Merge branch 'master' into gnome-team

Change-Id: I88d3789460d1a89917451d80405d89a2824006ac

68 files changed, 6264 insertions, 2238 deletions

diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm
index 8f72b0eeae..afbcf7fda6 100644
--- a/gnu/packages/admin.scm
+++ b/gnu/packages/admin.scm
@@ -406,7 +406,7 @@ interface and is based on GNU Guile.")
 (define-public swineherd
   (package
     (name "swineherd")
-    (version "0.0.1")
+    (version "0.0.3")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -415,7 +415,7 @@ interface and is based on GNU Guile.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "18nk0sy5s0dm2rhxnrrn8g0m098b110mxnnxa2vnl1dnvfdzszw8"))))
+                "0il1ikaj478n7xs4vqgawbshvmwq3nd0gp235mwqvmf4knra6j3g"))))
     (build-system gnu-build-system)
     (arguments
      '(#:configure-flags '("--localstatedir=/var")
@@ -2835,13 +2835,13 @@ specified directories.")
 (define-public ansible-core
   (package
     (name "ansible-core")
-    (version "2.14.4")
+    (version "2.15.5")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "ansible-core" version))
        (sha256
-        (base32 "057g87smxcn6zc558xk4zr6ga4q8clmkyxghn5gx60a94sy61clh"))))
+        (base32 "00hnwjk4dxgxbz4xlza2wqx20yks5xr7074hzlzsyja3ip5kkicc"))))
     (build-system python-build-system)
     (arguments
      `(#:modules ((guix build python-build-system)
@@ -2911,14 +2911,6 @@ test_context)" all)
              (when tests?
                ;; Otherwise Ansible fails to create its config directory.
                (setenv "HOME" "/tmp")
-               ;; This test module messes up with sys.path and causes many
-               ;; test failures.
-               (delete-file "test/units/_vendor/test_vendor.py")
-               ;; The test fails when run in the container, for reasons
-               ;; unknown.
-               (delete-file "test/units/utils/test_display.py")
-               ;; This test fail for reasons unknown.
-               (delete-file "test/units/cli/test_adhoc.py")
                ;; These tests fail in the container; it appears that the
                ;; mocking of the absolute file names such as /usr/bin/svcs do
                ;; not work as intended there.
@@ -2933,7 +2925,7 @@ test_command_nonexisting.py")
                ;; does some extra environment setup.  Taken from
                ;; https://raw.githubusercontent.com/ansible/ansible/\
                ;; devel/test/utils/shippable/shippable.sh.
-               (invoke "ansible-test" "units" "-v"
+               (invoke "./bin/ansible-test" "units" "-v"
                        "--num-workers" (number->string
                                         (parallel-job-count)))))))))
     (native-inputs
@@ -2954,7 +2946,7 @@ test_command_nonexisting.py")
            python-jinja2
            python-pyyaml
            python-packaging             ;for version number parsing
-           python-resolvelib-0.5))
+           python-resolvelib))
     (home-page "https://www.ansible.com/")
     (synopsis "Radically simple IT automation")
     (description "Ansible aims to be a radically simple IT automation system.
@@ -2981,13 +2973,13 @@ provides the following commands:
 (define-public ansible
   (package
     (name "ansible")
-    (version "7.4.0")
+    (version "8.5.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "ansible" version))
        (sha256
-        (base32 "142barhwz0wx5kn74xi0bfl21iwq2yq3jp14kxajsg9nggndcr09"))))
+        (base32 "0bazj5h12wraf30bb2schzwk553y20n9vh45km4b5kgmvadm0z1j"))))
     (build-system python-build-system)
     (propagated-inputs (list ansible-core))
     ;; The Ansible collections are found by ansible-core via the Python search
diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm
index c061184aee..c0fe75ddfd 100644
--- a/gnu/packages/algebra.scm
+++ b/gnu/packages/algebra.scm
@@ -936,7 +936,7 @@ algorithms from the FORTRAN library MINPACK.")
 (define-public symengine
   (package
     (name "symengine")
-    (version "0.10.1")
+    (version "0.11.1")
     (source
      (origin
        (method git-fetch)
@@ -945,7 +945,7 @@ algorithms from the FORTRAN library MINPACK.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0qy5w5msq0zy7drbhdy0vx451zglha8jm5s4zzmvmsja5yyv8fx9"))))
+        (base32 "105rnnf33vx2n03wwv4962az7bfzgsn1gx6a6wyakmyrfdkb07jc"))))
     (build-system cmake-build-system)
     (arguments
      '(#:configure-flags
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 764a674a6d..908c3ada3a 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -493,6 +493,60 @@ in FITS files.")
     (license (license:non-copyleft "file://License.txt"
                                    "See License.txt in the distribution."))))
 
+(define-public python-aplpy
+  (package
+    (name "python-aplpy")
+    (version "2.1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "aplpy" version))
+       (sha256
+        (base32 "0ph9jhv4q4i4z6nkqr6hjw9148kdlnayxsn83qgv5dqn0h3nc9r8"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs
+     (list python-astropy
+           python-matplotlib
+           python-numpy
+           python-pillow
+           python-pyavm
+           python-pyregion
+           python-reproject
+           python-scikit-image
+           python-shapely))
+    (native-inputs
+     (list python-pytest-astropy
+           python-pytest-mpl
+           python-semantic-version))
+    (home-page "http://aplpy.github.io")
+    (synopsis "Astronomical Plotting Library in Python")
+    (description
+     "@acronym{APLpy, the Astronomical Plotting Library in Python} is a Python
+module aimed at producing publication-quality plots of astronomical imaging data
+in FITS format.  The module uses @code{matplotlib}, a powerful and interactive
+plotting package.  It is capable of creating output files in several graphical
+formats, including EPS, PDF, PS, PNG, and SVG.
+
+Main features:
+@itemize
+@item Make plots interactively or using scripts
+@item Show grayscale, colorscale, and 3-color RGB images of FITS files
+@item Generate co-aligned FITS cubes to make 3-color RGB images
+@item Make plots from FITS files with arbitrary WCS (e.g. position-velocity)
+@item Slice multi-dimensional FITS cubes
+@item Overlay any number of contour sets
+@item Overlay markers with fully customizable symbols
+@item Plot customizable shapes like circles, ellipses, and rectangles
+@item Overlay ds9 region files
+@item Overlay coordinate grids
+@item Show colorbars, scalebars, and beams
+@item Customize the appearance of labels and ticks
+@item Hide, show, and remove different contour and marker layers
+@item Pan, zoom, and save any view as a full publication-quality plot
+@item Save plots as EPS, PDF, PS, PNG, and SVG
+@end itemize")
+    (license license:expat)))
+
 (define-public python-astroml
   (package
     (name "python-astroml")
@@ -2166,6 +2220,29 @@ cases for which diffractive rather than geometric optics is the topic of
 interest, and which require portability between platforms or ease of scripting.")
     (license license:bsd-3)))
 
+(define-public python-pyavm
+  (package
+    (name "python-pyavm")
+    (version "0.9.6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "PyAVM" version))
+       (sha256
+        (base32 "0vgjqvddq4a5lnmg8msm7fwqs3r6fc748xzvnhyvc387h0z8pdxk"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs
+     (list python-astropy python-numpy))
+    (native-inputs
+     (list python-pillow python-pytest python-setuptools-scm))
+    (home-page "https://astrofrog.github.io/pyavm/")
+    (synopsis "Simple pure-python AVM meta-data handling")
+    (description
+     "PyAVM is a module to represent, read, and write metadata following the
+@acronym{AVM, Astronomy Visualization Metadata} standard provided by
+@url{https://www.virtualastronomy.org/avm_metadata.php, vamp} project.")
+    (license license:expat)))
+
 (define-public python-pyvo
   (package
     (name "python-pyvo")
@@ -2455,6 +2532,60 @@ positions of the sun: dawn, sunrise, solar noon, sunset, dusk, solar
 elevation, solar azimuth, rahukaalam, and the phases of the moon.")
     (license license:asl2.0)))
 
+(define-public python-spectral-cube
+  (package
+    (name "python-spectral-cube")
+    (version "0.6.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "spectral-cube" version))
+       (sha256
+        (base32 "10q76rsgf9w4j7y68mfa870bpxf06m6kqvivj4340jmgnsrfy1zg"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs
+     (list python-astropy
+           python-aplpy
+           python-casa-formats-io
+           python-dask
+           python-distributed
+           python-fsspec
+           ;; python-glue-core ; Not packed http://glueviz.org/, optional.
+           python-joblib
+           python-matplotlib
+           python-numpy
+           python-radio-beam
+           python-reproject
+           python-scipy
+           python-six
+           ;; python-yt ; Not packed https://yt-project.org/, optional.
+           python-zarr))
+    (native-inputs
+     (list ;; XXX: Introduce cycle with pvextractor, listed as extra requiremnts
+           ;; in [noviz] option.
+           ;; python-pvextractor
+           python-pytest-astropy
+           python-regions
+           python-semantic-version
+           python-setuptools-scm))
+    (home-page "https://spectral-cube.readthedocs.io/en/latest/")
+    (synopsis "Library for reading and analyzing astrophysical spectral data cubes")
+    (description
+     "The spectral-cube package provides an easy way to read, manipulate,
+analyze, and write data cubes with two positional dimensions and one spectral
+dimension, optionally with Stokes parameters.
+
+It provides the following main features:
+@itemize
+@item A uniform interface to spectral cubes, robust to the wide range of conventions
+of axis order, spatial projections, and spectral units that exist in the wild.
+@item Easy extraction of cube sub-regions using physical coordinates.
+@item Ability to easily create, combine, and apply masks to datasets.
+@item Basic summary statistic methods like moments and array aggregates.
+@item Designed to work with datasets too large to load into memory.
+@end itemize")
+    (license license:bsd-3)))
+
 (define-public python-spherical-geometry
   (package
     (name "python-spherical-geometry")
@@ -3471,6 +3602,46 @@ astrophysical simulations supporting PKDGRAV/Gasoline, Gadget, Gadget4/Arepo,
 N-Chilada and RAMSES AMR outputs.")
     (license license:gpl3+)))
 
+(define-public python-pyregion
+  (package
+    (name "python-pyregion")
+    (version "2.2.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "pyregion" version))
+       (sha256
+        (base32 "0l7qb7r8fnv46mdih4m5b8jaxixgpw6m7v37dpikjkblgh0vigaw"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'check 'build-extensions
+            (lambda _
+              ;; Cython extensions have to be built before running the tests.
+              (invoke "python" "setup.py" "build_ext" "--inplace"))))))
+    (propagated-inputs
+     (list python-astropy python-numpy python-pyparsing))
+    (native-inputs
+     (list python-cython
+           python-pytest
+           python-pytest-astropy-header
+           python-setuptools-scm))
+    (home-page "https://github.com/astropy/pyregion")
+    (synopsis "Python parser for ds9 region files")
+    (description
+     "@code{pyregion} is a python module to parse ds9 region files.  It also
+supports ciao region files.
+Features:
+@itemize
+@item ds9 and ciao region files.
+@item (physical, WCS) coordinate conversion to the image coordinate.
+@item convert regions to matplotlib patches.
+@item convert regions to spatial filter (i.e., generate mask images)
+@end itemize")
+    (license license:expat)))
+
 (define-public python-pysynphot
   (package
     (name "python-pysynphot")
@@ -3955,6 +4126,40 @@ format, which are used by ASDF to serialize and deserialize data for the Nancy
 Grace Roman Space Telescope.")
     (license license:bsd-3)))
 
+(define-public python-radio-beam
+  (package
+    (name "python-radio-beam")
+    (version "0.3.6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "radio-beam" version))
+       (sha256
+        (base32 "19c6gmm1wvyp5nn1yfbzl428rkysdq273j2yaarxpivv7cwj7qjk"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs
+     (list python-astropy
+           python-matplotlib
+           python-numpy
+           python-scipy
+           python-six))
+    (native-inputs (list python-pytest-astropy python-setuptools-scm))
+    (home-page "https://radio-beam.readthedocs.io/en/latest/")
+    (synopsis "Operations for radio astronomy beams with Astropy")
+    (description
+     "Radio Beam is a simple toolkit for reading beam information from FITS
+headers and manipulating beams.
+Some example applications include:
+@itemize
+@item Convolution and deconvolution
+@item Unit conversion (Jy to/from K)
+@item Handle sets of beams for spectral cubes with varying resolution between
+channels
+@item Find the smallest common beam from a set of beams
+@item Add the beam shape to a matplotlib plot
+@end itemize")
+    (license license:bsd-3)))
+
 (define-public python-roman-datamodels
   (package
     (name "python-roman-datamodels")
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index d3ff0b1127..b15a856fb9 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -68,6 +68,59 @@
 
 ;;; Annotations
 
+(define-public r-hpo-db
+  (package
+    (name "r-hpo-db")
+    (version "0.99.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "HPO.db" version
+                              'annotation))
+       (sha256
+        (base32 "1brzrnafvyh76h8a663gk5lprhixxpi9xi65vwgxwf7jh6yw0was"))))
+    (properties `((upstream-name . "HPO.db")))
+    (build-system r-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'avoid-internet-access
+            (lambda* (#:key inputs #:allow-other-keys)
+              (let* ((cache (string-append #$output "/share/HPO.db/cache"))
+                     (file (string-append cache "/118333")))
+                (mkdir-p cache)
+                (copy-file #$(this-package-native-input "HPO.sqlite") file)
+                (substitute* "R/zzz.R"
+                  (("ah <- suppressMessages\\(AnnotationHub\\(\\)\\)" m)
+                   (string-append
+                    "if (Sys.getenv(\"NIX_BUILD_TOP\") == \"\") { " m " };"))
+                  (("dbfile <- ah.*" m)
+                   (string-append
+                    "if (Sys.getenv(\"NIX_BUILD_TOP\") != \"\") { dbfile <- \""
+                    file "\";} else { " m " }\n")))))))))
+    (propagated-inputs
+     (list r-annotationdbi r-annotationhub r-biocfilecache r-dbi))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)
+       ("HPO.sqlite"
+        ,(origin
+           (method url-fetch)
+           (uri "https://annotationhub.bioconductor.org/fetch/118333")
+           (file-name "HPO.sqlite")
+           (sha256
+            (base32 "1wwdwf27iil0p41183qgygh2ifphhmlljjkgjm2h8sr25qycf0md"))))))
+    (home-page "https://bioconductor.org/packages/HPO.db")
+    (synopsis
+     "Annotation maps describing the entire Human Phenotype Ontology")
+    (description
+     "Human Phenotype Ontology (HPO) was developed to create a consistent
+description of gene products with disease perspectives, and is essential for
+supporting functional genomics in disease context.  Accurate disease
+descriptions can discover new relationships between genes and disease, and new
+functions for previous uncharacteried genes and alleles.")
+    (license license:artistic2.0)))
+
 (define-public r-mafh5-gnomad-v3-1-2-grch38
   (package
     (name "r-mafh5-gnomad-v3-1-2-grch38")
@@ -98,6 +151,65 @@ It retrieves this data from the Genome Aggregation Database
 (@code{gnomAD} version 3.1.2) for the human genome version GRCh38.")
     (license license:artistic2.0)))
 
+(define-public r-mpo-db
+  (package
+    (name "r-mpo-db")
+    (version "0.99.7")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "MPO.db" version
+                              'annotation))
+       (sha256
+        (base32 "0x1rcikg189akbd71yh0p02482km9hry6i69s2srdf5mlgqficvl"))))
+    (properties `((upstream-name . "MPO.db")))
+    (build-system r-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'avoid-internet-access
+            (lambda* (#:key inputs #:allow-other-keys)
+              (let* ((cache (string-append #$output "/share/MPO.db/cache"))
+                     (file (string-append cache "/118299")))
+                (mkdir-p cache)
+                (copy-file #$(this-package-native-input "MPO.sqlite") file)
+                (substitute* "R/zzz.R"
+                  (("ah <- suppressMessages\\(AnnotationHub\\(\\)\\)" m)
+                   (string-append
+                    "if (Sys.getenv(\"NIX_BUILD_TOP\") == \"\") { " m " };"))
+                  (("dbfile <- ah.*" m)
+                   (string-append
+                    "if (Sys.getenv(\"NIX_BUILD_TOP\") != \"\") { dbfile <- \""
+                    file "\";} else { " m " }\n")))))))))
+    (propagated-inputs
+     (list r-annotationdbi r-annotationhub r-biocfilecache r-dbi))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)
+       ("MPO.sqlite"
+        ,(origin
+           (method url-fetch)
+           (uri "https://annotationhub.bioconductor.org/fetch/118299")
+           (file-name "MPO.sqlite")
+           (sha256
+            (base32 "12rf5dpnjrpw55bgnbn68dni2g0p87nvs9c7mamqk0ayafs61zl0"))))))
+    (home-page "https://github.com/YuLab-SMU/MPO.db")
+    (synopsis "set of annotation maps describing the Mouse Phenotype Ontology")
+    (description
+     "This is the human disease ontology R package HDO.db, which provides the
+semantic relationship between human diseases.  Relying on the DOSE and
+GO@code{SemSim} packages, this package can carry out disease enrichment and
+semantic similarity analyses.  Many biological studies are achieved through
+mouse models, and a large number of data indicate the association between
+genotypes and phenotypes or diseases.  The study of model organisms can be
+transformed into useful knowledge about normal human biology and disease to
+facilitate treatment and early screening for diseases.  Organism-specific
+genotype-phenotypic associations can be applied to cross-species phenotypic
+studies to clarify previously unknown phenotypic connections in other species.
+Using the same principle to diseases can identify genetic associations and
+even help to identify disease associations that are not obvious.")
+    (license license:artistic2.0)))
+
 (define-public r-org-eck12-eg-db
   (package
     (name "r-org-eck12-eg-db")
@@ -1841,6 +1953,40 @@ LC-MSMS and MRM files from proteomics experiments; and PSI mzIdentML example
 files for various search engines.")
     (license license:gpl2+)))
 
+(define-public r-msexperiment
+  (package
+    (name "r-msexperiment")
+    (version "1.4.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "MsExperiment" version))
+       (sha256
+        (base32 "06m0i60zh3xjqmsz6dpp0il833xzdfj0fm6xbhl7kmicvfrcnyfg"))))
+    (properties `((upstream-name . "MsExperiment")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-iranges
+                             r-protgenerics
+                             r-qfeatures
+                             r-s4vectors
+                             r-spectra
+                             r-summarizedexperiment))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/RforMassSpectrometry/MsExperiment")
+    (synopsis "Infrastructure for Mass Spectrometry experiments")
+    (description
+     "This package provides infrastructure to store and manage all aspects
+related to a complete proteomics or metabolomics mass spectrometry (MS)
+experiment.  The @code{MsExperiment} package provides light-weight and
+flexible containers for MS experiments building on the new MS infrastructure
+provided by the Spectra, QFeatures and related packages.  Along with raw data
+representations, links to original data files and sample annotations,
+additional metadata or annotations can also be stored within the
+@code{MsExperiment} container.  To guarantee maximum flexibility only minimal
+constraints are put on the type and content of the data within the
+containers.")
+    (license license:artistic2.0)))
+
 (define-public r-msigdb
   (package
     (name "r-msigdb")
@@ -2135,13 +2281,13 @@ and @code{Sailfish}.  Alevin example output is also included.")
 (define-public r-abarray
   (package
     (name "r-abarray")
-    (version "1.68.0")
+    (version "1.70.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "ABarray" version))
               (sha256
                (base32
-                "0vrsyx06acdkb3hq350zdnx3bqzz43grf1w8n0pmxlcr2dncchv9"))))
+                "0p9q2x6n6n1d4w2hfbhhj54qflc6rf1w1qm9p2zqv9fcrm3g153v"))))
     (properties `((upstream-name . "ABarray")))
     (build-system r-build-system)
     (propagated-inputs (list r-biobase r-multtest))
@@ -2161,13 +2307,13 @@ into folders according to the analysis settings used.")
 (define-public r-absseq
   (package
     (name "r-absseq")
-    (version "1.54.0")
+    (version "1.56.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "ABSSeq" version))
               (sha256
                (base32
-                "1my2slp88qpb15qidjd646hlslvn8brv6i553h21c4c76jzxzsiz"))))
+                "0y8j66yargvipwxg2ffcs62idk5q5r8vracfldbd1x5rgq7lf6nq"))))
     (properties `((upstream-name . "ABSSeq")))
     (build-system r-build-system)
     (propagated-inputs (list r-limma r-locfit))
@@ -2190,13 +2336,13 @@ ranking by fold-change and visualization.")
 (define-public r-adacgh2
   (package
     (name "r-adacgh2")
-    (version "2.40.0")
+    (version "2.42.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ADaCGH2" version))
        (sha256
-        (base32 "1mmckrxhv23kl3g4d3n4hfdm97sfg2k36khzy9i6d73g7c033hsv"))))
+        (base32 "0lzgn4zqckv37jsgd1azvshblb38khrlcncm98g74qhkswqj5wx3"))))
     (properties `((upstream-name . "ADaCGH2")))
     (build-system r-build-system)
     (arguments
@@ -2232,13 +2378,13 @@ storing data.")
 (define-public r-adam
   (package
     (name "r-adam")
-    (version "1.16.0")
+    (version "1.18.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "ADAM" version))
               (sha256
                (base32
-                "1hy7xdf6v2fqggvc9rdl90gn0l6vfbmvb23c61i8q45s3qsaxksp"))))
+                "0gz3mpkj1q4j7w08ylfzclpa6saxsz7wyp0cldllhxpcj9lxljs5"))))
     (properties `((upstream-name . "ADAM")))
     (build-system r-build-system)
     (propagated-inputs (list r-dplyr
@@ -2267,13 +2413,13 @@ functionally associated genes} (GFAG).")
 (define-public r-adamgui
   (package
     (name "r-adamgui")
-    (version "1.16.0")
+    (version "1.18.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "ADAMgui" version))
               (sha256
                (base32
-                "0jc0sbmmc98z75x73ns3qwcvklvx73wqla87cki8sls6ywa8w93j"))))
+                "10m5dplkzxsxm7dxcmybihv81yflm3f7q6fmgb1dvwr8lsn1dm03"))))
     (properties `((upstream-name . "ADAMgui")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2315,13 +2461,13 @@ the @code{GFAGpathUi} function.")
 (define-public r-adimpute
   (package
     (name "r-adimpute")
-    (version "1.10.0")
+    (version "1.12.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "ADImpute" version))
               (sha256
                (base32
-                "0a3r4bkf6g28lgsq21077ag9ba6zrfv6yflawx9fg73zdx4266jp"))))
+                "0299yyin2j8577db2w6mrxmsq68cjlzwyh7z1wvhbj0n1p75r871"))))
     (properties `((upstream-name . "ADImpute")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2364,13 +2510,13 @@ results from different methods into an ensemble.")
 (define-public r-adsplit
   (package
     (name "r-adsplit")
-    (version "1.70.0")
+    (version "1.72.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "adSplit" version))
               (sha256
                (base32
-                "0nbdcrc2wiq3mkpayjslz66ik2vk3h3f18zg6df9xaivanxrkk5z"))))
+                "0av0kji4r788cn5808g13svqpydq6xk4d2awpzpsckz7xbjyx0ya"))))
     (properties `((upstream-name . "adSplit")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2392,13 +2538,13 @@ the supporting gene set is determined.")
 (define-public r-affixcan
   (package
     (name "r-affixcan")
-    (version "1.18.0")
+    (version "1.20.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "AffiXcan" version))
               (sha256
                (base32
-                "0nf5dkidar6zp5rvpd7i19gdb7mnam9rmca3z3anxi0pdnalwc9d"))))
+                "1f508sz5vsmmmvp2mcyd2l4hislg2xhnn11xxva010l3i7by8c2r"))))
     (properties `((upstream-name . "AffiXcan")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2420,13 +2566,13 @@ expression values are known.")
 (define-public r-affyilm
   (package
     (name "r-affyilm")
-    (version "1.52.0")
+    (version "1.54.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "affyILM" version))
        (sha256
-        (base32 "02g0bg21ms0gmq6dvdcj91b0p47ppqcfvgj73y0mbdx6prrmcagx"))))
+        (base32 "1sbgc787gvcnpjhm0hv80rsms679wlvphq2ch7s28zdlaa2vz7sv"))))
     (properties `((upstream-name . "affyILM")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2447,13 +2593,13 @@ concentrations on behal of the Langmuir model.")
 (define-public r-affylmgui
   (package
     (name "r-affylmgui")
-    (version "1.74.0")
+    (version "1.76.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "affylmGUI" version))
        (sha256
-        (base32 "1m1gvz313h4x080889b05fjq60wn57dxlgq03qkwy65scl3x2fcn"))))
+        (base32 "1431zmh9van9605lh0i96as48zih17s3cfhjw94v37rswfq09fkg"))))
     (properties `((upstream-name . "affylmGUI")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2479,13 +2625,13 @@ limma packages.")
 (define-public r-affyplm
   (package
     (name "r-affyplm")
-    (version "1.76.1")
+    (version "1.78.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "affyPLM" version))
        (sha256
-        (base32 "1660nn4541f2k5qpzxkkkf9h92ndzqr0j1jpzh4czs466766kn8y"))))
+        (base32 "0l7rfwj1bdkk9vd5j0zby2ijpapmd5k0s6l84zy4ld47vabxyaa6"))))
     (properties `((upstream-name . "affyPLM")))
     (build-system r-build-system)
     (inputs (list zlib))
@@ -2510,13 +2656,13 @@ also provided.")
 (define-public r-affyrnadegradation
   (package
     (name "r-affyrnadegradation")
-    (version "1.46.0")
+    (version "1.48.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "AffyRNADegradation" version))
               (sha256
                (base32
-                "14s3kvxcc3qj931bf5ya088flijmn5z89hps3di98kkdsl3w6d4g"))))
+                "0i7929cyqvbx81v1d629g53480m48cbdpxfv0k6lwjfzf4yvazhf"))))
     (properties `((upstream-name . "AffyRNADegradation")))
     (build-system r-build-system)
     (propagated-inputs (list r-affy))
@@ -2535,13 +2681,13 @@ of samples that are affected by RNA degradation.")
 (define-public r-agdex
   (package
     (name "r-agdex")
-    (version "1.48.0")
+    (version "1.50.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "AGDEX" version))
               (sha256
                (base32
-                "0p9qmwhi4ik24m51cvgxnny4yfqv4v0rvra16bj5d3w9bw9yf3an"))))
+                "06z74p3khw3r8dnwrpyyikq3ifcdvffxgfwcic9j8vc9s8pf921s"))))
     (properties `((upstream-name . "AGDEX")))
     (build-system r-build-system)
     (propagated-inputs (list r-biobase r-gseabase))
@@ -2562,13 +2708,13 @@ experiment.")
 (define-public r-aggregatebiovar
   (package
     (name "r-aggregatebiovar")
-    (version "1.10.0")
+    (version "1.12.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "aggregateBioVar" version))
               (sha256
                (base32
-                "0g7n6dj1scad833y2182946hn3yh4jad20wvw9ic8gmqb438vihj"))))
+                "1i04hhncz9lhjp730gyknd8v7zakz1whc2a5pw3pn37h8k9mq5la"))))
     (properties `((upstream-name . "aggregateBioVar")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2596,13 +2742,13 @@ bulk RNA-seq tools.")
 (define-public r-agilp
   (package
     (name "r-agilp")
-    (version "3.32.0")
+    (version "3.34.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "agilp" version))
               (sha256
                (base32
-                "0rm646iqc8hf8vfk0pdg064hm9k4k371bp1q4k7z2l16zhs8a07r"))))
+                "0xbbcmnbnj7y3a1wndv6zhqhrwdpdj6207wh4n0qz794akciw84a"))))
     (properties `((upstream-name . "agilp")))
     (build-system r-build-system)
     (home-page "https://bioconductor.org/packages/agilp")
@@ -2618,13 +2764,13 @@ but which also provides utilities which may be useful for other platforms.")
 (define-public r-adductomicsr
   (package
     (name "r-adductomicsr")
-    (version "1.16.0")
+    (version "1.18.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "adductomicsR" version))
               (sha256
                (base32
-                "17cm65n2awbwmk5i8h1n30abk6pww42ngcy9m24dxz1qdbnvx5fn"))))
+                "0fb670gxzl5aq6vmb5d2l04r0408gxrqs06k1a3b3pzkdbd7qxwm"))))
     (properties `((upstream-name . "adductomicsR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2693,13 +2839,13 @@ objects are used so that other packages could be used as well.")
 (define-public r-aims
   (package
     (name "r-aims")
-    (version "1.32.0")
+    (version "1.34.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "AIMS" version))
               (sha256
                (base32
-                "1mbwv70ypkb3x086css94m89wq9pqzd23i7nar1844vbqpw3j83q"))))
+                "0fmzyd8vypcfadqfa8w11mxr12h4a9shgiqpi2n2y150fvhlqf6c"))))
     (properties `((upstream-name . "AIMS")))
     (build-system r-build-system)
     (propagated-inputs (list r-biobase r-e1071))
@@ -2717,13 +2863,13 @@ well as on dataset of gene expression data.")
 (define-public r-airpart
   (package
     (name "r-airpart")
-    (version "1.8.0")
+    (version "1.10.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "airpart" version))
               (sha256
                (base32
-                "024vcxf23irlysc8srqii3zqhhldpwdcj0i4zzhz18x3bdy9cbj0"))))
+                "1bdlg078nlpibbn3y1cbkglhlm440crx3alzhv9k0psv6arg2kqb"))))
     (properties `((upstream-name . "airpart")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2764,13 +2910,13 @@ datasets.")
 (define-public r-amountain
   (package
     (name "r-amountain")
-    (version "1.26.0")
+    (version "1.28.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "AMOUNTAIN" version))
               (sha256
                (base32
-                "12ml67882lscv05np4m80fg9d48dwkaa6kx5cga6x19kdx6xs2cj"))))
+                "1c65vn2k3hzzymik9ia7nk32sf0hr83q27yzf561a1hgv3m67d65"))))
     (properties `((upstream-name . "AMOUNTAIN")))
     (build-system r-build-system)
     (inputs (list gsl))
@@ -2788,13 +2934,13 @@ in multi-layer WGCN using a continuous optimization approach.")
 (define-public r-amplican
   (package
     (name "r-amplican")
-    (version "1.22.1")
+    (version "1.24.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "amplican" version))
               (sha256
                (base32
-                "1bws4awpjvswzj53zwn9x5ra76ngpqn2h8hlr6y0x7j9wwwqldc7"))))
+                "0xsw6226yyyl5zgmcyfim6dxj04zrpzbd1288l0hysq1s3b1yslw"))))
     (properties `((upstream-name . "amplican")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2835,13 +2981,13 @@ problems.")
 (define-public r-amaretto
   (package
     (name "r-amaretto")
-    (version "1.16.0")
+    (version "1.18.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "AMARETTO" version))
               (sha256
                (base32
-                "1yp2npw9mdjy0wchbp0y1r1ifyy63hdz2y3y8cia9c76nfv4627f"))))
+                "1h0ci2sak2x5dhcshmgk4hy53ggjvrz3kaj61m47w5fjkj0lz79s"))))
     (properties `((upstream-name . "AMARETTO")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2887,13 +3033,13 @@ canonical cancer pathways.")
 (define-public r-anaquin
   (package
     (name "r-anaquin")
-    (version "2.24.0")
+    (version "2.26.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Anaquin" version))
               (sha256
                (base32
-                "0f2xc0pm7ld72fnmqirr0q2a5xfh12cag6s2yysblslh9ajyzcmw"))))
+                "1f2xf1i9l1s7433mvqjsralpm77qg0m73dw1rq9jsxbpk1f502ld"))))
     (properties `((upstream-name . "Anaquin")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2917,13 +3063,13 @@ analysis, modelling, and visualization of spike-in controls.")
 (define-public r-ancombc
   (package
     (name "r-ancombc")
-    (version "2.2.2")
+    (version "2.4.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "ANCOMBC" version))
               (sha256
                (base32
-                "0jws3wqgwc0gnp7smc0lsqfw9jbcik36pl7vz9a8ndgwpp9c8653"))))
+                "1m63k1b9xh5mv4zb5m9nlrdcqkh2h477x1zyfk8j89idcvk9jil7"))))
     (properties `((upstream-name . "ANCOMBC")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3025,13 +3171,13 @@ to understand their data better and discover new insights.")
 (define-public r-annotationhubdata
   (package
     (name "r-annotationhubdata")
-    (version "1.30.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "AnnotationHubData" version))
        (sha256
-        (base32 "109gi5cs82j135q00wg9dfx0z5m9bs1kc7s246ym13ik43z0h3qq"))))
+        (base32 "0jkz65z7l9vaxid6vpsr4rdavarkayfrgkybzhwf9va82jsnkd3z"))))
     (properties `((upstream-name . "AnnotationHubData")))
     (build-system r-build-system)
     (arguments
@@ -3076,13 +3222,13 @@ for use in Bioconductor’s AnnotationHub.")
 (define-public r-anvil
   (package
     (name "r-anvil")
-    (version "1.12.4")
+    (version "1.14.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "AnVIL" version))
               (sha256
                (base32
-                "05wgrr16vaqb7982j7nyri6rrhx90ljgxc37afhw190wc5dj07n0"))))
+                "0syd1m992i2xqw2djw6s07zwwvrzvd0aksix1cbhx9plpswd2245"))))
     (properties `((upstream-name . "AnVIL")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3117,19 +3263,22 @@ to transform JSON responses to formats more amenable to manipulation in R.")
 (define-public r-aldex2
   (package
     (name "r-aldex2")
-    (version "1.32.0")
+    (version "1.34.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "ALDEx2" version))
               (sha256
                (base32
-                "0gdkc8qwx3vpk5i09znlfrag7gk87piz61z90k96v6bm6x8sclb8"))))
+                "0wchlw9dprw7vkw26h26ypx06xv2j0cxbidw61pcqaxmrrh14dhz"))))
     (properties `((upstream-name . "ALDEx2")))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biocparallel
+           r-directlabels
            r-genomicranges
            r-iranges
+           r-lattice
+           r-latticeextra
            r-multtest
            r-rfast
            r-s4vectors
@@ -3158,13 +3307,13 @@ paired or unpaired study designs.")
 (define-public r-alevinqc
   (package
     (name "r-alevinqc")
-    (version "1.16.1")
+    (version "1.18.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "alevinQC" version))
               (sha256
                (base32
-                "137bvqyh1cqmhf9x3xl6n1dv0380lpcr2nxhd60b7zqiw4p14i5a"))))
+                "0lhbh9xgkbrad9fqvxl4c6y0f2kgibn6sinp8znysk5m9z0ngpwp"))))
     (properties `((upstream-name . "alevinQC")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3192,13 +3341,13 @@ generated as HTML or PDF files, or as Shiny applications.")
 (define-public r-alphabeta
   (package
     (name "r-alphabeta")
-    (version "1.14.0")
+    (version "1.16.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "AlphaBeta" version))
               (sha256
                (base32
-                "11431d453xszzjyxr10npnblhlrfw8hl5jgabpxla7cj77w02wnr"))))
+                "0zja8mysw0ljkvk6vqdx4c9wpf45zs64iyazh90mlf6xhbrvqfvq"))))
     (properties `((upstream-name . "AlphaBeta")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3272,13 +3421,13 @@ data.")
 (define-public r-alpsnmr
   (package
     (name "r-alpsnmr")
-    (version "4.2.0")
+    (version "4.4.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "AlpsNMR" version))
               (sha256
                (base32
-                "0rp82y7163pjbl7n6fyywh4l0sgzn1z8kp83v0kg7xk3810mj9sm"))))
+                "0141kayx20mm8skqr2210bpl76ra560ik7gf71iar03r3izcfczq"))))
     (properties `((upstream-name . "AlpsNMR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3326,13 +3475,13 @@ data.  Efficient plotting with 1-D data is also available.  Basic reading of
 (define-public r-altcdfenvs
   (package
     (name "r-altcdfenvs")
-    (version "2.62.0")
+    (version "2.64.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "altcdfenvs" version))
               (sha256
                (base32
-                "1jpimj195rdw86pp623ylrmcxkxmn8qmc84vsw9prnf3gdz3q18b"))))
+                "17kgiqa5dbfp74jrm565wlx9sj4ydbds2y8ahs7dikvdvm725qsn"))))
     (properties `((upstream-name . "altcdfenvs")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3357,37 +3506,37 @@ create an alternative mapping from sequences.")
 (define-public r-aneufinder
   (package
     (name "r-aneufinder")
-    (version "1.28.0")
+    (version "1.30.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "AneuFinder" version))
               (sha256
                (base32
-                "1l33yb20pynkvlla1dmgbwjhnhxh067fci0ciryxmbzqwq2sn1kc"))))
+                "0x7v60j1c1g12qlqxgshpmbnwzjbmlnkrfh60wl43inr0wyllq1l"))))
     (build-system r-build-system)
     (native-inputs
      (list r-knitr))
     (propagated-inputs
-     (list r-genomicranges
-           r-aneufinderdata
+     (list r-aneufinderdata
+           r-bamsignals
+           r-biocgenerics
+           r-biostrings
+           r-cowplot
+           r-dnacopy
+           r-doparallel
            r-ecp
            r-foreach
-           r-doparallel
-           r-biocgenerics
-           r-s4vectors
            r-genomeinfodb
-           r-iranges
-           r-rsamtools
-           r-bamsignals
-           r-dnacopy
-           r-biostrings
            r-genomicalignments
-           r-ggplot2
-           r-reshape2
+           r-genomicranges
            r-ggdendro
+           r-ggplot2
            r-ggrepel
+           r-iranges
            r-mclust
-           r-cowplot))
+           r-reshape2
+           r-rsamtools
+           r-s4vectors))
     (home-page "https://bioconductor.org/packages/AneuFinder/")
     (synopsis "Copy number variation analysis in single-cell-sequencing data")
     (description "This package implements functions for copy number variant
@@ -3426,13 +3575,13 @@ network fusion.")
 (define-public r-annmap
   (package
     (name "r-annmap")
-    (version "1.42.0")
+    (version "1.44.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "annmap" version))
               (sha256
                (base32
-                "0gilb8yxba1cqi678w9xkq77m8lf3k8dqcldh68cll61xsgihl1v"))))
+                "1gf0qdhj4ijgb6b67fh94zx084k5r87la3d7vc0qxs413rvr4mj8"))))
     (properties `((upstream-name . "annmap")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3460,13 +3609,13 @@ Functions to plot gene architecture and BAM file data are also provided.")
 (define-public r-antiprofiles
   (package
     (name "r-antiprofiles")
-    (version "1.40.0")
+    (version "1.42.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "antiProfiles" version))
               (sha256
                (base32
-                "0ix0r36fs6vr0gyryi1j15pcc0hvpynsg9505w95dsn3p4fdnhg8"))))
+                "14lzyq08gnm9r99xwaqh50sz0dwzhmiyyylkg239dlbw80zmv404"))))
     (properties `((upstream-name . "antiProfiles")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3486,13 +3635,13 @@ tumor samples from healthy controls.")
 (define-public r-arrayexpress
   (package
     (name "r-arrayexpress")
-    (version "1.60.0")
+    (version "1.62.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "ArrayExpress" version))
               (sha256
                (base32
-                "1ib33fw379sakk084csa3pwcc3wvba38ily6mmv2ax1wh16i0pfz"))))
+                "0cnb6r6rqbz5qph32aa1mghr0w2rhl6znyiblj0cbkv45mx2k4jr"))))
     (properties `((upstream-name . "ArrayExpress")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3513,13 +3662,13 @@ structures: @code{ExpressionSet}, @code{AffyBatch}, @code{NChannelSet}.")
 (define-public r-arrayqualitymetrics
   (package
     (name "r-arrayqualitymetrics")
-    (version "3.56.0")
+    (version "3.58.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "arrayQualityMetrics" version))
               (sha256
                (base32
-                "06plgmgla7hvryqfcid4y35s24r50s39d9f8sjchwbxqciwy72wj"))))
+                "1k80ih7r3hf48r9rp9dl2wl8m17620dqr4fch49kdsq97hm5q5dm"))))
     (properties `((upstream-name . "arrayQualityMetrics")))
     (build-system r-build-system)
     (propagated-inputs (list r-affy
@@ -3551,13 +3700,13 @@ supported.")
 (define-public r-arraymvout
   (package
     (name "r-arraymvout")
-    (version "1.58.0")
+    (version "1.60.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "arrayMvout" version))
        (sha256
-        (base32 "1wdqcfa0h070lky4m2h5k4wg8lg7014y0gk95gip5zags29zjwqb"))))
+        (base32 "0z3ksx0yigan5aiq7vsdx78khlrcdxa4yd5b46rfn83gsrjbxzhz"))))
     (properties `((upstream-name . "arrayMvout")))
     (build-system r-build-system)
     (arguments
@@ -3587,13 +3736,13 @@ fixed Type I error rate.")
 (define-public r-arrayquality
   (package
     (name "r-arrayquality")
-    (version "1.78.0")
+    (version "1.80.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "arrayQuality" version))
        (sha256
-        (base32 "0lq59y4pi13z4v1i1ah78xlchxy34x1lplsh0n42wlk88rk0rqxd"))))
+        (base32 "1bm46zf5c1i7fd848bqajv3agl05b93xsvam7034033ypyx6bf1z"))))
     (properties `((upstream-name . "arrayQuality")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3612,13 +3761,13 @@ quality assessment.")
 (define-public r-asafe
   (package
     (name "r-asafe")
-    (version "1.26.0")
+    (version "1.28.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "ASAFE" version))
               (sha256
                (base32
-                "05xw42552x7by63psb05hvjraax66flg94i331ca61zx107q7fai"))))
+                "13pn2s59npp8lhc2sk9sa7dq8fy6jlq22c71n3rcjgxrrh690nb8"))))
     (properties `((upstream-name . "ASAFE")))
     (build-system r-build-system)
     (native-inputs (list r-knitr))
@@ -3635,13 +3784,13 @@ pairs.")
 (define-public r-aseb
   (package
     (name "r-aseb")
-    (version "1.44.0")
+    (version "1.46.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "ASEB" version))
               (sha256
                (base32
-                "1dq6b5rg9iw6hdjmd7g0w64z7cxm52yg1cjyv355qs064dx26nph"))))
+                "1hiapxdbp1fg6wk62s31nkv9mkxzvd23hn3zhmf9n0nvqfhi7bdf"))))
     (properties `((upstream-name . "ASEB")))
     (build-system r-build-system)
     (home-page "https://bioconductor.org/packages/ASEB")
@@ -3662,13 +3811,13 @@ RNAs.")
 (define-public r-asgsca
   (package
     (name "r-asgsca")
-    (version "1.34.0")
+    (version "1.36.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "ASGSCA" version))
               (sha256
                (base32
-                "0vb37rvrb08qvv0i2k9jnqpajzpj044ww05w3kq1kypbby0c84zs"))))
+                "13nk19rccrp0xl1s5gjwydpl1ayc7zc2izjrij9iz7fh2r79gn7f"))))
     (properties `((upstream-name . "ASGSCA")))
     (build-system r-build-system)
     (propagated-inputs (list r-mass r-matrix))
@@ -3685,13 +3834,13 @@ model as latent variables.")
 (define-public r-asics
   (package
     (name "r-asics")
-    (version "2.16.0")
+    (version "2.18.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "ASICS" version))
               (sha256
                (base32
-                "0svl9wnfn9z88j1yyl30b1f3d14h01x4cga8q04x530723xnjws7"))))
+                "10wlmnlpn6ji256fp81rhsm2rsbsqsbvbjqqpw9vib11cwpam9wd"))))
     (properties `((upstream-name . "ASICS")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3719,13 +3868,13 @@ the spectra of the library with a sparse penalty.")
 (define-public r-aspli
   (package
     (name "r-aspli")
-    (version "2.10.0")
+    (version "2.12.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "ASpli" version))
               (sha256
                (base32
-                "0462hf7anpmmqq4585kmjilw1q229r38lijbxq8xg0f3m8xvr1ga"))))
+                "0rj103vvff2c20r018491i71393x0idq22ri4zg3qibx2accd7jy"))))
     (properties `((upstream-name . "ASpli")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3767,13 +3916,13 @@ that might arise in splicing patterns.")
 (define-public r-assessorf
   (package
     (name "r-assessorf")
-    (version "1.18.0")
+    (version "1.20.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "AssessORF" version))
               (sha256
                (base32
-                "16nv6sh7z3l6ff3a7zrixkc04mhrak38q045xlirgljkcragz1c5"))))
+                "0v64d3nmvcj6bz8zplyqzslm7kz6j3y0nl316h76g094hify64lk"))))
     (properties `((upstream-name . "AssessORF")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3796,13 +3945,13 @@ start codons as the forms of evidence.")
 (define-public r-asset
   (package
     (name "r-asset")
-    (version "2.18.0")
+    (version "2.20.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "ASSET" version))
               (sha256
                (base32
-                "1vksbfd4wd2xcc0nl3wp53vm0jyqy97p0hqps2aml04745vkg023"))))
+                "0mm15i59vsnz8zh2d10xnab3a6kq08hwd3pzm3r12g4wcrdsxfxc"))))
     (properties `((upstream-name . "ASSET")))
     (build-system r-build-system)
     (propagated-inputs (list r-mass r-msm r-rmeta))
@@ -3823,13 +3972,13 @@ variant.")
 (define-public r-atena
   (package
     (name "r-atena")
-    (version "1.6.0")
+    (version "1.8.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "atena" version))
               (sha256
                (base32
-                "1057mkxrjfnqhb1mydhd7vlb1s8h7n4zc4cl063gw4sgj6mw99ij"))))
+                "1qfgy76d65hbx32fw1yf20n1vavylcafb9fgqqp02r455vk3xzng"))))
     (properties `((upstream-name . "atena")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3864,13 +4013,13 @@ transcripts in an integrated manner.")
 (define-public r-atsnp
   (package
     (name "r-atsnp")
-    (version "1.16.0")
+    (version "1.18.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "atSNP" version))
               (sha256
                (base32
-                "14j8lbry4wpn8izch1nra5npg4qsh49ql4bf21jvvr3gl3qa1g7l"))))
+                "1nksx6al1cr6apknvrabi3gdbr7m61ms81nmkq4qykx5aysmp8mv"))))
     (properties `((upstream-name . "atSNP")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3897,13 +4046,13 @@ SNP-led changes in motif matches.")
 (define-public r-attract
   (package
     (name "r-attract")
-    (version "1.52.0")
+    (version "1.54.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "attract" version))
               (sha256
                (base32
-                "1lb6npxm5f82z8278v6fh7k5w8d4z73881iplm3ashc27wiw6sz3"))))
+                "0lk8gfbccrxly7gn629497sxz0mj3m9wcwdahqv1m7l6fjnf5563"))))
     (properties `((upstream-name . "attract")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3928,13 +4077,13 @@ transcriptionally-coordinated changes in gene expression.")
 (define-public r-awfisher
   (package
     (name "r-awfisher")
-    (version "1.14.0")
+    (version "1.16.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "AWFisher" version))
               (sha256
                (base32
-                "1c6rr1z1rhvn8w1kb3nnjlfacfr22vwm1rsa1xqm2hmghs01bq4x"))))
+                "10c5qi040z2w46k7qdcd2yap11mzllllrbr0nx7gd9gfzwlx089s"))))
     (properties `((upstream-name . "AWFisher")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3952,13 +4101,13 @@ meta-pattern.")
 (define-public r-awst
   (package
     (name "r-awst")
-    (version "1.8.0")
+    (version "1.10.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "awst" version))
               (sha256
                (base32
-                "0nwpfxfrx9rw4vl02vr311ivmmk96ajlwyhwms642hjv74j2yiji"))))
+                "0hry7ynv69hqbwyhlsilf1f9w8yadidbn2ckm5dx9mnb5ihgkyvj"))))
     (properties `((upstream-name . "awst")))
     (build-system r-build-system)
     (propagated-inputs (list r-summarizedexperiment))
@@ -3979,13 +4128,13 @@ artifacts.")
 (define-public r-baalchip
   (package
     (name "r-baalchip")
-    (version "1.26.0")
+    (version "1.28.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BaalChIP" version))
               (sha256
                (base32
-                "0bp8p7cn59iv08cf4yw9xl1f83dcr6v1kqvggxjals8y4gmls9nz"))))
+                "0d08mp12lw4qdy7w7i474ywcy2zgv940nc44w0gbb9h9dfl22crv"))))
     (properties `((upstream-name . "BaalChIP")))
     (build-system r-build-system)
     (inputs (list perl)) ; extra/get.overlaps.v2_chrXY.perl
@@ -4019,13 +4168,13 @@ alleles, a known phenotypical feature of cancer samples.")
 (define-public r-basespacer
   (package
     (name "r-basespacer")
-    (version "1.44.0")
+    (version "1.46.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BaseSpaceR" version))
               (sha256
                (base32
-                "15aqf2s51gl6gcnv24170v9hlq1vgya58qh1f5vjmark7j2k8vvm"))))
+                "1ldsgrhxb1nm8xj7mws461apjknp9c2bhq3738f63i2qj9g25j4g"))))
     (properties `((upstream-name . "BaseSpaceR")))
     (build-system r-build-system)
     (propagated-inputs (list r-rcurl r-rjsonio))
@@ -4066,13 +4215,13 @@ you will have to normalize your data beforehand.")
 (define-public r-bader
   (package
     (name "r-bader")
-    (version "1.38.0")
+    (version "1.40.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BADER" version))
               (sha256
                (base32
-                "0g3yvgrarpdcxpvjrxg0gbdcagknh80cr0xyzinzpmiiz0rywmzc"))))
+                "0zmf7a7lwsnk9gcg48vmzdvfmzhvnbawwg77pb4gy3cw9sjdz5ym"))))
     (properties `((upstream-name . "BADER")))
     (build-system r-build-system)
     (home-page "https://bioconductor.org/packages/BADER")
@@ -4090,13 +4239,13 @@ can be used for further down-stream analyses such as gene set enrichment.")
 (define-public r-badregionfinder
   (package
     (name "r-badregionfinder")
-    (version "1.28.0")
+    (version "1.30.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BadRegionFinder" version))
               (sha256
                (base32
-                "04bzb3i461gwkq9ygkjljpjk32c3arqr08hfzxyig1sarrryzl3q"))))
+                "17smlghl8s667n6cjx64mqli9drmv0pkq51mhjlyjy2v019im7l9"))))
     (properties `((upstream-name . "BadRegionFinder")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4117,13 +4266,13 @@ Various visual and textual types of output are available.")
 (define-public r-bambu
   (package
     (name "r-bambu")
-    (version "3.2.6")
+    (version "3.4.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "bambu" version))
               (sha256
                (base32
-                "0h7ps32vbcn4hjpfb343nn8b50zq9my0k61847fi69vc4siwcx5k"))))
+                "02pcab8jfwlx4y00yky63anba61bb1h884m0f6ajvasfpgl30w6i"))))
     (properties `((upstream-name . "bambu")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4160,13 +4309,13 @@ usage.")
 (define-public r-bandits
   (package
     (name "r-bandits")
-    (version "1.16.1")
+    (version "1.18.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BANDITS" version))
               (sha256
                (base32
-                "04l6iy0sij7zhzswhxjzir3xmrjnp6aapp0a93xp01xiv2sgdzni"))))
+                "1xdyi61scfay5l5v7c40wjjl83kcvagvypxnfvsws4avh08x3ni3"))))
     (properties `((upstream-name . "BANDITS")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4198,13 +4347,13 @@ the posterior densities for the average relative abundance of transcripts.")
 (define-public r-banocc
   (package
     (name "r-banocc")
-    (version "1.24.0")
+    (version "1.26.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "banocc" version))
               (sha256
                (base32
-                "0yi70y87isb34jc1wrnz4gr0d0f2zw44555s50j3qdnj1x8cld9y"))))
+                "0y6mizkbx3s2x6465g53q87q0sixxrxhjvjmvwiilhirxf4x7hgp"))))
     (properties `((upstream-name . "banocc")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4226,13 +4375,13 @@ estimates for each correlation element.")
 (define-public r-barcodetrackr
   (package
     (name "r-barcodetrackr")
-    (version "1.8.0")
+    (version "1.10.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "barcodetrackR" version))
               (sha256
                (base32
-                "155lxqqq2mgrz9i04xvv8y7gh2iacw6qd3mzijzbvrbm605qb3p8"))))
+                "1w5p6dqagf3g27ymqsxdim0qhnwm11rrs3nnpp4mj8jcxm8wjsh9"))))
     (properties `((upstream-name . "barcodetrackR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4268,14 +4417,14 @@ retrieval analyses, or similar technologies.")
 (define-public r-biocversion
   (package
     (name "r-biocversion")
-    (version "3.17.1")
+    (version "3.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocVersion" version))
        (sha256
         (base32
-         "0n29adnb62agp9li8rmn68z653d2m41iy9zjz75h43a05drlgp33"))))
+         "07zcf19gcbki2d18xgyrdzp3vn90cz2ww45p8ra4lc1mif5gy0c3"))))
     (properties `((upstream-name . "BiocVersion")))
     (build-system r-build-system)
     (home-page "https://bioconductor.org/packages/BiocVersion/")
@@ -4288,13 +4437,13 @@ of Bioconductor.")
 (define-public r-biocgenerics
   (package
     (name "r-biocgenerics")
-    (version "0.46.0")
+    (version "0.48.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocGenerics" version))
               (sha256
                (base32
-                "19kwpis282i8x31xlh8nc3z6vvn23p3wpx7wmrqhclf8ymq61c7z"))))
+                "0av525j9l0y3kjdy5wl6s35sh4nsabmdclq3687l5258kmq2dq8k"))))
     (properties
      `((upstream-name . "BiocGenerics")))
     (build-system r-build-system)
@@ -4308,13 +4457,13 @@ packages.")
 (define-public r-breakpointr
   (package
     (name "r-breakpointr")
-    (version "1.18.0")
+    (version "1.20.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "breakpointR" version))
               (sha256
                (base32
-                "001n99lilymgqxmpi4v89gw60j1mx13rvppv1ff1pbnk1zcmg53n"))))
+                "1jhgimybc2ib201k6vs5nfyi1whpkkzn7nj562yhz74208fx793a"))))
     (properties `((upstream-name . "breakpointR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4342,13 +4491,13 @@ export of Strand-seq data.")
 (define-public r-cardelino
   (package
     (name "r-cardelino")
-    (version "1.2.0")
+    (version "1.4.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "cardelino" version))
               (sha256
                (base32
-                "0ivhqd3da23iy2qklk2nljkjjr943m9r2y1q51fphld33izmv64v"))))
+                "0y4d3db01jwahz01hx3dswc4gg0x5k7325v4n1illgw3ddj2mvgn"))))
     (properties `((upstream-name . "cardelino")))
     (build-system r-build-system)
     (propagated-inputs (list r-combinat
@@ -4380,20 +4529,20 @@ stochastic dropout events as well as systematic allelic imbalance is used.")
 (define-public r-cellid
   (package
     (name "r-cellid")
-    (version "1.8.1")
+    (version "1.10.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "CelliD" version))
               (sha256
                (base32
-                "0vigvqjrlqbi5kviaj8qvyq3v8afgbc5pjrz7zmx2ckf4hdp0g03"))))
+                "1x4kp8i204rqas2bgg4qanwdncafilymlpvxvfyv39zpdji91yv5"))))
     (properties `((upstream-name . "CelliD")))
     (build-system r-build-system)
     (propagated-inputs
-     (list r-data-table
-           r-biocparallel
+     (list r-biocparallel
+           r-data-table
            r-fastmatch
-	   r-fgsea
+           r-fgsea
            r-ggplot2
            r-glue
            r-irlba
@@ -4404,13 +4553,14 @@ stochastic dropout events as well as systematic allelic imbalance is used.")
            r-rcpparmadillo
            r-reticulate
            r-rtsne
+           r-scater
            r-seurat
+           r-singlecellexperiment
            r-stringr
-           r-tictoc
-	   r-singlecellexperiment
            r-summarizedexperiment
+           r-tictoc
            r-umap))
-    (native-inputs (list r-knitr r-scater))
+    (native-inputs (list r-knitr))
     (home-page "https://bioconductor.org/packages/CelliD")
     (synopsis
      "Single cell gene signature extraction using multiple correspondence analysis")
@@ -4422,24 +4572,69 @@ omics protocols.  The package can also be used to explore functional pathways
 enrichment in single cell data.")
     (license license:gpl3)))
 
+(define-public r-coregx
+  (package
+    (name "r-coregx")
+    (version "2.6.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "CoreGx" version))
+       (sha256
+        (base32 "0ffbi5afw759mi5r657h67hdh9yr5jrzvl3aigp960jzb5542105"))))
+    (properties `((upstream-name . "CoreGx")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-bench
+           r-biobase
+           r-biocgenerics
+           r-biocparallel
+           r-bumpymatrix
+           r-checkmate
+           r-crayon
+           r-data-table
+           r-glue
+           r-lsa
+           r-matrixgenerics
+           r-multiassayexperiment
+           r-piano
+           r-rlang
+           r-s4vectors
+           r-summarizedexperiment))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/CoreGx")
+    (synopsis
+     "Classes and functions to serve as the basis for other Gx packages")
+    (description
+     "This package provides a collection of functions and classes which serve
+as the foundation for packages such as PharmacoGx and RadioGx.  It was created
+to abstract shared functionality to increase ease of maintainability and
+reduce code repetition in current and future Gx suite programs.  Major
+features include a @code{CoreSet} class, from which RadioSet and PharmacoSet
+are derived, along with get and set methods for each respective slot.
+Additional functions related to fitting and plotting dose response curves,
+quantifying statistical correlation and calculating @acronym{AUC, area under
+the curve} or @acronym{SF, survival fraction} are included.")
+    (license license:gpl3+)))
+
 (define-public r-coverageview
   (package
     (name "r-coverageview")
-    (version "1.38.0")
+    (version "1.40.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "CoverageView" version))
               (sha256
                (base32
-                "1ci07y75nvvv1mxy23v6jp5xb6n023fvlqh9il5lsdqwyfl5nz9s"))))
+                "1sj1vr84nsbygkh5mmp7zm21zzk4zcw3bwcvcazmy54zs553blpf"))))
     (build-system r-build-system)
     (propagated-inputs
-     (list r-s4vectors
-           r-iranges
+     (list r-genomicalignments
            r-genomicranges
-           r-genomicalignments
+           r-iranges
+           r-rsamtools
            r-rtracklayer
-           r-rsamtools))
+           r-s4vectors))
     (home-page "https://bioconductor.org/packages/CoverageView/")
     (synopsis "Coverage visualization package for R")
     (description "This package provides a framework for the visualization of
@@ -4452,13 +4647,13 @@ how the coverage distributed across the genome.")
 (define-public r-cummerbund
   (package
    (name "r-cummerbund")
-   (version "2.42.0")
+   (version "2.44.0")
    (source (origin
              (method url-fetch)
              (uri (bioconductor-uri "cummeRbund" version))
              (sha256
               (base32
-               "1xin1azby96xxp4yyd4wc3rfcjc2g9p01ksfd89bk2vxcclccqxn"))))
+               "1a5x3jzagd1a385yk1brs4say02r0l21qqjak4cl6fsv8ihhy05s"))))
    (build-system r-build-system)
    (propagated-inputs
     (list r-biobase
@@ -4482,13 +4677,13 @@ used visualizations.")
 (define-public r-dama
   (package
     (name "r-dama")
-    (version "1.72.0")
+    (version "1.74.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "daMA" version))
               (sha256
                (base32
-                "0z4y57hna312pkhkchair8calm7wl40rx8lcm8i6h1789hba063d"))))
+                "1ckk8h6adylaxq6bh14ym9vvrrhsfglnaigqz16v96vsj8q9i336"))))
     (properties `((upstream-name . "daMA")))
     (build-system r-build-system)
     (propagated-inputs (list r-mass))
@@ -4504,13 +4699,13 @@ factorial microarray data.")
 (define-public r-damefinder
   (package
     (name "r-damefinder")
-    (version "1.12.0")
+    (version "1.14.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "DAMEfinder" version))
               (sha256
                (base32
-                "0m8g1sp55mxa0qswpqkzk73myhhy3s49c21hf97sk0lxis5lagcd"))))
+                "0mbm884dm30b4fwf3qr1w96j18dxdmr2bn11dw83hh0wrbhp8njm"))))
     (properties `((upstream-name . "DAMEfinder")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4545,14 +4740,14 @@ offers nice visualization of methyl-circle plots.")
 (define-public r-dearseq
   (package
     (name "r-dearseq")
-    (version "1.12.1")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "dearseq" version))
        (sha256
         (base32
-         "12ld1f3892ag1a3lmkwjlkk6pd79ibykg8jrmddx2x33k23cv67g"))))
+         "1ldxw457zsfphm6izxz2kvxy3719gszhxb8mymx8njg6islljy27"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-compquadform
@@ -4584,13 +4779,13 @@ set analyses, and can deal with repeated or longitudinal data.")
 (define-public r-debcam
   (package
     (name "r-debcam")
-    (version "1.18.0")
+    (version "1.20.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "debCAM" version))
               (sha256
                (base32
-                "11vqfkyd3fklc8fhn850kklph8x4pmwclb9xbqji4i21222m89hh"))
+                "1swqqrlwin2i2qq46qyfziblbfsfyd5hf6w39hygp7fdkpic14b7"))
               (snippet
                '(for-each delete-file
                           '("inst/java/CornerDetect.jar"
@@ -4599,9 +4794,6 @@ set analyses, and can deal with repeated or longitudinal data.")
     (build-system r-build-system)
     (arguments
      (list
-      ;; XXX: since the upgrade to R 4.3.0 this package takes too long to be
-      ;; loaded.
-      #:tests? #false
       #:configure-flags '(list "--fake")
       #:modules
       '((guix build r-build-system)
@@ -4629,7 +4821,7 @@ set analyses, and can deal with repeated or longitudinal data.")
          (add-after 'install 'strip-jar-timestamps
            (assoc-ref ant:%standard-phases 'strip-jar-timestamps)))))
     (inputs
-     (list (list icedtea "jdk")
+     (list (list openjdk11 "jdk")
            java-pj))
     (propagated-inputs
      (list r-apcluster
@@ -4661,13 +4853,13 @@ knowledge can achieve semi-supervised deconvolution of mixtures.")
 (define-public r-decipher
   (package
     (name "r-decipher")
-    (version "2.28.0")
+    (version "2.30.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "DECIPHER" version))
               (sha256
                (base32
-                "16z6yk8rr2115z6g1l7fl01binxm29vnxsnsm2wzfvc5vv49927n"))))
+                "1ri8ldx3dqcpfvn3mz0022f77zi6ki04mh27qp132bbrjkj6zl79"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biostrings
@@ -4760,13 +4952,13 @@ mechanism based on the shared signatures.")
 (define-public r-decomptumor2sig
   (package
     (name "r-decomptumor2sig")
-    (version "2.16.0")
+    (version "2.18.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "decompTumor2Sig" version))
               (sha256
                (base32
-                "028sczy1d108i05ymr1wpj6jdrcds476wbmmc7rzzflzyg4aix75"))))
+                "13vwrg82zprb9h72azdqd0rkm5k2xm4mw7viawbzwkkqvg6azsdj"))))
     (properties `((upstream-name . "decompTumor2Sig")))
     (build-system r-build-system)
     (inputs (list perl))                ;script/extractSpecColumns.pl
@@ -4803,13 +4995,13 @@ of the signatures to the mutation load of the tumor.")
 (define-public r-deconrnaseq
   (package
     (name "r-deconrnaseq")
-    (version "1.42.0")
+    (version "1.44.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "DeconRNASeq" version))
               (sha256
                (base32
-                "0bmkyci31p7g097i8fvc0s1fz47hv6vp5rcfqqkvclm86wfkkmkc"))))
+                "1k5xrx97w9g0jfvjzawyfsqyz2fj9r463nj849djxgmcw8vp53vg"))))
     (properties `((upstream-name . "DeconRNASeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4830,13 +5022,13 @@ single expression profiles.")
 (define-public r-decontam
   (package
     (name "r-decontam")
-    (version "1.20.0")
+    (version "1.22.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "decontam" version))
               (sha256
                (base32
-                "08niwixy4m6gqmazisxzbbla9nsxicpa685jy3r6knapwaznvcb2"))))
+                "0m4zd6qxsrp7w9a8psg8xcrviim6plwgwn4rgdxy8ag0c442fsvk"))))
     (properties `((upstream-name . "decontam")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4856,13 +5048,13 @@ negative control samples.")
 (define-public r-deconvr
   (package
     (name "r-deconvr")
-    (version "1.6.0")
+    (version "1.8.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "deconvR" version))
               (sha256
                (base32
-                "1r5js5prwy1libnf1g1a4pdi15pj216bb8ajhzii3symn5r0cdj9"))))
+                "0pl4nwaf8swwz9nl2ynf9mm38d0x223gpz89qrj03yihxszy2n13"))))
     (properties `((upstream-name . "deconvR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4901,13 +5093,13 @@ make mapping WGBS data to their probe IDs easier.")
 (define-public r-decoupler
   (package
     (name "r-decoupler")
-    (version "2.6.0")
+    (version "2.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "decoupleR" version))
        (sha256
-        (base32 "012d76jwgg6fwfjc00zdws59y6jbj0grzd4lgjrqs2afp2ycmh9s"))))
+        (base32 "1vnlrkza33nb80qf810yfz66m3j84p8chhfdxak5lvpciqwx7dh9"))))
     (properties `((upstream-name . "decoupleR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4942,13 +5134,13 @@ targeted by a kinase.")
 (define-public r-deepsnv
   (package
     (name "r-deepsnv")
-    (version "1.46.0")
+    (version "1.48.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "deepSNV" version))
               (sha256
                (base32
-                "11cnyy3hyn8akhmax25293mx2blcs8ba5vfax6mx6hjhb577hkwb"))))
+                "16dkjqy9ba5v8nikaxdjcz7rr60dg46sfsgrjjlp82rf3256bf8r"))))
     (properties `((upstream-name . "deepSNV")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4978,13 +5170,13 @@ bases such as COSMIC.")
 (define-public r-degreport
   (package
     (name "r-degreport")
-    (version "1.36.0")
+    (version "1.38.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "DEGreport" version))
               (sha256
                (base32
-                "15xm1l2qgsyzaw820a1fq5qdzh5pj4dmr1hx6s6b6wm2p02cvvai"))
+                "1ska9fh1bzdqd9pi67vqgx0vz4wz2r5kzmh73fb9zh9m0gnjjr23"))
               (snippet
                '(delete-file "docs/jquery.sticky-kit.min.js"))))
     (properties `((upstream-name . "DEGreport")))
@@ -5049,13 +5241,13 @@ fold changes mean and variability for each selected gene.")
 (define-public r-delayedarray
   (package
     (name "r-delayedarray")
-    (version "0.26.7")
+    (version "0.28.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "DelayedArray" version))
               (sha256
                (base32
-                "1xsq85nm1gk537mw6ppsyykpw70kczv6wn1nll63b0k8xs4wj0ha"))))
+                "0mf30vdns64mpm11zcz9qx6nh5clr6krjvcmr7dqv2xg5ig0a1f7"))))
     (properties
      `((upstream-name . "DelayedArray")))
     (build-system r-build-system)
@@ -5065,7 +5257,8 @@ fold changes mean and variability for each selected gene.")
            r-matrix
            r-matrixgenerics
            r-s4arrays
-           r-s4vectors))
+           r-s4vectors
+           r-sparsearray))
     (native-inputs
      (list r-knitr))
     (home-page "https://bioconductor.org/packages/DelayedArray")
@@ -5083,17 +5276,21 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns),
 (define-public r-densvis
   (package
     (name "r-densvis")
-    (version "1.10.3")
+    (version "1.12.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "densvis" version))
               (sha256
                (base32
-                "1nkii02bj49z9qm3rj8lzwpz7dllrsa5zf7dn5ffcczyxr3b1ap9"))))
+                "164pyy5l69qhdgqkxjginapvfjy0rjx4p6m83cijz6jbz6kf6gks"))))
     (properties `((upstream-name . "densvis")))
     (build-system r-build-system)
-    (propagated-inputs (list r-assertthat r-basilisk r-irlba r-rcpp
-                             r-reticulate))
+    (propagated-inputs (list r-assertthat
+                             r-basilisk
+                             r-irlba
+                             r-rcpp
+                             r-reticulate
+                             r-rtsne))
     (native-inputs (list r-knitr))
     (home-page "https://bioconductor.org/packages/densvis")
     (synopsis
@@ -5114,13 +5311,13 @@ heterogeneity in the original high-dimensional space.")
 (define-public r-derfinder
   (package
     (name "r-derfinder")
-    (version "1.34.0")
+    (version "1.36.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "derfinder" version))
               (sha256
                (base32
-                "1gb65hk26ffn0njsgwgk43z9i9bcvx89pz5m9x951c2a07c1xrcw"))))
+                "0rj3szlpbxiwj3rajmr6ccnbs1mkcskql12iip8zgswmhz76rxh1"))))
     (properties `((upstream-name . "derfinder")))
     (build-system r-build-system)
     (propagated-inputs (list r-annotationdbi
@@ -5160,13 +5357,13 @@ The DER Finder approach can also be used to identify differentially bounded
 (define-public r-derfinderhelper
   (package
     (name "r-derfinderhelper")
-    (version "1.34.0")
+    (version "1.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "derfinderHelper" version))
        (sha256
-        (base32 "0ww4lvwmm8rf44wgksg98bqh7zlm503c4gc8dwilb1w0dz2k7qll"))))
+        (base32 "01vq8xnszxqhijranzaciapw8mcn6px0jhx9zb9lyqhsvaffjh5r"))))
     (properties `((upstream-name . "derfinderHelper")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5226,13 +5423,13 @@ possibly confounded by SNPs and cross-hybridisation.  It includes
 (define-public r-drimseq
   (package
     (name "r-drimseq")
-    (version "1.28.0")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DRIMSeq" version))
        (sha256
-        (base32 "1i9lcp31g94mllkwcyfablj27qr8v7vqk9j96ywrdfpj8dmcrw98"))))
+        (base32 "1nf044cfqywfnglm081xbppamva87z2j2xz0f51z8mra11apj6i6"))))
     (properties `((upstream-name . "DRIMSeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5261,13 +5458,13 @@ results.")
 (define-public r-dropletutils
   (package
     (name "r-dropletutils")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DropletUtils" version))
        (sha256
-        (base32 "09xwfb4ihpsp465vb1zbcwm6ww6qi3spn9d8p4i1gczyc0p9pf1y"))))
+        (base32 "0bnxk72a0ygh4nqwyjzzi79zc4md8pwk0pr6jn43in0wdk054wf6"))))
     (properties `((upstream-name . "DropletUtils")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5331,13 +5528,13 @@ Beta-Binomial distributions.")
 (define-public r-dyndoc
   (package
     (name "r-dyndoc")
-    (version "1.78.0")
+    (version "1.80.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "DynDoc" version))
               (sha256
                (base32
-                "16cb4pby6ja0xy8ygbgr6zfbyp4agyhlds5sayc5ryq50vafykah"))))
+                "0d2axaszy7rpi47yg4vhd1z70m53nx40znapgg5pq6ahrx7if5f1"))))
     (properties `((upstream-name . "DynDoc")))
     (build-system r-build-system)
     (home-page "https://bioconductor.org/packages/DynDoc")
@@ -5350,13 +5547,13 @@ dynamic documents and vignettes.")
 (define-public r-bluster
   (package
    (name "r-bluster")
-   (version "1.10.0")
+   (version "1.12.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "bluster" version))
             (sha256
              (base32
-              "15f103lpl686730vl8g69fhki9iq2ncgr5dm6qm2xc9bq9vh65s9"))))
+              "16zkv567d39258syhfb215y04sq3pnfjh9pgbp5z85hcfpz4qmhc"))))
    (properties `((upstream-name . "bluster")))
    (build-system r-build-system)
    (propagated-inputs
@@ -5380,21 +5577,21 @@ and evaluate clustering results.")
 (define-public r-ideoviz
   (package
     (name "r-ideoviz")
-    (version "1.36.0")
+    (version "1.37.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "IdeoViz" version))
               (sha256
                (base32
-                "1za1cxf734mar9hbvqrijdg61g0jag9jdzmi8p8ka62xbikxqa3s"))))
+                "1bhari5ghag5f5dlrgm79hckbh0bamd9567z04qi0spnfr97wf3s"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biobase
-           r-iranges
+           r-genomeinfodb
            r-genomicranges
+           r-iranges
            r-rcolorbrewer
-           r-rtracklayer
-           r-genomeinfodb))
+           r-rtracklayer))
     (home-page "https://bioconductor.org/packages/IdeoViz/")
     (synopsis "Plots data along a chromosomal ideogram")
     (description "This package provides functions to plot data associated with
@@ -5404,14 +5601,14 @@ arbitrary genomic intervals along chromosomal ideogram.")
 (define-public r-infercnv
   (package
     (name "r-infercnv")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "infercnv" version))
        (sha256
         (base32
-         "19fk4pzhwj9pfh4vg943xb4cdfpq65ax75d61w1mm3f71gg56z5g"))))
+         "1yxg04644yqy3wbqbsf4hcvvimkk8z60xizpy4rc48i3hxjm7nbf"))))
     (properties `((upstream-name . "infercnv")))
     (build-system r-build-system)
     (inputs (list python))
@@ -5443,8 +5640,8 @@ arbitrary genomic intervals along chromosomal ideogram.")
            r-rcolorbrewer
            r-reshape2
            r-rjags
-           r-singlecellexperiment
            r-seurat
+           r-singlecellexperiment
            r-summarizedexperiment
            r-tidyr))
     (native-inputs (list r-knitr))
@@ -5464,13 +5661,13 @@ over-abundant or less-abundant as compared to that of normal cells.")
 (define-public r-iranges
   (package
     (name "r-iranges")
-    (version "2.34.1")
+    (version "2.36.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "IRanges" version))
               (sha256
                (base32
-                "013a3vcw1v5vn0sg2d9cwrdksch48kilvxp8cr79y0nr4vk58q9z"))))
+                "0rhh82hrsm32bdjamfah84p7zi8fvr4shyq2rdjfxzdp9qy5rh2q"))))
     (properties
      `((upstream-name . "IRanges")))
     (build-system r-build-system)
@@ -5492,13 +5689,13 @@ possible.")
 (define-public r-isoformswitchanalyzer
   (package
     (name "r-isoformswitchanalyzer")
-    (version "2.0.1")
+    (version "2.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "IsoformSwitchAnalyzeR" version))
        (sha256
-        (base32 "1zjwhxlayz2sb77vspw280didhawj282i5gvxnydcdparg165zwf"))))
+        (base32 "1yin2jv06g3jrzadq6yjcr14jz1zzwyxipzna5csgr013dkkrl8h"))))
     (properties `((upstream-name . "IsoformSwitchAnalyzeR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5573,13 +5770,13 @@ AE et al 2011, <doi: 10.1093/bioinformatics/btr171>).")
 (define-public r-italics
   (package
     (name "r-italics")
-    (version "2.60.0")
+    (version "2.62.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ITALICS" version))
        (sha256
-        (base32 "09yia158mrv9r32iw88jlbfd6l7hzmglv8ni7i28x18qvnhp2a08"))))
+        (base32 "0zk9n94nqw6vpw908ka32zppxwqkki9krzxib06y1nic3bri3w9i"))))
     (properties `((upstream-name . "ITALICS")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5708,13 +5905,13 @@ mapping.")
 (define-public r-nebulosa
   (package
     (name "r-nebulosa")
-    (version "1.10.0")
+    (version "1.12.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Nebulosa" version))
               (sha256
                (base32
-                "0lqm9mfmaxdhhs9di2kjg2rixng78lrrikyp7blmpyqk4c41j3nh"))))
+                "0kzkdwxrhl7plbcbqr58gnadhhbhx2811ian0s4kds14y4mxl26c"))))
     (properties `((upstream-name . "Nebulosa")))
     (build-system r-build-system)
     (propagated-inputs (list r-ggplot2
@@ -5784,14 +5981,14 @@ performing parallel computations on multicore machines.")
 (define-public r-affy
   (package
     (name "r-affy")
-    (version "1.78.2")
+    (version "1.80.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "affy" version))
        (sha256
         (base32
-         "0zsr87zsw5rp5rgdiv1bbsi6fx6b7qzlgjirzczky6fmf4dqwgnm"))))
+         "0lsvcv7nprmsh62d0r2v44a5n915crvv1cbj9ba6fdggj7wp8zyk"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-affyio
@@ -5812,14 +6009,14 @@ analysis.")
 (define-public r-affycomp
   (package
     (name "r-affycomp")
-    (version "1.76.1")
+    (version "1.78.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "affycomp" version))
        (sha256
         (base32
-         "0wccj8q8sl0zc68nr5qf1qih8awqf1h6bwi5hq9d7r59p4g4r9n1"))))
+         "0818mgwny9hznw7lawrvmk11nwy0wxgjnlkf083vv3js4aq31gfp"))))
     (properties `((upstream-name . "affycomp")))
     (build-system r-build-system)
     (propagated-inputs (list r-biobase))
@@ -5878,14 +6075,14 @@ Command Console} (AGCC)-compatible sample annotation files.")
 (define-public r-affycontam
   (package
     (name "r-affycontam")
-    (version "1.58.0")
+    (version "1.60.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "affyContam" version))
        (sha256
         (base32
-         "07a6kd51rlj433yxmyd2j8nl8qn1hw8wv3mk270dp8xxlk613y3p"))))
+         "1jxp4qacclfl07ig8dfwy5gpnsqrfqnjbci1a7znc7acqg0kv0zv"))))
     (properties `((upstream-name . "affyContam")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5943,14 +6140,14 @@ to streamline the more common analyses that a Biostatistician might see.")
 (define-public r-affyio
   (package
     (name "r-affyio")
-    (version "1.70.0")
+    (version "1.72.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "affyio" version))
        (sha256
         (base32
-         "1r1c0iwix0n8r433x4bv8hvzhkablc4xkdgg2b1fk4ijhd1iwf3c"))))
+         "01shv7936cb5yynxkdssczl752ayv2rx4qkrkddqhi5smksw13z9"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-zlibbioc))
@@ -5967,14 +6164,14 @@ CDF file formats.")
 (define-public r-affxparser
   (package
     (name "r-affxparser")
-    (version "1.72.0")
+    (version "1.74.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "affxparser" version))
        (sha256
         (base32
-         "0n86my3bzy3g7xn60kizs5ym5m016zrkg7dv96kx246mrnv0ax8y"))))
+         "18qjdsgkmdhwv2c4sbixp7fn69sbjdipn363jnms95dksdj2xvr9"))))
     (properties `((upstream-name . "affxparser")))
     (build-system r-build-system)
     (home-page "https://github.com/HenrikBengtsson/affxparser")
@@ -5995,14 +6192,14 @@ structure.")
 (define-public r-annotate
   (package
     (name "r-annotate")
-    (version "1.78.0")
+    (version "1.80.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "annotate" version))
        (sha256
         (base32
-         "1104r6jdy3nza8329xmq428ljfbfi2xwkd92sw519g0yqryh09vy"))))
+         "10mdlbgbvdj967bih6wpvxmy91r10p8frhgcwv8mhv4g94ardasd"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-annotationdbi
@@ -6022,13 +6219,13 @@ microarrays.")
 (define-public r-annotationdbi
   (package
     (name "r-annotationdbi")
-    (version "1.62.2")
+    (version "1.64.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "AnnotationDbi" version))
               (sha256
                (base32
-                "0vprm84k79pfnkkg9vf3gyb1nhzmin5lp5375rsaj6fnzbd46dw9"))))
+                "0nyw3x5ivq969p2w788zi4pp0pwjv5hhpjpl5lyfzhak9ydylgh6"))))
     (properties
      `((upstream-name . "AnnotationDbi")))
     (build-system r-build-system)
@@ -6052,13 +6249,13 @@ annotation data packages using SQLite data storage.")
 (define-public r-annotationfilter
   (package
     (name "r-annotationfilter")
-    (version "1.24.0")
+    (version "1.26.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "AnnotationFilter" version))
               (sha256
                (base32
-                "10jkxjmsshrr08c397qvkgrcfwzvrbd2hci1nal4vd5mm77f9cl9"))))
+                "0cd2vcnx0pn5wba3x5q32vddjjp7fvix7yd7jrwv07a2fkv9c4p5"))))
     (properties
      `((upstream-name . "AnnotationFilter")))
     (build-system r-build-system)
@@ -6077,14 +6274,14 @@ used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.")
 (define-public r-annotationforge
   (package
     (name "r-annotationforge")
-    (version "1.42.2")
+    (version "1.44.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "AnnotationForge" version))
        (sha256
         (base32
-         "0b4dmjv7y50c1rn76wlhnlz93kidvg1byj72vq2s11kdzyq3pmss"))))
+         "0dbbg0wvk1ndv20d5j80waaz0z1bsp7y2k2m17jly4ax2hc5frc9"))))
     (properties
      `((upstream-name . "AnnotationForge")))
     (build-system r-build-system)
@@ -6109,14 +6306,14 @@ databases.  Packages produced are intended to be used with AnnotationDbi.")
 (define-public r-annotationhub
   (package
     (name "r-annotationhub")
-    (version "3.8.0")
+    (version "3.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "AnnotationHub" version))
        (sha256
         (base32
-         "0ri8qj5j10bhprkb810c2hl5sl944kpb8rf5lab6nxykzgyz73v0"))))
+         "1mx3vip1rx5lq0vnkxpmkyksnq4vygmww85vxq3spr0fah1pwnkr"))))
     (properties `((upstream-name . "AnnotationHub")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6150,14 +6347,14 @@ by the user, helping with quick and reproducible access.")
 (define-public r-aroma-light
   (package
     (name "r-aroma-light")
-    (version "3.30.0")
+    (version "3.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "aroma.light" version))
        (sha256
         (base32
-         "118yqvbj4ad2b2bik0zi3ir15kxh9fbdi9qqyk52isvcdbv6069p"))))
+         "1i6rml0slfsf01a3sphyzrxp2z759psq5bv9cfy5dxx44fnav8b8"))))
     (properties `((upstream-name . "aroma.light")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6174,14 +6371,14 @@ classes.")
 (define-public r-bamsignals
   (package
     (name "r-bamsignals")
-    (version "1.32.0")
+    (version "1.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bamsignals" version))
        (sha256
         (base32
-         "18058j3fc47qcwvzgpb8mbc7cd1pywzrz3a36iqz93ihzjmymydk"))))
+         "1qv2gydn8awrkbhdrgxm8zxpicphqc29rwzkj3vyaa9glmnx2y34"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biocgenerics
@@ -6204,13 +6401,13 @@ paired-end data.")
 (define-public r-biobase
   (package
     (name "r-biobase")
-    (version "2.60.0")
+    (version "2.62.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Biobase" version))
               (sha256
                (base32
-                "1xjs5nxr3dffllp599hf0cx71a2czqmhf7zj2sp6rz06kcxib905"))))
+                "0znkawzr3hgbp2dkdk30ziqa6ylbq2nf0xmz4vi089cw9763lxgg"))))
     (properties
      `((upstream-name . "Biobase")))
     (build-system r-build-system)
@@ -6227,13 +6424,13 @@ on Bioconductor or which replace R functions.")
 (define-public r-biomart
   (package
     (name "r-biomart")
-    (version "2.56.1")
+    (version "2.58.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "biomaRt" version))
               (sha256
                (base32
-                "0jqv2mv4ridi5lffva20a5s479bzpxhblyymricb17fd400rag8f"))))
+                "1m6c6m9z0d1k6s2q0ikd78ahcq72gzqnhlprdn0xvkjxrgh1i2lf"))))
     (properties
      `((upstream-name . "biomaRt")))
     (build-system r-build-system)
@@ -6267,13 +6464,13 @@ powerful online queries from gene annotation to database mining.")
 (define-public r-biomartr
   (package
     (name "r-biomartr")
-    (version "1.0.5")
+    (version "1.0.6")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "biomartr" version))
               (sha256
                (base32
-                "14nw44dkyrfw43dc4zwsnvkrmdhsl131m9w1wa80j3qkbhyaypfl"))))
+                "06wd8s2cssw58xp9d078fc7iycpxryccnclrk3gnh757j1h0vzim"))))
     (properties `((upstream-name . "biomartr")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6312,13 +6509,13 @@ only one command.")
 (define-public r-biocparallel
   (package
     (name "r-biocparallel")
-    (version "1.34.2")
+    (version "1.36.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocParallel" version))
               (sha256
                (base32
-                "0j0yi0g0zri0liy9xm2j3k848smhib5mmkvwcw6281iwnpn7yypq"))))
+                "19h80qf0zdxfg3pkcwwywh9gg0ymv92n51qpimnw4c3w5iaszy6b"))))
     (properties
      `((upstream-name . "BiocParallel")))
     (build-system r-build-system)
@@ -6363,13 +6560,13 @@ objects.")
 (define-public r-biostrings
   (package
     (name "r-biostrings")
-    (version "2.68.1")
+    (version "2.70.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Biostrings" version))
               (sha256
                (base32
-                "13cnjbq2iykv83ycb4151d7yys21s3v15fc72v3s02m1i92lqyq4"))))
+                "198y36yfkncsp4sw00ij8cal45al67f9nx84bbszhygaq0jh504y"))))
     (properties
      `((upstream-name . "Biostrings")))
     (build-system r-build-system)
@@ -6380,6 +6577,7 @@ objects.")
            r-iranges
            r-s4vectors
            r-xvector))
+    (native-inputs (list r-knitr))
     (home-page "https://bioconductor.org/packages/Biostrings")
     (synopsis "String objects and algorithms for biological sequences")
     (description
@@ -6391,14 +6589,14 @@ biological sequences or sets of sequences.")
 (define-public r-biovizbase
   (package
     (name "r-biovizbase")
-    (version "1.48.0")
+    (version "1.50.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biovizBase" version))
        (sha256
         (base32
-         "0na37f2nfavgxd2xhprfb6bv68zm2h6glbkffspc3gsnw1q5h6da"))))
+         "01hli49aq1fjjgpk465znq1ki0qi7nxg71pqg18fz6nblg3ny9z5"))))
     (properties `((upstream-name . "biovizBase")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6433,18 +6631,19 @@ effort and encourages consistency.")
 (define-public r-bsgenome
   (package
     (name "r-bsgenome")
-    (version "1.68.0")
+    (version "1.70.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BSgenome" version))
               (sha256
                (base32
-                "0fx2mkzyhbn8iayw14nr913wd4xhp76b1zjb85akrxaab2dm4zz8"))))
+                "1bdrh1kp7ihnlyvgdvwdzly69l9zy5rr09gizm0l59zy4kh59nih"))))
     (properties
      `((upstream-name . "BSgenome")))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biocgenerics
+           r-biocio
            r-biostrings
            r-genomeinfodb
            r-genomicranges
@@ -6464,14 +6663,14 @@ genome data packages and support for efficient SNP representation.")
 (define-public r-category
   (package
     (name "r-category")
-    (version "2.66.0")
+    (version "2.68.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Category" version))
        (sha256
         (base32
-         "1wjf6xbnys7nv8z4xrzck1wk5xifkdni672kigs0aqdxqj8d80f5"))))
+         "19qyxqky1gsrjylmc2h0sndbqlk2ibrps7123gqwn19p8kg4nhf0"))))
     (properties `((upstream-name . "Category")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6479,12 +6678,12 @@ genome data packages and support for efficient SNP representation.")
            r-annotationdbi
            r-biobase
            r-biocgenerics
+           r-dbi
            r-genefilter
            r-graph
            r-gseabase
            r-matrix
-           r-rbgl
-           r-dbi))
+           r-rbgl))
     (home-page "https://bioconductor.org/packages/Category")
     (synopsis "Category analysis")
     (description
@@ -6557,13 +6756,13 @@ regions and to highlight copy number alterations.")
 (define-public r-chipseeker
   (package
     (name "r-chipseeker")
-    (version "1.36.0")
+    (version "1.38.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "ChIPseeker" version))
               (sha256
                (base32
-                "0nngygci1g8bb3rsica348zi59hskr6hf8319csia6cman89gvqm"))))
+                "0bx85y5888w85miif73y0yd9j4kdmjn1cfck1xshnqnsrh7p3m50"))))
     (build-system r-build-system)
     (native-inputs
      (list r-knitr))
@@ -6572,18 +6771,17 @@ regions and to highlight copy number alterations.")
            r-aplot
            r-biocgenerics
            r-boot
+           r-dplyr
            r-enrichplot
-           r-iranges
            r-genomeinfodb
-           r-genomicranges
            r-genomicfeatures
+           r-genomicranges
            r-ggplot2
            r-gplots
            r-gtools
-           r-dplyr
-           r-plotrix
-           r-dplyr
+           r-iranges
            r-magrittr
+           r-plotrix
            r-rtracklayer
            r-s4vectors
            r-tibble
@@ -6605,14 +6803,14 @@ annotation, distance to TSS, and overlap of peaks or genes.")
 (define-public r-chipseq
   (package
     (name "r-chipseq")
-    (version "1.50.0")
+    (version "1.52.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "chipseq" version))
        (sha256
         (base32
-         "0q83c4dm9qbdxlh4cbdzp357fn4sa16d7dqb4s65650pcnjg3a48"))))
+         "1fw99xnll4jwdmp49jh59zxcbp3qs2850pjdg403sv4cg1bgfdyi"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biocgenerics
@@ -6632,14 +6830,14 @@ experiments.")
 (define-public r-complexheatmap
   (package
     (name "r-complexheatmap")
-    (version "2.16.0")
+    (version "2.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ComplexHeatmap" version))
        (sha256
         (base32
-         "08jpbw7qns736zq1fwk9lyr4qm7rgzzw3hksv59zwb1458a79pzy"))))
+         "0zzp0kci5daffpyv56advdcs05pz3nmjn07bmm7r3hwpk0nr3fcf"))))
     (properties
      `((upstream-name . "ComplexHeatmap")))
     (build-system r-build-system)
@@ -6794,14 +6992,14 @@ distribution.")
 (define-public r-deseq2
   (package
     (name "r-deseq2")
-    (version "1.40.2")
+    (version "1.42.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DESeq2" version))
        (sha256
         (base32
-         "0rb6b2aqn3an5ria4yjasjr7aldr5606rkc4yw275x9ddii22djg"))))
+         "1mz7v0vcl741zjvj63mk48hhbq6sk2fl2dwn9y1a6hr8fb79vy1a"))))
     (properties `((upstream-name . "DESeq2")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6812,6 +7010,7 @@ distribution.")
            r-ggplot2
            r-iranges
            r-locfit
+           r-matrixgenerics
            r-matrixstats
            r-rcpp
            r-rcpparmadillo
@@ -6831,14 +7030,14 @@ distribution.")
 (define-public r-dexseq
   (package
     (name "r-dexseq")
-    (version "1.46.0")
+    (version "1.48.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DEXSeq" version))
        (sha256
         (base32
-         "0z4i3lsaziq3hprk64akx7jl6b757kmd8k6gv5pn36pavc6x1a0g"))))
+         "1q59agaidf0nkq599iz54a253sjxzillj39za86ihfj5xws24f8w"))))
     (properties `((upstream-name . "DEXSeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6876,13 +7075,13 @@ exploration of the results.")
 (define-public r-diffcyt
   (package
     (name "r-diffcyt")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "diffcyt" version))
        (sha256
-        (base32 "1vsn9z06vmfw6741x7dri3d9wh4rqhzak9r506y3c3h2gjjwilv1"))))
+        (base32 "1k3gzzgda29m2v7v8hqw7c2s8z778p0plqxag443lhsxcm6izcxi"))))
     (properties `((upstream-name . "diffcyt")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6914,14 +7113,14 @@ adapted from transcriptomics.")
 (define-public r-dirichletmultinomial
   (package
     (name "r-dirichletmultinomial")
-    (version "1.42.0")
+    (version "1.44.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DirichletMultinomial" version))
        (sha256
         (base32
-         "1vslg6hp498ar4l1b8rdxscz5wj1xci866j8975wr378lnymb942"))))
+         "1rvic3acrf4qdag423f8xa6bnqrqr31vj7k4l7a5kzf1fjm359wy"))))
     (properties
      `((upstream-name . "DirichletMultinomial")))
     (build-system r-build-system)
@@ -6941,13 +7140,13 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2):
 (define-public r-dittoseq
   (package
     (name "r-dittoseq")
-    (version "1.12.1")
+    (version "1.14.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "dittoSeq" version))
               (sha256
                (base32
-                "0gpgmy1yqgxvxiyrinxnn78w68w81ldqyhzwz3yxj2brlld6ycd1"))))
+                "17ks6bbhv8iw8grzlkibgqmwggrqp5hikg1p49m4a6b6bayillv2"))))
     (properties `((upstream-name . "dittoSeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6985,14 +7184,14 @@ code{dittoColors()}.")
 (define-public r-edaseq
   (package
     (name "r-edaseq")
-    (version "2.34.0")
+    (version "2.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "EDASeq" version))
        (sha256
         (base32
-         "0gf4k02b5qywrg5rpg6hs9gyzcdlpw36ndgz3ca19plicair4mih"))))
+         "0xvi5mynkf1n74bn2k6gxmyhp1piwzsljd37biibdfzy14r1ir08"))))
     (properties `((upstream-name . "EDASeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7025,17 +7224,18 @@ global-scaling and full-quantile normalization.")
 (define-public r-edger
   (package
     (name "r-edger")
-    (version "3.42.4")
+    (version "4.0.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "edgeR" version))
               (sha256
                (base32
-                "1lyn017jqgn6d987zrk0kp2p2nw3mxf8zjspk31pky532p9pkhs3"))))
+                "0vjydwjazl7br0hvshy7jip3z6w73bif9vaky20im5rv40pqnchh"))))
     (properties `((upstream-name . "edgeR")))
     (build-system r-build-system)
     (propagated-inputs
      (list r-limma r-locfit r-rcpp))
+    (native-inputs (list r-knitr))
     (home-page "https://bioinf.wehi.edu.au/edgeR")
     (synopsis "EdgeR does empirical analysis of digital gene expression data")
     (description "This package can do differential expression analysis of
@@ -7050,13 +7250,13 @@ CAGE.")
 (define-public r-enhancedvolcano
   (package
     (name "r-enhancedvolcano")
-    (version "1.18.0")
+    (version "1.20.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "EnhancedVolcano" version))
               (sha256
                (base32
-                "1mcyhgdvfmkkh0rlhf51an7j1zi96lqdhifki2aqmlx0lqvg4qxq"))))
+                "097w3957m47m03iy8xc1m7pdgm3qy0kzqbllic8pd79qglrla802"))))
     (properties `((upstream-name . "EnhancedVolcano")))
     (build-system r-build-system)
     (propagated-inputs (list r-ggplot2 r-ggrepel))
@@ -7078,13 +7278,13 @@ parameter configurations.")
 (define-public r-enmix
   (package
     (name "r-enmix")
-    (version "1.36.0")
+    (version "1.38.01")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "ENmix" version))
               (sha256
                (base32
-                "1cwj45rnb6ra1bnd0plkjfvfsix25xr51yh6rwrfj524c35r70w1"))))
+                "1wh9lri9dp3904c2n6562z7p9gqx39dmag55imx8zrqnayxamc03"))))
     (properties `((upstream-name . "ENmix")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7101,9 +7301,9 @@ parameter configurations.")
            r-illuminaio
            r-impute
            r-iranges
+           r-irlba
            r-matrixstats
            r-minfi
-           r-preprocesscore
            r-quadprog
            r-rpmm
            r-s4vectors
@@ -7120,14 +7320,14 @@ visualization of Illumina DNA methylation array data.")
 (define-public r-ensembldb
   (package
     (name "r-ensembldb")
-    (version "2.24.1")
+    (version "2.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ensembldb" version))
        (sha256
         (base32
-         "1x73lln0rlnypl8iia54srl3wrazs94f8rspmjsaqsxwknkym319"))))
+         "010fp03x1splddxmhpxlfv1i3paqgbcxm7l9z2lmm6zfixhb158a"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-annotationdbi
@@ -7165,18 +7365,19 @@ chromosome region or transcript models of lincRNA genes.")
 (define-public r-fastseg
   (package
     (name "r-fastseg")
-    (version "1.46.0")
+    (version "1.48.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "fastseg" version))
        (sha256
         (base32
-         "0gygyf1xq1z6vzand43n965p366zh0k3rv58gnyqa81whj4dvcq3"))))
+         "10g9mdh7nzdz2b1k5gg5hk35lpapcnbs3p3z17k15aq040lpm236"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biobase r-biocgenerics r-genomicranges r-iranges
            r-s4vectors))
+    (native-inputs (list r-knitr))
     (home-page "https://www.bioinf.jku.at/software/fastseg/index.html")
     (synopsis "Fast segmentation algorithm for genetic sequencing data")
     (description
@@ -7192,14 +7393,14 @@ microarrays or GRanges for sequencing data.")
 (define-public r-gage
   (package
     (name "r-gage")
-    (version "2.50.0")
+    (version "2.52.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gage" version))
        (sha256
         (base32
-         "16wx2w70i12420022xz2zx8pizzyxb7z1pcmqn515cs89f1qcnli"))))
+         "0bm5hvy3cdcm46527w45mnnnk95qm28xzdk1m53615gh55ix4iy8"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-annotationdbi r-go-db r-graph r-keggrest))
@@ -7220,14 +7421,14 @@ analysis using other methods.")
 (define-public r-genefilter
   (package
     (name "r-genefilter")
-    (version "1.82.1")
+    (version "1.84.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "genefilter" version))
        (sha256
         (base32
-         "1wpg8banz6s6smycfqf9hqryp4kf2gs069s7npyvpq53wy0kxyny"))))
+         "0q80z872d3z1jy69b53qxzvmshf5zx4qssmp4gj7fwdpfxj9qqjw"))))
     (build-system r-build-system)
     (native-inputs
      (list gfortran r-knitr))
@@ -7244,16 +7445,16 @@ high-throughput sequencing experiments.")
 (define-public r-geneoverlap
   (package
     (name "r-geneoverlap")
-    (version "1.36.0")
+    (version "1.38.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GeneOverlap" version))
               (sha256
                (base32
-                "1bimsayaf68j15im591r6rbvydhbmiqcp1pphd5zzg6hzp6va927"))))
+                "074d3inz8sh8xxjliisa0p99rgy6r9fg9ljaka5bf1waxwpknzpw"))))
     (build-system r-build-system)
     (propagated-inputs
-     (list r-rcolorbrewer r-gplots))
+     (list r-gplots r-rcolorbrewer))
     (home-page "https://www.bioconductor.org/packages/GeneOverlap/")
     (synopsis "Test and visualize gene overlaps")
     (description "This package can be used to test two sets of gene lists
@@ -7263,13 +7464,13 @@ and visualize the results.")
 (define-public r-genomation
   (package
     (name "r-genomation")
-    (version "1.32.0")
+    (version "1.34.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "genomation" version))
               (sha256
                (base32
-                "0y6a2qxxp5mnkllcq46j00069z22ixnrbkd15s007a35lhkibz21"))))
+                "1vbpx187m5d5g307f4jiwyy1sw4jgj1s18622y3a458ixv540zkc"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biostrings
@@ -7310,13 +7511,13 @@ genomic intervals.  In addition, it can use BAM or BigWig files as input.")
 (define-public r-genomeinfodb
   (package
     (name "r-genomeinfodb")
-    (version "1.36.4")
+    (version "1.38.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomeInfoDb" version))
               (sha256
                (base32
-                "0wwh72sj894m3awk4g2zmkkwqafdjyxzsr49vnd1fiyz909hw02a"))))
+                "1a82xx1ijmfxk6d4pjqy45cdrnf75yrs7l7l64brl5d5dif45s42"))))
     (properties
      `((upstream-name . "GenomeInfoDb")))
     (build-system r-build-system)
@@ -7336,13 +7537,13 @@ names in their natural, rather than lexicographic, order.")
 (define-public r-genomicalignments
   (package
     (name "r-genomicalignments")
-    (version "1.36.0")
+    (version "1.38.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicAlignments" version))
               (sha256
                (base32
-                "1irzcz9s97gqbyj9j71wxv2ikdfd8g14296fg33w2ykfdm80nzf0"))))
+                "06xa3dcdk6jprvpyvr3pfbv6qv8xrqw2n6rrfp8q8qizx3ifj431"))))
     (properties
      `((upstream-name . "GenomicAlignments")))
     (build-system r-build-system)
@@ -7369,13 +7570,13 @@ alignments.")
 (define-public r-genomicdatacommons
   (package
     (name "r-genomicdatacommons")
-    (version "1.24.3")
+    (version "1.26.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicDataCommons" version))
               (sha256
                (base32
-                "1grvria7lx7p0py3w8yi0j41bpfx951lds5db7jdiq0j8l75fh38"))))
+                "1inikcczkhav6h6a46ix9ixkf7b1n8rf766m5hmhmx09sspzsm5w"))))
     (properties `((upstream-name . "GenomicDataCommons")))
     (build-system r-build-system)
     (propagated-inputs (list r-dplyr
@@ -7401,13 +7602,13 @@ Commons RESTful service.")
 (define-public r-genomicfeatures
   (package
     (name "r-genomicfeatures")
-    (version "1.52.2")
+    (version "1.54.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicFeatures" version))
               (sha256
                (base32
-                "0givyx77gvx24wgq180jsb2q1b8g4j49rs6bxdmd0l04a87hm9cr"))))
+                "1b2rx16l7zd4lisqssbkcwi534s7m7h1w6k72km6c835x2cdxfs4"))))
     (properties
      `((upstream-name . "GenomicFeatures")))
     (build-system r-build-system)
@@ -7445,14 +7646,14 @@ extracting the desired features in a convenient format.")
 (define-public r-genomicfiles
   (package
     (name "r-genomicfiles")
-    (version "1.36.0")
+    (version "1.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GenomicFiles" version))
        (sha256
         (base32
-         "0nxz8lvpmyllgs1ksgbha8qqs4fhppkg5casppnas9x47dj4bxph"))))
+         "1kvys60hhb0ndjvjdanfgciq3jc42iag8r0a199gv6w5bjaxp6wm"))))
     (properties `((upstream-name . "GenomicFiles")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7480,13 +7681,13 @@ provide added flexibility for data combination and manipulation.")
 (define-public r-genomicranges
   (package
     (name "r-genomicranges")
-    (version "1.52.0")
+    (version "1.54.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicRanges" version))
               (sha256
                (base32
-                "0vbr8nqn4pk0w3wx94q4f44psy6lxgx4b7p8hp0vf46flwggj2lj"))))
+                "1vrs3r8dyhhwj0s3vwvr168s84x5hj10lnpg1xf5c2kbj26bdv0w"))))
     (properties
      `((upstream-name . "GenomicRanges")))
     (build-system r-build-system)
@@ -7507,13 +7708,13 @@ manipulating genomic intervals and variables defined along a genome.")
 (define-public r-glad
   (package
     (name "r-glad")
-    (version "2.64.0")
+    (version "2.66.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GLAD" version))
               (sha256
                (base32
-                "0fi7wwn0ai4bwy8wgwl4dh3fbl6zhrkcy662dc1fcnk5i7rnv3y5"))))
+                "04wyzn56crz7sa453qj07p90vvg8nwrqz54m9ms9vf9z8adpck51"))))
     (properties `((upstream-name . "GLAD")))
     (build-system r-build-system)
     (inputs (list gsl))
@@ -7531,13 +7732,13 @@ regions identified.")
 (define-public r-globalancova
   (package
     (name "r-globalancova")
-    (version "4.18.0")
+    (version "4.20.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GlobalAncova" version))
               (sha256
                (base32
-                "1fld18rmi6rqm2nr549a4740w1iq3mf5df67v9ba6h42r4abs1ar"))))
+                "0j1ma04zjsvf668idms8hx1vnw3sh5yy8fbhwscyk1qbfy708cfh"))))
     (properties `((upstream-name . "GlobalAncova")))
     (build-system r-build-system)
     (propagated-inputs (list r-annotate
@@ -7563,13 +7764,13 @@ linear models via the extra sum of squares principle.")
 (define-public r-globaltest
   (package
     (name "r-globaltest")
-    (version "5.54.0")
+    (version "5.56.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "globaltest" version))
               (sha256
                (base32
-                "0jjhhg4vi44xqlvmcd80m30m93qyd4c79i7m9jn5hz3mw211xaig"))))
+                "14kcsx1gynl0fijq67qb5zvfxn4yqj8809p7535y455rd0vddp5r"))))
     (properties `((upstream-name . "globaltest")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7587,14 +7788,14 @@ facilitate the use of this test for gene set testing of GO and KEGG terms.")
 (define-public r-gostats
   (package
     (name "r-gostats")
-    (version "2.66.0")
+    (version "2.68.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GOstats" version))
        (sha256
         (base32
-         "1jjcjc1zp42l3gw36rr84al07ghih0cjx4p8gn8rlmv1jsz6kp1h"))))
+         "1v10ss1gf4a3qp6hbwa2f0la9sgiwhszg4c45qd6gv0dja2v30fs"))))
     (properties `((upstream-name . "GOstats")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7605,8 +7806,8 @@ facilitate the use of this test for gene set testing of GO and KEGG terms.")
            r-category
            r-go-db
            r-graph
-           r-rgraphviz
-           r-rbgl))
+           r-rbgl
+           r-rgraphviz))
     (native-inputs (list r-knitr))
     (home-page "https://bioconductor.org/packages/GOstats")
     (synopsis "Tools for manipulating GO and microarrays")
@@ -7619,14 +7820,14 @@ testing and other simple calculations.")
 (define-public r-gseabase
   (package
     (name "r-gseabase")
-    (version "1.62.0")
+    (version "1.64.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GSEABase" version))
        (sha256
         (base32
-         "0xfcgvsglcwkwsb1azmp4n4hx95fxnjk7rlwggb1f5rjw440qjnh"))))
+         "1y7z3627shskwss8bzjz1xm02rv4s7cdi91v1xqdsbdayjkrh1nb"))))
     (properties `((upstream-name . "GSEABase")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7648,13 +7849,13 @@ Enrichment Analysis} (GSEA).")
 (define-public r-gsva
   (package
     (name "r-gsva")
-    (version "1.48.3")
+    (version "1.50.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GSVA" version))
               (sha256
                (base32
-                "0ljfw65ray9ks8g55bfzn0c1w4412y4a7996zddywn5qj5pkjkfb"))))
+                "01w5j7fmi3hsfd282kcn4v41mi58z2yfhapff2zgf9swdfps4m6z"))))
     (properties `((upstream-name . "GSVA")))
     (build-system r-build-system)
     (propagated-inputs (list r-biobase
@@ -7688,13 +7889,13 @@ manner.")
 (define-public r-harshlight
   (package
     (name "r-harshlight")
-    (version "1.72.0")
+    (version "1.74.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Harshlight" version))
               (sha256
                (base32
-                "1rg3gx42a68jqbdmbqx7lh97y0rird1lci7146hnxa4svj827d5p"))))
+                "1djs95l04b3qrqcb7jkzhfmxzbsn2riyydz8p2lmilg6z9rkdqx7"))))
     (properties `((upstream-name . "Harshlight")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7715,14 +7916,14 @@ matrix to solve the memory problem.")
 (define-public r-hpar
   (package
     (name "r-hpar")
-    (version "1.42.0")
+    (version "1.44.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "hpar" version))
        (sha256
         (base32
-         "1sg0mjada72a13xh3k6xsiaff7xj4mp76r6i8iab8nfkvng07p4i"))))
+         "19jdy0q3larl5lxjzqlnyynq9rya56fyvf1yx9pwsyag1c148z08"))))
     (build-system r-build-system)
     (arguments
      (list
@@ -7747,19 +7948,120 @@ matrix to solve the memory problem.")
 the Human Protein Atlas project.")
     (license license:artistic2.0)))
 
+(define-public r-r3cseq
+  (package
+    (name "r-r3cseq")
+    (version "1.48.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "r3Cseq" version))
+       (sha256
+        (base32 "1llkfcy13h0c973703jmpgp2n6xxfsizb9iw1wxzgkbp1v0iy268"))))
+    (properties `((upstream-name . "r3Cseq")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biostrings
+           r-data-table
+           r-genomeinfodb
+           r-genomicranges
+           r-iranges
+           r-qvalue
+           r-rcolorbrewer
+           r-rsamtools
+           r-rtracklayer
+           r-sqldf
+           r-vgam))
+    (home-page "http://r3cseq.genereg.net/Site/index.html")
+    (synopsis
+     "Analysis of Chromosome conformation capture and Next-generation sequencing")
+    (description
+     "This package is used for the analysis of long-range chromatin
+interactions from 3C-seq assay.")
+    (license license:gpl3)))
+
+(define-public r-r4rna
+  (package
+    (name "r-r4rna")
+    (version "1.30.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "R4RNA" version))
+       (sha256
+        (base32 "1qmr1s7z2f126wkwxjpr9fvak4i7mzgvfflkycgavbdqshn1rk6l"))))
+    (properties `((upstream-name . "R4RNA")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-biostrings))
+    (home-page "https://www.e-rna.org/r-chie/")
+    (synopsis "RNA visualization and analysis")
+    (description
+     "This package provides a package for RNA basepair analysis, including the
+visualization of basepairs as arc diagrams for easy comparison and annotation of
+sequence and structure.  Arc diagrams can additionally be projected onto
+multiple sequence alignments to assess basepair conservation and covariation,
+with numerical methods for computing statistics for each.")
+    (license license:gpl3)))
+
+(define-public r-radiogx
+  (package
+    (name "r-radiogx")
+    (version "2.6.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "RadioGx" version))
+       (sha256
+        (base32 "0ykmvva5h1y7x9bxhqqfc18car9nasy06v1jjban7dlm95dl8nmk"))))
+    (properties `((upstream-name . "RadioGx")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-assertthat
+           r-biobase
+           r-biocgenerics
+           r-biocparallel
+           r-catools
+           r-coregx
+           r-data-table
+           r-downloader
+           r-magicaxis
+           r-matrixstats
+           r-rcolorbrewer
+           r-reshape2
+           r-s4vectors
+           r-scales
+           r-summarizedexperiment))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/RadioGx")
+    (synopsis "Analysis of large-scale radio-genomic data")
+    (description
+     "This package is a computational tool box for radio-genomic analysis
+which integrates radio-response data, radio-biological modelling and
+comprehensive cell line annotations for hundreds of cancer cell lines.  The
+@code{RadioSet} class enables creation and manipulation of standardized
+datasets including information about cancer cells lines, radio-response assays
+and dose-response indicators.  Included methods allow fitting and plotting
+dose-response data using established radio-biological models along with
+quality control to validate results.  Additional functions related to fitting
+and plotting dose response curves, quantifying statistical correlation and
+calculating @acronym{AUC, area under the curve} or @acronym{SF, survival
+fraction} are included.")
+    (license license:gpl3)))
+
 (define-public r-raggedexperiment
   (package
     (name "r-raggedexperiment")
-    (version "1.24.2")
+    (version "1.26.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "RaggedExperiment" version))
               (sha256
                (base32
-                "0aa886mmk1c5h1i3xnk4niq4ylrawpsn2f62hwmfj5dsyl8a36ka"))))
+                "07wx2icvxgrds1w7cx9pn99z6rzk2ih938j8g1laxmgx9sya74v6"))))
     (properties `((upstream-name . "RaggedExperiment")))
     (build-system r-build-system)
-    (propagated-inputs (list r-biocgenerics
+    (propagated-inputs (list r-biocbaseutils
+                             r-biocgenerics
                              r-genomeinfodb
                              r-genomicranges
                              r-iranges
@@ -7783,13 +8085,13 @@ rectangular dataset.")
 (define-public r-rdisop
   (package
     (name "r-rdisop")
-    (version "1.60.0")
+    (version "1.62.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Rdisop" version))
               (sha256
                (base32
-                "02mj02sa9qxc6678irx7g3yzab4sa5sf4jkdjzsi9i6519xd7sa4"))))
+                "1jz063hsrrbrqqx8p5yknagw19hsw51arck591h95dckncxd0006"))))
     (properties `((upstream-name . "Rdisop")))
     (build-system r-build-system)
     (propagated-inputs (list r-rcpp))
@@ -7805,14 +8107,14 @@ be calculated to search in MS peak lists.")
 (define-public r-rhtslib
   (package
     (name "r-rhtslib")
-    (version "2.2.0")
+    (version "2.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rhtslib" version))
        (sha256
         (base32
-         "1p8imns26knh21r254n7i9xvy8xzz3zizx0kq4si7cdaf2b4xayi"))))
+         "1h0hzs4f4mmnpi436dgib9lakljacznkyyssy7c4mdd419431aq2"))))
     (properties `((upstream-name . "Rhtslib")))
     (build-system r-build-system)
     ;; Without this a temporary directory ends up in the Rhtslib.so binary,
@@ -7834,13 +8136,13 @@ of other R packages who wish to make use of HTSlib.")
 (define-public r-impute
   (package
     (name "r-impute")
-    (version "1.74.1")
+    (version "1.76.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "impute" version))
               (sha256
                (base32
-                "0nz8ggzk2g5w20yyhp6av6hy69kbmg3ncfpq9ppmq6p5a0msx92l"))))
+                "0q7mnx99ndna1r2r0v7jc3w8ly8qw33flwbgkcvrfhk6dzvbn4pl"))))
     (native-inputs
      (list gfortran))
     (build-system r-build-system)
@@ -7851,16 +8153,17 @@ of other R packages who wish to make use of HTSlib.")
 microarray data, using nearest neighbor averaging.")
     (license license:gpl2+)))
 
+;; TODO: check javascript
 (define-public r-interactivedisplay
   (package
     (name "r-interactivedisplay")
-    (version "1.38.0")
+    (version "1.40.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "interactiveDisplay" version))
               (sha256
                (base32
-                "1y9fdnpz1bagrwhyj8jikp2q5fd9y74j48l5z7f0s88v88sa7szl"))
+                "0w81c5kc48gjavln50ysgr3vaf8s4fb6632ckzb1q225j9ik2gia"))
               (snippet
                '(for-each delete-file
                           '("inst/www/js/jquery.js"
@@ -7897,9 +8200,7 @@ microarray data, using nearest neighbor averaging.")
     (propagated-inputs
      (list r-annotationdbi
            r-biocgenerics
-           r-biocmanager
            r-category
-           r-dt
            r-ggplot2
            r-gridsvg
            r-interactivedisplaybase
@@ -7907,7 +8208,6 @@ microarray data, using nearest neighbor averaging.")
            r-rcolorbrewer
            r-reshape2
            r-shiny
-           r-zlibbioc
            r-xml))
     (native-inputs
      `(("esbuild" ,esbuild)
@@ -7938,14 +8238,14 @@ visualizations and interfaces for working with Bioconductor data.")
 (define-public r-interactivedisplaybase
   (package
     (name "r-interactivedisplaybase")
-    (version "1.38.0")
+    (version "1.40.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "interactiveDisplayBase" version))
        (sha256
         (base32
-         "1p3lwk8g14srkhl3x3i0v2d9071251ldy9964mii11k1bp2g08am"))))
+         "14cw90qlp8y4k0fs7xim8qvhzwbb8sn334mc72fkxg1h4bs8bxjw"))))
     (properties
      `((upstream-name . "interactiveDisplayBase")))
     (build-system r-build-system)
@@ -7963,14 +8263,14 @@ Shiny-based display methods for Bioconductor objects.")
 (define-public r-keggrest
   (package
     (name "r-keggrest")
-    (version "1.40.1")
+    (version "1.42.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "KEGGREST" version))
        (sha256
         (base32
-         "13pbw5nlkjwplliv2pdwazv2idfjklvw0ykx5ja8rchvzs5f1vk4"))))
+         "05fc1i1bcdvvy4mr4m2cdqxd3jrj1rxkxy7c43yrliv5dlikyb07"))))
     (properties `((upstream-name . "KEGGREST")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7987,13 +8287,13 @@ Shiny-based display methods for Bioconductor objects.")
 (define-public r-lea
   (package
     (name "r-lea")
-    (version "3.12.2")
+    (version "3.14.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "LEA" version))
               (sha256
                (base32
-                "1kxrrl8pxhaipmzsw8gs4gs8g8xbp8169z9f7bcpgrfapnawafm9"))))
+                "1rhlrcp9rzf64rkabgk3gd8jqdg8ldwpkxvpfb6g49bgpkg1h6b1"))))
     (properties `((upstream-name . "LEA")))
     (build-system r-build-system)
     (native-inputs (list r-knitr))
@@ -8018,13 +8318,13 @@ scale with the dimensions of large data sets.")
 (define-public r-lfa
   (package
     (name "r-lfa")
-    (version "2.0.11")
+    (version "2.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "lfa" version))
        (sha256
-        (base32 "0x169fxwlccsqwj1bpviaky3hfr0zdwsdrlgfvrb4j6j95qfgnns"))))
+        (base32 "1xrwvw7227znd1h7426k8l86197yc24b4v608issh5fqglmhljns"))))
     (properties `((upstream-name . "lfa")))
     (build-system r-build-system)
     (propagated-inputs (list r-corpcor r-rspectra))
@@ -8039,14 +8339,16 @@ Binomial data via estimation of latent structure in the natural parameter.")
 (define-public r-limma
   (package
     (name "r-limma")
-    (version "3.56.2")
+    (version "3.58.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "limma" version))
               (sha256
                (base32
-                "0miyba9frn1p4pkclzpr0bfazsk0br2jgpwpwwh773d3103hkn0r"))))
+                "01byjnhhjyxk9x871rk8bgqq6lkp1a6dylqbdphpzp88b1jf2f9m"))))
     (build-system r-build-system)
+    (native-inputs (list r-knitr))
+    (propagated-inputs (list r-statmod))
     (home-page "https://bioinf.wehi.edu.au/limma")
     (synopsis "Package for linear models for microarray and RNA-seq data")
     (description "This package can be used for the analysis of gene expression
@@ -8058,13 +8360,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.")
 (define-public r-maaslin2
   (package
     (name "r-maaslin2")
-    (version "1.14.1")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Maaslin2" version))
        (sha256
-        (base32 "06mb72hbzihdficv73yqbb2m86bkw78w3vbw1rm98n0npxq2fch6"))))
+        (base32 "1d95dv46b36ncwb7zdn0wvshg4v73qjfs3hij0jmbkkxvf2il9iq"))))
     (properties `((upstream-name . "Maaslin2")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8106,13 +8408,13 @@ of data exploration, normalization, and transformation methods.")
 (define-public r-made4
   (package
     (name "r-made4")
-    (version "1.74.0")
+    (version "1.76.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "made4" version))
               (sha256
                (base32
-                "1233l5160msxp85vm2h0j3k073vv5d9wj55709x4s657fi9la6ij"))))
+                "03fhiszlmjh8nvz3gppf45r9kpcjrdb601ar17c4f2aygjpkf0cg"))))
     (properties `((upstream-name . "made4")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8135,13 +8437,13 @@ datasets (coinertia analysis).")
 (define-public r-makecdfenv
   (package
     (name "r-makecdfenv")
-    (version "1.76.0")
+    (version "1.78.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "makecdfenv" version))
               (sha256
                (base32
-                "1a6kngwmc7nvzlgpnhdv4j180847gjh4i3dshld0pcvy3b6bjv8r"))))
+                "0mggcw0390i1y2wn4k8570gjmbsx6hbipi8fkhz2zj9icsx89x1l"))))
     (properties `((upstream-name . "makecdfenv")))
     (build-system r-build-system)
     (inputs (list zlib))
@@ -8162,13 +8464,13 @@ package that automatically loads that environment.")
 (define-public r-manor
   (package
     (name "r-manor")
-    (version "1.72.0")
+    (version "1.74.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MANOR" version))
        (sha256
-        (base32 "0ili9xy7vvw17mz44lxadv1vkf3ahpks2l34qa9yfccpalwhzriw"))))
+        (base32 "10zf6c1vx6cp4wg6axpmbpxk2hlmf6mga7rdh765fznwb71r4h0x"))))
     (properties `((upstream-name . "MANOR")))
     (build-system r-build-system)
     (propagated-inputs (list r-glad))
@@ -8185,13 +8487,13 @@ experiments.")
 (define-public r-maser
   (package
     (name "r-maser")
-    (version "1.18.0")
+    (version "1.20.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "maser" version))
               (sha256
                (base32
-                "1ma5d1i56gw8hm2pgvzzvmdd1cm2xb42rgf5lb6sf4v47yzlyb9f"))))
+                "0h7x1fyfvnjc30w9ydbnlqijz58q2kcxv4yy784rf4adsrdhwh45"))))
     (properties `((upstream-name . "maser")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8217,13 +8519,13 @@ and visualizaton of alternative splicing events generated by rMATS.")
 (define-public r-mdqc
   (package
     (name "r-mdqc")
-    (version "1.62.0")
+    (version "1.64.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "mdqc" version))
        (sha256
-        (base32 "0y35z9sw3h77a5g4ah0fxrk5xh7irdw9z0y2jhh6dp0xxcqh6i0k"))))
+        (base32 "0q6ig9qdf2s9329wysrvgh13yq5c7n76as2c3mahqm78xb0mpplf"))))
     (properties `((upstream-name . "mdqc")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8239,16 +8541,42 @@ array against the quality of the other arrays.  Then, arrays with unusually
 high distances can be flagged as potentially low-quality.")
     (license license:lgpl2.0+)))
 
+(define-public r-metabocoreutils
+  (package
+    (name "r-metabocoreutils")
+    (version "1.10.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "MetaboCoreUtils" version))
+       (sha256
+        (base32 "0bs24dwqlm8isp231jds51l7v16q0gjli1qmhjxyva3qmi5yb4dl"))))
+    (properties `((upstream-name . "MetaboCoreUtils")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-mscoreutils))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/RforMassSpectrometry/MetaboCoreUtils")
+    (synopsis "Core utils for Metabolomics data")
+    (description
+     "@code{MetaboCoreUtils} defines metabolomics-related core functionality
+provided as low-level functions to allow a data structure-independent usage
+across various R packages.  This includes functions to calculate between
+ion (adduct) and compound mass-to-charge ratios and masses or functions to
+work with chemical formulas.  The package provides also a set of adduct
+definitions and information on some commercially available internal standard
+mixes commonly used in MS experiments.")
+    (license license:artistic2.0)))
+
 (define-public r-metagenomeseq
   (package
     (name "r-metagenomeseq")
-    (version "1.42.0")
+    (version "1.43.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "metagenomeSeq" version))
        (sha256
-        (base32 "0293c531l0sjz8qxy7nrajfl081v9df0af9242017msbvyszq6wk"))))
+        (base32 "1m19qkwrbfr4yhbr1izfjka3brn1qasqql6alczv55l5h52m4s4b"))))
     (properties `((upstream-name . "metagenomeSeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8276,13 +8604,13 @@ correlations.")
 (define-public r-metaneighbor
   (package
     (name "r-metaneighbor")
-    (version "1.20.0")
+    (version "1.22.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "MetaNeighbor" version))
               (sha256
                (base32
-                "151ip70la12kj80c0airi1yyjbj69gnkshd6kfk88wsvq7s179id"))))
+                "0y8nk9jq0z48phg13mf6hsfg8l54w6z6b67g0k1c9gmsb7aqq04d"))))
     (properties `((upstream-name . "MetaNeighbor")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8312,13 +8640,13 @@ profiles than cells of different types.")
 (define-public r-methylkit
   (package
     (name "r-methylkit")
-    (version "1.26.0")
+    (version "1.28.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "methylKit" version))
               (sha256
                (base32
-                "1qi4gwlxsxr4cgs8s12qybrs89vr79xwd7n9in1af3hyn0swikn1"))))
+                "0y45wa45kblm2g3nylvybvyfc34sjlynhsz3dirhs1favb83sdiv"))))
     (properties `((upstream-name . "methylKit")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8359,13 +8687,13 @@ TAB-Seq.")
 (define-public r-mfuzz
   (package
     (name "r-mfuzz")
-    (version "2.60.0")
+    (version "2.62.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Mfuzz" version))
               (sha256
                (base32
-                "0rfna5ycwkx4xb2gv1wpfn7f7nz6f79w5nlkb7719l5730d81wnz"))))
+                "0v2l3fi9331lxfam6az265rfk52g4n75hh4rg12ykhp86ihplzpf"))))
     (properties `((upstream-name . "Mfuzz")))
     (build-system r-build-system)
     (propagated-inputs (list r-biobase r-e1071 r-tkwidgets))
@@ -8379,13 +8707,13 @@ time-series data (including a graphical user interface).")
 (define-public r-mmuphin
   (package
     (name "r-mmuphin")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MMUPHin" version))
        (sha256
-        (base32 "14cn1mg9ffhzy1vgschl2h0wzah3c1g67q367f2m050a3z2i2ndy"))
+        (base32 "0lhvsx5yjvqh5d3h860sv8cf3h73nrzvljpkqrd9ks0irc4gcm6d"))
        ;; Delete generated files.
        (snippet
         '(for-each delete-file
@@ -8474,14 +8802,14 @@ throughput genetic sequencing data sets using regression methods.")
 (define-public r-muscat
   (package
     (name "r-muscat")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "muscat" version))
        (sha256
         (base32
-         "1jcy07m8ywpgsmwkq6s7zj32w7gvxqj52j562irv2h2q429awdxk"))))
+         "0vasr9rwnfjxbb3y2saq7gqzis5xyamgvns2rlywdxv1jm0nr8y3"))))
     (properties `((upstream-name . "muscat")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8524,14 +8852,14 @@ platform that mimics both single and multi-sample scRNA-seq data.")
 (define-public r-mutationalpatterns
   (package
     (name "r-mutationalpatterns")
-    (version "3.10.0")
+    (version "3.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MutationalPatterns" version))
        (sha256
         (base32
-         "1p9n5afnr4cx690w9d5q1hkwqffsbnsn72wibqcl5rbqgfsvhf8h"))))
+         "19ya4ax6pa727hdn0118l9pwa9dxgh89dz54mm66dawxga3jhar4"))))
     (build-system r-build-system)
     (native-inputs
      (list r-knitr))
@@ -8570,13 +8898,13 @@ in SNV base substitution data.")
 (define-public r-msa
   (package
     (name "r-msa")
-    (version "1.32.0")
+    (version "1.34.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "msa" version))
               (sha256
                (base32
-                "08fg4y8rmkvilsx2hxqwxa90p2wqrl4iyndp7wfjicvplmaxp708"))))
+                "1csa8j64xrfr6kdnndr3876bplclca9wf6ydy9kg97xsjq7gz8q5"))))
     (properties `((upstream-name . "msa")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8601,14 +8929,14 @@ package TeXshade.")
 (define-public r-msnbase
   (package
     (name "r-msnbase")
-    (version "2.26.0")
+    (version "2.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MSnbase" version))
        (sha256
         (base32
-         "0qpgpvzg0vw45ia3dpkpfs56dj06crjrrg4i9l46bj8f2pgzcf0g"))))
+         "0dway94j3k2dq5p8lqzj49ql85xrxxxgmlgppqg0h8k56xqrmf5i"))))
     (properties `((upstream-name . "MSnbase")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8646,14 +8974,14 @@ of mass spectrometry based proteomics data.")
 (define-public r-msnid
   (package
     (name "r-msnid")
-    (version "1.34.0")
+    (version "1.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MSnID" version))
        (sha256
         (base32
-         "1mxlr76xrgp3limhr20naanhqr6b0d2wbk9l63j0pi2yckszxjjc"))))
+         "1hmfh7v7p5d741x2wh1njqwkmfmf3xmwkqy88kalrcjzrdwfpv9b"))))
     (properties `((upstream-name . "MSnID")))
     (build-system r-build-system)
     (arguments
@@ -8674,8 +9002,8 @@ of mass spectrometry based proteomics data.")
            r-foreach
            r-ggplot2
            r-iterators
-           r-msnbase
            r-msmstests
+           r-msnbase
            r-mzid
            r-mzr
            r-protgenerics
@@ -8703,14 +9031,14 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.")
 (define-public r-mzid
   (package
     (name "r-mzid")
-    (version "1.38.0")
+    (version "1.40.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "mzID" version))
        (sha256
         (base32
-         "0grl7798vnpxb6nw98zj0lbvsrhkjfsyn0y15bi4v7vhyhkk26xm"))))
+         "1rgkd9iv0lxj1zxh96sifwa312ivw5kl5jw82ma4fmapr4iqhzsh"))))
     (properties `((upstream-name . "mzID")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8734,14 +9062,14 @@ specific parser.")
 (define-public r-mzr
   (package
     (name "r-mzr")
-    (version "2.34.1")
+    (version "2.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "mzR" version))
        (sha256
         (base32
-         "1jsna4xwyph1gg72wwqlpavb65g5nc3db1vmcs1qcw1mdgasdjhk"))
+         "0z6ckp69syrdzhp6n4n399k2lar3w4n2d1ji2f90951c4ds6hkh8"))
        (modules '((guix build utils)))
        (snippet
         '(delete-file-recursively "src/boost"))))
@@ -8854,14 +9182,14 @@ Gao et al in Nature Biotechnology 2022}.")
 (define-public r-organism-dplyr
   (package
     (name "r-organism-dplyr")
-    (version "1.28.0")
+    (version "1.30.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Organism.dplyr" version))
        (sha256
         (base32
-         "0yrd7a7c0n6c987gyy76jidpvsdwrv2097f9wkvh4y5dd1w0mk7p"))))
+         "1s55fiqgxrdznn43qhm5yv9gp8d1msr2f39wxih0b5bm4wxhkq45"))))
     (properties `((upstream-name . "Organism.dplyr")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8893,14 +9221,14 @@ functionality of the @code{TxDb} packages (e.g.,
 (define-public r-organismdbi
   (package
     (name "r-organismdbi")
-    (version "1.42.0")
+    (version "1.44.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "OrganismDbi" version))
        (sha256
         (base32
-         "1pw3qd6n0xf7vq3x73612bndcqhwrqkpi29f6crazdzjcy3fivlb"))))
+         "0g75y21lqmwsh28nx99zp2gxr6rhlhbw76f66qx5hrh6bm2zpm7j"))))
     (properties `((upstream-name . "OrganismDbi")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8926,13 +9254,13 @@ the fact that each of these packages implements a select methods.")
 (define-public r-oscope
   (package
     (name "r-oscope")
-    (version "1.30.0")
+    (version "1.32.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Oscope" version))
               (sha256
                (base32
-                "055j7y1icikqivc795hzl1l5v5ga2bfcqk2x0kivawbrqvj4yq5v"))))
+                "1li2l9mdq2q0580a7qzvfid5n15v62fr9ys87j42k3l2w5a26smf"))))
     (properties `((upstream-name . "Oscope")))
     (build-system r-build-system)
     (propagated-inputs (list r-biocparallel r-cluster r-ebseq r-testthat))
@@ -8952,14 +9280,14 @@ insertion module to recover the base cycle order for each oscillator group.")
 (define-public r-pcaexplorer
   (package
     (name "r-pcaexplorer")
-    (version "2.26.1")
+    (version "2.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "pcaExplorer" version))
        (sha256
         (base32
-         "04r4qsiasbfb0pwqyqmw2w3qdkhgwixwffp1s8hjflwnb63hxzjx"))))
+         "0ihc9jqjy0nl4pfgcxczfdf973nb99325agk73y0222ad1mpkc07"))))
     (properties `((upstream-name . "pcaExplorer")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9007,14 +9335,14 @@ application encapsulates the whole analysis.")
 (define-public r-pcamethods
   (package
     (name "r-pcamethods")
-    (version "1.92.0")
+    (version "1.94.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "pcaMethods" version))
        (sha256
         (base32
-         "14awrgq56s948x74j4iv9k1yy5b7axw1kqzg827y5znjc1i3aqy6"))))
+         "1asm4iafdzm98iv2j9sxvn5y9ss2p679cx7gwjipq8mf1d7bzfp0"))))
     (properties `((upstream-name . "pcaMethods")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9034,13 +9362,13 @@ structure (pcaRes) to provide a common interface to the PCA results.")
 (define-public r-pfamanalyzer
   (package
     (name "r-pfamanalyzer")
-    (version "1.0.1")
+    (version "1.2.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "pfamAnalyzeR" version))
               (sha256
                (base32
-                "0zff887lc4bjrv683kqsw47vjwmf6886wybklsf2wd6hpy23mxfy"))))
+                "0qxxp7kfwbb9q471mgwc4bd8dmyid56ddyzw2jlg4gb1wcq9py67"))))
     (properties `((upstream-name . "pfamAnalyzeR")))
     (build-system r-build-system)
     (propagated-inputs (list r-dplyr r-magrittr r-readr r-stringr r-tibble))
@@ -9054,6 +9382,43 @@ isotypes. This R package enables the identification and classification of such
 domain isotypes from pfam data.")
     (license license:expat)))
 
+(define-public r-piano
+  (package
+    (name "r-piano")
+    (version "2.18.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "piano" version))
+       (sha256
+        (base32 "0rw55ig3pbvi2kyg10rx60ldcncsd4gki2h1zpr1nhmqg3fv0l5y"))))
+    (properties `((upstream-name . "piano")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biobase
+           r-biocgenerics
+           r-dt
+           r-fgsea
+           r-gplots
+           r-htmlwidgets
+           r-igraph
+           r-marray
+           r-relations
+           r-scales
+           r-shiny
+           r-shinydashboard
+           r-shinyjs
+           r-visnetwork))
+    (native-inputs (list r-knitr))
+    (home-page "https://varemo.github.io/piano/")
+    (synopsis "Platform for integrative analysis of omics data")
+    (description
+     "Piano performs gene set analysis using various statistical methods, from
+different gene level statistics and a wide range of gene-set collections.  The
+package contains functions for combining the results of multiple runs of gene
+set analyses.")
+    (license license:gpl2+)))
+
 ;; This is a CRAN package, but it depends on a Bioconductor package:
 ;; r-aroma-light, r-dnacopy..
 (define-public r-pscbs
@@ -9099,14 +9464,14 @@ chromosome.  Both tumor-normal paired and tumor-only analyses are supported.")
 (define-public r-protgenerics
   (package
     (name "r-protgenerics")
-    (version "1.32.0")
+    (version "1.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ProtGenerics" version))
        (sha256
         (base32
-         "0fgsb47qrvrl4y3yr094mas22rai5h5yl9mciadd6zcpamp2p01i"))))
+         "1gjva76nxa9nzzmc9hya3bq7hswfmjd768v21f6m3gyygxvl581m"))))
     (properties `((upstream-name . "ProtGenerics")))
     (build-system r-build-system)
     (home-page "https://github.com/lgatto/ProtGenerics")
@@ -9119,14 +9484,14 @@ proteomics packages.")
 (define-public r-rbgl
   (package
     (name "r-rbgl")
-    (version "1.76.0")
+    (version "1.78.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "RBGL" version))
        (sha256
         (base32
-         "0y6ghiwraw3whs57i31qnvlvqlbl9143wxv2yg48rp7qxipxvn6s"))))
+         "0hxhl1l6qdi355w5y7fdq8vlba2pknfizggkgr2fp8f1f3zqh494"))))
     (properties `((upstream-name . "RBGL")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9142,13 +9507,13 @@ the graph algorithms contained in the Boost library.")
 (define-public r-rcas
   (package
     (name "r-rcas")
-    (version "1.26.0")
+    (version "1.28.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "RCAS" version))
               (sha256
                (base32
-                "073fhbh0pzyca90q2irbaiwj21sci8jf9ksflx9pm9fr1giy37i4"))))
+                "19ildsck3g8v4w0g2f473sb8hyhn4avprdi78fim0prva5f9nqnv"))))
     (properties `((upstream-name . "RCAS")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9174,9 +9539,9 @@ the graph algorithms contained in the Boost library.")
            r-plotrix
            r-proxy
            r-ranger
+           r-rmarkdown
            r-rsqlite
            r-rtracklayer
-           r-rmarkdown
            r-s4vectors
            pandoc))
     (native-inputs
@@ -9192,14 +9557,14 @@ library implementing most of the pipeline's features.")
 (define-public r-regioner
   (package
     (name "r-regioner")
-    (version "1.32.0")
+    (version "1.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "regioneR" version))
        (sha256
         (base32
-         "0grlqga9d6mch9l487fdll65wi0m2kpq2097igfhx185i8jvwsz1"))))
+         "1qcgbj7d2fngs3p9a9apnj14x35kc651fy3m0651dnqrxz8j5yij"))))
     (properties `((upstream-name . "regioneR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9306,16 +9671,16 @@ browser.")
 (define-public r-rhdf5
   (package
     (name "r-rhdf5")
-    (version "2.44.0")
+    (version "2.46.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "rhdf5" version))
               (sha256
                (base32
-                "1akbr55lylwp20b2j351h1gcj1sc5y2j2pjjdpz43m6b7mji23a0"))))
+                "1csf5nrg2nkdwh8cz26idz6wrhj7bgnfh559mzlpdj4licnf1ymc"))))
     (build-system r-build-system)
     (propagated-inputs
-     (list r-rhdf5filters r-rhdf5lib))
+     (list r-rhdf5filters r-rhdf5lib r-s4vectors))
     (native-inputs
      (list r-knitr))
     (home-page "https://bioconductor.org/packages/rhdf5")
@@ -9333,42 +9698,26 @@ the available RAM.")
 (define-public r-rhdf5filters
   (package
     (name "r-rhdf5filters")
-    (version "1.12.1")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "rhdf5filters" version))
        (sha256
         (base32
-         "1v9wxa5q0iwphrmkf9x70jpbq9r9rqz2hm94smqnnpfxszila49m"))))
+         "1appjnggyljrn77nvv9adkwxplbrrlgkrrd1bf2b5r0nsa505hdc"))))
     (properties `((upstream-name . "rhdf5filters")))
     (build-system r-build-system)
     (arguments
      (list
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'unpack 'use-system-libraries
-            (lambda _
-              (substitute* "src/blosc/Makefile.in"
-                (("libblosc.a: blosc") "libwhatever.a:")
-                (("libblosc.a")
-                 (string-append #$(this-package-input "c-blosc")
-                                "/lib/libblosc.so"))
-                (("../zstd/libzstd.a") "-lzstd"))
-              (substitute* "src/bzip2/Makefile"
-                (("libH5Zbz2.so: bzip2-1.0.8/libbz2.a") "libH5Zbz2.so:")
-                (("./bzip2-1.0.8/libbz2.a") "-lbz2"))
-              (substitute* "src/zstd/Makefile"
-                (("libH5Zzstd.so: libzstd.a") "libH5Zzstd.so:")
-                (("libzstd.a") "-lzstd"))
-              (substitute* "src/vbz/Makefile"
-                (("../zstd/libzstd.a") "-lzstd")))))))
+      #:configure-flags
+      '(list "--without-bundled-libs")))
     (propagated-inputs
      (list r-rhdf5lib))
     (inputs
      (list bzip2 c-blosc zlib (list zstd "lib")))
     (native-inputs
-     (list r-biocstyle r-knitr r-rmarkdown))
+     (list r-knitr))
     (home-page "https://github.com/grimbough/rhdf5filters")
     (synopsis "HDF5 compression filters")
     (description
@@ -9379,13 +9728,13 @@ HDF5 datasets.")
 (define-public r-rsamtools
   (package
     (name "r-rsamtools")
-    (version "2.16.0")
+    (version "2.18.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Rsamtools" version))
               (sha256
                (base32
-                "18kh6vmyjmv7zklqr5ifpfixjwldxgwj550c69mqfkk7m0zk52cl"))))
+                "0bcapiwdzv7rqgs4hmw7hq290r3pz5vvhg4apxard0yybq83na1g"))))
     (properties
      `((upstream-name . "Rsamtools")))
     (build-system r-build-system)
@@ -9408,7 +9757,8 @@ HDF5 datasets.")
            r-iranges
            r-rhtslib
            r-s4vectors
-           r-xvector))
+           r-xvector
+           r-zlibbioc))
     (native-inputs (list r-knitr))
     (home-page "https://bioconductor.org/packages/release/bioc/html/Rsamtools.html")
     (synopsis "Interface to samtools, bcftools, and tabix")
@@ -9445,13 +9795,13 @@ tab-delimited (tabix) files.")
 (define-public r-rtcga
   (package
     (name "r-rtcga")
-    (version "1.30.0")
+    (version "1.32.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "RTCGA" version))
               (sha256
                (base32
-                "1y7ciq1270dc1c9y490fygrsylyzwl52fqi1vj7r75hy3rnwnv25"))))
+                "1lzdwkisvzj1wyx3wx4ll1c2j9ww3xz8kpbngmpf8cdrw4h3jrg1"))))
     (properties `((upstream-name . "RTCGA")))
     (build-system r-build-system)
     (propagated-inputs (list r-assertthat
@@ -9490,13 +9840,13 @@ transforms TCGA data to tidy form which is convenient to use.")
 (define-public r-rtcgatoolbox
   (package
     (name "r-rtcgatoolbox")
-    (version "2.30.0")
+    (version "2.32.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "RTCGAToolbox" version))
               (sha256
                (base32
-                "03p5rgjzc1265q60jkvk92vhcib5wdnv6bz997r70q9c39y03wm5"))))
+                "1a38b30nsg2bnlnijf4aa4rn4db2y4v86awfbf6a6qzqwlzknrcq"))))
     (properties `((upstream-name . "RTCGAToolbox")))
     (build-system r-build-system)
     (propagated-inputs (list r-biocgenerics
@@ -9506,7 +9856,6 @@ transforms TCGA data to tidy form which is convenient to use.")
                              r-genomicranges
                              r-httr
                              r-raggedexperiment
-                             r-rcircos
                              r-rcurl
                              r-rjsonio
                              r-rvest
@@ -9530,13 +9879,13 @@ pre-processed data.")
 (define-public r-rtracklayer
   (package
     (name "r-rtracklayer")
-    (version "1.60.1")
+    (version "1.62.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "rtracklayer" version))
               (sha256
                (base32
-                "06z02sz8zjg2lxp2q4qwhvh6dsi6srirdmhcdvmi3as50nnjmzd8"))))
+                "1jxhv2fq62lz0j6kbwq43c8ggk14ccsjg0xgfqjqy941dj9ig0n2"))))
     (build-system r-build-system)
     (arguments
      `(#:phases
@@ -9609,13 +9958,13 @@ differential expression analysis, RNAseq data and related problems.")
 (define-public r-saturn
   (package
     (name "r-saturn")
-    (version "1.8.0")
+    (version "1.10.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "satuRn" version))
               (sha256
                (base32
-                "0frm7iblxkc8ajcdqrfgsvf4krn6x8cr3mx7fnzq06xij0mqm3sj"))))
+                "12bivj0cnp38apwi3jqmil8bwsfa96cjp5f132a5raacd2z87gqf"))))
     (properties `((upstream-name . "satuRn")))
     (build-system r-build-system)
     (propagated-inputs (list r-biocparallel
@@ -9643,13 +9992,13 @@ transcripts in groups of interest.")
 (define-public r-scannotatr
   (package
     (name "r-scannotatr")
-    (version "1.6.0")
+    (version "1.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "scAnnotatR" version))
        (sha256
-        (base32 "0mxq2dknrhgj1487kfshkayx963c7qdgxwmlh9fbfr0lwc7gljfn"))))
+        (base32 "13wrxxdwphngi0f9vxakykk54bqngw8g38w6wkk96999lzb3p57p"))))
     (properties `((upstream-name . "scAnnotatR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9680,13 +10029,13 @@ cell types based on specific research needs.")
 (define-public r-scdblfinder
   (package
     (name "r-scdblfinder")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "scDblFinder" version))
        (sha256
-        (base32 "0lvacrgfj9i8mwlcv5ykxs69hd3bm6bvr6fsddxffsr7cckpn31w"))))
+        (base32 "1f3n1m6fjx965wm2jllzk51ssj92ifxb4bln4vwk25qxd3g0bna8"))))
     (properties `((upstream-name . "scDblFinder")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9762,13 +10111,13 @@ method applicable to massive single-cell datasets (>10,000 cells).")
 (define-public r-scmap
   (package
     (name "r-scmap")
-    (version "1.22.3")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "scmap" version))
        (sha256
-        (base32 "06i3r7zybwcgnak9ml2jaz7fy70zjqdh28v03ckaqhvck49kdqdm"))))
+        (base32 "1sd5ixs8fbiqqp1p4p505l1f0lncmagkhzh4xrk8wrca6db6k6d8"))))
     (properties `((upstream-name . "scmap")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9804,13 +10153,13 @@ different experiment.")
 (define-public r-scry
   (package
     (name "r-scry")
-    (version "1.12.0")
+    (version "1.14.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "scry" version))
               (sha256
                (base32
-                "0406slld468m9lxswv1akcdmap6izvzz6zljyrs5av546nfxpmrz"))))
+                "0hbdsjsn0jl0dr2ly5vx0wb4bnz7nl15kkypryywjvis9rdasjj3"))))
     (properties `((upstream-name . "scry")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9835,13 +10184,13 @@ single-cell RNA-seq.")
 (define-public r-seqarray
   (package
     (name "r-seqarray")
-    (version "1.40.1")
+    (version "1.42.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "SeqArray" version))
               (sha256
                (base32
-                "1771vk23psjavvi1nf2z8i2xawygdh4amawlijnskci8y9w4x5dm"))))
+                "0zs60yh3x6kgy6izn11d400vw59ww2w6bmhg6fw5ijinknyr3ixc"))))
     (properties `((upstream-name . "SeqArray")))
     (build-system r-build-system)
     (propagated-inputs (list r-biostrings
@@ -9865,14 +10214,14 @@ data access using the R programming language.")
 (define-public r-seqlogo
   (package
     (name "r-seqlogo")
-    (version "1.66.0")
+    (version "1.68.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "seqLogo" version))
        (sha256
         (base32
-         "0727yrmm194gskrcpmq4fh0qmi6dnp70gx627psrpvzlk6vlcl8k"))))
+         "106359wn4v0m53b33x4zjsyjsj4j8h7bnvd1whamsig982h6szp2"))))
     (properties `((upstream-name . "seqLogo")))
     (build-system r-build-system)
     (native-inputs
@@ -9888,13 +10237,13 @@ Stephens (1990).")
 (define-public r-seqpattern
   (package
     (name "r-seqpattern")
-    (version "1.32.0")
+    (version "1.34.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "seqPattern" version))
               (sha256
                (base32
-                "033hss67dxi6fbvn6ya7vc61f60m20hwms9kmdia0icyp8nv2yil"))))
+                "0rs9dy540d4agp7fc8glbrcnly4s6qcxqsq4yv8y555bbdld6dv0"))))
     (properties
      `((upstream-name . "seqPattern")))
     (build-system r-build-system)
@@ -9911,13 +10260,13 @@ reference point and sorted by a user defined feature.")
 (define-public r-sesame
   (package
     (name "r-sesame")
-    (version "1.18.4")
+    (version "1.20.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "sesame" version))
               (sha256
                (base32
-                "1il33ygys6y72l8p3fhx301q16w9kylfy6w92b64n8gqkn6dmsmn"))))
+                "0yh4mrsj3pqhjkrq5dwmcpcqwixs0pmjy7dfa3cr0mf52fgzcvmr"))))
     (properties `((upstream-name . "sesame")))
     (build-system r-build-system)
     (propagated-inputs (list r-biocfilecache
@@ -9953,13 +10302,13 @@ and advanced quality control routines.")
 (define-public r-shinymethyl
   (package
     (name "r-shinymethyl")
-    (version "1.36.1")
+    (version "1.38.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "shinyMethyl" version))
               (sha256
                (base32
-                "0hq1q66vjd9pwdwm9zx8q45ws65bn6cm87zmjmyc3md8dwvb8cck"))))
+                "1gkj15q1rxvsdzbsp3gkk02kvvx0kq4wsqycf3ln1bszb9688jw6"))))
     (properties `((upstream-name . "shinyMethyl")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9981,14 +10330,14 @@ methylation array data.  Both the 450k and EPIC array are supported.")
 (define-public r-shortread
   (package
     (name "r-shortread")
-    (version "1.58.0")
+    (version "1.60.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ShortRead" version))
        (sha256
         (base32
-         "0wpr3ksr7j5yk6m1zaa47dwdgznajsz8as4p9vf7schaqvhq1wc4"))))
+         "0fgiszb5qhplppfngpi4s33sx62ff5sdhd6n31a3b6l7fnlvk51m"))))
     (properties `((upstream-name . "ShortRead")))
     (build-system r-build-system)
     (inputs
@@ -10001,11 +10350,11 @@ methylation array data.  Both the 450k and EPIC array are supported.")
            r-genomeinfodb
            r-genomicalignments
            r-genomicranges
-           r-rhtslib
            r-hwriter
            r-iranges
            r-lattice
            r-latticeextra
+           r-rhtslib
            r-rsamtools
            r-s4vectors
            r-xvector
@@ -10024,14 +10373,14 @@ ungapped alignment formats.")
 (define-public r-simplifyenrichment
   (package
     (name "r-simplifyenrichment")
-    (version "1.10.0")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "simplifyEnrichment" version))
        (sha256
         (base32
-         "1vs57j361fbwv7vaybs71vc208qn76djmbmakhwwcvxwrx77jp5f"))))
+         "0qhrlhf881mi2v0n0y410c0bf2cm3imrlglq8argnw86n9xj51pw"))))
     (properties
      `((upstream-name . "simplifyEnrichment")))
     (build-system r-build-system)
@@ -10065,13 +10414,13 @@ and comparing the clusterings.")
 (define-public r-singscore
   (package
     (name "r-singscore")
-    (version "1.20.0")
+    (version "1.22.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "singscore" version))
               (sha256
                (base32
-                "1s1kyvkbfgwskf0hi4b44c2yx256rjp1yk9ijpld9qlm7z7pi67q"))))
+                "0hafzbhbik1512pisjvnnzmy8pl2shrgra6l06kpvsrczkqlmi04"))))
     (properties `((upstream-name . "singscore")))
     (build-system r-build-system)
     (propagated-inputs (list r-biobase
@@ -10103,13 +10452,13 @@ level.")
 (define-public r-tcgautils
   (package
     (name "r-tcgautils")
-    (version "1.20.4")
+    (version "1.22.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "TCGAutils" version))
               (sha256
                (base32
-                "02mkijvh2h58wg7hsi76ycw6gapl0ai190agckaw4l54sqpsx91q"))))
+                "0r79iiqv7q83wz5w3lm271dn3jdrkggmvjdyj1wnjsih1n2viy7d"))))
     (properties `((upstream-name . "TCGAutils")))
     (build-system r-build-system)
     (propagated-inputs (list r-annotationdbi
@@ -10142,13 +10491,13 @@ identifier translation via the GDC API.")
 (define-public r-tkwidgets
   (package
     (name "r-tkwidgets")
-    (version "1.78.0")
+    (version "1.80.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "tkWidgets" version))
               (sha256
                (base32
-                "1xp0gdfrhhfzfww4ig3y90f7334y24rhzrmlxmm4wav8slvcran2"))))
+                "11a8rflmga2d63l5nzdlbkyfnzsf20dzg2sy6qr143hg9sjzqrrj"))))
     (properties `((upstream-name . "tkWidgets")))
     (build-system r-build-system)
     (propagated-inputs (list r-dyndoc r-widgettools))
@@ -10158,16 +10507,17 @@ identifier translation via the GDC API.")
      "This package implements widgets to provide user interfaces.")
     (license license:artistic2.0)))
 
+;; TODO: check javascript
 (define-public r-trackviewer
   (package
     (name "r-trackviewer")
-    (version "1.36.2")
+    (version "1.38.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "trackViewer" version))
               (sha256
                (base32
-                "1ngfpd308y8i3vgv07cggk2azs64lsyyc9zfi3pz0gapr33ha6a1"))
+                "15agkyqx6gl5zzdxra5nl0czd4j7mw456r587w039l9hzwznwbr8"))
               (snippet
                '(delete-file "inst/htmlwidgets/lib/d3/d3.v4.min.js"))))
     (properties `((upstream-name . "trackViewer")))
@@ -10227,13 +10577,13 @@ methylation data.")
 (define-public r-transcriptr
   (package
     (name "r-transcriptr")
-    (version "1.28.0")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "transcriptR" version))
        (sha256
-        (base32 "0i38zs33drzk9szy2mdfs9ff9c3ccjgiyyynrrsinrx0szc8l22r"))))
+        (base32 "1lbla2syljpmgdf7da7vl1260fy54xs3hk6m2gjpark0dka0kqbh"))))
     (properties `((upstream-name . "transcriptR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10277,14 +10627,14 @@ able to deal also with novel and case specific events.")
 (define-public r-trajectoryutils
   (package
     (name "r-trajectoryutils")
-    (version "1.8.0")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "TrajectoryUtils" version))
        (sha256
         (base32
-         "1q3c226fskl45gq28xj2w5paz2s9n9kxm0bkkgg0329w399cs09k"))))
+         "0pqdl0v16q90ffxla34rp07mq0if1q9izpbimfnq0rx7633mk95v"))))
     (properties
      `((upstream-name . "TrajectoryUtils")))
     (build-system r-build-system)
@@ -10304,13 +10654,13 @@ structures to hold pseudotime inference results.")
 (define-public r-scds
   (package
     (name "r-scds")
-    (version "1.16.0")
+    (version "1.18.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "scds" version))
               (sha256
                (base32
-                "059gahl679if8xsfgpxmi3h9fiagb6v08rd6rs7yv96s3pb8qywn"))))
+                "0cmzvc1m29ijhzs2p407bhhxfqbflzsnrk7nq0jshjyw6v6pkfn0"))))
     (properties `((upstream-name . "scds")))
     (build-system r-build-system)
     (propagated-inputs (list r-dplyr
@@ -10332,13 +10682,13 @@ scRNA-seq data computationally.")
 (define-public r-slingshot
   (package
    (name "r-slingshot")
-   (version "2.8.0")
+   (version "2.10.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "slingshot" version))
             (sha256
              (base32
-              "1xr17rg8nfpcvdwa19qrcaqffkz048l5lkqlm6gw0abm8bg2k8x7"))))
+              "0q3j0jpc4mnmjb3xha5cmfhk1qdr1jiz7kdghznk4zqxn4bchc1d"))))
    (build-system r-build-system)
    (propagated-inputs
     (list r-igraph
@@ -10404,19 +10754,20 @@ tools either included in speaq or available elsewhere on CRAN.")
 (define-public r-spectra
   (package
     (name "r-spectra")
-    (version "1.10.3")
+    (version "1.12.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Spectra" version))
               (sha256
                (base32
-                "1fx6xkl29frfk8bzz5jvr1cn0hjyi46ck23izb1cypiag4lsrf8v"))))
+                "07zs9x5fzxzwicjc5x29sv33yidmq1ar70ss91py094zbw9i63qy"))))
     (properties `((upstream-name . "Spectra")))
     (build-system r-build-system)
     (propagated-inputs (list r-biocgenerics
                              r-biocparallel
                              r-fs
                              r-iranges
+                             r-metabocoreutils
                              r-mscoreutils
                              r-protgenerics
                              r-s4vectors))
@@ -10435,13 +10786,13 @@ data sets ensuring a small memory footprint.")
 (define-public r-stager
   (package
     (name "r-stager")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "stageR" version))
        (sha256
-        (base32 "0advih0g2g5w8bx9f21chz8a66f4v84qn3p5skxi084pp142v5ms"))))
+        (base32 "064hvx8qyw5hdhihwl9k0jqhg6saz4ng2m37d2ipr5pz9v8adspb"))))
     (properties `((upstream-name . "stageR")))
     (build-system r-build-system)
     (propagated-inputs (list r-summarizedexperiment))
@@ -10458,13 +10809,13 @@ Biology at
 (define-public r-stringdb
   (package
     (name "r-stringdb")
-    (version "2.12.1")
+    (version "2.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "STRINGdb" version))
        (sha256
-        (base32 "1c0m9k3gjmj160k8xyj2r60lpx4qgp7xibljfg8ljxr33f8aqyaz"))))
+        (base32 "1ffn73sx0qbzbh8cjil9r159g0fjnvi6y8rlbg6nf7p3zx3aya54"))))
     (properties `((upstream-name . "STRINGdb")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10491,13 +10842,13 @@ that integrates the various evidences.")
 (define-public r-structuralvariantannotation
   (package
     (name "r-structuralvariantannotation")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "StructuralVariantAnnotation" version))
        (sha256
-        (base32 "0gkps2pls9bpqr8sxm8zwdkn156g8r6mhf4bx17nif5s35qld1rb"))))
+        (base32 "1h3l3xbxwf2w2dl0qz72v68h5g77zhd2rr0g86l2dhn67mhy8ml2"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-assertthat
@@ -10528,13 +10879,13 @@ involving two separate genomic loci encoded as GRanges objects.")
 (define-public r-summarizedexperiment
   (package
     (name "r-summarizedexperiment")
-    (version "1.30.2")
+    (version "1.32.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "SummarizedExperiment" version))
               (sha256
                (base32
-                "05dy57fi43rpq9bhbsc4apa62xki99r84098pbvi3rjmac811425"))))
+                "1949k2658drmcrrr7v6748b40g2qym39n0ch50jxf0xmmlb1r04z"))))
     (properties
      `((upstream-name . "SummarizedExperiment")))
     (build-system r-build-system)
@@ -10563,13 +10914,13 @@ samples.")
 (define-public r-survcomp
   (package
     (name "r-survcomp")
-    (version "1.50.0")
+    (version "1.52.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "survcomp" version))
               (sha256
                (base32
-                "1va0ijx3qk3rjhzaflygfwlzn5a670y833qly8in8p5r3al9bdj6"))))
+                "18a81vv88xj3frkdy5l6w2fc4xzr1k6vgbz4j4marlmh6mz6skin"))))
     (properties `((upstream-name . "survcomp")))
     (build-system r-build-system)
     (propagated-inputs (list r-bootstrap
@@ -10590,22 +10941,22 @@ of risk prediction (survival) models.")
 (define-public r-sva
   (package
     (name "r-sva")
-    (version "3.48.0")
+    (version "3.50.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "sva" version))
        (sha256
         (base32
-         "1f6ia57fn2sn7c2zdfswvj9kx8xayssrgf5q6hrr9nrxc0jq19g3"))))
+         "0p4zgw1pi5vnaqxn6jmvhpy0h5hnnqp41n0k2v0chhqgqxgn67x1"))))
     (build-system r-build-system)
     (propagated-inputs
-     (list r-edger
+     (list r-biocparallel
+           r-edger
            r-genefilter
-           r-mgcv
-           r-biocparallel
+           r-limma
            r-matrixstats
-           r-limma))
+           r-mgcv))
     (home-page "https://bioconductor.org/packages/sva")
     (synopsis "Surrogate variable analysis")
     (description
@@ -10621,14 +10972,14 @@ unmodeled, or latent sources of noise.")
 (define-public r-systempiper
   (package
     (name "r-systempiper")
-    (version "2.6.3")
+    (version "2.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "systemPipeR" version))
        (sha256
         (base32
-         "068rikfq32awhvj0abl30bghv5k2z4zlfkbxpmsdapxhmdzhgnba"))))
+         "01amqib9ahrf19xpy4ivlsss82zyp3w7fbgwrwp53zfbg0cninga"))))
     (properties `((upstream-name . "systemPipeR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10664,21 +11015,21 @@ annotation infrastructure.")
 (define-public r-topgo
   (package
     (name "r-topgo")
-    (version "2.52.0")
+    (version "2.54.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "topGO" version))
               (sha256
                (base32
-                "0avjjvih387qhw8n4vjz4jq66q7sicgacsw53b85lq2c6ppib662"))))
+                "1sznyx11kzw8d8zg5ynl9sp6m0daf2yw3f2b24maxbpr1xkif9nx"))))
     (properties
      `((upstream-name . "topGO")))
     (build-system r-build-system)
     (propagated-inputs
      (list r-annotationdbi
-           r-dbi
            r-biobase
            r-biocgenerics
+           r-dbi
            r-go-db
            r-graph
            r-lattice
@@ -10697,13 +11048,13 @@ dependencies between GO terms can be implemented and applied.")
 (define-public r-tximport
   (package
     (name "r-tximport")
-    (version "1.28.0")
+    (version "1.30.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "tximport" version))
               (sha256
                (base32
-                "0km1vfn4jcp05jk5srrqanjngq6ghh5im6h1c424b926g9s7w7k1"))))
+                "0m6avd815xcv3py5sym083pdccvd4crdyyc7sfpxccnksgchyrf2"))))
     (build-system r-build-system)
     (native-inputs
      (list r-knitr))
@@ -10756,15 +11107,16 @@ R, enabling interactive analysis and visualization of genome-scale data.")
 (define-public r-variantannotation
   (package
     (name "r-variantannotation")
-    (version "1.46.0")
+    (version "1.48.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "VariantAnnotation" version))
               (sha256
                (base32
-                "0masx496cd4ypz6r0l8kk8vi81sipqdnx4iyifjvkrds1p87mvsm"))))
+                "1r1cyimr5l5jzgxvmrm3vq8mvz3f1klfdwy9mz31xvnvgjacr58p"))))
     (properties
      `((upstream-name . "VariantAnnotation")))
+    (build-system r-build-system)
     (propagated-inputs
      (list r-annotationdbi
            r-biobase
@@ -10777,14 +11129,14 @@ R, enabling interactive analysis and visualization of genome-scale data.")
            r-genomicranges
            r-iranges
            r-matrixgenerics
-           r-summarizedexperiment
            r-rhtslib
            r-rsamtools
            r-rtracklayer
            r-s4vectors
+           r-summarizedexperiment
            r-xvector
            r-zlibbioc))
-    (build-system r-build-system)
+    (native-inputs (list r-knitr))
     (home-page "https://bioconductor.org/packages/VariantAnnotation")
     (synopsis "Package for annotation of genetic variants")
     (description "This R package can annotate variants, compute amino acid
@@ -10794,14 +11146,14 @@ coding changes and predict coding outcomes.")
 (define-public r-vsn
   (package
     (name "r-vsn")
-    (version "3.68.0")
+    (version "3.70.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "vsn" version))
        (sha256
         (base32
-         "0i6c0wyhj0gcq0mw13zyk60cza2baq4yrj1n2dzqgsqkmhm5lfla"))))
+         "0li0yxf8m34xpmrgv5vciy8zdsbfdlajl9cmnxr4g4nmarik2bkh"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-affy r-biobase r-ggplot2 r-lattice r-limma))
@@ -10863,13 +11215,13 @@ inference.")
 (define-public r-xina
   (package
     (name "r-xina")
-    (version "1.18.0")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "XINA" version))
        (sha256
-        (base32 "1byk8xgn9rwfbi677b99ysxi4a9n58fr3hbnwjzhnziy2n2cd703"))))
+        (base32 "1cnw2zbjfs8qcgqrx557g00m59h5pldcx788v9r4gn2f70rx7vx3"))))
     (properties `((upstream-name . "XINA")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10899,13 +11251,13 @@ molecular functions, respectively, and produces intuitive graphical outputs.")
 (define-public r-xmapbridge
   (package
     (name "r-xmapbridge")
-    (version "1.58.0")
+    (version "1.60.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "xmapbridge" version))
        (sha256
-        (base32 "09pskmhjymqvhk26mk5yy1k195v536a2qp4k6xdd67xhf5ag260i"))))
+        (base32 "0pby2h8m12xlngpk33dvh3nkrpgqi4f2mb7g9jafyiv3sl8pjd19"))))
     (properties `((upstream-name . "xmapbridge")))
     (build-system r-build-system)
     (home-page "https://git.bioconductor.org/packages/xmapbridge")
@@ -10926,13 +11278,13 @@ describing each of the graphs.")
 (define-public r-xvector
   (package
     (name "r-xvector")
-    (version "0.40.0")
+    (version "0.42.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "XVector" version))
               (sha256
                (base32
-                "1v10hfz658gnb6p7pzdl28jbyypv91wx70i0dvi384nfgznhvmj2"))))
+                "0h03imdl0pyy714kmddsdnsv69bd8kr7bhi9wq9z18y8ahg5cqx1"))))
     (properties
      `((upstream-name . "XVector")))
     (build-system r-build-system)
@@ -10949,7 +11301,7 @@ describing each of the graphs.")
     (inputs
      (list zlib))
     (propagated-inputs
-     (list r-biocgenerics r-iranges r-s4vectors))
+     (list r-biocgenerics r-iranges r-s4vectors r-zlibbioc))
     (home-page "https://bioconductor.org/packages/XVector")
     (synopsis "Representation and manpulation of external sequences")
     (description
@@ -10960,13 +11312,13 @@ describing each of the graphs.")
 (define-public r-zlibbioc
   (package
     (name "r-zlibbioc")
-    (version "1.46.0")
+    (version "1.48.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "zlibbioc" version))
               (sha256
                (base32
-                "0x3d5kihckqnfjkc7dxk6mc194vwwr03jfjx2qh15g5494gfmm53"))))
+                "043xwgw3yclxnxlfl7fdwf7qf7fajzvqdv34qxnngxj9wpgha3gv"))))
     (properties
      `((upstream-name . "zlibbioc")))
     (build-system r-build-system)
@@ -10979,13 +11331,13 @@ libraries for systems that do not have these available via other means.")
 (define-public r-zellkonverter
   (package
     (name "r-zellkonverter")
-    (version "1.10.1")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "zellkonverter" version))
        (sha256
-        (base32 "1p89i2dfwcgrdchdnxrywp3jjjn5jjs5bisrx5kav26yh2pyx1wk"))))
+        (base32 "02q9icblcnh0l7vah29mnhcczw8w0gpgd57v19gy7222nrqpcd9m"))))
     (properties `((upstream-name . "zellkonverter")))
     (build-system r-build-system)
     (propagated-inputs
@@ -11011,14 +11363,14 @@ saving AnnData objects to disk.")
 (define-public r-geneplotter
   (package
     (name "r-geneplotter")
-    (version "1.78.0")
+    (version "1.80.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "geneplotter" version))
        (sha256
         (base32
-         "03x90l7rvxk0z03p5immqbyyhiygi3mkik636al1cjdcxl9dr5f8"))))
+         "0zvb84jlsvmr2dvwyy4xjqv353qrxpls0v2vz0nmj1q4m7lrpl1k"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-annotate
@@ -11027,6 +11379,8 @@ saving AnnData objects to disk.")
            r-biocgenerics
            r-lattice
            r-rcolorbrewer))
+    (native-inputs
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/geneplotter")
     (synopsis "Graphics functions for genomic data")
     (description
@@ -11036,14 +11390,14 @@ saving AnnData objects to disk.")
 (define-public r-oligoclasses
   (package
     (name "r-oligoclasses")
-    (version "1.62.0")
+    (version "1.64.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "oligoClasses" version))
        (sha256
         (base32
-         "0i745q2kx7rdfbkz3cwzzp1m4diny25mc301vy0sh4z5lpi5mdm8"))))
+         "1gdvjvyjfpvvrqyj9rq1l4dnq00hr8vr8knnlb9gnjk21sbcf1d7"))))
     (properties `((upstream-name . "oligoClasses")))
     (build-system r-build-system)
     (propagated-inputs
@@ -11071,14 +11425,14 @@ packages.")
 (define-public r-oligo
   (package
     (name "r-oligo")
-    (version "1.64.1")
+    (version "1.66.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "oligo" version))
        (sha256
         (base32
-         "0gs26h0hm8xlv3aayz4w0vwmw15x5602g02728spsm3n0qra3b1j"))))
+         "0pqn5qslynylx235wknwj71a6j7xf5i6pb7wjm00jwrdbqwvdlp6"))))
     (properties `((upstream-name . "oligo")))
     (build-system r-build-system)
     (inputs (list zlib))
@@ -11107,13 +11461,13 @@ Affymetrix (CEL files) and NimbleGen arrays (XYS files).")
 (define-public r-qfeatures
   (package
     (name "r-qfeatures")
-    (version "1.10.0")
+    (version "1.12.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "QFeatures" version))
               (sha256
                (base32
-                "1xnmd14nf4cqbfxkjsl6af312k7l27ars5g8qdnljylkn8kq276z"))))
+                "1g744fpb6g690bjbjs4v2899wwv6qc7n5cyq977pm8f3wln0m7mx"))))
     (properties `((upstream-name . "QFeatures")))
     (build-system r-build-system)
     (propagated-inputs (list r-annotationfilter
@@ -11142,13 +11496,13 @@ proteins) in a coherent and tractable format.")
 (define-public r-quantsmooth
   (package
     (name "r-quantsmooth")
-    (version "1.66.0")
+    (version "1.68.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "quantsmooth" version))
        (sha256
-        (base32 "05lja0viz5jgc7g3b8qfhd1x596vczid0dz8278qpl4zwv9i17vx"))))
+        (base32 "050nnwhxk3ld615f6ij4cc3d6wzrrxykvv02fr20fg5gzdj0z08a"))))
     (properties `((upstream-name . "quantsmooth")))
     (build-system r-build-system)
     (propagated-inputs (list r-quantreg))
@@ -11169,14 +11523,14 @@ on the location of the probe, and other useful tools.")
 (define-public r-qvalue
   (package
     (name "r-qvalue")
-    (version "2.32.0")
+    (version "2.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "qvalue" version))
        (sha256
         (base32
-         "1552390pf3wrrir6c9xshgll69a33fhbdnh2cvpnznma1ag490ki"))))
+         "10v5khnrs1fa84d430zy52f9466rwb1byaw1l3c9nivbhmaxhvyi"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-ggplot2 r-reshape2))
@@ -11224,13 +11578,13 @@ problems in genomics, brain imaging, astrophysics, and data mining.")
 (define-public r-apcomplex
   (package
     (name "r-apcomplex")
-    (version "2.66.0")
+    (version "2.68.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "apComplex" version))
        (sha256
-        (base32 "057p1bsqqw3r49bsx78prqc4jha468bfx50gpl62giix0cfs007f"))))
+        (base32 "1y3c3358y7ynn5lj2gcy9ll2gxnnlv689pj0bgr2gsnhbss1kw1r"))))
     (properties `((upstream-name . "apComplex")))
     (build-system r-build-system)
     (propagated-inputs
@@ -11249,13 +11603,13 @@ spectrometry} data.")
 (define-public r-apeglm
   (package
     (name "r-apeglm")
-    (version "1.22.1")
+    (version "1.24.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "apeglm" version))
               (sha256
                (base32
-                "19r1mhpkn3xy6l188c14k9xgn25xqc718bwrlmnz63lak6mp4ws7"))))
+                "0cj9yzmh9w3fk3rxmk2k5j55r42mmz9znszmr4l160mr23alkzx4"))))
     (properties `((upstream-name . "apeglm")))
     (build-system r-build-system)
     (propagated-inputs
@@ -11276,13 +11630,13 @@ posterior for individual coefficients.")
 (define-public r-greylistchip
   (package
    (name "r-greylistchip")
-   (version "1.32.1")
+   (version "1.34.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "GreyListChIP" version))
             (sha256
              (base32
-              "0z89yikglx077x18qhq6f8f2fa9xni12jz8my9p5sa6zmvnj4dnm"))))
+              "1k974cvfbkl8ffn7k2la843bv2pf33cr5f6fahiiy24d68lxwifr"))))
    (properties `((upstream-name . "GreyListChIP")))
    (build-system r-build-system)
    (propagated-inputs
@@ -11303,14 +11657,14 @@ signal in the input, that lead to spurious peaks during peak calling.")
 (define-public r-diffbind
   (package
     (name "r-diffbind")
-    (version "3.10.1")
+    (version "3.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DiffBind" version))
        (sha256
         (base32
-         "12frl2wfvfz4gpq4fjsmglqyqfxdk3zjbhqkc78rzylbw37xx3bf"))))
+         "1nlcx4fl1cpcg38cn9p55f75bv6pcg6h2jv4z94g2b7g1gwjd686"))))
     (properties `((upstream-name . "DiffBind")))
     (build-system r-build-system)
     (propagated-inputs
@@ -11381,13 +11735,13 @@ processing to visualization and annotation.")
 (define-public r-mbecs
   (package
     (name "r-mbecs")
-    (version "1.4.0")
+    (version "1.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MBECS" version))
        (sha256
-        (base32 "0gfr3c5k7xjd342zfdksgh22mrk3ryr4cp89nar0mlpgzxg4l4vz"))))
+        (base32 "1j7vb26n2fnf5fkk8hfz552yx91g4zg719alhg4hg2vvjd1qx2l1"))))
     (properties `((upstream-name . "MBECS")))
     (build-system r-build-system)
     (arguments
@@ -11406,7 +11760,6 @@ processing to visualization and annotation.")
            r-lme4
            r-lmertest
            r-magrittr
-           r-markdown
            r-matrix
            r-pheatmap
            r-phyloseq
@@ -11432,13 +11785,13 @@ before and after correcting for batch effects.")
 (define-public r-mbkmeans
   (package
     (name "r-mbkmeans")
-    (version "1.16.0")
+    (version "1.18.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "mbkmeans" version))
               (sha256
                (base32
-                "0c48ycgba1m10p1w2qz9r7yxw15nqzlz8fp44d6lbrvj3svmgjwi"))))
+                "1x7azijfs28iz2w40b9hnpgwh4jxgihl8cj6h91b2wgz79sq649l"))))
     (build-system r-build-system)
     (native-inputs
      (list r-knitr))
@@ -11464,13 +11817,13 @@ large datasets, including support for on-disk data representation.")
 (define-public r-multibac
   (package
     (name "r-multibac")
-    (version "1.10.0")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MultiBaC" version))
        (sha256
-        (base32 "1qwf1mvw81hb929xpnx5x910f7qnax9lkylhwzcdw1814s4zj25i"))))
+        (base32 "1mwfibakrxgs3r572bqqqmzq7ys6cs0bpn0wfrcb08ww2197xc4j"))))
     (properties `((upstream-name . "MultiBaC")))
     (build-system r-build-system)
     (propagated-inputs
@@ -11494,17 +11847,17 @@ the batches considered.")
 (define-public r-multtest
   (package
     (name "r-multtest")
-    (version "2.56.0")
+    (version "2.58.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "multtest" version))
        (sha256
         (base32
-         "19c6l8pkyp0m2zdzhr81cnmx5lqf501sap9h6ig5iiv66sf2ysmz"))))
+         "0s8x2rg2xp6awg2cikybgxrxpi9f91jah7dskk5dnfkazd20di4j"))))
     (build-system r-build-system)
     (propagated-inputs
-     (list r-survival r-biocgenerics r-biobase r-mass))
+     (list r-biobase r-biocgenerics r-mass r-survival))
     (home-page "https://bioconductor.org/packages/multtest")
     (synopsis "Resampling-based multiple hypothesis testing")
     (description
@@ -11529,13 +11882,13 @@ expressed genes in DNA microarray experiments.")
 (define-public r-graph
   (package
     (name "r-graph")
-    (version "1.78.0")
+    (version "1.80.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "graph" version))
               (sha256
                (base32
-                "184izzxc8bpagcac8wqinjp8kmf9zpvjibl0g32nnr64kp9f4rsn"))))
+                "0p7g7ykpkngbs3h1dsackfy93l8lvc301lr64ffsiaw60gllcx01"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biocgenerics))
@@ -11572,13 +11925,13 @@ fitting of some classes of graphical Markov models.")
 (define-public r-ggtreeextra
   (package
     (name "r-ggtreeextra")
-    (version "1.10.0")
+    (version "1.12.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "ggtreeExtra" version))
               (sha256
                (base32
-                "19xikly6ksh03kgpz35wj2d2gdbpikhrk71ahj9ghhkmlwdyjbcr"))))
+                "0q8k81mq5q9fym4zyrkzapgyww23lkxpkyj2s9r1y0ciclk90zdc"))))
     (properties `((upstream-name . "ggtreeExtra")))
     (build-system r-build-system)
     (propagated-inputs (list r-cli
@@ -11672,13 +12025,13 @@ a given recall, F-score for single and multiple classes are available.")
 (define-public r-pepsnmr
   (package
     (name "r-pepsnmr")
-    (version "1.18.0")
+    (version "1.20.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "PepsNMR" version))
               (sha256
                (base32
-                "17rbadvay3kbp4r6p023yww4biw9cl359q200ciygr7d2ffcas85"))))
+                "013jw9l7r87j4bmpjrvq5qn91kp44wj5vd68cl5axbqhjg7fq4ww"))))
     (properties `((upstream-name . "PepsNMR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -11728,14 +12081,14 @@ determining dependencies between variables, code improvement suggestions.")
 (define-public r-chippeakanno
   (package
     (name "r-chippeakanno")
-    (version "3.34.1")
+    (version "3.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ChIPpeakAnno" version))
        (sha256
         (base32
-         "0y9qskkdkl2vdbn66md4xisny0i7g2biasylp357vrkv41d3al6l"))))
+         "012hhakhk81qk1hi4igfa4vji678gmyvdxi05z9mdsx721lwwy2i"))))
     (properties `((upstream-name . "ChIPpeakAnno")))
     (build-system r-build-system)
     (propagated-inputs
@@ -11782,13 +12135,13 @@ enrichedGO (addGeneIDs).")
 (define-public r-matrixgenerics
   (package
    (name "r-matrixgenerics")
-   (version "1.12.3")
+   (version "1.14.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "MatrixGenerics" version))
             (sha256
              (base32
-              "07hrafzn3787vprdwdk3cfyhi8df7hjvxg9vq7ad8raqzb37lqil"))))
+              "14x5jib5xh2006lg96v3b9n2pnbjcbsd5igqybqsv0c53rk9394d"))))
    (properties
     `((upstream-name . "MatrixGenerics")))
    (build-system r-build-system)
@@ -11809,12 +12162,12 @@ incompatibilities.")
 (define-public r-marray
   (package
     (name "r-marray")
-    (version "1.78.0")
+    (version "1.80.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "marray" version))
               (sha256
-               (base32 "1z8fx47ng1av8nfpk0i7wpb8k8lsrn66k613p36mbh19m5fx05ks"))))
+               (base32 "1gj4mdbni5fk2z3zrk2cnhy610ihhhwjb9l1crglkklwxhkqlkvd"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-limma))
@@ -11828,12 +12181,12 @@ normalization and quality checking.")
 (define-public r-cghbase
   (package
    (name "r-cghbase")
-   (version "1.60.0")
+   (version "1.62.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "CGHbase" version))
             (sha256
-             (base32 "1r050acahvfp2ib88sy9xj4yjzy2d8h73hndi1s075h0zv12mjj7"))))
+             (base32 "1iw03gq1kvmn9a6h0kw389l9i7h99fbxcsag9f3gkfznjv0vp5k4"))))
    (properties `((upstream-name . "CGHbase")))
    (build-system r-build-system)
    (propagated-inputs
@@ -11847,16 +12200,16 @@ the @code{arrayCGH} packages.")
 (define-public r-cghcall
   (package
    (name "r-cghcall")
-   (version "2.62.0")
+   (version "2.64.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "CGHcall" version))
             (sha256
-             (base32 "02d8j0al062k33h6n3ihn7kwbqp3pjwg9zzbr45ay1m1jm6bappi"))))
+             (base32 "1x2zfr40bm42zd1bljwpbz3cz1q23a3yy1g277lwsp78gxbn3zly"))))
    (properties `((upstream-name . "CGHcall")))
    (build-system r-build-system)
    (propagated-inputs
-    (list r-biobase r-cghbase r-impute r-dnacopy r-snowfall))
+    (list r-biobase r-cghbase r-dnacopy r-impute r-snowfall))
    (home-page "https://bioconductor.org/packages/CGHcall")
    (synopsis "Base functions and classes for arrayCGH data analysis")
    (description "This package contains functions and classes that are needed by
@@ -11866,12 +12219,12 @@ the @code{arrayCGH} packages.")
 (define-public r-qdnaseq
   (package
     (name "r-qdnaseq")
-    (version "1.36.0")
+    (version "1.38.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "QDNAseq" version))
               (sha256
-               (base32 "0lcf5zkv44s7xsa2svxia7inv6iz2k1kilfj5zcq80r339pj3vx4"))))
+               (base32 "1n2qngqqw3hfv1yscksnpg8wslc85dlvaqw1hz2qvsxf1gcq2mks"))))
     (properties `((upstream-name . "QDNAseq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -11898,14 +12251,14 @@ respectively.")
 (define-public r-bayseq
   (package
     (name "r-bayseq")
-    (version "2.31.0")
+    (version "2.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "baySeq" version))
        (sha256
         (base32
-         "0lq2wfm3ibrpha9mqhhp6dgsx4jm2kwxvvrj0b62dzqspvg743wh"))))
+         "1b5vvzl0kkm6kb03vr6m6sdlr3azpc24933a7ayxkiffmf2wbi0g"))))
     (properties `((upstream-name . "baySeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -11922,14 +12275,14 @@ more complex hypotheses) via empirical Bayesian methods.")
 (define-public r-chipcomp
   (package
     (name "r-chipcomp")
-    (version "1.30.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ChIPComp" version))
        (sha256
         (base32
-         "1v27bqik5cgcvs1kb67s52r56v6fakvmi81iybvvvbxvcn1dmy9r"))))
+         "061d2z1rrcyad6cf19si14ab9a3dxdi17sfbkx3vx8kdsfs3djy9"))))
     (properties `((upstream-name . "ChIPComp")))
     (build-system r-build-system)
     (propagated-inputs
@@ -11956,14 +12309,14 @@ datasets.")
 (define-public r-riboprofiling
   (package
     (name "r-riboprofiling")
-    (version "1.30.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "RiboProfiling" version))
        (sha256
         (base32
-         "0qgzq82v4glkc0krk81zj9z71cnrvflsf1w45r9zmaw6bq45rfqd"))))
+         "1bd37ypxsj9p94p2851hhc9ind59b5pkg1lyalha1nfw5gf8iay3"))))
     (properties `((upstream-name . "RiboProfiling")))
     (build-system r-build-system)
     (propagated-inputs
@@ -11997,14 +12350,14 @@ assessment, principal component analysis on codon coverage.")
 (define-public r-riboseqr
   (package
     (name "r-riboseqr")
-    (version "1.32.0")
+    (version "1.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "riboSeqR" version))
        (sha256
         (base32
-         "0la8kmxxh5jnqsrmmvyhi313bjdbqkiq16hcxar6mgyjhxlsm610"))))
+         "1cigbp3pc70ipja9mmprkrs91723r1zwgxbzyp87n5mb0i4q8xqh"))))
     (properties `((upstream-name . "riboSeqR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -12025,14 +12378,14 @@ parsing of genetic sequencing data from ribosome profiling experiments.")
 (define-public r-interactionset
   (package
     (name "r-interactionset")
-    (version "1.28.1")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "InteractionSet" version))
        (sha256
         (base32
-         "1vs3mqf3x8zk7p83jkv41kag1bmn5zxrr3j1ldqk6wxsl77h55c5"))))
+         "0mpgxcwhb734pyn6bj93xknb704yrjkprxpa7kqwl24rbqyjydqs"))))
     (properties
      `((upstream-name . "InteractionSet")))
     (build-system r-build-system)
@@ -12059,14 +12412,14 @@ experiments.")
 (define-public r-genomicinteractions
   (package
     (name "r-genomicinteractions")
-    (version "1.34.0")
+    (version "1.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GenomicInteractions" version))
        (sha256
         (base32
-         "0qhb2mm5nynnw0cj5da0i6hb1bz7cyns0gp7xy0wscmfyh2wahbv"))))
+         "13rnxig22agykzv3q7wm4wr9c5aw56q6q1zv8m5g5ngjcssy8l4c"))))
     (properties
      `((upstream-name . "GenomicInteractions")))
     (build-system r-build-system)
@@ -12100,14 +12453,14 @@ information and producing various plots and statistics.")
 (define-public r-ctc
   (package
     (name "r-ctc")
-    (version "1.74.0")
+    (version "1.76.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ctc" version))
        (sha256
         (base32
-         "0ph22v1an2havnh9sm7hms0q2pq4fjad2cm4dffiy3344cv70sn1"))))
+         "10a83rr0qhnzdhvlbyn0y690hxnl8q86z47dpimr6sq41w463im3"))))
     (build-system r-build-system)
     (propagated-inputs (list r-amap))
     (home-page "https://bioconductor.org/packages/ctc/")
@@ -12120,14 +12473,14 @@ trees and clusters to other programs.")
 (define-public r-goseq
   (package
     (name "r-goseq")
-    (version "1.52.0")
+    (version "1.54.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "goseq" version))
        (sha256
         (base32
-         "1r13n64s9fbx951yaa4mpna71vynbkjz78irk96yzh2x2zzxpjvx"))))
+         "0waw5hhxh8yab8fqw9gnd3l39s6wkmp8690rhs4llarpqz6ssrhk"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-annotationdbi
@@ -12146,14 +12499,14 @@ defined categories which are over/under represented in RNA-seq data.")
 (define-public r-glimma
   (package
     (name "r-glimma")
-    (version "2.10.0")
+    (version "2.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Glimma" version))
        (sha256
         (base32
-         "0171wizl516chzzwnbc2z2bf5sk4a491fcs4yhq5ycqaqpjmbg35"))
+         "0pkh15jjjb83pq7d49yzwb2gyc95x4rww78qnzpdrzhycgmcapii"))
        (modules '((guix build utils)))
        (snippet
         '(with-directory-excursion "inst/htmlwidgets/lib/"
@@ -12231,13 +12584,13 @@ information.")
 (define-public r-glmgampoi
   (package
     (name "r-glmgampoi")
-    (version "1.12.2")
+    (version "1.14.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "glmGamPoi" version))
               (sha256
                (base32
-                "0d6q8vn8z90k8ffskcn9jmgg5x5pfb3wjv67bqskasy38inn1zg7"))))
+                "1qc3f1spzkcjk95b07jpxgrjiwmlamwwx6mlhml4lgzy5qby7dpw"))))
     (properties `((upstream-name . "glmGamPoi")))
     (build-system r-build-system)
     (propagated-inputs
@@ -12267,14 +12620,14 @@ experiments.")
 (define-public r-rots
   (package
     (name "r-rots")
-    (version "1.28.0")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ROTS" version))
        (sha256
         (base32
-         "0b2fl4wn696ia2kxihc6088ncnvd87ffq40bz58qi1bhq6krcmwv"))))
+         "1zd5w3mq0vjs3ivdb23x6d28sqq0dsfv13d64k1yijr4vdk3wvp6"))))
     (properties `((upstream-name . "ROTS")))
     (build-system r-build-system)
     (propagated-inputs
@@ -12290,14 +12643,14 @@ in omics data.")
 (define-public r-plgem
   (package
     (name "r-plgem")
-    (version "1.72.0")
+    (version "1.74.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "plgem" version))
        (sha256
         (base32
-         "1kzrscaqsrsvdq2c9g93l7bjmv1s5p1l3cbrz6skkqls9h4gsw08"))))
+         "0s5hia3xvddi0gaawcr5zsh34v6sh2zdi5gsjis8ar2g2p7agqgg"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biobase r-mass))
@@ -12314,13 +12667,13 @@ genes or proteins in these datasets.")
 (define-public r-plyranges
   (package
     (name "r-plyranges")
-    (version "1.20.0")
+    (version "1.22.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "plyranges" version))
               (sha256
                (base32
-                "1qv8snpcxpg16v5ji7sq3bnmgrgghz9h4mh246mcnnxfhi44b6nv"))))
+                "1z4pc9slbd6ji3c6g9flxhvvf0anjmywrlnjblv1mpgsh88avp7w"))))
     (properties `((upstream-name . "plyranges")))
     (build-system r-build-system)
     (propagated-inputs (list r-biocgenerics
@@ -12348,14 +12701,14 @@ accessiblity for new Bioconductor users is hopefully increased.")
 (define-public r-inspect
   (package
     (name "r-inspect")
-    (version "1.30.0")
+    (version "1.31.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "INSPEcT" version))
        (sha256
         (base32
-         "1nyfl78fjj956bk1xf32k3jdqhlffx6grbl7vajn48q5ldsx8kcx"))))
+         "0c7bw9cnav41vals2scv2gh5mj5nx2mgzagdb8g99sprdqv5924n"))))
     (properties `((upstream-name . "INSPEcT")))
     (build-system r-build-system)
     (propagated-inputs
@@ -12394,14 +12747,14 @@ modeling the rates that determines changes in mature mRNA levels.")
 (define-public r-dnabarcodes
   (package
     (name "r-dnabarcodes")
-    (version "1.30.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DNABarcodes" version))
        (sha256
         (base32
-         "1jys0lj92zkqa3bb22fg35q5y8ij5pqhy3yvzg8zc8bjpzdvrg3a"))))
+         "12x4k55kshvwyzl83zkgkp0ylryr8wd3kz44ngp60k4pkwhkl9h9"))))
     (properties `((upstream-name . "DNABarcodes")))
     (build-system r-build-system)
     (propagated-inputs
@@ -12421,14 +12774,14 @@ demultiplexed, i.e. assigned to their original reference barcode.")
 (define-public r-ruvseq
   (package
     (name "r-ruvseq")
-    (version "1.34.0")
+    (version "1.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "RUVSeq" version))
        (sha256
         (base32
-         "0kxaaqf6py7kfndgpd0faxv6g610zj16pyvn9b4x9s3b22ib06j1"))))
+         "04byggwsvmqrl77268smbas0wax460cdshmp4v5iqc5fghl7n0p2"))))
     (properties `((upstream-name . "RUVSeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -12446,14 +12799,14 @@ samples.")
 (define-public r-biocneighbors
   (package
     (name "r-biocneighbors")
-    (version "1.18.0")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocNeighbors" version))
        (sha256
         (base32
-         "1i4b37n9darizfq9i4vvbnxgrwhkvvd25a4cpfjv7nqywjfbsfjd"))))
+         "0a5wg099fgwjbzd6r3mr4l02rcmjqlkdcz1w97qzwx1mir41fmas"))))
     (properties `((upstream-name . "BiocNeighbors")))
     (build-system r-build-system)
     (propagated-inputs
@@ -12474,14 +12827,14 @@ achieved for all methods using the BiocParallel framework.")
 (define-public r-scaledmatrix
   (package
     (name "r-scaledmatrix")
-    (version "1.8.1")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ScaledMatrix" version))
        (sha256
         (base32
-         "0xhw77w28r3agv0hw7fjpn1fp2p9bz7kdzwzx7gsa8411nffmd4d"))))
+         "1aigca0s8cmi46458pl9p9vwlkrmqawbgi0xmbwslz646x2s2h4a"))))
     (properties `((upstream-name . "ScaledMatrix")))
     (build-system r-build-system)
     (propagated-inputs
@@ -12500,19 +12853,18 @@ multiplication.")
 (define-public r-treeio
   (package
     (name "r-treeio")
-    (version "1.24.3")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "treeio" version))
        (sha256
         (base32
-         "0shm0mdqvsk5qipdqbz3251kks6ii1vpx1pph0ms271nzs6fcvif"))))
+         "1kvzdryw74r74gwxddsrng81ww49p3s7hgxn8ggl0p8fvz3sfgir"))))
     (properties `((upstream-name . "treeio")))
     (build-system r-build-system)
     (propagated-inputs
      (list r-ape
-           r-cli
            r-dplyr
            r-jsonlite
            r-magrittr
@@ -12533,13 +12885,13 @@ platform for merging tree with associated data and converting file formats.")
 (define-public r-treesummarizedexperiment
   (package
     (name "r-treesummarizedexperiment")
-    (version "2.8.0")
+    (version "2.10.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "TreeSummarizedExperiment" version))
               (sha256
                (base32
-                "1grnz82a7l5dpwssc24yxhllqdcvza2gc4h4cc6zxjcdg5r4l1ra"))))
+                "1yvqixlivapasx0ircfhmc8ckr7sw86d9vfvnqj97p4r667x6z6g"))))
     (properties `((upstream-name . "TreeSummarizedExperiment")))
     (build-system r-build-system)
     (propagated-inputs
@@ -12566,14 +12918,14 @@ data.")
 (define-public r-ggtree
   (package
     (name "r-ggtree")
-    (version "3.8.2")
+    (version "3.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ggtree" version))
        (sha256
         (base32
-         "0l8llnvmg8k5qgag6vfgx1gdv0x46p3ypfz5apv23qhlbx4jfjja"))))
+         "12w2l1q0c5aznd5fls04wvgsmjidqhr1kkqj4gajz1abj9f49cqf"))))
     (properties `((upstream-name . "ggtree")))
     (build-system r-build-system)
     (propagated-inputs
@@ -12604,14 +12956,14 @@ data.")
 (define-public r-metapod
   (package
     (name "r-metapod")
-    (version "1.8.0")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "metapod" version))
        (sha256
         (base32
-         "0lr2sgbgdbqq626nsm3vyhghs8nalg5cxycr4cwsqh9nqrmip3wa"))))
+         "1nhxwj6gwc3hqji7icp1q6n0hj1gnvv1y5zhd2myhm7kj3sic2qc"))))
     (properties `((upstream-name . "metapod")))
     (build-system r-build-system)
     (propagated-inputs
@@ -12633,14 +12985,14 @@ missing values and weighting where appropriate.")
 (define-public r-biocsingular
   (package
     (name "r-biocsingular")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocSingular" version))
        (sha256
         (base32
-         "1a33zsw353pryq30178sbj9jzsmb4m7spqbx11hsicri8s1c0lb9"))))
+         "0z1p02329wk2x058ij42q5pyvp0vhsihaxmizgzcj4sww6i28j33"))))
     (properties `((upstream-name . "BiocSingular")))
     (build-system r-build-system)
     (propagated-inputs
@@ -12668,14 +13020,14 @@ possible, parallelization is achieved using the BiocParallel framework.")
 (define-public r-destiny
   (package
     (name "r-destiny")
-    (version "3.14.0")
+    (version "3.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "destiny" version))
        (sha256
         (base32
-         "0hc85dq68h7dy5jcflpjj05231ny7na9i4lksfsw89jhmxgzhacd"))))
+         "06xwyqlsas98lxmd0qw5ysjwbk397kyapd5jq5pzjrynsj4r9xn6"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biobase
@@ -12733,14 +13085,14 @@ Viewer (SAV) files, access data, and generate QC plots.")
 (define-public r-chipexoqual
   (package
     (name "r-chipexoqual")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ChIPexoQual" version))
        (sha256
         (base32
-         "1iysqs2k0xxiwd48ymahf6rywwj9ingjcfmnhx9d1x6w2h00v7lz"))))
+         "04dhkm8cq87x3c9f114z6q1pcw77xgs33rmhgzk4ajzxywhklq4j"))))
     (properties `((upstream-name . "ChIPexoQual")))
     (build-system r-build-system)
     (propagated-inputs
@@ -12793,14 +13145,14 @@ penalized least squares regression method.")
 (define-public r-dnacopy
   (package
     (name "r-dnacopy")
-    (version "1.74.1")
+    (version "1.76.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DNAcopy" version))
        (sha256
         (base32
-         "1bj87ksvch5cm5zxwgfiiql0j94pvzbpn59wp6bacyip65z7w3ax"))))
+         "0hyjin75v8l2a8qymsd6rjb8m7svv2q07s6z1dllqag09wja1yfz"))))
     (properties `((upstream-name . "DNAcopy")))
     (build-system r-build-system)
     (native-inputs (list gfortran))
@@ -12891,18 +13243,23 @@ and regression inferences from RNA-sequencing data.")
 (define-public r-ebseq
   (package
     (name "r-ebseq")
-    (version "1.40.0")
+    (version "2.0.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "EBSeq" version))
        (sha256
         (base32
-         "0y23k607f61csj2ciaqnl8pzsjisqlcnnhlasv36446n8f3silx5"))))
+         "07x9fh8akgiixsv1xddkvs2q8xxfsibas01kdx0kw6wak3nihn4w"))))
     (properties `((upstream-name . "EBSeq")))
     (build-system r-build-system)
     (propagated-inputs
-     (list r-blockmodeling r-gplots r-testthat))
+     (list r-bh
+           r-blockmodeling
+           r-gplots
+           r-rcpp
+           r-rcppeigen
+           r-testthat))
     (home-page "https://bioconductor.org/packages/EBSeq")
     (synopsis "Differential expression analysis of RNA-seq data")
     (description
@@ -12913,13 +13270,13 @@ gene and isoform level using RNA-seq data")
 (define-public r-karyoploter
   (package
     (name "r-karyoploter")
-    (version "1.26.0")
+    (version "1.28.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "karyoploteR" version))
               (sha256
                (base32
-                "1nqcm2jlazm8wsa4p6a59m1j8y1qdwg0w3kii4dqnkann3q2q68x"))))
+                "0jr9lp250s9066hh40vxb6c6yhdd8yrnk0zklwylkf3jpbdgl621"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-annotationdbi
@@ -12951,14 +13308,14 @@ coordinates.")
 (define-public r-lpsymphony
   (package
     (name "r-lpsymphony")
-    (version "1.28.1")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "lpsymphony" version))
        (sha256
         (base32
-         "08b4d7k5qx19bpg12pw89ckk8x6r2n28qjdxbmy1cxn6dcgzhijd"))))
+         "1946wlw9zvyxdd99rs2rliks54ff5dkibavxd48aj7cqjsjh6b7g"))))
     (build-system r-build-system)
     (arguments
      (list
@@ -12973,7 +13330,7 @@ coordinates.")
     (inputs
      (list zlib))
     (native-inputs
-     (list gfortran pkg-config r-knitr))
+     (list pkg-config r-knitr))
     (home-page "https://r-forge.r-project.org/projects/rsymphony")
     (synopsis "Symphony integer linear programming solver in R")
     (description
@@ -12990,14 +13347,14 @@ to install interface to SYMPHONY.")
 (define-public r-ihw
   (package
     (name "r-ihw")
-    (version "1.28.0")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "IHW" version))
        (sha256
         (base32
-         "0i4yahgkrg9rnc0xldm026k6bd1bn5nkgkaf6kpyyday41rxzyq8"))))
+         "1pix38lg9snw0jdihh8sifnmckyw1lniwp95r93ca524g6swfc8b"))))
     (properties `((upstream-name . "IHW")))
     (build-system r-build-system)
     (propagated-inputs
@@ -13019,14 +13376,14 @@ independent of the p-value under the null hypothesis.")
 (define-public r-icobra
   (package
     (name "r-icobra")
-    (version "1.28.1")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "iCOBRA" version))
        (sha256
         (base32
-         "120bcakhhl6xqsfclzgmn7rcxmld289bjl6j7nrli7aiq5ilz8h4"))))
+         "1f0j10wha60vv592vsnv2pcqwz7g2fkld8pnar9rpwwb7qd0wcnf"))))
     (properties `((upstream-name . "iCOBRA")))
     (build-system r-build-system)
     (propagated-inputs
@@ -13056,14 +13413,14 @@ interactive exploration of results.")
 (define-public r-residualmatrix
   (package
     (name "r-residualmatrix")
-    (version "1.10.0")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ResidualMatrix" version))
        (sha256
         (base32
-         "1yay0i0nh2ax35ayqlpnmq0839syl5991hacyrbv3li3gqjc9qqv"))))
+         "06py71xbygfwq55kawh2x340idrf5mmxmnsz5m6lph2ka086dc5v"))))
     (properties
      `((upstream-name . "ResidualMatrix")))
     (build-system r-build-system)
@@ -13085,14 +13442,14 @@ multiplication and calculation of row/column sums or means.")
 (define-public r-batchelor
   (package
     (name "r-batchelor")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "batchelor" version))
        (sha256
         (base32
-         "1cswij2mdjsdh99rmyh68wscg6h7cs0cff69gnki4gzzjfxy8x3f"))))
+         "1d5zik3bhz26ky2kpxd9kdzs9ff696qqys5gl8qwmmp8qym520l2"))))
     (properties `((upstream-name . "batchelor")))
     (build-system r-build-system)
     (propagated-inputs
@@ -13128,14 +13485,14 @@ the numbers of cells across batches.")
 (define-public r-mast
   (package
     (name "r-mast")
-    (version "1.26.0")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MAST" version))
        (sha256
         (base32
-         "0vm7v2anbrci6mcans9y9svd6xjm4waf2kny3rz0cjgsasw60ycx"))
+         "17iycxxp6jb56ra21546kh2zlrm8by2vrlvsxvx8xmbpk32fb4lp"))
        (snippet
         '(delete-file "docs/jquery.sticky-kit.min.js"))))
     (properties `((upstream-name . "MAST")))
@@ -13185,14 +13542,14 @@ single cell assay data.")
 (define-public r-monocle
   (package
     (name "r-monocle")
-    (version "2.28.0")
+    (version "2.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "monocle" version))
        (sha256
         (base32
-         "05pix638s4hkig2i048m5jjhvw6cqr2b5qvfkk14i64p9kpifmqj"))))
+         "0i1qnmiaf3gf8955nlqzd81xzg4siliq154k699jmsz0fyyykia1"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biobase
@@ -13276,13 +13633,13 @@ several functions from the R igraph package.")
 (define-public r-sangerseqr
   (package
     (name "r-sangerseqr")
-    (version "1.36.0")
+    (version "1.38.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "sangerseqR" version))
               (sha256
                (base32
-                "0hhq5zsx4srd9ndr370m44f80qdlrqafjv1838wf65gzijffhfqb"))))
+                "1vggjvxfmmm2gcyfay22wahkib15i164ic148jdps36pxapl6hi3"))))
     (properties `((upstream-name . "sangerseqR")))
     (build-system r-build-system)
     (propagated-inputs (list r-biostrings r-shiny r-stringr))
@@ -13392,14 +13749,14 @@ user-defined and/or data-driven sets of hypotheses.")
 (define-public r-noiseq
   (package
     (name "r-noiseq")
-    (version "2.44.0")
+    (version "2.46.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "NOISeq" version))
        (sha256
         (base32
-         "0cxhy4yrww6bh4z603389fikhix8rhfy04ylhm74fdmdng4jblg6"))))
+         "0qs0sc47n3p9wmf5cmc39cb30i8pbsyizhr29b3ld197pi1ba5wb"))))
     (properties `((upstream-name . "NOISeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -13418,14 +13775,14 @@ assumptions.")
 (define-public r-scdd
   (package
     (name "r-scdd")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "scDD" version))
        (sha256
         (base32
-         "1ndb1zcbdy00xkfx18slrm5bnld9ci5scysc37clhsq2lq5xb25z"))))
+         "15hzsq8ckw8v8ccz30kia9qr1iymmcszc9z31g5arrx1y816zgbq"))))
     (properties `((upstream-name . "scDD")))
     (build-system r-build-system)
     (propagated-inputs
@@ -13456,14 +13813,14 @@ distributions.")
 (define-public r-scone
   (package
     (name "r-scone")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "scone" version))
        (sha256
         (base32
-         "0v3rd2h0n52qz9kqxa3l49rjfssfk252dy7j2nvi34y85win2p1w"))))
+         "1y0blhh75hb60h9jmvz2naqfzky4zgw5gn81fbj74jfph9y712lp"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-aroma-light
@@ -13500,14 +13857,14 @@ high-throughput analyses.")
 (define-public r-geoquery
   (package
     (name "r-geoquery")
-    (version "2.68.0")
+    (version "2.70.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GEOquery" version))
        (sha256
         (base32
-         "1xyrfj8b7j2wdjlbmwhx1c0hfbvr7l7jxyw2v64fbw8604zprv4s"))))
+         "1xjfh9lx2cfwzkk61pdarajsa86nzhy3dz7r4zws20pz4xkhwv87"))))
     (properties `((upstream-name . "GEOquery")))
     (build-system r-build-system)
     (propagated-inputs
@@ -13535,14 +13892,14 @@ the bridge between GEO and BioConductor.")
 (define-public r-illuminaio
   (package
     (name "r-illuminaio")
-    (version "0.42.0")
+    (version "0.44.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "illuminaio" version))
        (sha256
         (base32
-         "190i3b9qmh26bic1lzi54mw4p1nrg57qijl1pg6b29w3i6srq692"))))
+         "15i47b995dqh0dlg60lss5vgj31as3cwhb2z5fqbnknx3lj7s6rl"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-base64))
@@ -13556,14 +13913,14 @@ files, including IDAT.")
 (define-public r-siggenes
   (package
     (name "r-siggenes")
-    (version "1.74.0")
+    (version "1.76.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "siggenes" version))
        (sha256
         (base32
-         "0h5asj2w4xgfj9xapjawmxldnhq789py39drlr8illyhcczkzkbz"))))
+         "0jzxwg28ih1i0f7hal99g60zply0g613b4wrjsbv738cmlsai2kc"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biobase r-multtest r-scrime))
@@ -13580,14 +13937,14 @@ Bayes Analyses of Microarrays} (EBAM).")
 (define-public r-bumphunter
   (package
     (name "r-bumphunter")
-    (version "1.42.0")
+    (version "1.44.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bumphunter" version))
        (sha256
         (base32
-         "1xghz87702fg9r6n1igygf4ybb8mw8ff0i02qkx9jmm6vmmfhv18"))))
+         "0vnm0m9abf8478f7lair58vw1v4mxj8sbmrxcpf8622ygf2na4qc"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-annotationdbi
@@ -13614,13 +13971,13 @@ studies.")
 (define-public r-bumpymatrix
   (package
     (name "r-bumpymatrix")
-    (version "1.8.0")
+    (version "1.10.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BumpyMatrix" version))
               (sha256
                (base32
-                "021xn5d08phmwv6g8a5d4ap5kcf5syhm6vpr784l4k54lflssr5i"))))
+                "0ic87fjxwb39nmys09zb6k3ghcx8mmmj9pifljs10449i2lgzl2r"))))
     (properties `((upstream-name . "BumpyMatrix")))
     (build-system r-build-system)
     (propagated-inputs (list r-iranges r-matrix r-s4vectors))
@@ -13640,13 +13997,13 @@ data in a format that is compatible with two-dimensional containers like the
 (define-public r-mia
   (package
     (name "r-mia")
-    (version "1.8.0")
+    (version "1.10.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "mia" version))
               (sha256
                (base32
-                "1p78yacx0cgihva7m2n3vnll5w4b47vl98hy12pq9rnmhk6r591z"))))
+                "044spfxsf7xijnbh0933cwdkycmg05zsfqhbx5pkfajysh6w5cxp"))))
     (properties `((upstream-name . "mia")))
     (build-system r-build-system)
     (propagated-inputs
@@ -13654,6 +14011,7 @@ data in a format that is compatible with two-dimensional containers like the
            r-biocgenerics
            r-biocparallel
            r-biostrings
+           r-bluster
            r-decipher
            r-decontam
            r-delayedarray
@@ -13662,6 +14020,7 @@ data in a format that is compatible with two-dimensional containers like the
            r-dplyr
            r-iranges
            r-mass
+           r-matrixgenerics
            r-multiassayexperiment
            r-rlang
            r-s4vectors
@@ -13688,13 +14047,13 @@ summarization.")
 (define-public r-microbiome
   (package
     (name "r-microbiome")
-    (version "1.22.0")
+    (version "1.24.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "microbiome" version))
               (sha256
                (base32
-                "120wyjv2r9cbjgxbp70nzf249hai8cqn59gcbgwnazynfy5ih1w8"))))
+                "0xmkwf7v89nwlpjrzqxv87lbsn6za99v7f0yxkgzfk5n6fadrf05"))))
     (properties `((upstream-name . "microbiome")))
     (build-system r-build-system)
     (propagated-inputs
@@ -13759,13 +14118,13 @@ experiments.")
 (define-public r-milor
   (package
     (name "r-milor")
-    (version "1.8.1")
+    (version "1.10.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "miloR" version))
               (sha256
                (base32
-                "073s239aqkixsrarqxfv4nmpcj025k32nhql63qaxrkrvvdd34di"))))
+                "1hnvw9x0xwjb0br4yvzkzn73nvm8p3j3wmcw8jrid105j0fz6vcj"))))
     (properties `((upstream-name . "miloR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -13807,14 +14166,14 @@ model.")
 (define-public r-minfi
   (package
     (name "r-minfi")
-    (version "1.46.0")
+    (version "1.48.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "minfi" version))
        (sha256
         (base32
-         "18b9yg9hnnm1saaiprm2hj86aajjwm1zwvpj0yadfa3s811pw4nq"))))
+         "13lldzj68vmmmrp5fi2rfxbchbivaa1scq56hl0v9mxxicw72a0x"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-beanplot
@@ -13858,13 +14217,13 @@ methylation arrays.")
 (define-public r-missmethyl
   (package
     (name "r-missmethyl")
-    (version "1.34.0")
+    (version "1.36.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "missMethyl" version))
               (sha256
                (base32
-                "1jvrdr57mv93pcbyazcg1bcx1zd0kp72hi1if839gw54hk3igs3h"))))
+                "1nv4rm5pbx0s7m5zak3jzmwz4pkf8ghkj0ckdcsnmw3k364ny856"))))
     (properties `((upstream-name . "missMethyl")))
     (build-system r-build-system)
     (propagated-inputs
@@ -13908,14 +14267,14 @@ into account multi-gene associated probes.")
 (define-public r-methylumi
   (package
     (name "r-methylumi")
-    (version "2.46.0")
+    (version "2.48.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "methylumi" version))
        (sha256
         (base32
-         "1aa0pwjyp2p9a4mx4n4qw88ndgrj56p669yzdkd7hxhc3x55nzlf"))))
+         "1vracrvy56kk3hc9midxdaxhad2zf1lspn0zzxjjbsyzx3r0ip0n"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-annotate
@@ -13955,13 +14314,13 @@ and Infinium HD arrays are also included.")
 (define-public r-lefser
   (package
     (name "r-lefser")
-    (version "1.10.1")
+    (version "1.11.5")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "lefser" version))
               (sha256
                (base32
-                "1ifmbbsbyzcyvjni9ww27c9qsqliv7vj2rv9mg9c7gnqgbg6h2c4"))))
+                "1fnccnjllgxf51dlmcvv0r66xs0wvfxrj66qrqisqd99hrpxhws2"))))
     (properties `((upstream-name . "lefser")))
     (build-system r-build-system)
     (propagated-inputs
@@ -13979,14 +14338,14 @@ to find biomarkers of groups and sub-groups.")
 (define-public r-lumi
   (package
     (name "r-lumi")
-    (version "2.52.0")
+    (version "2.54.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "lumi" version))
        (sha256
         (base32
-         "1lxxqr7x9jdjrsj5j95jb0dbd7p208vifxw3j4s4140zh1ppxnpj"))))
+         "0iwkag84w1sc703jcdfx0h799hlchdiqvlps8g8lwmil5b0xlsw5"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-affy
@@ -14018,14 +14377,14 @@ especially Illumina Infinium methylation microarrays.")
 (define-public r-linnorm
   (package
     (name "r-linnorm")
-    (version "2.24.1")
+    (version "2.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Linnorm" version))
        (sha256
         (base32
-         "1sqkmjah2lxahnvwv04a970za2b8kzvmxnb41k9xrnvj0akigc2d"))))
+         "1ax5zmby8zw0mgxjd8yhlk4ai0s03zq59qwzqgv8zqlms8yjpvs2"))))
     (properties `((upstream-name . "Linnorm")))
     (build-system r-build-system)
     (propagated-inputs
@@ -14079,14 +14438,14 @@ evaluation of DEG analysis methods.")
 (define-public r-ioniser
   (package
     (name "r-ioniser")
-    (version "2.24.0")
+    (version "2.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "IONiseR" version))
        (sha256
         (base32
-         "1yrsd5n9zam6wslc6savfn122v3wzzcc46w20mb849qq2np4frf0"))))
+         "1y595hq40kpsasp74wsbf3ngd2rrriqg65z9y4svcwdygj03pgrz"))))
     (properties `((upstream-name . "IONiseR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -14146,14 +14505,14 @@ are standardized and usable by the accompanying mutossGUI package.")
 (define-public r-metap
   (package
     (name "r-metap")
-    (version "1.8")
+    (version "1.9")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "metap" version))
        (sha256
         (base32
-         "0asmypxfxly4xmcjf3yzid5zqlzg88z0brij2splfk4avsl035gf"))))
+         "1w4mv7vb94d4pkllvabz9az8sbrbfhigxw4is3j0jzi1pnlyc8kg"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-lattice
@@ -14175,13 +14534,13 @@ published results; and a routine for graphical display.")
 (define-public r-tradeseq
   (package
    (name "r-tradeseq")
-   (version "1.14.0")
+   (version "1.16.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "tradeSeq" version))
             (sha256
              (base32
-              "14b90x9h34mhbc4sdpzkygrrswf84pi1ddwpzxhvlvr9gs443xqs"))))
+              "06k0jib20nq7zqc5vbgag8v1lbadjlg0idh5jwn5bcjc74dx15vj"))))
    (build-system r-build-system)
    (propagated-inputs
     (list r-biobase
@@ -14244,14 +14603,14 @@ peak definition in combination with known profile characteristics.")
 (define-public r-varianttools
   (package
     (name "r-varianttools")
-    (version "1.42.0")
+    (version "1.44.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "VariantTools" version))
        (sha256
         (base32
-         "1vkdw626r1ffdsvry6qwhd1i3lkyb9wzrp9zf3dfafi02cap6r47"))))
+         "1ibg4cdpbv4ph3y4r90j8zfwr1cy1z33p4bazhzyi2zv3xa1nrq6"))))
     (properties `((upstream-name . "VariantTools")))
     (build-system r-build-system)
     (propagated-inputs
@@ -14284,14 +14643,14 @@ gmapR.")
 (define-public r-heatplus
   (package
     (name "r-heatplus")
-    (version "3.8.0")
+    (version "3.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Heatplus" version))
        (sha256
         (base32
-         "031f25w960jp5nhd78v3iv6pib266cpbawhi9rrd7csw89vnswfx"))))
+         "1vs7x4dc2vrfi2wi300bjr2hl1wwp4v27sgzycr6qv6x2nx9i5xq"))))
     (properties `((upstream-name . "Heatplus")))
     (build-system r-build-system)
     (propagated-inputs
@@ -14309,18 +14668,18 @@ information about samples and features can be added to the plot.")
 (define-public r-gosemsim
   (package
     (name "r-gosemsim")
-    (version "2.26.1")
+    (version "2.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GOSemSim" version))
        (sha256
         (base32
-         "15z7wqnp0s8fiysl3qc76pjaj3xik2br2mz2z3nmf28vxig69mx9"))))
+         "10jhjzgf10w9cmr97qzc3mqvgvgx9h7pqk7zkkqwhg7anv6wa788"))))
     (properties `((upstream-name . "GOSemSim")))
     (build-system r-build-system)
     (propagated-inputs
-     (list r-annotationdbi r-go-db r-rcpp))
+     (list r-annotationdbi r-go-db r-rcpp r-rlang))
     (native-inputs
      (list r-knitr))
     (home-page "https://guangchuangyu.github.io/software/GOSemSim")
@@ -14336,14 +14695,14 @@ sets of GO terms, gene products and gene clusters.")
 (define-public r-anota
   (package
     (name "r-anota")
-    (version "1.48.0")
+    (version "1.50.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "anota" version))
        (sha256
         (base32
-         "0ic12p1qyfrmh3l1wv7s9yi8sr84crj4nksmcx0lybb6rak9gy0x"))))
+         "1b1r7jwilwvl89fw3rqascyhy8wnm8y81lnx85pwjk55ld56jlb1"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-multtest r-qvalue))
@@ -14366,13 +14725,13 @@ the data set is suitable for such analysis.")
 (define-public r-anota2seq
   (package
     (name "r-anota2seq")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "anota2seq" version))
        (sha256
-        (base32 "0pmk45276bl3qppzxlp4jpc8bsvdpca8nzrdl6c4n9r3xhzfpyq0"))))
+        (base32 "0kyxwhj5vq5z4v3x3hfb9ks3h37axqskyj9rzyj2bzsy2yk9hajn"))))
     (properties `((upstream-name . "anota2seq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -14399,38 +14758,16 @@ mRNA levels or buffering, a mechanism regulating translational efficiency so
 that protein levels remain constant despite fluctuating total mRNA levels.")
     (license license:gpl3)))
 
-(define-public r-sigpathway
-  (package
-    (name "r-sigpathway")
-    (version "1.66.2")
-    (source
-      (origin
-        (method url-fetch)
-        (uri (bioconductor-uri "sigPathway" version))
-        (sha256
-          (base32
-            "0k86hlz7zbbw7559bd2sl59pr441kihgwvg8nr75mj8d50n783sy"))))
-    (properties `((upstream-name . "sigPathway")))
-    (build-system r-build-system)
-    (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
-    (synopsis "Pathway analysis")
-    (description
-     "This package is used to conduct pathway analysis by calculating the NT_k
-and NE_k statistics in a statistical framework for determining whether a
-specified group of genes for a pathway has a coordinated association with a
-phenotype of interest.")
-    (license license:gpl2)))
-
 (define-public r-fcscan
   (package
     (name "r-fcscan")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "fcScan" version))
        (sha256
-        (base32 "071sylwwj27bk39pkn5a29r7bmfpmyaixkkg7dqcdq230c1dsrps"))))
+        (base32 "0hhad9vg43j0yz8fp2w7qdhvdy77yr7anv0fi170042x3piq1q7r"))))
     (properties `((upstream-name . "fcScan")))
     (build-system r-build-system)
     (propagated-inputs
@@ -14457,14 +14794,14 @@ presence of additional sites within the allowed window size.")
 (define-public r-fgsea
   (package
     (name "r-fgsea")
-    (version "1.26.0")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "fgsea" version))
        (sha256
         (base32
-         "0chnrwiwk31crrx4am1yrbxjdqd3jycgjgczqzj7lxaa9v7lvm7z"))))
+         "0sykd4ingpw41615hbr3vw9yd1ks225hdb5qxnhbk4m4wxj814ql"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-bh
@@ -14490,14 +14827,14 @@ to multiple hypothesis correction.")
 (define-public r-dose
   (package
     (name "r-dose")
-    (version "3.26.1")
+    (version "3.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DOSE" version))
        (sha256
         (base32
-         "1whvgzw8p0nm3kchdndrxj4x3fhmq0vgbz77d54sqq1qri4j35qx"))))
+         "1xirazskw2d0fllyf27jvsm69amcil1znx81m9d613vl03dpwswy"))))
     (properties `((upstream-name . "DOSE")))
     (build-system r-build-system)
     (propagated-inputs
@@ -14507,6 +14844,8 @@ to multiple hypothesis correction.")
            r-ggplot2
            r-gosemsim
            r-hdo-db
+           r-hpo-db
+           r-mpo-db
            r-qvalue
            r-reshape2))
     (native-inputs
@@ -14525,13 +14864,13 @@ data.")
 (define-public r-enrichedheatmap
   (package
     (name "r-enrichedheatmap")
-    (version "1.30.0")
+    (version "1.32.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "EnrichedHeatmap" version))
               (sha256
                (base32
-                "18p2vjcg76rrjzjl03zgm4yxrgllbd42hg8rvsdbfb0s7brzr7ya"))))
+                "0j87x26qimsx4gi311bm1g9bldwq9r4z3aflxf8p91zlavjbv8zp"))))
     (properties `((upstream-name . "EnrichedHeatmap")))
     (build-system r-build-system)
     (propagated-inputs (list r-circlize
@@ -14557,14 +14896,14 @@ correspondance between different data sources.")
 (define-public r-enrichplot
   (package
     (name "r-enrichplot")
-    (version "1.20.3")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "enrichplot" version))
        (sha256
         (base32
-         "11hgxs42wvirv6b9ywr2jb51s67k4r0pm21dkvm7xjbsbarlkhmh"))))
+         "05ps96adbn4h8i0mqflzm1h6chjlrmfz6hx393232bhb995jfllx"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-aplot
@@ -14625,14 +14964,14 @@ attempts to assess their statistical significance.")
 (define-public r-clusterprofiler
   (package
     (name "r-clusterprofiler")
-    (version "4.8.3")
+    (version "4.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "clusterProfiler" version))
        (sha256
         (base32
-         "1kihrpa8cb2bqk5dck0w6yzgfpl72qxlrxwpidg1ar27q3ivz8w3"))))
+         "1vlrybyczfci5qnw50k0y2j2853r2p1ff5bpj35rdca4ja0iqh2q"))))
     (properties
      `((upstream-name . "clusterProfiler")))
     (build-system r-build-system)
@@ -14645,6 +14984,8 @@ attempts to assess their statistical significance.")
            r-go-db
            r-gosemsim
            r-gson
+           r-httr
+           r-igraph
            r-magrittr
            r-plyr
            r-qvalue
@@ -14663,13 +15004,13 @@ profiles (GO and KEGG) of gene and gene clusters.")
 (define-public r-clusterexperiment
   (package
     (name "r-clusterexperiment")
-    (version "2.20.0")
+    (version "2.22.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "clusterExperiment" version))
               (sha256
                (base32
-                "0h22zh6jpd2wsh6b9rnrmx8897aqlrsnw82kwphx8lay4r1vv706"))))
+                "1qnxrdpp75m342q4chwaig413l52giz1h7nd4p9y4b472dqx9hh4"))))
     (build-system r-build-system)
     (native-inputs
      (list r-knitr))
@@ -14709,14 +15050,14 @@ expression data sets.")
 (define-public r-mlinterfaces
   (package
     (name "r-mlinterfaces")
-    (version "1.80.0")
+    (version "1.82.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MLInterfaces" version))
        (sha256
         (base32
-         "1s5b27n01crfzrpshhiv6g0q0qf0dip1gw4nkrkg5sh5x9dsikq6"))))
+         "0aga7xhx5d1xp09n2im7yqi9y1b3v22l554hi35ahg2lwwvxjiw1"))))
     (properties `((upstream-name . "MLInterfaces")))
     (build-system r-build-system)
     (propagated-inputs
@@ -14753,14 +15094,14 @@ data in R and Bioconductor containers.")
 (define-public r-annaffy
   (package
     (name "r-annaffy")
-    (version "1.72.0")
+    (version "1.74.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "annaffy" version))
        (sha256
         (base32
-         "0jy3qk31lb11bixncb2w2hw1ibvik31bfi2l5vyq5wjyxndfyax6"))))
+         "1mdv0x9lnr0bm96h5f9104nqg2j6cjqvp5prrxx10j0d6464vmkw"))))
     (build-system r-build-system)
     (arguments
      `(#:phases
@@ -14785,14 +15126,14 @@ It allows searching of biological metadata using various criteria.")
 (define-public r-a4core
   (package
     (name "r-a4core")
-    (version "1.48.0")
+    (version "1.50.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "a4Core" version))
        (sha256
         (base32
-         "14q9q3dxnmmm491af53hd0dwwqiz47xxrwy05axh85x4fh01j3xx"))))
+         "0iismcsnkyb7m4dwmxw5pyvscj2bhp6zw9hpdb2ff91viynbknq1"))))
     (properties `((upstream-name . "a4Core")))
     (build-system r-build-system)
     (propagated-inputs
@@ -14809,14 +15150,14 @@ arrays.")
 (define-public r-a4classif
   (package
     (name "r-a4classif")
-    (version "1.48.0")
+    (version "1.50.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "a4Classif" version))
        (sha256
         (base32
-         "1z5xypz5jvb06pk71x6953iirhh1w1mggm0pxqibg0ag9lx2zzmv"))))
+         "1wxkyqyhb3mj04kmaisd09dapywjpc081ihaig5rs04k611ddvhi"))))
     (properties `((upstream-name . "a4Classif")))
     (build-system r-build-system)
     (propagated-inputs
@@ -14839,14 +15180,14 @@ Affymetrix arrays.")
 (define-public r-a4preproc
   (package
     (name "r-a4preproc")
-    (version "1.48.0")
+    (version "1.50.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "a4Preproc" version))
        (sha256
         (base32
-         "1dxh0zbv4z4gqnwbv7yn247gx7cqv68vb43p6f98c2kyqilfpjg9"))))
+         "19nf3bc0gdwixif50f3bs47a1kw1w1lir1dz4l8zqdp3h8gfmj60"))))
     (properties `((upstream-name . "a4Preproc")))
     (build-system r-build-system)
     (propagated-inputs
@@ -14863,14 +15204,14 @@ is used for preprocessing the arrays.")
 (define-public r-a4reporting
   (package
     (name "r-a4reporting")
-    (version "1.48.0")
+    (version "1.50.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "a4Reporting" version))
        (sha256
         (base32
-         "0lx7fx2vlpq3c347gx842qlcvnzl0r25i5a55l0qbf8rb5liq2yv"))))
+         "16lgbwsgwp77x9a8c3hr1aqhp36skzz72xhbzm0a7w3kagmd8gn6"))))
     (properties `((upstream-name . "a4Reporting")))
     (build-system r-build-system)
     (propagated-inputs
@@ -14887,14 +15228,14 @@ provides reporting features.")
 (define-public r-a4base
   (package
     (name "r-a4base")
-    (version "1.48.0")
+    (version "1.50.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "a4Base" version))
        (sha256
         (base32
-         "01c8rps321820b0pchfqv8shglb26rys7hqkwygpzzx3jj310v8x"))))
+         "0hin5lpwa7cxa862jh3y7d8kq3q9bv76ri08b27jxzyr5p7xwcr2"))))
     (properties `((upstream-name . "a4Base")))
     (build-system r-build-system)
     (propagated-inputs
@@ -14918,14 +15259,14 @@ Affymetrix arrays.")
 (define-public r-a4
   (package
     (name "r-a4")
-    (version "1.48.0")
+    (version "1.50.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "a4" version))
        (sha256
         (base32
-         "0n49scwwmg51gcakbc0bfjcy1lcpdxg974l11yk35kj0bg9ynpgi"))))
+         "1hdqnipg326z2k7vs6sc1brc9lvvhmr2l6cjp4f9a205g4q7r9rr"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-a4base r-a4classif r-a4core r-a4preproc r-a4reporting))
@@ -14939,14 +15280,14 @@ Affymetrix arrays.")
 (define-public r-abseqr
   (package
     (name "r-abseqr")
-    (version "1.18.0")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "abseqR" version))
        (sha256
         (base32
-         "05kcwmv3d59lrdnpi82701biwawnnpfvpwr170xdi3hfdff6g59c"))))
+         "0s865nahgm0by2nvjydkjlhkj2sxmrvcrhw7rmm46ld4g10xsrc8"))))
     (properties `((upstream-name . "abseqR")))
     (build-system r-build-system)
     (inputs
@@ -14987,14 +15328,14 @@ further downstream analysis on its output.")
 (define-public r-bacon
   (package
     (name "r-bacon")
-    (version "1.28.0")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bacon" version))
        (sha256
         (base32
-         "1h2yh85c6d4j2abdh5l7m6zcxh9i5xzrwwjkwas4nfs48h74z293"))))
+         "065b4xf5i1bx08494nm3r497bs47s5vf99l2g37nlpvxf7pypvrz"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biocparallel r-ellipse r-ggplot2))
@@ -15012,14 +15353,14 @@ fitting a three-component normal mixture on z-scores.")
 (define-public r-rgadem
   (package
     (name "r-rgadem")
-    (version "2.48.0")
+    (version "2.50.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "rGADEM" version))
        (sha256
         (base32
-         "08li2wql2zhg06z0rjws9qcnv3ishgnpc6k8xyjcf7yfyg7qpk1d"))))
+         "14jcsqb56vn67hjmcjjnwswzbilsarkk8kblc715c7da72q7fzpn"))))
     (properties `((upstream-name . "rGADEM")))
     (build-system r-build-system)
     (propagated-inputs
@@ -15066,12 +15407,12 @@ distributions, modules and filter motifs.")
 (define-public r-motifdb
   (package
    (name "r-motifdb")
-   (version "1.42.0")
+   (version "1.44.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "MotifDb" version))
             (sha256
-             (base32 "18d0qj9sn4bhfjy2mwsz2nnm41xlsqjslsv69nkhv19w9zd842pw"))))
+             (base32 "1z72f5f3sh2ak6zjcfc6j6rblkllmdkli0kb57nwxg2j5hrys3xr"))))
    (properties `((upstream-name . "MotifDb")))
    (build-system r-build-system)
    (propagated-inputs
@@ -15093,12 +15434,12 @@ frequency matrices from nine public sources, for multiple organisms.")
 (define-public r-motifbreakr
   (package
    (name "r-motifbreakr")
-   (version "2.14.2")
+   (version "2.16.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "motifbreakR" version))
             (sha256
-             (base32 "13fv0rkyb32grswlgzd3zr35p9xpibj2iq62sr23if4w6z5nbml2"))))
+             (base32 "02i3hkffhhsbzmn97mv8wc2px5caq9xnp45z0l53dp1jxbmms1h0"))))
    (properties `((upstream-name . "motifbreakR")))
    (build-system r-build-system)
    (propagated-inputs
@@ -15143,40 +15484,29 @@ Bioconductor.")
 (define-public r-motifstack
   (package
     (name "r-motifstack")
-    (version "1.44.1")
+    (version "1.46.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "motifStack" version))
        (sha256
         (base32
-         "1g46cxn1h3cqr0yrj6ancshzygiqr9finf1vmmig3h9g0ijgr5lz"))
+         "10hmqwkysifd59as9zx00p3gj595lwj30ywn9pqb1920q6f5mx2i"))
        (snippet
         '(delete-file "inst/htmlwidgets/lib/d3/d3.v4.min.js"))))
     (properties `((upstream-name . "motifStack")))
     (build-system r-build-system)
     (arguments
      (list
-      #:modules '((guix build utils)
-                  (guix build r-build-system)
-                  (srfi srfi-1))
       #:phases
       '(modify-phases %standard-phases
          (add-after 'unpack 'process-javascript
            (lambda* (#:key inputs #:allow-other-keys)
              (with-directory-excursion "inst/htmlwidgets/lib/d3"
-               (call-with-values
-                   (lambda ()
-                     (unzip2
-                      `((,(assoc-ref inputs "_")
-                         "d3.v4.min.js"))))
-                 (lambda (sources targets)
-                   (for-each (lambda (source target)
-                               (format #true "Processing ~a --> ~a~%"
-                                       source target)
-                               (invoke "esbuild" source "--minify"
-                                       (string-append "--outfile=" target)))
-                             sources targets)))))))))
+               (let ((source (assoc-ref inputs "_"))
+                     (target "d3.v4.min.js"))
+                 (invoke "esbuild" source "--minify"
+                         (string-append "--outfile=" target)))))))))
     (propagated-inputs
      (list r-ade4
            r-biostrings
@@ -15206,14 +15536,14 @@ type and symbol colors.")
 (define-public r-genomicscores
   (package
     (name "r-genomicscores")
-    (version "2.12.0")
+    (version "2.14.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GenomicScores" version))
        (sha256
         (base32
-         "1z8h9sbr6xqwbsfisr33qdxg0xdrw8r4vvxl1pf4x8vv08zw0vx6"))))
+         "1plpmi1sb9vv03480njf3awnc7i19f9iaxi3j6bvjzpi6zmw40dq"))))
     (properties `((upstream-name . "GenomicScores")))
     (build-system r-build-system)
     (propagated-inputs
@@ -15244,14 +15574,14 @@ position-specific scores within R and Bioconductor.")
 (define-public r-atacseqqc
   (package
     (name "r-atacseqqc")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ATACseqQC" version))
        (sha256
         (base32
-         "0mcrkmirss484d2mskikyjdz5cmbhdk52yxkffz9g8g5m9lkq5xk"))))
+         "1b53rkhyqnyh5vangh3hy4yccx1yackwbv1pxdimbp840ji6d122"))))
     (properties `((upstream-name . "ATACseqQC")))
     (build-system r-build-system)
     (propagated-inputs
@@ -15291,14 +15621,14 @@ footprints.")
 (define-public r-gofuncr
   (package
     (name "r-gofuncr")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GOfuncR" version))
        (sha256
         (base32
-         "05509xf768x8asqadjj5s50m0yqnklrxi28bmqd22cn6cbmahszw"))))
+         "1baa3aabkhmwq66xkzf4jk5nz85kkx1ks0mqc91s2ra9916wj6cd"))))
     (properties `((upstream-name . "GOfuncR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -15396,14 +15726,14 @@ different identifieres using the Biocore Data Team data-packages (e.g.
 (define-public r-annotationtools
   (package
     (name "r-annotationtools")
-    (version "1.74.0")
+    (version "1.76.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "annotationTools" version))
        (sha256
         (base32
-         "0dwbh2h2mp8gy0kwqmkri3q2glnzcj8cn83j1qyh7lk15anc33g8"))))
+         "0g086rj06k3wac24zx66dw1yc1bzv25bmlbjbpcpgdcmyjb1i8sf"))))
     (properties
      `((upstream-name . "annotationTools")))
     (build-system r-build-system)
@@ -15421,14 +15751,14 @@ text files).")
 (define-public r-allelicimbalance
   (package
     (name "r-allelicimbalance")
-    (version "1.38.0")
+    (version "1.40.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "AllelicImbalance" version))
        (sha256
         (base32
-         "1ms3x3x2gvhgllff3nwawg5jlpmgx6dhwll0dghklnv3lssbx4c7"))))
+         "0p7l856a46zzla8brsg901pmh5738j63h7h7rn3da94ny8k417mf"))))
     (properties
      `((upstream-name . "AllelicImbalance")))
     (build-system r-build-system)
@@ -15464,14 +15794,14 @@ investigation using RNA-seq data.")
 (define-public r-aucell
   (package
     (name "r-aucell")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "AUCell" version))
        (sha256
         (base32
-         "1zqjmg8nxxj30lxppl685ihynbz44vw7qm3kwjq6cp83c5556hz9"))))
+         "1d1icbq8i7mwsc7lv9pn4r0vs7azx1lwng5p3ghnray1ygqclbi0"))))
     (properties `((upstream-name . "AUCell")))
     (build-system r-build-system)
     (propagated-inputs
@@ -15505,14 +15835,14 @@ needed.")
 (define-public r-ebimage
   (package
     (name "r-ebimage")
-    (version "4.42.0")
+    (version "4.44.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "EBImage" version))
        (sha256
         (base32
-         "0z0ajmy1zx7mqcjm2ibyk2qg3cj00kl76padyksbdbmwdncxs8yb"))))
+         "0jdi5cn4v5ll43xb3l6sy062snd5p9n2nrryc5aqd2ki18mdmghy"))))
     (properties `((upstream-name . "EBImage")))
     (build-system r-build-system)
     (propagated-inputs
@@ -15544,14 +15874,14 @@ visualization with image data.")
 (define-public r-yamss
   (package
     (name "r-yamss")
-    (version "1.26.0")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "yamss" version))
        (sha256
         (base32
-         "0kjlp62s2393jdwp0crizsgp4iqagbgnd3hdl9vpbr9qrjxg4s7m"))))
+         "16rdy35wmydcx322pf9j7l7z2mzgrksg1whr8i8xdmdqfnqz3xyb"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biocgenerics
@@ -15577,14 +15907,14 @@ analysis.")
 (define-public r-gtrellis
   (package
     (name "r-gtrellis")
-    (version "1.32.0")
+    (version "1.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gtrellis" version))
        (sha256
         (base32
-         "1kk7ysscq8xdbn35b20s8sn8gl93sy0c718fmvr1yrhiqaxq5alr"))))
+         "022wn0l2wfizlz6d5plkphjsjbmxw2wcvxrzr4vanczjzzyxv5c5"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-circlize r-genomicranges r-getoptlong r-iranges))
@@ -15603,14 +15933,14 @@ genomic categories and to add self-defined graphics in the plot.")
 (define-public r-somaticsignatures
   (package
     (name "r-somaticsignatures")
-    (version "2.36.0")
+    (version "2.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "SomaticSignatures" version))
        (sha256
         (base32
-         "075w88x7lv2fkp2ipqgxp4pzh6kbjw3nmp0qra2p4fss4j3g8d6s"))))
+         "0s9kjjh1n4a55ycjvcw8ymjcclcj8b35aygx4x1k5af1hf3f7wyb"))))
     (properties
      `((upstream-name . "SomaticSignatures")))
     (build-system r-build-system)
@@ -15642,14 +15972,14 @@ decomposition algorithms.")
 (define-public r-yapsa
   (package
     (name "r-yapsa")
-    (version "1.26.8")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "YAPSA" version))
        (sha256
         (base32
-         "16rr2bkni3jx5qskr5fz5lvf23d03xgd3m4068mnd3n9r23hpb4p"))))
+         "07dxhaywad9ivkrc454hhizfw6a5yvarrc5fp5za2jgsznv408wl"))))
     (properties `((upstream-name . "YAPSA")))
     (build-system r-build-system)
     (propagated-inputs
@@ -15691,14 +16021,14 @@ provided.")
 (define-public r-gcrma
   (package
     (name "r-gcrma")
-    (version "2.72.0")
+    (version "2.74.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gcrma" version))
        (sha256
         (base32
-         "0k4fsmqkv82d3a6v3gwphvbri5sgbd3f1s4qyv960rhyk2xj2b4p"))))
+         "07ina8w8p5bm382v452i2wpmv90gvgli393lsgp7xy0h9in7h6yg"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-affy
@@ -15773,14 +16103,14 @@ chips with the MAQC reference datasets.")
 (define-public r-quantro
   (package
     (name "r-quantro")
-    (version "1.34.0")
+    (version "1.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "quantro" version))
        (sha256
         (base32
-         "08m94q65c11isbkx9xljm2bx2aq2rml1bqh5i1cg81xg2ilm9h6a"))))
+         "032qxwgldl1hbgsgb5q3fi7nfg1nx3k0yppqkvim5cif613m1nzq"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biobase
@@ -15806,14 +16136,14 @@ groups.")
 (define-public r-yarn
   (package
     (name "r-yarn")
-    (version "1.26.0")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "yarn" version))
        (sha256
         (base32
-         "0ddfl4jp0n8sb665hcpsij959fl28rj22n1h61wp2374kpc0fwfj"))))
+         "12d806pyiks5xbvxng4pxn0xqvgs4c526gp2pp2qhdxw0w2m29rj"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biobase
@@ -15843,14 +16173,14 @@ large RNA-seq experiments.")
 (define-public r-roar
   (package
     (name "r-roar")
-    (version "1.36.0")
+    (version "1.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "roar" version))
        (sha256
         (base32
-         "0p5q6nyp8d0gl95rd89xrs08gv87m1q6d0x4ws2b6sd4gc1nw2ny"))))
+         "0pibk6zdqlbm0rxnb95pd94v6lbg67rwmjnpfxizq7wv36pw6kdr"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biocgenerics
@@ -15911,14 +16241,14 @@ genes.")
 (define-public r-massspecwavelet
   (package
     (name "r-massspecwavelet")
-    (version "1.66.0")
+    (version "1.68.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MassSpecWavelet" version))
        (sha256
         (base32
-         "1nc1imxia71sxxvi77f91yhwxza2l8kk1d7zkp5680xzw6yd6ajr"))))
+         "044rz2xsz2v8i9ha20hxn2cwf7wa74p5f25jql8ancp6r3gim9sy"))))
     (properties
      `((upstream-name . "MassSpecWavelet")))
     (build-system r-build-system)
@@ -15935,14 +16265,14 @@ based on @dfn{Continuous Wavelet Transform} (CWT).")
 (define-public r-xcms
   (package
     (name "r-xcms")
-    (version "3.22.0")
+    (version "4.0.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "xcms" version))
        (sha256
         (base32
-         "112g2lpi074cr8g09cqwjbcwv9aw4djr7ashxpnxjycd3ayc0j3v"))))
+         "10bvxww489mb4bl5v9ma6klyg359zb9ady5rl95q1mkp54hahdw8"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biobase
@@ -15952,16 +16282,19 @@ based on @dfn{Continuous Wavelet Transform} (CWT).")
            r-lattice
            r-massspecwavelet
            r-mscoreutils
+           r-msexperiment
            r-msfeatures
            r-msnbase
            r-multtest
            r-mzr
            r-plyr
+           r-progress
            r-protgenerics
            r-rann
            r-rcolorbrewer
            r-robustbase
            r-s4vectors
+           r-spectra
            r-summarizedexperiment))
     (native-inputs
      (list r-knitr))
@@ -15977,13 +16310,13 @@ data for high-throughput, untargeted analyte profiling.")
 (define-public r-wppi
   (package
     (name "r-wppi")
-    (version "1.8.0")
+    (version "1.10.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "wppi" version))
               (sha256
                (base32
-                "06y4pq8msjzwrw1jgyj9yskgpfhvcz54qcsv0h14bakhyrwk00pg"))))
+                "04wg645c0gww8mq3vg70gqlwm12dmqxmvk704zvmxcpifhrvpn2b"))))
     (properties `((upstream-name . "wppi")))
     (build-system r-build-system)
     ;; This is necessary because omnipathr attempts to write a configuration
@@ -16018,14 +16351,14 @@ scores and a path search algorithm.")
 (define-public r-wrench
   (package
     (name "r-wrench")
-    (version "1.18.0")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Wrench" version))
        (sha256
         (base32
-         "18x12395928d0mf8kffmdjqkdxrzgqzzhhvs7sdzldwyas6hfg2h"))))
+         "11g6a2315hllf197ssccybhv6i7p48n7bv2amzpgxs7bs7qg3k9d"))))
     (properties `((upstream-name . "Wrench")))
     (build-system r-build-system)
     (propagated-inputs
@@ -16042,14 +16375,14 @@ that arising from 16s metagenomic surveys.")
 (define-public r-wiggleplotr
   (package
     (name "r-wiggleplotr")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "wiggleplotr" version))
        (sha256
         (base32
-         "15gbs10bi1alxxbxaj4h3hzfgck4nxygy896y34x81w1rn7in3vp"))))
+         "1gq0hxmnnis0g1y6hiphz02dmk3pfjz874xb2bxqw49z7387fwm8"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-assertthat
@@ -16076,14 +16409,14 @@ visualization of exonic read coverage.")
 (define-public r-widgettools
   (package
     (name "r-widgettools")
-    (version "1.78.0")
+    (version "1.80.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "widgetTools" version))
        (sha256
         (base32
-         "03bvh2jk97jj40z35q5n1is2wxrs4dggw08ndyywy4pzx1diqdc4"))))
+         "1zkc275sb1qbban7sghqziv3xkg7wjdpghddklv451n7j282k6w1"))))
     (properties `((upstream-name . "widgetTools")))
     (build-system r-build-system)
     (home-page "https://bioconductor.org/packages/widgetTools/")
@@ -16097,14 +16430,14 @@ widgets in R.")
 (define-public r-webbioc
   (package
     (name "r-webbioc")
-    (version "1.72.0")
+    (version "1.74.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "webbioc" version))
        (sha256
         (base32
-         "0z2sixzs0rwdwdhxs5mqzghgiw4g64l8p9ag5lw289bzs4c4kqnd"))))
+         "1ca41q7hxy6p8kvc3qbjplvn40k4jwhf0mb03njifry4xi1xipgy"))))
     (build-system r-build-system)
     (inputs
      (list netpbm perl))
@@ -16129,14 +16462,14 @@ Currently only Affymetrix oligonucleotide analysis is supported.")
 (define-public r-zinbwave
   (package
     (name "r-zinbwave")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "zinbwave" version))
        (sha256
         (base32
-         "1bmxbzpgmwama42a3vi1n0sic166v5zs0kl9mhmrh0rrx0nv303k"))))
+         "1lp8x9grc07kaz9iy7yc45mk708g9dplsl86fq0ip8rs51c8f31i"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biocparallel
@@ -16162,14 +16495,14 @@ the data.")
 (define-public r-zfpkm
   (package
     (name "r-zfpkm")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "zFPKM" version))
        (sha256
         (base32
-         "1fkzyq282xafyapgi5xi1c2dmfkyikqvf622pycjs80fas38044h"))))
+         "18pnzc51r7l1ypnhavl83r3gy7l91qnqzvl6771zid04g99pk844"))))
     (properties `((upstream-name . "zFPKM")))
     (build-system r-build-system)
     (propagated-inputs
@@ -16187,14 +16520,14 @@ This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
 (define-public r-rbowtie2
   (package
     (name "r-rbowtie2")
-    (version "2.6.0")
+    (version "2.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rbowtie2" version))
        (sha256
         (base32
-         "11h4irhi0pxd0l378im455amqfamqypyl0ri2cs8nk1lg184ridr"))))
+         "0dx1psk6f27p1kiw4qwj1nf55gpqgisibzipvlnn5m9q3q8g70gv"))))
     (properties `((upstream-name . "Rbowtie2")))
     (build-system r-build-system)
     (propagated-inputs
@@ -16214,14 +16547,14 @@ rapid adapter trimming, identification, and read merging.")
 (define-public r-progeny
   (package
     (name "r-progeny")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "progeny" version))
        (sha256
         (base32
-         "047x6by3xa15gvi3kny5pkqxaq8d2kzcfi55ic5j7a351715l6l7"))))
+         "1plgwi2fmx7bh648fqpzzfqnh84fsgnn5jfcbdf9yia6zzigicql"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biobase
@@ -16246,14 +16579,14 @@ expression\".")
 (define-public r-arrmnormalization
   (package
     (name "r-arrmnormalization")
-    (version "1.40.0")
+    (version "1.42.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ARRmNormalization" version))
        (sha256
         (base32
-         "001nwl605prg942vmnbb1rwjwgpscpjs27ssic3h10rlmpb65yzp"))))
+         "1fd1pfw2ggqb0k2npvibfy8liix57m01cxfxp10shvfbzjjy4wjm"))))
     (properties
      `((upstream-name . "ARRmNormalization")))
     (build-system r-build-system)
@@ -16269,14 +16602,14 @@ Infinium HumanMethylation 450k assay.")
 (define-public r-biocfilecache
   (package
     (name "r-biocfilecache")
-    (version "2.8.0")
+    (version "2.10.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocFileCache" version))
        (sha256
         (base32
-         "1qk1n50arlk0mfkv9p3zl3lqbapzfkjdbadv51hsp4h9lyaw9sbg"))))
+         "044kh1rfgb608y2v4wzbzddirhw5crj3k6i28wr78qgnzqc89mdm"))))
     (properties `((upstream-name . "BiocFileCache")))
     (build-system r-build-system)
     (propagated-inputs
@@ -16301,14 +16634,14 @@ and data files used across sessions.")
 (define-public r-iclusterplus
   (package
     (name "r-iclusterplus")
-    (version "1.36.1")
+    (version "1.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "iClusterPlus" version))
        (sha256
         (base32
-         "1lbkmin9pkk9yzpmwrfyniyqnwmp0wcgiirq8prmzi5mvndl6wm3"))))
+         "0p56w6431jg921416dkyiykccvr7alq6x6r1gcx5d9hkcpyncks1"))))
     (properties `((upstream-name . "iClusterPlus")))
     (build-system r-build-system)
     (native-inputs (list gfortran))
@@ -16331,14 +16664,14 @@ Gaussian distributions.")
 (define-public r-rbowtie
   (package
     (name "r-rbowtie")
-    (version "1.40.0")
+    (version "1.42.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rbowtie" version))
        (sha256
         (base32
-         "1hfr1zdvikvygzgyy58f5rnz5jkmsrhwa930h331wx5012hhmnv7"))))
+         "1arwr8gisc5g9bwxlachf3lvxpd2767ahnwdf2p1lidwpfism8l8"))))
     (properties `((upstream-name . "Rbowtie")))
     (build-system r-build-system)
     (arguments
@@ -16367,14 +16700,14 @@ alignment tool.")
 (define-public r-sgseq
   (package
     (name "r-sgseq")
-    (version "1.34.0")
+    (version "1.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "SGSeq" version))
        (sha256
         (base32
-         "0qsmy85400in2xvw3bnzjnk8ni3lipqjc81npk3fmvbp6cb85njq"))))
+         "1h44r0frrw54s9nqa539ifg270ggmm634gj9cyhn4z7nhxxh134c"))))
     (properties `((upstream-name . "SGSeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -16410,14 +16743,14 @@ interpretation.")
 (define-public r-rhisat2
   (package
     (name "r-rhisat2")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rhisat2" version))
        (sha256
         (base32
-         "1x9phnrk27v2r3ldqa9cd6yp2q3y5p2rm9wmra3wgrmhz9gxq1qy"))))
+         "1pxlpwqzbdii0b1swy9vcq905934yfmyqwfx2j3f7n5n4dgglc2q"))))
     (properties `((upstream-name . "Rhisat2")))
     (build-system r-build-system)
     (arguments
@@ -16448,14 +16781,14 @@ index.")
 (define-public r-quasr
   (package
     (name "r-quasr")
-    (version "1.40.1")
+    (version "1.42.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "QuasR" version))
        (sha256
         (base32
-         "08vns1wbgpxw1x6djp84f9hl3gqaybbw9917ghfzk0x3ijpvggbg"))))
+         "0695pjvp742qn629kxly4a9crbg6vakdx1ygnyshprjsz6xz2vnn"))))
     (properties `((upstream-name . "QuasR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -16490,14 +16823,14 @@ quantification of genomic regions of interest.")
 (define-public r-rqc
   (package
     (name "r-rqc")
-    (version "1.34.0")
+    (version "1.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rqc" version))
        (sha256
         (base32
-         "15w5bmcl7h3fz6qhdqz4qc3qkg3pxcmzapg4mnnckzmyg8kh0i4l"))))
+         "0hrhfgv0b9ycw2vmzkpmrv9m9jvvq1n6asnxnrgvzlz81xak84ic"))))
     (properties `((upstream-name . "Rqc")))
     (build-system r-build-system)
     (propagated-inputs
@@ -16533,14 +16866,14 @@ graphics.")
 (define-public r-birewire
   (package
     (name "r-birewire")
-    (version "3.32.0")
+    (version "3.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiRewire" version))
        (sha256
         (base32
-         "1741raw1834093y5zhgx9jywfgz0wl0idlkynvab2c8vi40kc9a8"))))
+         "1h5pmd38b9zpbz1nngmk1s0cag4z0vx93yi2n7r85nca9z02cxad"))))
     (properties `((upstream-name . "BiRewire")))
     (build-system r-build-system)
     (propagated-inputs
@@ -16586,14 +16919,14 @@ Markov-Chain-Monte-Carlo is applied to sample the activity states.")
 (define-public r-multidataset
   (package
     (name "r-multidataset")
-    (version "1.28.0")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MultiDataSet" version))
        (sha256
         (base32
-         "1qyvwhmdv27xsyljyzyh52pn6x0wqx8rslvr2j7vqcjyywv270x6"))))
+         "1n17bpzj95hkljvgqpyv92jm4bk1d3j3mdg7106pb3dffvwv52sk"))))
     (properties `((upstream-name . "MultiDataSet")))
     (build-system r-build-system)
     (propagated-inputs
@@ -16623,14 +16956,14 @@ packages.")
 (define-public r-ropls
   (package
     (name "r-ropls")
-    (version "1.32.0")
+    (version "1.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ropls" version))
        (sha256
         (base32
-         "1cq5ixaxag5r6nvl73c8bznxkdjhxw1r7qx90ml7qm4jr7wyi173"))))
+         "1k3j1cbapzqk0qr3v4gijskp487xyz2n4lv4kia9y5pmplddxp7v"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biobase
@@ -16665,14 +16998,14 @@ coefficients).")
 (define-public r-biosigner
   (package
     (name "r-biosigner")
-    (version "1.28.0")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biosigner" version))
        (sha256
         (base32
-         "19sl75168zv6qqmgsfnhcyw1z0lp0phmky40lsl6bbmy4k2hfw38"))))
+         "1j3wkqvha6pzd6d3wm2q4lihn8p9ycw0wmddjqpnqvglb1x7c0f8"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biobase
@@ -16700,14 +17033,14 @@ datasets.")
 (define-public r-annotatr
   (package
     (name "r-annotatr")
-    (version "1.26.0")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "annotatr" version))
        (sha256
         (base32
-         "1vjbk1vpqjxy9wv2a6sc32yyk0bhkbvdx9hl3vs5yjifwdswh2pw"))))
+         "16nkxnbsmr0y6km794x2iwbkyrkf0svg6ln3qkqnw0a47a3cbm65"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-annotationdbi
@@ -16741,14 +17074,14 @@ annotations.")
 (define-public r-rsubread
   (package
     (name "r-rsubread")
-    (version "2.14.2")
+    (version "2.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rsubread" version))
        (sha256
         (base32
-         "1dgbvhsd0rki1skwrb4acd3cfy7c9slsjq1s7r2469zbs3xf12xc"))))
+         "0bhq8q3dch09r3digf3snfvhyj6w7j1qqw8gl28b29in8azg6v4d"))))
     (properties `((upstream-name . "Rsubread")))
     (build-system r-build-system)
     (inputs (list zlib))
@@ -16767,13 +17100,13 @@ and to both short and long sequence reads.")
 (define-public r-flowai
   (package
     (name "r-flowai")
-    (version "1.30.0")
+    (version "1.32.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "flowAI" version))
               (sha256
                (base32
-                "0ydy98qsiqpw0b6fvmlv09kza94qjcl40ma9pknzgbq21ac4z25g"))))
+                "1bi13f8q7267lai71sl640w9zgd5a1iln5r4ri2dcskkwb2qxzkz"))))
     (properties `((upstream-name . "flowAI")))
     (build-system r-build-system)
     (propagated-inputs
@@ -16833,14 +17166,14 @@ the quality control enables the detection and removal of anomalies.")
 (define-public r-consensusclusterplus
   (package
     (name "r-consensusclusterplus")
-    (version "1.64.0")
+    (version "1.66.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ConsensusClusterPlus" version))
        (sha256
         (base32
-         "0ig6xfhd70my5j4xrdy8srg1wi8nb3kcxlrld9py47psrq9vdadm"))))
+         "11xcz9b4mg3inz8c8f2vckgai67s740qjyynjim4ahf9zd0j7rxs"))))
     (properties
      `((upstream-name . "ConsensusClusterPlus")))
     (build-system r-build-system)
@@ -16899,14 +17232,14 @@ of the analyses while minimizing technical noise.")
 (define-public r-cytolib
   (package
     (name "r-cytolib")
-    (version "2.12.1")
+    (version "2.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "cytolib" version))
        (sha256
         (base32
-         "0mfv259k92vz0g7zv8zir2av2nlmx6na1f6q9zyj24s18m7mrkqz"))))
+         "1r2slhzrp3gf45k5gknqgj3vjz7p0rx2yjzrbp020inj82fp4mgi"))))
     (properties `((upstream-name . "cytolib")))
     (build-system r-build-system)
     (native-inputs
@@ -16923,14 +17256,14 @@ interact with gated cytometry data.")
 (define-public r-flowcore
   (package
     (name "r-flowcore")
-    (version "2.12.2")
+    (version "2.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "flowCore" version))
        (sha256
         (base32
-         "1z3xsp1ymvdjhwcj5mkhl1d586rlr5i8vji9y5gs595w3naa4r0h"))))
+         "11aic1nzlw0gdpcpmky5jzljxgxcrimi29f0zl3yjvgb48qa88bd"))))
     (properties `((upstream-name . "flowCore")))
     (build-system r-build-system)
     (propagated-inputs
@@ -16955,14 +17288,14 @@ with flow cytometry data.")
 (define-public r-flowmeans
   (package
     (name "r-flowmeans")
-    (version "1.60.0")
+    (version "1.62.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "flowMeans" version))
        (sha256
         (base32
-         "18lp1pickpd68fl7a4nidyvyh4yf53gbgn2f2yxaxfp2mk3mj88w"))))
+         "06n35c5fdkd3l8d5q8a23yslanirwhbf07b4f0zmf9a43zi642bv"))))
     (properties `((upstream-name . "flowMeans")))
     (build-system r-build-system)
     (propagated-inputs
@@ -16978,14 +17311,14 @@ change point detection.")
 (define-public r-ncdfflow
   (package
     (name "r-ncdfflow")
-    (version "2.46.0")
+    (version "2.48.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ncdfFlow" version))
        (sha256
         (base32
-         "0nrj4g02kx763wb70fzvhidmzp82gr1g3fp1aa1bv34cj4lnp47q"))))
+         "0z9vgd8v69iq8gv23iiaxrk77j2aq8y2n5k8x9jmxphbm0cm19a0"))))
     (properties `((upstream-name . "ncdfFlow")))
     (build-system r-build-system)
     (propagated-inputs
@@ -17008,14 +17341,14 @@ manipulation of flow cytometry data.")
 (define-public r-ggcyto
   (package
     (name "r-ggcyto")
-    (version "1.28.1")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ggcyto" version))
        (sha256
         (base32
-         "1hgw8g0b62k2lyswp3m81qczzwsyid7zdrnyjvl9388k29w2105s"))))
+         "13zc5952drl187fl07v1nh6gv0g6ba11vxpxl4ghvavnknvi5phd"))))
     (properties `((upstream-name . "ggcyto")))
     (build-system r-build-system)
     (propagated-inputs
@@ -17045,14 +17378,14 @@ statistics to the plot.")
 (define-public r-flowviz
   (package
     (name "r-flowviz")
-    (version "1.64.0")
+    (version "1.66.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "flowViz" version))
        (sha256
         (base32
-         "0y16hzadpr5c99cwkphc07vh6lypgfk5nacbmn7mmrw01b3gbk67"))))
+         "1hn021p2220a47qzlya8qabc9xgmxk9gcs505m7wx6gx6ysdn418"))))
     (properties `((upstream-name . "flowViz")))
     (build-system r-build-system)
     (propagated-inputs
@@ -17076,14 +17409,14 @@ statistics to the plot.")
 (define-public r-flowclust
   (package
     (name "r-flowclust")
-    (version "3.38.0")
+    (version "3.40.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "flowClust" version))
        (sha256
         (base32
-         "1gmkmx6gzx4w39ijcad3lx2xnr2b833mhs8gcmc6k21k57aznzs2"))))
+         "1xg0hdxh0c1c1wc6d8gcynq8168hi61c3gjdf1223qvqwc39nsby"))))
     (properties `((upstream-name . "flowClust")))
     (build-system r-build-system)
     (arguments
@@ -17110,14 +17443,14 @@ model with Box-Cox transformation.")
 (define-public r-rprotobuflib
   (package
     (name "r-rprotobuflib")
-    (version "2.12.1")
+    (version "2.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "RProtoBufLib" version))
        (sha256
         (base32
-         "097nxjijblqyz6nbpal7292qfijmk7x8dbx7plryr132xbaw5hdm"))))
+         "1i1a4ikfdyrrn0r53y1aipfm9dzzn6yzp5w651hvd6zav77cdh6q"))))
     (properties `((upstream-name . "RProtoBufLib")))
     (build-system r-build-system)
     (arguments
@@ -17139,14 +17472,14 @@ for other R packages to compile and link against.")
 (define-public r-flowworkspace
   (package
     (name "r-flowworkspace")
-    (version "4.12.2")
+    (version "4.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "flowWorkspace" version))
        (sha256
         (base32
-         "1g1hym2anysgy7v46fnnxyzac3wzi1713vlih2gqzi23k8r2xx26"))))
+         "09cpbf33b3x9b06yf41qy2fy8zviwrznrpkb9fq3an8vg8gf51lp"))))
     (properties `((upstream-name . "flowWorkspace")))
     (build-system r-build-system)
     (propagated-inputs
@@ -17186,19 +17519,20 @@ matches the flowJo analysis.")
 (define-public r-flowstats
   (package
     (name "r-flowstats")
-    (version "4.12.0")
+    (version "4.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "flowStats" version))
        (sha256
         (base32
-         "13mdpdndalm0d6azjancw0xcbdc674ivkj8kp6ccfpdd7gydhr4j"))))
+         "1f7qawn9wb8221npnmmygmvi4w1rq5lb74j3vmfzcak5kyga5xck"))))
     (properties `((upstream-name . "flowStats")))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biobase
            r-biocgenerics
+           r-clue
            r-cluster
            r-corpcor
            r-fda
@@ -17224,14 +17558,14 @@ package.")
 (define-public r-opencyto
   (package
     (name "r-opencyto")
-    (version "2.12.0")
+    (version "2.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "openCyto" version))
        (sha256
         (base32
-         "0z0p09mkap1jqlq1x33i2ik87pbhwq85xgqyfsx4r360nhv06pna"))))
+         "12b4a65zgswzddkfdyl4j06qp7w9lkxv4h05m4z8hfff8c9x5bls"))))
     (properties `((upstream-name . "openCyto")))
     (build-system r-build-system)
     (propagated-inputs
@@ -17260,14 +17594,14 @@ sequential way to mimic the manual gating strategy.")
 (define-public r-cytoml
   (package
     (name "r-cytoml")
-    (version "2.12.0")
+    (version "2.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "CytoML" version))
        (sha256
         (base32
-         "19rlg15nk2205vma4whpqmvlazww5i3ibxhmk9cljsaj4ql560vf"))))
+         "0wq9ganas6l2jw8bnajr7vwli35kykpgv2lca4qh79nfgxlicff9"))))
     (properties `((upstream-name . "CytoML")))
     (build-system r-build-system)
     (inputs
@@ -17305,14 +17639,14 @@ standard to exchange gated cytometry data with other software platforms.")
 (define-public r-flowsom
   (package
     (name "r-flowsom")
-    (version "2.8.0")
+    (version "2.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "FlowSOM" version))
        (sha256
         (base32
-         "13y0ny61skj14mfhjwpa5zmflzdqxy2vf6gd4m9358g4wxfbhkv0"))))
+         "170xz3b4kfsxpqirfz9vk4j8dkdmz4qd0a1nm3yaya1rddpg9m3l"))))
     (properties `((upstream-name . "FlowSOM")))
     (build-system r-build-system)
     (propagated-inputs
@@ -17341,14 +17675,14 @@ self-organizing map clustering and minimal spanning trees.")
 (define-public r-mixomics
   (package
     (name "r-mixomics")
-    (version "6.24.0")
+    (version "6.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "mixOmics" version))
        (sha256
         (base32
-         "0dqndpmi56g772sra49vdrkjs4m9h2gzimwv3bwmw2l0krh2ax8s"))))
+         "0ifi89s611kblncnpvsrbl6sq2zi36binz63njrhya9wkyaxj6pc"))))
     (properties `((upstream-name . "mixOmics")))
     (build-system r-build-system)
     (propagated-inputs
@@ -17356,8 +17690,8 @@ self-organizing map clustering and minimal spanning trees.")
            r-corpcor
            r-dplyr
            r-ellipse
-           r-ggrepel
            r-ggplot2
+           r-ggrepel
            r-gridextra
            r-igraph
            r-lattice
@@ -17387,18 +17721,19 @@ delete entire rows with missing data.")
 (define-public r-depecher
   (package                              ;Source/Weave error
     (name "r-depecher")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DepecheR" version))
        (sha256
         (base32
-         "1kn1w1fs19gjvg8nhbvj6hyp32h6k81dnal4ab12xl1jgaa3xj5p"))))
+         "1b3c1wg5xnhh4bdcjls26j6nsp0vx1g5y3grqv7x4ds01vmh3q2w"))))
     (properties `((upstream-name . "DepecheR")))
     (build-system r-build-system)
     (propagated-inputs
      (list r-beanplot
+           r-collapse
            r-dosnow
            r-dplyr
            r-fnn
@@ -17475,14 +17810,14 @@ genes in the gene-set that are ranked above the leading edge).")
 (define-public r-chicago
   (package
     (name "r-chicago")
-    (version "1.28.0")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Chicago" version))
        (sha256
         (base32
-         "04h4a5nyc78jlsg9pj8ay559bwb8y1nm80v9zvyxd7r490yn7k7s"))))
+         "1mcpx785ag0jcsh08df34hx3wp55zd1vggnl3fflkinb78178n38"))))
     (properties `((upstream-name . "Chicago")))
     (build-system r-build-system)
     (propagated-inputs
@@ -17521,14 +17856,14 @@ expression space.")
 (define-public r-cicero
   (package
     (name "r-cicero")
-    (version "1.18.0")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "cicero" version))
        (sha256
         (base32
-         "12zdygnwqjla99wzvvxzcmiwmh4v0rmnx4yix02gbj8xl4bxmm51"))))
+         "19vn31w74r45pq5m9pn5db1sz1qg757mghzzs933cdssnqf4m6y5"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-assertthat
@@ -17588,14 +17923,14 @@ accessibility data.")
 (define-public r-circrnaprofiler
   (package
     (name "r-circrnaprofiler")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "circRNAprofiler" version))
        (sha256
         (base32
-         "0gagfm7v5bnnfj1zy6zf4cg91bj8nvv4vm38f3a1s4q2xc8pcvfj"))))
+         "098fbrszph5cnh4n9zjhj92sg1bi6h6k57wm2vlaqkq0nab63r63"))))
     (properties
      `((upstream-name . "circRNAprofiler")))
     (build-system r-build-system)
@@ -17723,14 +18058,14 @@ cisTopics and explore the nature and regulatory proteins driving them.")
 (define-public r-genie3
   (package
     (name "r-genie3")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GENIE3" version))
        (sha256
         (base32
-         "1q4wi3k95c8vsyfx6359p2p29ascjg1cxmpp9bf99ixbjs71rd33"))))
+         "0bsid8qhcqgalqghr2b2592pzm4viyi7wq8h5dmhrrl7gky8l60k"))))
     (properties `((upstream-name . "GENIE3")))
     (build-system r-build-system)
     (propagated-inputs
@@ -17747,14 +18082,14 @@ regulatory networks from expression data.")
 (define-public r-roc
   (package
     (name "r-roc")
-    (version "1.76.0")
+    (version "1.78.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ROC" version))
        (sha256
         (base32
-         "0fq59bwc5i8zdw0v0jr5j5lm4hk6p7b88i2xndsgj4fq65yr50g1"))))
+         "12msc6skvcx4ajk20l71k32rj8lsiafjxwcsrd51kyy5x2yj2v4m"))))
     (properties `((upstream-name . "ROC")))
     (build-system r-build-system)
     (native-inputs
@@ -17769,14 +18104,14 @@ Characteristic} (ROC) curves, with a focus on micro arrays.")
 (define-public r-watermelon
   (package
     (name "r-watermelon")
-    (version "2.6.0")
+    (version "2.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "wateRmelon" version))
        (sha256
         (base32
-         "0qslh2xhhyaf0nsgcqav6qgh05n8kp0s6p1zggc02iid30i1ibrj"))))
+         "1ra21qzni9cny52ag9zxi46vb9grabyqjyk01dqqp3r9i0b4999l"))))
     (properties `((upstream-name . "wateRmelon")))
     (build-system r-build-system)
     (propagated-inputs
@@ -17807,14 +18142,14 @@ metrics, with methods for objects produced by the @code{methylumi} and
 (define-public r-gdsfmt
   (package
     (name "r-gdsfmt")
-    (version "1.36.1")
+    (version "1.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gdsfmt" version))
        (sha256
         (base32
-         "11qib2znznzvyb0x9qm1nfg9lhyqy63yrdjicy7n3n6l8dfd2lx7"))
+         "03qgiww523kijrkciln3fw3djn20rnvwz2j0i3p518h6fbl7vlpm"))
        (modules '((guix build utils)))
        ;; Remove bundled sources of zlib, lz4, and xz.  Don't attempt to build
        ;; them and link with system libraries instead.
@@ -17865,14 +18200,14 @@ with multiple R processes supported by the package @code{parallel}.")
 (define-public r-bigmelon
   (package
     (name "r-bigmelon")
-    (version "1.26.0")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bigmelon" version))
        (sha256
         (base32
-         "1l1ym89qqbq6qx07bm2p8gcl5zd9xh0nbw10fb7s0pfbrkj8xy64"))))
+         "1j80f7k39p23s6fym3nia73g8d1v44hdiv73igcq6fnsllxg40hr"))))
     (properties `((upstream-name . "bigmelon")))
     (build-system r-build-system)
     (propagated-inputs
@@ -17895,18 +18230,18 @@ with multiple R processes supported by the package @code{parallel}.")
 (define-public r-seqbias
   (package
     (name "r-seqbias")
-    (version "1.48.0")
+    (version "1.50.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "seqbias" version))
        (sha256
         (base32
-         "1sspl03m2hf6s5rw6nfqrycb236nvcgygql6apdlg3cjnikf090j"))))
+         "18pdpi855y1hhka96xc5886nqffjn1jhz9jr9p305iikdrsvmjp1"))))
     (properties `((upstream-name . "seqbias")))
     (build-system r-build-system)
     (propagated-inputs
-     (list r-biostrings r-genomicranges r-rhtslib))
+     (list r-biostrings r-genomicranges r-rhtslib r-zlibbioc))
     (home-page "https://bioconductor.org/packages/seqbias/")
     (synopsis "Estimation of per-position bias in high-throughput sequencing data")
     (description
@@ -17919,14 +18254,14 @@ genome sequence.")
 (define-public r-reqon
   (package
     (name "r-reqon")
-    (version "1.46.0")
+    (version "1.48.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ReQON" version))
        (sha256
         (base32
-         "1knzla5d8n22121a9licrjh2rxrmh05304a9d4bs2f1r7aiwhgnh"))))
+         "0w28b3ma8r8rshijdm5jj1z64v91my7hcvw18r9pdwjprh05bw0g"))))
     (properties `((upstream-name . "ReQON")))
     (build-system r-build-system)
     (propagated-inputs
@@ -17942,14 +18277,14 @@ format.")
 (define-public r-wavcluster
   (package
     (name "r-wavcluster")
-    (version "2.34.0")
+    (version "2.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "wavClusteR" version))
        (sha256
         (base32
-         "0491x3m0015g83m6a7pkc4783768clgykhlcmd2xr6cgrhih10g2"))))
+         "1y2bk1kla0l72xgdam2l9c0k7584ckdqscqnc184cxvqm6fb335j"))))
     (properties `((upstream-name . "wavClusteR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -17989,13 +18324,13 @@ procedures that induce nucleotide substitutions (e.g. BisSeq).")
 (define-public r-tilingarray
   (package
     (name "r-tilingarray")
-    (version "1.78.0")
+    (version "1.80.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "tilingArray" version))
               (sha256
                (base32
-                "0wj3wb4x9s0v189p20rlwghsx82x314yyhhsnfmrl266qb1ambrn"))))
+                "01j4wj0mdfrlyhp2alf1xfy78f17x43w9i0wb41ljw6pm313np58"))))
     (properties `((upstream-name . "tilingArray")))
     (build-system r-build-system)
     (propagated-inputs
@@ -18071,14 +18406,14 @@ provides methods for retrieving enriched pathways.")
 (define-public r-variantfiltering
   (package
     (name "r-variantfiltering")
-    (version "1.36.1")
+    (version "1.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "VariantFiltering" version))
        (sha256
         (base32
-         "0v0shsv0s9fzakdb4p84jfc4z57ryan27r1dkbvb3v25kjrhd8fi"))))
+         "01czx88dzqm8qv44kyy1n7b999wgfklxzgvmjh10chf677phnzsr"))))
     (properties
      `((upstream-name . "VariantFiltering")))
     (build-system r-build-system)
@@ -18115,76 +18450,17 @@ model, amino acid change consequence, minor allele frequencies across human
 populations, splice site strength, conservation, etc.")
     (license license:artistic2.0)))
 
-(define-public r-genomegraphs
-  (package
-    (name "r-genomegraphs")
-    (version "1.46.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "GenomeGraphs" version))
-       (sha256
-        (base32
-         "05vavhz936v7cknig2f2mn3fd9fiy54r3swlvifpawramblp1ags"))))
-    (properties `((upstream-name . "GenomeGraphs")))
-    (build-system r-build-system)
-    (propagated-inputs
-     (list r-biomart))
-    (home-page "https://bioconductor.org/packages/GenomeGraphs/")
-    (synopsis "Plotting genomic information from Ensembl")
-    (description
-     "Genomic data analyses requires integrated visualization of known genomic
-information and new experimental data.  GenomeGraphs uses the biomaRt package
-to perform live annotation queries to Ensembl and translates this to e.g.
-gene/transcript structures in viewports of the grid graphics package.  This
-results in genomic information plotted together with your data.  Another
-strength of GenomeGraphs is to plot different data types such as array CGH,
-gene expression, sequencing and other data, together in one plot using the
-same genome coordinate system.")
-    (license license:artistic2.0)))
-
-(define-public r-wavetiling
-  (package
-    (name "r-wavetiling")
-    (version "1.28.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "waveTiling" version))
-       (sha256
-        (base32
-         "0d7l559zlmly8mncmh1zhkqmsml0bwwfpm7ccp8l26y852vwf7hf"))))
-    (properties `((upstream-name . "waveTiling")))
-    (build-system r-build-system)
-    (propagated-inputs
-     (list r-affy
-           r-biobase
-           r-biostrings
-           r-genomegraphs
-           r-genomicranges
-           r-iranges
-           r-oligo
-           r-oligoclasses
-           r-preprocesscore
-           r-waveslim))
-    (home-page "https://r-forge.r-project.org/projects/wavetiling/")
-    (synopsis "Wavelet-based models for tiling array transcriptome analysis")
-    (description
-     "This package is designed to conduct transcriptome analysis for tiling
-arrays based on fast wavelet-based functional models.")
-    (license license:gpl2+)))
-
 (define-public r-variancepartition
   (package
     (name "r-variancepartition")
-    (version "1.30.2")
+    (version "1.32.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "variancePartition" version))
        (sha256
         (base32
-         "17jssd327l0miw52iadag2dbk8w4mhv2vwjpzdw89p8gww47bmbv"))))
+         "1pr321hv5q2sl8lc998hkwdl2mfyzcgf2l70ny2m3hfmlclq5lnn"))))
     (properties
      `((upstream-name . "variancePartition")))
     (build-system r-build-system)
@@ -18192,8 +18468,8 @@ arrays based on fast wavelet-based functional models.")
      (list r-aod
            r-biobase
            r-biocparallel
-           r-doparallel
-           r-foreach
+           r-corpcor
+           r-fancova
            r-ggplot2
            r-gplots
            r-iterators
@@ -18203,7 +18479,6 @@ arrays based on fast wavelet-based functional models.")
            r-mass
            r-matrix
            r-pbkrtest
-           r-progress
            r-rdpack
            r-remacor
            r-reshape2
@@ -18226,14 +18501,14 @@ measures.")
 (define-public r-htqpcr
   (package
     (name "r-htqpcr")
-    (version "1.54.0")
+    (version "1.56.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "HTqPCR" version))
        (sha256
         (base32
-         "12p0jb9bpz4x612vwj77d6l5h8rihfkzmhp8qy1gvv2zmn2a54jf"))))
+         "14cff36ikbqhd5xizihpxzsv9jimcpbgnd381jd154pgi60bil0m"))))
     (properties `((upstream-name . "HTqPCR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -18256,13 +18531,13 @@ features (e.g.  genes, microRNAs).")
 (define-public r-ucell
   (package
     (name "r-ucell")
-    (version "2.4.0")
+    (version "2.6.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "UCell" version))
               (sha256
                (base32
-                "01qcwmiqri4xvwr3j4k1g062rfj6bbc0bvh0ifq1jq2xrm1azw9y"))))
+                "1ds11f1q6v89sfcj1sinrkv7aw3s0prf5nxf7pz4hdsvqn4zp467"))))
     (properties `((upstream-name . "UCell")))
     (build-system r-build-system)
     (propagated-inputs (list r-biocneighbors
@@ -18287,14 +18562,14 @@ directly interact with SingleCellExperiment and Seurat objects.")
 (define-public r-unifiedwmwqpcr
   (package
     (name "r-unifiedwmwqpcr")
-    (version "1.36.0")
+    (version "1.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "unifiedWMWqPCR" version))
        (sha256
         (base32
-         "1gza678sd5m2rbki0l5hniki6gmds2cljkmywmk5v5m9swh9azq7"))))
+         "0v3jpnm3nq66xvckmc8447xl7wngfhhiwq6vjx54wgc6f586vmgd"))))
     (properties
      `((upstream-name . "unifiedWMWqPCR")))
     (build-system r-build-system)
@@ -18311,14 +18586,14 @@ data.")
 (define-public r-universalmotif
   (package
     (name "r-universalmotif")
-    (version "1.18.1")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "universalmotif" version))
        (sha256
         (base32
-         "0v1085dl16a3494f1fxc9rk1ffz3si89mdwbmnnczyhj5p13pfx8"))))
+         "0wy7zplypjiqv4wjq0l30xb5xj63fxb7z2wmmfrmzfkbgbm0xyha"))))
     (properties
      `((upstream-name . "universalmotif")))
     (build-system r-build-system)
@@ -18360,13 +18635,13 @@ motifs, and others.")
 (define-public r-ace
   (package
     (name "r-ace")
-    (version "1.18.0")
+    (version "1.20.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "ACE" version))
               (sha256
                (base32
-                "158v25ivbmsh54ywb5spfsd1nrmvfq83s8fkp14i7q5ckr2kvjhm"))))
+                "0ll0lksz6nzfj5ivmyrp5w24bhfl083amjpr0m8qlzpdw6k3wi98"))))
     (properties `((upstream-name . "ACE")))
     (build-system r-build-system)
     (propagated-inputs (list r-biobase r-genomicranges r-ggplot2 r-qdnaseq))
@@ -18389,13 +18664,13 @@ of @dfn{tumor cells} (cells with divergent segments).")
 (define-public r-acgh
   (package
     (name "r-acgh")
-    (version "1.78.0")
+    (version "1.80.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "aCGH" version))
               (sha256
                (base32
-                "0k8fbwhh1w0b0zy5qgixmcnwxi3v78f1bjmjg1yx6paniwk58bzn"))))
+                "1qckqdil1cq8lbrj9di96w9934r1fp48xpmfdwp4f2vw9pjadi1q"))))
     (properties `((upstream-name . "aCGH")))
     (build-system r-build-system)
     (propagated-inputs (list r-biobase r-cluster r-multtest r-survival))
@@ -18413,13 +18688,13 @@ printing and plotting @code{aCGH} objects.")
 (define-public r-acme
   (package
     (name "r-acme")
-    (version "2.56.0")
+    (version "2.58.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "ACME" version))
               (sha256
                (base32
-                "1z6j4wy355pljn9wf12zzq4zqrhaik0i2phy7jg89jsys7n2mlxy"))))
+                "0cy1f4ki4j7yxc9cws5s17ljd4ac0yxhijms0pm31im81qz2djax"))))
     (properties `((upstream-name . "ACME")))
     (build-system r-build-system)
     (propagated-inputs (list r-biobase r-biocgenerics))
@@ -18440,13 +18715,13 @@ on whole-genome tiling array experiments quite easily with enough memory.")
 (define-public r-acde
   (package
     (name "r-acde")
-    (version "1.30.0")
+    (version "1.32.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "acde" version))
               (sha256
                (base32
-                "088dq6mc9m1bx0dprcz8cdpfp447lnxq7420r139mhcik0z21vky"))))
+                "1rqyjj4lgqxs372qx8p3qx2napww0djh4jz8hzgv86x9r202kk9p"))))
     (properties `((upstream-name . "acde")))
     (build-system r-build-system)
     (propagated-inputs (list r-boot))
@@ -18566,14 +18841,14 @@ gene expression.")
 (define-public r-bgx
   (package
     (name "r-bgx")
-    (version "1.66.0")
+    (version "1.68.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bgx" version))
        (sha256
         (base32
-         "1g6k3ryj8dz17asa4imnrk77z4dk9an5ssrqr17r0g797d5f4qjm"))))
+         "0v85i0lwmxq5yq9ygfzljgy8fsflqq1p53rq8aasnndd6gsm8ld2"))))
     (properties `((upstream-name . "bgx")))
     (build-system r-build-system)
     (arguments
@@ -18602,14 +18877,14 @@ Affymetrix GeneChips.")
 (define-public r-bhc
   (package
     (name "r-bhc")
-    (version "1.52.0")
+    (version "1.54.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BHC" version))
        (sha256
         (base32
-         "0w60h1jr9kwvgg5d6bcrq4gl1aa1v6xrn43ymsc2312019psrrjy"))))
+         "1m289q9bs7i7d15g5mzdmzw7yppnqspr8illkya8kxlv1i2sify1"))))
     (properties `((upstream-name . "BHC")))
     (build-system r-build-system)
     (home-page "https://bioconductor.org/packages/BHC/")
@@ -18628,14 +18903,14 @@ algorithm which is more efficient for larger data sets.")
 (define-public r-bicare
   (package
     (name "r-bicare")
-    (version "1.58.0")
+    (version "1.60.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BicARE" version))
        (sha256
         (base32
-         "1q7dsvj6nvczs76jcxyy77298vgk4zk083bldmbbgnwparrgjii9"))))
+         "10inwxl1cmkdp8037wcwkj5wzxsrrcysxfbqhnkh7pzhzvwnzz9h"))))
     (properties `((upstream-name . "BicARE")))
     (build-system r-build-system)
     (propagated-inputs
@@ -18650,14 +18925,14 @@ results.")
 (define-public r-bifet
   (package
     (name "r-bifet")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiFET" version))
        (sha256
         (base32
-         "05lwz2pw2vnhmlhp5vv9j45jrc5ssdw4lx6mkxnsvds8zl3y9294"))))
+         "056zqlql39q44snvx5nzc5snrihpr1kj3jdbpbb401hxi9r64f4r"))))
     (properties `((upstream-name . "BiFET")))
     (build-system r-build-system)
     (propagated-inputs
@@ -18679,14 +18954,14 @@ the read count and GC content bias.")
 (define-public r-rsbml
   (package
     (name "r-rsbml")
-    (version "2.58.0")
+    (version "2.60.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "rsbml" version))
        (sha256
         (base32
-         "0mgg1qfvxgyjk6fw4x0cv486vrsgf1kbqr6nqhgxj6lk8w6909fm"))))
+         "0pvj0qgc6hd02g9ppfc610gvfn412rw69rxh43y4dr3n894kdm2i"))))
     (properties `((upstream-name . "rsbml")))
     (build-system r-build-system)
     (inputs
@@ -18705,13 +18980,13 @@ validating output, provides an S4 SBML DOM, converts SBML to R graph objects.")
 (define-public r-hybridmtest
   (package
     (name "r-hybridmtest")
-    (version "1.44.0")
+    (version "1.46.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "HybridMTest" version))
        (sha256
-        (base32 "19pycad35hc7ylnsz75bv029y1r6j9xvrbhzk4i64i7jn8gi7ngh"))))
+        (base32 "1jkihcad453d7jqb78fl03yfqz169jz75c40y53569ndp2j4rg71"))))
     (properties `((upstream-name . "HybridMTest")))
     (build-system r-build-system)
     (propagated-inputs
@@ -18736,14 +19011,14 @@ then the law of total EBPs.")
 (define-public r-hypergraph
   (package
     (name "r-hypergraph")
-    (version "1.72.0")
+    (version "1.74.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "hypergraph" version))
        (sha256
         (base32
-         "13f3m8m6i99hzm94hriry645jcn0a1ki8z8wmn3mkasdi6bzx20h"))))
+         "16bjjfzcndjfqsywzw2cn551fgqlnll2gi975w0qqxhkh3jssgmi"))))
     (properties `((upstream-name . "hypergraph")))
     (build-system r-build-system)
     (propagated-inputs
@@ -18758,14 +19033,14 @@ manipulating hypergraphs.")
 (define-public r-hyperdraw
   (package
     (name "r-hyperdraw")
-    (version "1.52.0")
+    (version "1.54.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "hyperdraw" version))
        (sha256
         (base32
-         "0vhfvmv6b3kab6a8hy2y9zwxgzwb5vliaaxhlrgz8i4pvvq5nhqb"))))
+         "1lgfpw9f7095lgk46gdpxq3z52c24xw4ajl7yid3pcgw19bfcgk5"))))
     (properties `((upstream-name . "hyperdraw")))
     (build-system r-build-system)
     (inputs (list graphviz))
@@ -18780,14 +19055,14 @@ manipulating hypergraphs.")
 (define-public r-biggr
   (package
     (name "r-biggr")
-    (version "1.36.0")
+    (version "1.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiGGR" version))
        (sha256
         (base32
-         "03pd4a3l912zdfk35flagikqimp01wp76nslid32l43d7yg9p57w"))))
+         "1pdsxkh9fkgn80f7p21902pb6xp2qafq10p29ifb55qwz8gma2ff"))))
     (properties `((upstream-name . "BiGGR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -18887,13 +19162,13 @@ visualizing RNA-sequencing datasets and differentially expressed genes.")
 (define-public r-chemmineob
   (package
     (name "r-chemmineob")
-    (version "1.38.0")
+    (version "1.40.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ChemmineOB" version))
        (sha256
-        (base32 "0l44d6l078k1w5nf7i4sarah1zn30zqjmcj9qpy4hhg97dfy45ci"))))
+        (base32 "0mfajzwzldmra6g5kni5yw7m2n719456p1vd3hxx2r7l1phdjixi"))))
     (properties `((upstream-name . "ChemmineOB")))
     (build-system r-build-system)
     (arguments
@@ -18928,14 +19203,14 @@ add-on package rather than used directly.")
 (define-public r-chemminer
   (package
     (name "r-chemminer")
-    (version "3.52.0")
+    (version "3.54.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ChemmineR" version))
        (sha256
         (base32
-         "1m4vgq3z0kya7kbncawr9csvbwnh74mh012w7g2ialwd3nwdf91x"))))
+         "1328mwmghflrvir1i3crlq8q36wq60x2an11saabg63hnx4paa81"))))
     (properties `((upstream-name . "ChemmineR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -18971,13 +19246,13 @@ structures.")
 (define-public r-fmcsr
   (package
     (name "r-fmcsr")
-    (version "1.42.0")
+    (version "1.44.0")
     (source
       (origin
         (method url-fetch)
         (uri (bioconductor-uri "fmcsR" version))
         (sha256
-          (base32 "0ci77gbz93i3s2j2gjp7y3ssn6bcdcmqnl23smnjai7qjmln64dp"))))
+          (base32 "17il9mi1iagl474ia1lz0ajx1wq67jw5famkr1fmjlis8ymw8hnd"))))
     (properties `((upstream-name . "fmcsR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -19000,14 +19275,14 @@ searching and clustering.")
 (define-public r-bioassayr
   (package
     (name "r-bioassayr")
-    (version "1.38.0")
+    (version "1.40.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bioassayR" version))
        (sha256
         (base32
-         "0ilwniyrp3m8mi1vmggd17f9g6wdw7a78l2db190w29alzpbfmp6"))))
+         "1mm1nzdz9cl8mf33yiyaspqkx4sbqhhs6m9jfgl42fhscrhaxfsi"))))
     (properties `((upstream-name . "bioassayR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -19035,14 +19310,14 @@ available bioactivity data.")
 (define-public r-biobroom
   (package
     (name "r-biobroom")
-    (version "1.32.0")
+    (version "1.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biobroom" version))
        (sha256
         (base32
-         "0kb6ylq94vywfky0mcrva109darcv361sqvwb19qn92p8vh5199l"))))
+         "1ivclipy2igf8ax7f0pqrcqflcm7h0a8ny6nfa0200vp99an8ymf"))))
     (properties `((upstream-name . "biobroom")))
     (build-system r-build-system)
     (propagated-inputs
@@ -19064,14 +19339,14 @@ visualize bioinformatics analyses.")
 (define-public r-graphite
   (package
     (name "r-graphite")
-    (version "1.46.0")
+    (version "1.48.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "graphite" version))
        (sha256
         (base32
-         "1fhjkgl6567qchi5sfdqnznalm1l7c7pabz8jc9d7ib9x4g922q5"))))
+         "1h8j10jx02zsxs6rzids3gy4xchdhgzkifa5grrfbn8faf9ycy2n"))))
     (properties `((upstream-name . "graphite")))
     (build-system r-build-system)
     (propagated-inputs
@@ -19088,14 +19363,14 @@ symbols).")
 (define-public r-reactomepa
   (package
     (name "r-reactomepa")
-    (version "1.44.0")
+    (version "1.46.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ReactomePA" version))
        (sha256
         (base32
-         "1hy8qz7d2826kf6pkl3v8cjwx35ap8xr92jw5wv445p3xcd1clzn"))))
+         "0kflwlmyckyivr8xh7fsmpl7jfkq5kavwpkswmvdfqckbd0n9xsc"))))
     (properties `((upstream-name . "ReactomePA")))
     (build-system r-build-system)
     (propagated-inputs
@@ -19121,14 +19396,14 @@ enrichment analysis and several functions for visualization.")
 (define-public r-ebarrays
   (package
     (name "r-ebarrays")
-    (version "2.64.0")
+    (version "2.66.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "EBarrays" version))
        (sha256
         (base32
-         "1k50br4hpkrwv1lnn0wp1c7kj32vk0gg19aivmw5d6brjdd39c1f"))))
+         "1m8dy1lmx9m8p5jjk0i7yllb4pvq77kynszk1nz8cc1niz6xs47q"))))
     (properties `((upstream-name . "EBarrays")))
     (build-system r-build-system)
     (propagated-inputs
@@ -19143,13 +19418,13 @@ microarray data.")
 (define-public r-biocbaseutils
   (package
     (name "r-biocbaseutils")
-    (version "1.2.0")
+    (version "1.4.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocBaseUtils" version))
               (sha256
                (base32
-                "143fmjbi8spaj3njvc1xvsjszfxs7bv3vxik8pisw5y8lqzx7hqm"))))
+                "189jz8krhv0vdnk47m3cmy95zfg3l328w6dbhg6djvlkca17i275"))))
     (properties `((upstream-name . "BiocBaseUtils")))
     (build-system r-build-system)
     (native-inputs (list r-knitr))
@@ -19187,20 +19462,22 @@ monograph.")
 (define-public r-bioccheck
   (package
     (name "r-bioccheck")
-    (version "1.36.1")
+    (version "1.38.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocCheck" version))
               (sha256
                (base32
-                "0a0fnmqln13iglnw8smbbr4k7hdvacipxa04zhqylygpsq1246bc"))))
+                "11d67dfwxc34n7yzpz58ficjk7sxnbxrajhnqlcxvsifgmybkb4d"))))
     (properties
      `((upstream-name . "BiocCheck")))
     (build-system r-build-system)
     (propagated-inputs
-     (list r-biocfilecache
+     (list r-biocbaseutils
+           r-biocfilecache
            r-biocmanager
            r-biocviews
+           r-callr
            r-codetools
            r-graph
            r-httr
@@ -19217,14 +19494,14 @@ checks on R packages that are to be submitted to the Bioconductor repository.")
 (define-public r-biocgraph
   (package
     (name "r-biocgraph")
-    (version "1.62.0")
+    (version "1.64.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biocGraph" version))
        (sha256
         (base32
-         "0fnncmi82qb9lkg1zfyps7n3nrw1s3wcqbixh420w53hmdyryryl"))))
+         "1yy0bwvfa5b531jvmbiwrd4xg8cdvrgwr8l6bxasrh6yrbv8drml"))))
     (properties `((upstream-name . "biocGraph")))
     (build-system r-build-system)
     (propagated-inputs
@@ -19239,13 +19516,13 @@ different graph related packages produced by Bioconductor.")
 (define-public r-biocstyle
   (package
     (name "r-biocstyle")
-    (version "2.28.1")
+    (version "2.30.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocStyle" version))
               (sha256
                (base32
-                "11v3gzy88fai0rhdymvj9k74g7hjc6n9fihfrrnw0qfr447z1d61"))))
+                "17pkdi3vn62pw1nzmgz0i45czynqjchq078ij8v1xvflg6lf7flw"))))
     (properties
      `((upstream-name . "BiocStyle")))
     (build-system r-build-system)
@@ -19263,13 +19540,13 @@ functionality.")
 (define-public r-biocviews
   (package
     (name "r-biocviews")
-    (version "1.68.2")
+    (version "1.70.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "biocViews" version))
               (sha256
                (base32
-                "1icnaj1ifndym7nl1yafzd0y0fxyhzjyb4qzqpcnsqhh4yi3pnm5"))))
+                "0fpka47shrxcbc1k057f5zv79406daic0y34v8p5lsvxbgzh0m8b"))))
     (properties
      `((upstream-name . "biocViews")))
     (build-system r-build-system)
@@ -19292,14 +19569,14 @@ also known as views, in a controlled vocabulary.")
 (define-public r-experimenthub
   (package
     (name "r-experimenthub")
-    (version "2.8.1")
+    (version "2.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ExperimentHub" version))
        (sha256
         (base32
-         "1md6lan98h95jv776zyvl5im39gz4h6fdxw571vfahgr4b2nxvm4"))))
+         "1prl24sg5l142155z3iaxrvig2wv2xqajq02nj30jjjih4p4936w"))))
     (properties `((upstream-name . "ExperimentHub")))
     (build-system r-build-system)
     (propagated-inputs
@@ -19325,14 +19602,14 @@ access.")
 (define-public r-grohmm
   (package
     (name "r-grohmm")
-    (version "1.34.0")
+    (version "1.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "groHMM" version))
        (sha256
         (base32
-         "1zg30cb4s97zdv6c0f53ix6a97aan5w3lx698sa4cqvi4hbz8f35"))))
+         "15ibdbpj7vqypxfnp2w06w9lync11z3azzss6s97xhadkgsbw4vq"))))
     (properties `((upstream-name . "groHMM")))
     (build-system r-build-system)
     (propagated-inputs
@@ -19352,14 +19629,14 @@ access.")
 (define-public r-multiassayexperiment
   (package
     (name "r-multiassayexperiment")
-    (version "1.26.0")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MultiAssayExperiment" version))
        (sha256
         (base32
-         "00xgca1q9ai5x730bvx73f25lpwkr3dn2sia3msa49fpl4nrzr20"))))
+         "0dmhqymh800mljcpdf817nbyg20czp8y9bg13p3r4bfj6axxckch"))))
     (properties
      `((upstream-name . "MultiAssayExperiment")))
     (build-system r-build-system)
@@ -19389,14 +19666,14 @@ rownames.")
 (define-public r-bioconcotk
   (package
     (name "r-bioconcotk")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocOncoTK" version))
        (sha256
         (base32
-         "11135a4l0vn84qmpyclz052zy45s0m38av94604jqxgb51q9lwyf"))))
+         "1xymgfiv9abyaq5s7m683ml8a1ls9mqvbh9qjiz3jqbbpvmsm502"))))
     (properties `((upstream-name . "BiocOncoTK")))
     (build-system r-build-system)
     (propagated-inputs
@@ -19435,14 +19712,14 @@ tools for genome-scale analysis of cancer studies.")
 (define-public r-biocor
   (package
     (name "r-biocor")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BioCor" version))
        (sha256
         (base32
-         "1aw8yh9l0jbjvkqgyzyr0wmwjh3ppmb0lwg8hxsfcv52ycsmvk7p"))))
+         "0710dl05hs590fimp3dhg5hzvk6s79i0kwk6w6sj59pcawx2l6il"))))
     (properties `((upstream-name . "BioCor")))
     (build-system r-build-system)
     (propagated-inputs
@@ -19462,14 +19739,14 @@ gene selection, testing relationships, and so on.")
 (define-public r-biocpkgtools
   (package
     (name "r-biocpkgtools")
-    (version "1.18.1")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocPkgTools" version))
        (sha256
         (base32
-         "16d0sjkzagc0jxha28qxplg6iihwg2q05sig0s1291lm7kh5k9j8"))
+         "0swi6xiads31xcndc2cfzh0ivdl0wc88s83s1p1gxh51rgmgkb14"))
        (snippet
         '(for-each delete-file
                    '("inst/htmlwidgets/lib/bioc_explore/bootstrap.min.js"
@@ -19576,14 +19853,14 @@ analytics on packages.")
 (define-public r-biocset
   (package
     (name "r-biocset")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocSet" version))
        (sha256
         (base32
-         "1q5794gsinpy9hv5n1vx79bkqxi1jxzxjl95jlw9pqjmlnki07i5"))))
+         "0sk4kmvl86xm85dqaf8gvii0qavyycyn2qp0v6dmfcjqai528v2x"))))
     (properties `((upstream-name . "BiocSet")))
     (build-system r-build-system)
     (propagated-inputs
@@ -19614,14 +19891,14 @@ accessing web references for elements/sets are also available in BiocSet.")
 (define-public r-biocworkflowtools
   (package
     (name "r-biocworkflowtools")
-    (version "1.26.0")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocWorkflowTools" version))
        (sha256
         (base32
-         "1zvjj0hpqwdv7yifqwyb14166ppxw91d964gz4xclism5z5lvyln"))))
+         "0mh7lsiprshq56ns3b8pbv1j1mjcbdzqydvli0ynmvf5smn2j4m5"))))
     (properties
      `((upstream-name . "BiocWorkflowTools")))
     (build-system r-build-system)
@@ -19647,14 +19924,14 @@ Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.")
 (define-public r-biodist
   (package
     (name "r-biodist")
-    (version "1.72.0")
+    (version "1.74.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bioDist" version))
        (sha256
         (base32
-         "1mx4abv7p76qsa0yzj0b4d03xklx09im01bx02lwa1w527gdmfc3"))))
+         "0ngpysb89wag4wvcq83ddjxhy1zhl32b2fy2fg5laa4g8xfrqaxz"))))
     (properties `((upstream-name . "bioDist")))
     (build-system r-build-system)
     (propagated-inputs
@@ -19669,14 +19946,14 @@ distance measures.")
 (define-public r-pcatools
   (package
     (name "r-pcatools")
-    (version "2.12.0")
+    (version "2.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "PCAtools" version))
        (sha256
         (base32
-         "07kl7s2zd7nkhg4hib2mr3w5lhqy780aw53yqsd7bfsjh53k8g95"))))
+         "18rzv4kldjmm2zvz9pzrpspig2hy6mcvb45hgmw49ba4jdcxh31s"))))
     (properties `((upstream-name . "PCAtools")))
     (build-system r-build-system)
     (propagated-inputs
@@ -19715,14 +19992,14 @@ dimensional mass cytometry data.")
 (define-public r-rgreat
   (package
     (name "r-rgreat")
-    (version "2.2.0")
+    (version "2.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "rGREAT" version))
        (sha256
         (base32
-         "0qq3fqzd973jlf6ibfww5yicnyz2qvs2b2mn35p77k2mp4d7qp52"))))
+         "09fvmfiavawfwbxaj1585l2n00fibx9z3r17dv06hc6b40a1sa12"))))
     (properties `((upstream-name . "rGREAT")))
     (build-system r-build-system)
     (propagated-inputs
@@ -19742,8 +20019,8 @@ dimensional mass cytometry data.")
            r-org-hs-eg-db
            r-progress
            r-rcolorbrewer
-           r-rcurl
            r-rcpp
+           r-rcurl
            r-rjson
            r-s4vectors
            r-shiny
@@ -19761,14 +20038,14 @@ user's input and automatically retrieving results from GREAT web server.")
 (define-public r-m3c
   (package
     (name "r-m3c")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "M3C" version))
        (sha256
         (base32
-         "158brq3w5h735s9yq93xx0y4p79yhgz72rpy0cyk4fjia5yaij5c"))))
+         "0q6npc5pglmhzm9270pi11kbp5wg3ncvflp4rhv3w778qza2zlk1"))))
     (properties `((upstream-name . "M3C")))
     (build-system r-build-system)
     (propagated-inputs
@@ -19794,14 +20071,14 @@ hypothesis @code{K=1}.")
 (define-public r-icens
   (package
     (name "r-icens")
-    (version "1.72.0")
+    (version "1.74.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Icens" version))
        (sha256
         (base32
-         "1aq4iwk1cp96jzldhx7d4q7i77zbdg8nzkzh12g29yhwzj39nl3q"))))
+         "0fz66bchf41jzgabs1s8drpi3f7g27lid5g50lxwh6ph3i02cpaw"))))
     (properties `((upstream-name . "Icens")))
     (build-system r-build-system)
     (propagated-inputs
@@ -19917,14 +20194,14 @@ generated.")
 (define-public r-preprocesscore
   (package
     (name "r-preprocesscore")
-    (version "1.62.1")
+    (version "1.64.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "preprocessCore" version))
        (sha256
         (base32
-         "0z37ag22j1wh80vwq1kyr99rvadj9ppkddapfqyql3vj5x44cf4d"))))
+         "15fy3vwnjx6rwrkhbwxyvdykkfdis8c0m18x6y7irvyij9lm6x1y"))))
     (properties
      `((upstream-name . "preprocessCore")))
     (build-system r-build-system)
@@ -19938,13 +20215,13 @@ routines.")
 (define-public r-s4arrays
   (package
     (name "r-s4arrays")
-    (version "1.0.6")
+    (version "1.2.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "S4Arrays" version))
               (sha256
                (base32
-                "011n4lyznlrya5l8d7m30x81k7h81wbp07b12s6a4s5sy9fzd5jb"))))
+                "0x420l98f6b10r3qrdjq5ijs2p0msdcg6d6aghr3yvj1f9g06h8y"))))
     (properties `((upstream-name . "S4Arrays")))
     (build-system r-build-system)
     (propagated-inputs
@@ -19975,13 +20252,13 @@ array-like semantic.  It also provides:
 (define-public r-s4vectors
   (package
     (name "r-s4vectors")
-    (version "0.38.2")
+    (version "0.40.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "S4Vectors" version))
               (sha256
                (base32
-                "0n1w451647pxii6qrrxbvdi9z6rqdwibczkbs7k7a9j33bv3nqv8"))))
+                "0pja00ssl1pd16v3bls3aybml2cwanylx8igf596zha5srcf5l5h"))))
     (properties
      `((upstream-name . "S4Vectors")))
     (build-system r-build-system)
@@ -20043,14 +20320,14 @@ data manipulation and visualization.")
 (define-public r-rgraphviz
   (package
     (name "r-rgraphviz")
-    (version "2.44.0")
+    (version "2.46.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rgraphviz" version))
        (sha256
         (base32
-         "1dv1vk73achjz5b5zzw2d517nbjfrlj7gppd48pfhk1w0mvz3q61"))))
+         "03l6yr76inv4fivy10g0h2qafgywrcjnnhs694lwqz1y6r0gm1sy"))))
     (properties `((upstream-name . "Rgraphviz")))
     (build-system r-build-system)
     (arguments
@@ -20081,13 +20358,13 @@ objects from the @code{graph} package.")
 (define-public r-fishpond
   (package
     (name "r-fishpond")
-    (version "2.6.2")
+    (version "2.8.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "fishpond" version))
               (sha256
                (base32
-                "0zsw4j6gk25303xpdwnkda2sq3mb4zb4p1mzwiyf7hdyf87zis05"))))
+                "04vl4cp0izghm7h4xk7x48lqkq0dpl47dkd068lva33jygwwpvcz"))))
     (properties `((upstream-name . "fishpond")))
     (build-system r-build-system)
     (propagated-inputs
@@ -20117,13 +20394,13 @@ working with Salmon and Alevin quantification files.")
 (define-public r-fithic
   (package
     (name "r-fithic")
-    (version "1.26.0")
+    (version "1.28.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "FitHiC" version))
               (sha256
                (base32
-                "0mqrzh1rcwyqlhq9wxcy4gp47hsb70qrsissm9nj0cb9j6ihi407"))))
+                "0ygcq3xi55swsmysn539cr3m504rfb6zm30w747pa46r63dfjda7"))))
     (properties `((upstream-name . "FitHiC")))
     (build-system r-build-system)
     (propagated-inputs
@@ -20141,13 +20418,13 @@ assays such as Hi-C.")
 (define-public r-hitc
   (package
     (name "r-hitc")
-    (version "1.44.0")
+    (version "1.46.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "HiTC" version))
               (sha256
                (base32
-                "00csfr3yhbllwc8797xg49qb0djpvbpfi6mbnps284nlqy5vpdwh"))))
+                "16svq29fm9xl3rl9v6lyxf564manvp8ryxj1mbxc4pb360wmi780"))))
     (properties `((upstream-name . "HiTC")))
     (build-system r-build-system)
     (propagated-inputs
@@ -20170,14 +20447,14 @@ provided.")
 (define-public r-hdf5array
   (package
     (name "r-hdf5array")
-    (version "1.28.1")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "HDF5Array" version))
        (sha256
         (base32
-         "1riwxxnbi4z0lf42psh3m3ivxlgmmlnqhgsih6911c754r6s39qg"))))
+         "0p52n96mydqszpq1ysmbh5xs4n4icqsd0gbxl5wpkcwvvhxliw8b"))))
     (properties `((upstream-name . "HDF5Array")))
     (build-system r-build-system)
     (inputs
@@ -20202,14 +20479,14 @@ block processing.")
 (define-public r-rhdf5lib
   (package
     (name "r-rhdf5lib")
-    (version "1.22.1")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rhdf5lib" version))
        (sha256
         (base32
-         "1007i2rzz86k04kswa4h53p8zzh52k31m9d8im6iw0n91inqbcj9"))
+         "10n2grfdnri686sx52shz7y0csmcz4cky23k07803dz6qm1ljvmf"))
        (modules '((guix build utils)))
        (snippet
         '(begin
@@ -20247,8 +20524,6 @@ block processing.")
                (substitute* "Makevars"
                  (("@BUILD_HDF5@") "")
                  (("@COPY_SZIP@") "")
-                 (("@ZLIB_LIB@") "-lz")
-                 (("@ZLIB_INCLUDE@") "")
                  (("HDF5_CXX_LIB=.*")
                   (string-append "HDF5_CXX_LIB="
                                  (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n"))
@@ -20265,6 +20540,9 @@ block processing.")
                  (("HDF5_HL_CXX_LIB=.*")
                   (string-append "HDF5_HL_CXX_LIB="
                                  (assoc-ref inputs "hdf5") "/lib/libhdf5_hl_cpp.a\n"))
+                 (("@ZLIB_LIB_PATH@") "-lz")
+                 (("@ZLIB_INCLUDE_PATH@") "")
+
                  ;; szip is non-free software
                  (("cp \"\\$\\{SZIP_LIB\\}.*") "")
                  (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n"))))))))
@@ -20282,17 +20560,17 @@ packages.")
 (define-public r-beachmat
   (package
     (name "r-beachmat")
-    (version "2.16.0")
+    (version "2.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "beachmat" version))
        (sha256
         (base32
-         "0ga9y9npl885jdx7gw5h6lh7fr0z5p7cvcwpz3hvwm4dy235j6gj"))))
+         "1yixv6vs1q2k4vx17bq4nar3g4v2076i5dq77gh63mlka46qr3g2"))))
     (build-system r-build-system)
     (propagated-inputs
-     (list r-biocgenerics r-delayedarray r-matrix r-rcpp))
+     (list r-biocgenerics r-delayedarray r-matrix r-rcpp r-sparsearray))
     (native-inputs
      (list r-knitr))
     (home-page "https://bioconductor.org/packages/beachmat")
@@ -20305,13 +20583,13 @@ matrices.")
 (define-public r-beadarray
   (package
     (name "r-beadarray")
-    (version "2.50.0")
+    (version "2.52.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "beadarray" version))
               (sha256
                (base32
-                "0rd41193rq6v4a97ibp0l2bz140nsv91plhn7iim8d8n9hgxqhjp"))))
+                "0qwka7549mlv2x80bjrzdsy4a6h35yxrhj2cxss9aigwsbjb7sjr"))))
     (properties `((upstream-name . "beadarray")))
     (build-system r-build-system)
     (propagated-inputs (list r-annotationdbi
@@ -20338,13 +20616,13 @@ quality assessment and low-level analysis are provided.")
 (define-public r-beadarraysnp
   (package
     (name "r-beadarraysnp")
-    (version "1.66.0")
+    (version "1.68.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "beadarraySNP" version))
        (sha256
-        (base32 "1pymsm4j3wiyjvgsjb3vhjwdvhfmh91pxdhg4ihrj71pqpif3w9m"))))
+        (base32 "1vrizh7fpzv1w2gki0qxhphrfj1jj6m6bjsjsbw0b4n4invybzps"))))
     (properties `((upstream-name . "beadarraySNP")))
     (build-system r-build-system)
     (propagated-inputs (list r-biobase r-quantsmooth))
@@ -20358,13 +20636,13 @@ performs copy number calculations and reports.")
 (define-public r-beaddatapackr
   (package
     (name "r-beaddatapackr")
-    (version "1.52.0")
+    (version "1.54.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BeadDataPackR" version))
               (sha256
                (base32
-                "0hm4brxg2rxazdcnhjiz6f4di2q8wssrrp35m79vm93sac9w42y3"))))
+                "0sfpdpw6qqffzb9skzx9w1ggcixc3wry9c6f2kwpsykbdsnk90xz"))))
     (properties `((upstream-name . "BeadDataPackR")))
     (build-system r-build-system)
     (native-inputs (list r-knitr))
@@ -20381,13 +20659,13 @@ decompression of raw bead-level data from the Illumina BeadArray platform.")
 (define-public r-cner
   (package
     (name "r-cner")
-    (version "1.36.0")
+    (version "1.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "CNEr" version))
        (sha256
-        (base32 "04arfcr2ay71hyy0xsh6jzappmcnnzfr1nyj1l7dqhhhk81ksjfd"))))
+        (base32 "0kpz15l3yz26s2kskxk4093313c7vwi131y24wbpcdahicpqys2m"))))
     (properties `((upstream-name . "CNEr")))
     (build-system r-build-system)
     (inputs (list zlib))
@@ -20429,14 +20707,14 @@ advanced visualization of sets of conserved noncoding elements.")
 (define-public r-tfbstools
   (package
     (name "r-tfbstools")
-    (version "1.38.0")
+    (version "1.40.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "TFBSTools" version))
        (sha256
         (base32
-         "136s96cmd1aq878xy9mqd4k46awywqpmm55lpvash8mv4gg02vg8"))))
+         "18msr889nygk1c3wsjxc9bv989zakkl9f1h2a6cnfy8rxhbxpvwq"))))
     (properties `((upstream-name . "TFBSTools")))
     (build-system r-build-system)
     (propagated-inputs
@@ -20475,13 +20753,13 @@ provides a wrapper of de novo motif discovery software.")
 (define-public r-maftools
   (package
     (name "r-maftools")
-    (version "2.16.0")
+    (version "2.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "maftools" version))
        (sha256
-        (base32 "1jvmqn33hxzscr8j7y9zw5sngglcy0zkl0386053lx5dl5s5iqyq"))))
+        (base32 "025wlqnx13ldzyrf72mrfj492d62i4xyjbhpmgavgld0jwfmr3ga"))))
     (properties `((upstream-name . "maftools")))
     (build-system r-build-system)
     (propagated-inputs
@@ -20504,14 +20782,14 @@ customizable visualzations with minimal effort.")
 (define-public r-motifmatchr
   (package
     (name "r-motifmatchr")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "motifmatchr" version))
        (sha256
         (base32
-         "0vqsxfbrxs25xr27vsr5syqjn6fwvn5dw0g76w4rdqk5d08p56ci"))))
+         "13kkg9xpyvgqpsaz5f96pd43i8a45jrbnzqmax793zkv4ai8p16j"))))
     (properties `((upstream-name . "motifmatchr")))
     (build-system r-build-system)
     (propagated-inputs
@@ -20538,13 +20816,13 @@ This package wraps C++ code from the MOODS motif calling library.")
 (define-public r-chromvar
   (package
     (name "r-chromvar")
-    (version "1.22.1")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "chromVAR" version))
        (sha256
-        (base32 "001133rfcwmf4p3dbif933y9i1mkr3krw38g646wj4ikycszwih4"))))
+        (base32 "1vy650625b9b2dgnkgh5h0kw5bkdvfin133091asf1nw4jgnn1vx"))))
     (properties `((upstream-name . "chromVAR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -20585,14 +20863,14 @@ sequence (@code{DNAse-seq}) experiments.")
 (define-public r-singlecellexperiment
   (package
     (name "r-singlecellexperiment")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "SingleCellExperiment" version))
        (sha256
         (base32
-         "1v2px6gvr0wzj2cyml57hxj5ghynlvizkchbywd3kx05j1h2mckd"))))
+         "0q44n97mly1ldh52r0sb1jwhz8bn4n7sfw99qs5h4s44w9s0fry4"))))
     (properties
      `((upstream-name . "SingleCellExperiment")))
     (build-system r-build-system)
@@ -20613,13 +20891,13 @@ libraries.")
 (define-public r-singler
   (package
     (name "r-singler")
-    (version "2.2.0")
+    (version "2.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "SingleR" version))
        (sha256
-        (base32 "0dwlg86wkivsag5ffjk81nlq34lwl3kk065k9l6lak24ziq6c4ij"))))
+        (base32 "0s7m3qdbgrqaq93k6rvyj34h36kdjvppn9ilflrcaa5w498fzfhf"))))
     (properties `((upstream-name . "SingleR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -20645,14 +20923,14 @@ cell types to infer the cell of origin of each single cell independently.")
 (define-public r-scuttle
   (package
     (name "r-scuttle")
-    (version "1.10.2")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "scuttle" version))
        (sha256
         (base32
-         "0225fk3ca540b9z3dd5q2zngxsa524nq7zrv1z5qnmr2knc0yxfb"))))
+         "090arfacfs09x7g60qxz4bj2gqb97y3kmhafywkgnrj7pz1z0qzq"))))
     (properties `((upstream-name . "scuttle")))
     (build-system r-build-system)
     (propagated-inputs
@@ -20680,13 +20958,13 @@ of other packages.")
 (define-public r-scater
   (package
     (name "r-scater")
-    (version "1.28.0")
+    (version "1.30.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "scater" version))
               (sha256
                (base32
-                "0v6qaflv7b504yxxv6bmnlikg36bhfahgqxigpq6qcfrhqapmqck"))))
+                "0a8wfrcp09z0aflalqhhwvz675aa32wgprqphk1axvdppknsg7vf"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-beachmat
@@ -20695,13 +20973,12 @@ of other packages.")
            r-biocparallel
            r-biocsingular
            r-delayedarray
-           r-delayedmatrixstats
-           r-densvis
            r-ggbeeswarm
            r-ggplot2
-           r-ggrepel
            r-ggrastr
+           r-ggrepel
            r-matrix
+           r-matrixgenerics
            r-pheatmap
            r-rcolorbrewer
            r-rcppml
@@ -20725,14 +21002,14 @@ quality control.")
 (define-public r-scran
   (package
     (name "r-scran")
-    (version "1.28.2")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "scran" version))
        (sha256
         (base32
-         "1la55s14frvsjp8ly02fbrkzvv7lzvcd7jc1axmwh494b9zy5jmd"))))
+         "0vq3216jk389mjnz5kx0i6fwmkypp21rshvv9ldcy327h6vk1ylj"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-beachmat
@@ -20765,17 +21042,54 @@ cell-specific biases, assignment of cell cycle phase, and detection of highly
 variable and significantly correlated genes.")
     (license license:gpl3)))
 
+(define-public r-sparsearray
+  (package
+    (name "r-sparsearray")
+    (version "1.2.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "SparseArray" version))
+       (sha256
+        (base32 "0a1xg8vkjybgdr09bk2z4i82m06qnw2nhbzviyijadxiwvz6pgsz"))))
+    (properties `((upstream-name . "SparseArray")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-biocgenerics
+                             r-iranges
+                             r-matrix
+                             r-matrixgenerics
+                             r-matrixstats
+                             r-s4arrays
+                             r-s4vectors
+                             r-xvector))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/SparseArray")
+    (synopsis
+     "Efficient in-memory representation of multidimensional sparse arrays")
+    (description
+     "The @code{SparseArray} package is an infrastructure package that
+provides an array-like container for efficient in-memory representation of
+multidimensional sparse data in R.  The package defines the @code{SparseArray}
+virtual class and two concrete subclasses: @code{COO_SparseArray} and
+@code{SVT_SparseArray}.  Each subclass uses its own internal representation of
+the nonzero multidimensional data, the \"COO layout\" and the \"SVT layout\",
+respectively.  @code{SVT_SparseArray} objects mimic as much as possible the
+behavior of ordinary matrix and array objects in base R.  In particular, they
+suppport most of the \"standard matrix and array API\" defined in base R and
+in the @code{matrixStats} package from CRAN.")
+    (license license:artistic2.0)))
+
 (define-public r-sparsematrixstats
   (package
     (name "r-sparsematrixstats")
-    (version "1.12.2")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "sparseMatrixStats" version))
        (sha256
         (base32
-         "00jalzg6yphi8ci4iid7x38jlsrvvdswrq7cqa7jybs26ayjldw1"))))
+         "0r2jxwha2xjp8iy7al85s5vib4xvl47gmlbbvvjj4wnz2gfzic9r"))))
     (properties
      `((upstream-name . "sparseMatrixStats")))
     (build-system r-build-system)
@@ -20793,18 +21107,17 @@ data in the column sparse format.")
 (define-public r-spatialexperiment
   (package
     (name "r-spatialexperiment")
-    (version "1.10.0")
+    (version "1.12.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "SpatialExperiment" version))
               (sha256
                (base32
-                "18fcfyjvp9nzadlicsnz62wva8ik0z6jqg1b906avm2vk6rbxw70"))))
+                "1s42jzq95f662h39zmbf06qmrrglbch8sgygpnwqblrjbrqgm7n4"))))
     (properties `((upstream-name . "SpatialExperiment")))
     (build-system r-build-system)
     (propagated-inputs (list r-biocfilecache
                              r-biocgenerics
-                             r-dropletutils
                              r-magick
                              r-rjson
                              r-s4vectors
@@ -20825,14 +21138,14 @@ Visium platform.")
 (define-public r-delayedmatrixstats
   (package
     (name "r-delayedmatrixstats")
-    (version "1.22.6")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DelayedMatrixStats" version))
        (sha256
         (base32
-         "0jaaqa2fm61dmsphm5y4rlwf2dm1l5rs0vpq0f5r35iyw2m12lh8"))))
+         "18r5rfx46lac0kaakha4gqs4pj8vb39z0908gpclmp3ajca4hzb1"))))
     (properties
      `((upstream-name . "DelayedMatrixStats")))
     (build-system r-build-system)
@@ -20841,7 +21154,6 @@ Visium platform.")
            r-iranges
            r-matrix
            r-matrixgenerics
-           r-matrixstats
            r-s4vectors
            r-sparsematrixstats))
     (native-inputs
@@ -20861,14 +21173,14 @@ memory usage and processing time is minimized.")
 (define-public r-mscoreutils
   (package
     (name "r-mscoreutils")
-    (version "1.12.0")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MsCoreUtils" version))
        (sha256
         (base32
-         "055xzlq37d75ghfk87bxbsv4yifidnwxc3w2gp8mcqxwkxxhd70a"))))
+         "0faj4fxfsv7ir935sn9zainhk55vdfi6abgr0s321kwmvs6prc0p"))))
     (properties `((upstream-name . "MsCoreUtils")))
     (build-system r-build-system)
     (propagated-inputs
@@ -20890,13 +21202,13 @@ within the R for Mass Spectrometry packages.")
 (define-public r-msfeatures
   (package
     (name "r-msfeatures")
-    (version "1.8.0")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MsFeatures" version))
        (sha256
-        (base32 "0cb4b0mf5yh8amqwa3r0mbk2f3rgq40gdlkhifk50fxnqdy4fjsh"))))
+        (base32 "0vpsc7i6j2skn6wba178iy406yvd4p8xf3lq2qmm2inimxl983cs"))))
     (properties `((upstream-name . "MsFeatures")))
     (build-system r-build-system)
     (propagated-inputs
@@ -20920,14 +21232,14 @@ the respective packages (such as e.g. @code{xcms}).")
 (define-public r-biocio
   (package
     (name "r-biocio")
-    (version "1.10.0")
+    (version "1.12.0")
     (source
       (origin
         (method url-fetch)
         (uri (bioconductor-uri "BiocIO" version))
         (sha256
           (base32
-            "03hslg7k6khchf54gmlbkvwbkfn5ppz0wp7lh75gsnr0licsjkwx"))))
+            "0bn2jknvj2ag1yv67kjqr7gsq771rmqv3my9njjkwcc9nzrxzhbp"))))
     (properties `((upstream-name . "BiocIO")))
     (build-system r-build-system)
     (propagated-inputs
@@ -20953,14 +21265,14 @@ as well as local access.  Developers can register a file extension, e.g.,
 (define-public r-msmseda
   (package
     (name "r-msmseda")
-    (version "1.38.0")
+    (version "1.40.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "msmsEDA" version))
        (sha256
         (base32
-         "108azzd6ibcgb1gqgcrz4shk3rdr3vfpzy0z6zknlsxwz7sbcnfi"))))
+         "0xxjkr3x654n61q2yda09cghvssyx4ml9g22gfzfhbzjp8j7pm2c"))))
     (properties `((upstream-name . "msmsEDA")))
     (build-system r-build-system)
     (propagated-inputs
@@ -20976,14 +21288,14 @@ experiments, and visualize de influence of the involved factors.")
 (define-public r-msmstests
   (package
     (name "r-msmstests")
-    (version "1.38.0")
+    (version "1.40.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "msmsTests" version))
        (sha256
         (base32
-         "1y3nklhlib2l9smcl6slv1653vyg9ip29if286l59rjrdwh50cwa"))))
+         "0dif4yvm9hfrnamjph5xa9cbf41f2v8lbgyr88f11alwwbf0dg69"))))
     (properties `((upstream-name . "msmsTests")))
     (build-system r-build-system)
     (propagated-inputs
@@ -21005,14 +21317,14 @@ relevant, and the minimum expression of the most abundant condition.")
 (define-public r-catalyst
   (package
     (name "r-catalyst")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
       (origin
         (method url-fetch)
         (uri (bioconductor-uri "CATALYST" version))
         (sha256
           (base32
-            "0f6h0qngv7my83k402rydvi1pla695r5kxq02k1s5caxcsi1caza"))))
+            "0dfg9ib0imk8bmhycqrspnn8yvfdlchwvx39wgqxi5fb9zrppfz4"))))
     (properties `((upstream-name . "CATALYST")))
     (build-system r-build-system)
     (propagated-inputs
@@ -21029,7 +21341,6 @@ relevant, and the minimum expression of the most abundant condition.")
             r-ggrepel
             r-ggridges
             r-gridextra
-            r-magrittr
             r-matrix
             r-matrixstats
             r-nnls
@@ -21068,14 +21379,14 @@ preprocessing of cytometry data, including:
 (define-public r-erma
   (package
     (name "r-erma")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "erma" version))
        (sha256
         (base32
-         "14rgj8g9x248p2cc86aqn289qamsd91d6fnydi5d34q605ph73yj"))))
+         "0vapjfzhwlzxd049fsr00jd7lp48h9qwd95m2sqhqryqz1vsi7hz"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-annotationdbi
@@ -21108,14 +21419,14 @@ by Ernst and Kellis.")
 (define-public r-ggbio
   (package
     (name "r-ggbio")
-    (version "1.48.0")
+    (version "1.50.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ggbio" version))
        (sha256
         (base32
-         "0n7nghrrs7fp0b7jk2pfbkzl0lbv55xxk2xqnq2i77ps22ms0h9y"))))
+         "1chs58ifpwz4crcl5ymnb8ah3wf2jrn9lla3ljsywqiqn0r3i1am"))))
     (build-system r-build-system)
     (arguments
      `(#:phases
@@ -21276,14 +21587,14 @@ family of feature/genome hypotheses.")
 (define-public r-gviz
   (package
     (name "r-gviz")
-    (version "1.44.2")
+    (version "1.46.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Gviz" version))
        (sha256
         (base32
-         "0laismy8kklzkg81r5vf1194fbhp2hw952g6jc3zvn2z5y2d4524"))))
+         "0b707xxi0ch4kfxid5id16gkh9pnqwrgqpsvgbm0rc89kg73g4jz"))))
     (properties `((upstream-name . "Gviz")))
     (build-system r-build-system)
     (propagated-inputs
@@ -21325,14 +21636,14 @@ with your data.")
 (define-public r-gwascat
   (package
     (name "r-gwascat")
-    (version "2.32.0")
+    (version "2.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gwascat" version))
        (sha256
         (base32
-         "1i64bk0ac2v0w5yjxdhnbjh05l6n9fi7gxap0zp73wxj7kl75wkd"))))
+         "028n8v1pgkr1q5s9wslql8ayk1cbx6a9a2rjka9pdwz6rq1iyagy"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-annotationdbi
@@ -21359,13 +21670,13 @@ EMBL-EBI GWAS catalog.")
 (define-public r-gwastools
   (package
     (name "r-gwastools")
-    (version "1.46.0")
+    (version "1.48.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GWASTools" version))
               (sha256
                (base32
-                "1g86xg2d9wi6xijhc89zxhbw190aviw9nkwvbwgz85jf71wf34hv"))))
+                "1rjgdcw65zmmg5dy9mdaz720nvqk03bfsfvkdsa1wwhvlnxmscp8"))))
     (properties `((upstream-name . "GWASTools")))
     (build-system r-build-system)
     (propagated-inputs (list r-biobase
@@ -21380,6 +21691,7 @@ EMBL-EBI GWAS catalog.")
                              r-rsqlite
                              r-sandwich
                              r-survival))
+    (native-inputs (list r-knitr))
     (home-page "https://github.com/smgogarten/GWASTools")
     (synopsis "Tools for Genome Wide Association Studies")
     (description
@@ -21390,13 +21702,13 @@ annotation, and functions for GWAS data cleaning and analysis.")
 (define-public r-kegggraph
   (package
     (name "r-kegggraph")
-    (version "1.60.0")
+    (version "1.62.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "KEGGgraph" version))
        (sha256
-        (base32 "0bgigkmnz5zvsygcifk2fc7i8rahmqr4brk65qa3104clqqvdfkl"))))
+        (base32 "0i9iqr87mqih0rkbjx3wa383x4yfyzpcb0b0xzairbqgygvcq4kl"))))
     (properties `((upstream-name . "KEGGgraph")))
     (build-system r-build-system)
     (propagated-inputs
@@ -21414,14 +21726,14 @@ functionalities including parsing, graph operation, visualization and etc.")
 (define-public r-ldblock
   (package
     (name "r-ldblock")
-    (version "1.30.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ldblock" version))
        (sha256
         (base32
-         "18gqmwwi1i4gndqljy809n5zzx38agawxxwhlknpas6k2iskd1xq"))))
+         "1caxzc99kga2c90m2ydmnvcd8lfp0igmmickpl0ikrhwjlbfnc0p"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biocgenerics
@@ -21470,14 +21782,14 @@ on the plot.")
 (define-public r-abn
   (package
     (name "r-abn")
-    (version "3.0.1")
+    (version "3.0.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "abn" version))
        (sha256
         (base32
-         "03g02450l3mckjzwd0w717dbmxhrngkwlfhm5c9q5zv4g10df7nj"))))
+         "06n69cbkdqpwpxks8276h43132c9v57n4hg33vsjjyxjifwbwxwh"))))
     (build-system r-build-system)
     (inputs
      (list gsl))
@@ -21536,13 +21848,13 @@ other functional sequencing data.")
 (define-public r-parody
   (package
     (name "r-parody")
-    (version "1.58.0")
+    (version "1.60.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "parody" version))
        (sha256
-        (base32 "0n2pmpnpwh16hb58v821xn42jm4a7wjsdf6sqxapjjw9w432mjac"))))
+        (base32 "05mhbkhyh92bwmx37fpviprr9i4z0i6g24l71zk17gq0f8hwb4jj"))))
     (properties `((upstream-name . "parody")))
     (build-system r-build-system)
     (native-inputs (list r-knitr))
@@ -21557,13 +21869,13 @@ methods based on resistant statistics.")
 (define-public r-pathview
   (package
     (name "r-pathview")
-    (version "1.40.0")
+    (version "1.42.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "pathview" version))
        (sha256
-        (base32 "0mld7vys6s5k8snk1gniph9wkw3726vsx430nhyyr76fp4ps2mks"))))
+        (base32 "17kl7yvpjhsb52kz1pw3jnk6s480lnpvvh9rragndixsl8bkmqmc"))))
     (properties `((upstream-name . "pathview")))
     (build-system r-build-system)
     (propagated-inputs
@@ -21591,13 +21903,13 @@ large-scale and fully automated analysis.")
 (define-public r-snapcgh
   (package
     (name "r-snapcgh")
-    (version "1.70.0")
+    (version "1.72.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "snapCGH" version))
               (sha256
                (base32
-                "0yz5q7w3lqv8ac6a764xlbm4hq3ncnngqng879qbpmzhgb4r155g"))))
+                "0knjspxzc3z5dhx0a6kx9rkic85w65l84vy552x5bv8jzxkcwrsj"))))
     (properties `((upstream-name . "snapCGH")))
     (build-system r-build-system)
     (propagated-inputs
@@ -21619,13 +21931,13 @@ segmented data for individual and multiple arrays.")
 (define-public r-snprelate
   (package
     (name "r-snprelate")
-    (version "1.34.1")
+    (version "1.36.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "SNPRelate" version))
               (sha256
                (base32
-                "0js932qvhlwmnrr2jfvsch2zm6w6a1z5wydns3r1bw24r817dlgh"))))
+                "0jw9ziz0a472mnnvmqwas5w646xfgx8dn1bdpwz8c99m663d8ayp"))))
     (properties `((upstream-name . "SNPRelate")))
     (build-system r-build-system)
     (propagated-inputs (list r-gdsfmt))
@@ -21654,14 +21966,14 @@ whole-genome and whole-exome variant data.")
 (define-public r-snpstats
   (package
     (name "r-snpstats")
-    (version "1.50.0")
+    (version "1.52.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "snpStats" version))
        (sha256
         (base32
-         "1v2j2943apphs8i68ap9c8sxd4j5a04qda5scq4dqqkzqd0c5b6i"))))
+         "0a4kyv93ljv7n62ghx66l81q6sw24llr0998nsalidyws1wldbyr"))))
     (properties `((upstream-name . "snpStats")))
     (build-system r-build-system)
     (inputs (list zlib))
@@ -21678,14 +21990,14 @@ the earlier snpMatrix package, allowing for uncertainty in genotypes.")
 (define-public r-chromstar
   (package
     (name "r-chromstar")
-    (version "1.26.0")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "chromstaR" version))
        (sha256
         (base32
-         "1qrcmydk080m1rzwbzx2km4vpbahnq5y73mrnpgjjjrxbndz9xz9"))))
+         "1yykcqxp8y7by4jgh6dfl25m0pnghj36qy21990n2sdfv1kpg2x6"))))
     (properties `((upstream-name . "chromstaR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -21716,14 +22028,14 @@ analyses.")
 (define-public r-guitar
   (package
     (name "r-guitar")
-    (version "2.16.0")
+    (version "2.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Guitar" version))
        (sha256
         (base32
-         "1v1yw90waq0ccj6pxdipipy5bnk0k762m5kadl4h3jgpcrkf2fvc"))))
+         "09i6j8dcmzvd9gh9629523hw0hbng18jdqw5gf1r31ck8m8wwmnc"))))
     (properties `((upstream-name . "Guitar")))
     (build-system r-build-system)
     (propagated-inputs
@@ -21769,14 +22081,14 @@ visualizations for publication-quality multi-panel figures.")
 (define-public r-ballgown
   (package
     (name "r-ballgown")
-    (version "2.32.0")
+    (version "2.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ballgown" version))
        (sha256
         (base32
-         "05lvpvy4gs3vg4ks23prx0mdp730h1m9kpg4al03ah062gyq3ahx"))))
+         "1r3qz6y97zhp7swcv2ls1h6cz0l66y5ap00wx9wlqxv14sljd135"))))
     (properties `((upstream-name . "ballgown")))
     (build-system r-build-system)
     (propagated-inputs
@@ -21803,14 +22115,14 @@ to annotation.")
 (define-public r-megadepth
   (package
     (name "r-megadepth")
-    (version "1.10.0")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "megadepth" version))
        (sha256
         (base32
-         "1zzhgfnrr3r5ismbbj9jcqss8mr8ll6p4d3z026ya2khb0i7clc7"))))
+         "0g9d4q6vh2ys1la15fqgbc4ckfbjbzzaqa49x9liqrhpnrp59vc3"))))
     (properties `((upstream-name . "megadepth")))
     (build-system r-build-system)
     (inputs (list megadepth))
@@ -21836,14 +22148,14 @@ regions or annotations of your choice from BigWig files.")
 (define-public r-beclear
   (package
     (name "r-beclear")
-    (version "2.16.0")
+    (version "2.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BEclear" version))
        (sha256
         (base32
-         "1sdw69dhrzkcpc7flvp1gkixvpsbrckyg756rlm17hjjwfxlz5lb"))))
+         "1a8jmlx17qcx9qzcaxbnlk6qji6hqxcnzmr8zvar9jrfhx0cv9x1"))))
     (properties `((upstream-name . "BEclear")))
     (build-system r-build-system)
     (propagated-inputs
@@ -21870,14 +22182,14 @@ real numbers.")
 (define-public r-bgeecall
   (package
     (name "r-bgeecall")
-    (version "1.16.0")
+    (version "1.18.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BgeeCall" version))
        (sha256
         (base32
-         "0j83scxpq51bhxwfps7chcawzsqrd7pk7x2jg29zj4zbp1jbrnl0"))))
+         "1ipypkyfqx6mahiwl0gzdsi7z9j9cm5rgfw4ybgh6blfq8kg9qyk"))))
     (properties `((upstream-name . "BgeeCall")))
     (build-system r-build-system)
     (propagated-inputs
@@ -21906,14 +22218,14 @@ all RNA-Seq libraries of each species integrated in Bgee.")
 (define-public r-bgeedb
   (package
     (name "r-bgeedb")
-    (version "2.26.0")
+    (version "2.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BgeeDB" version))
        (sha256
         (base32
-         "1s6v17bavidlfy6habi4bv6lmwkrx8c5was1zcq0kb05qdvpn4ph"))))
+         "1ahip21wihwg9yhq0ya1cyzd2cq423hz9pd6iql6y3yhld4j5rnn"))))
     (properties `((upstream-name . "BgeeDB")))
     (build-system r-build-system)
     (propagated-inputs
@@ -21940,14 +22252,14 @@ anatomical terms, mapped to genes by expression patterns.")
 (define-public r-biobtreer
   (package
     (name "r-biobtreer")
-    (version "1.12.0")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biobtreeR" version))
        (sha256
         (base32
-         "0cbhlxh0w736695niyjd59fcvplna2f2x2av9k0sd1r3dy6lrcd4"))))
+         "18p5r67ppkw8wxxkrj76q68ljlhdbhar5hc89ffdsgr3zzdyk875"))))
     (properties `((upstream-name . "biobtreeR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -21964,14 +22276,14 @@ mappings functionalities.")
 (define-public r-minet
   (package
     (name "r-minet")
-    (version "3.58.0")
+    (version "3.60.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "minet" version))
        (sha256
         (base32
-         "04ll8nqhmyj2v12n2xskia8dh5px8mzj8fbyw1pzahk9vp085gkr"))))
+         "17v2x7cyw74h0zfsz33pyl1kqk976pdzw7mrgprz9l7w5120niw5"))))
     (properties `((upstream-name . "minet")))
     (build-system r-build-system)
     (propagated-inputs
@@ -21986,14 +22298,14 @@ information networks from data.")
 (define-public r-genetclassifier
   (package
     (name "r-genetclassifier")
-    (version "1.40.0")
+    (version "1.42.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "geNetClassifier" version))
        (sha256
         (base32
-         "1bn7h8jwmmgqzp0s3xdbsicm8pxmrgvnxmjnjs10d1rvp8znzjnn"))))
+         "1k61aka780xmf1vhqm6zvzjr2626hv71f8gp1s81az939crxlrqd"))))
     (properties
      `((upstream-name . "geNetClassifier")))
     (build-system r-build-system)
@@ -22011,14 +22323,14 @@ interface to query the classifier.")
 (define-public r-dir-expiry
   (package
     (name "r-dir-expiry")
-    (version "1.8.0")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "dir.expiry" version))
        (sha256
         (base32
-         "1vccq28734s7zk7pc7i9zq4rzbi373xqqvgkzamjpii36phkdmlw"))))
+         "191b8qhldxvsw09l2c0ffc1ldmx0mqxgsx6m074f28l01d3c1d9q"))))
     (properties `((upstream-name . "dir.expiry")))
     (build-system r-build-system)
     (propagated-inputs (list r-filelock))
@@ -22035,14 +22347,14 @@ eliminating obsolete caches generated by old versions of packages.")
 (define-public r-basilisk-utils
   (package
     (name "r-basilisk-utils")
-    (version "1.12.1")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "basilisk.utils" version))
        (sha256
         (base32
-         "0g5apvna9wzjlm7g9hdafy44nrg5rp3qh4anwpgwwp2vr0vxn37k"))))
+         "08wsn2znw56svyv5vpxxzcynz93h5hzw1n2r6hb9h3rvc7afyvxl"))))
     (properties
      `((upstream-name . "basilisk.utils")))
     (build-system r-build-system)
@@ -22059,14 +22371,14 @@ package, primarily for creation of the underlying Conda instance.")
 (define-public r-basilisk
   (package
     (name "r-basilisk")
-    (version "1.12.1")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "basilisk" version))
        (sha256
         (base32
-         "0bg6jfl12jsmhgby7x7g2vfmi61rx0jdksi97hb0zajgh1nvhirh"))))
+         "1z482gw04psvkgspclmxlkd9qi7srgbnr56ajngcng28sc6zqdhs"))))
     (properties `((upstream-name . "basilisk")))
     (build-system r-build-system)
     (propagated-inputs
@@ -22085,14 +22397,14 @@ Python environments in a single R session.")
 (define-public r-biocthis
   (package
     (name "r-biocthis")
-    (version "1.10.3")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biocthis" version))
        (sha256
         (base32
-         "1v0qrypdzl1bg85k8i7qamb6709cgk4ypmisjh6bn5r36nqd5qx4"))))
+         "0lxcsw70ib8wvkp3ii1l8vd4g2ddhj6g0x22dwcmwacr2myk3bg8"))))
     (properties `((upstream-name . "biocthis")))
     (build-system r-build-system)
     (arguments
@@ -22149,14 +22461,14 @@ the Bioconductor project.")
 (define-public r-biodb
   (package
     (name "r-biodb")
-    (version "1.8.1")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biodb" version))
        (sha256
         (base32
-         "18j70ma85qb42qqpzz8fw3g4x6cav4j0pc2ab5ym22791dr8izck"))))
+         "18w062s0wwdisl6a9a79in6h4052x3janinc5isip0x6p9g9d9bk"))))
     (properties `((upstream-name . "biodb")))
     (build-system r-build-system)
     (propagated-inputs
@@ -22195,14 +22507,14 @@ separate published packages.")
 (define-public r-biomformat
   (package
     (name "r-biomformat")
-    (version "1.28.0")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biomformat" version))
        (sha256
         (base32
-         "04kl2432wq6ybdhispvp98ylgyk3kkhmjx1nxdvcal7bfpy2vskk"))))
+         "1ccnrz8rkg533kil3sc8wnjqsmiyrpqqmk7av7ls01avglcjdjq1"))))
     (properties `((upstream-name . "biomformat")))
     (build-system r-build-system)
     (propagated-inputs
@@ -22224,14 +22536,14 @@ as extensions of common core functions/methods.")
 (define-public r-mvcclass
   (package
     (name "r-mvcclass")
-    (version "1.74.0")
+    (version "1.76.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MVCClass" version))
        (sha256
         (base32
-         "1vrn2c5m4w7g13s1zd1am5b02lp026zg6gvpg8dvsras0j56rhr6"))))
+         "16finp6q89n6x5q2v1khpfp5ys7d4dvlh3kacv5qbdh1bsb3fpax"))))
     (properties `((upstream-name . "MVCClass")))
     (build-system r-build-system)
     (home-page "https://bioconductor.org/packages/MVCClass")
@@ -22244,14 +22556,14 @@ design.")
 (define-public r-biomvcclass
   (package
     (name "r-biomvcclass")
-    (version "1.68.0")
+    (version "1.70.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BioMVCClass" version))
        (sha256
         (base32
-         "07iay2dpq3margh1ny2snlc75g7fpfs5bf2gmhv88d31b8blg57r"))))
+         "04ckv1y5iqawd0dvnn0bbpnmyys0ivcmf0my6dld3hib3idjzwfx"))))
     (properties `((upstream-name . "BioMVCClass")))
     (build-system r-build-system)
     (propagated-inputs
@@ -22300,14 +22612,14 @@ using aCGH or sequencing.")
 (define-public r-bionero
   (package
     (name "r-bionero")
-    (version "1.8.7")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BioNERO" version))
        (sha256
         (base32
-         "0yvd05yikvblnhimnmn4srcsimab4qml5k582n0c9h4rppffmvy4"))))
+         "0pq5fiacb2x8l5jk3p6bnha9bcwg91grpklgx2nirrlwwr80gf2h"))))
     (properties `((upstream-name . "BioNERO")))
     (build-system r-build-system)
     (propagated-inputs
@@ -22356,14 +22668,14 @@ networks.")
 (define-public r-bionet
   (package
     (name "r-bionet")
-    (version "1.60.0")
+    (version "1.62.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BioNet" version))
        (sha256
         (base32
-         "19caj3aj6gndkxkrd9s2x8v59hcdwdyxrx0ji473c3d5qrykskl1"))))
+         "122rj6rg4j9q9brhxyrbkc91fml3davk044s2yxwyjnwn2yjw0bq"))))
     (properties `((upstream-name . "BioNet")))
     (build-system r-build-system)
     (propagated-inputs
@@ -22385,14 +22697,14 @@ scoring subnetwork.")
 (define-public r-bionetstat
   (package
     (name "r-bionetstat")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BioNetStat" version))
        (sha256
         (base32
-         "0bvfgppsdih6s70iizd7zh3zkb0hg4s4h1728xmyjqbvkl8fsdf4"))
+         "1rbb36v64b9xbk2dsf6wsyrhwwbkysrj8fp1g22y3gisdk170sg8"))
        (snippet
         '(delete-file "inst/datatables/js/jquery.dataTables.min.js"))))
     (properties `((upstream-name . "BioNetStat")))
@@ -22440,14 +22752,14 @@ network and metabolic pathways view.")
 (define-public r-bioqc
   (package
     (name "r-bioqc")
-    (version "1.28.0")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BioQC" version))
        (sha256
         (base32
-         "0g6imi03l4xm0chx3i9wd2vdy0ls78lnylp294fq0jldl4n6y0nw"))))
+         "15kmg102259h2yl3b6ncq2p545kdac4hk4kwm1s5492y5rg7qkla"))))
     (properties `((upstream-name . "BioQC")))
     (build-system r-build-system)
     (propagated-inputs
@@ -22466,14 +22778,14 @@ optimised for high performance.")
 (define-public r-biotip
   (package
     (name "r-biotip")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BioTIP" version))
        (sha256
         (base32
-         "0lqnxaycrva2092h4swmk6na2pq2kp951dmicyw399djd1i7yj50"))))
+         "1bbjfv3bi20xlk8h7r5ipav6mfs27lmj0zjb5mk1gmp071dmnk0y"))))
     (properties `((upstream-name . "BioTIP")))
     (build-system r-build-system)
     (propagated-inputs
@@ -22496,14 +22808,14 @@ help unravel disease regulatory trajectory.")
 (define-public r-biotmle
   (package
     (name "r-biotmle")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biotmle" version))
        (sha256
         (base32
-         "1hjkhwbld8m52lsy2ba6cnp02n0xykaxm9650r5zmzry38dw9nb5"))))
+         "0h796sxv7fvwx9m8ikamf3bvaac7rimp33lv1j3ngsjifigdkvfy"))))
     (properties `((upstream-name . "biotmle")))
     (build-system r-build-system)
     (propagated-inputs
@@ -22538,14 +22850,14 @@ ensemble machine learning for the estimation of nuisance functions.")
 (define-public r-bsseq
   (package
     (name "r-bsseq")
-    (version "1.36.0")
+    (version "1.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bsseq" version))
        (sha256
         (base32
-         "1mvhh99h1l6f5rlz0fzqkjpz9hblj2rbv8nx4j9n93g8riz7wsi3"))))
+         "0afpzr52mf2ab7gr9swdf6609787ymw8s8wksis0d4ap0y0wdgg0"))))
     (properties `((upstream-name . "bsseq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -22584,13 +22896,13 @@ visualizing bisulfite sequencing data.")
 (define-public r-dada2
   (package
     (name "r-dada2")
-    (version "1.28.0")
+    (version "1.30.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "dada2" version))
               (sha256
                (base32
-                "1vxy2106rzygy0dr38wmw84zrqp9gsvaphliikdmhx0n2gv6xhd1"))))
+                "0rvnwbknvwksm50f4rw9965gnhy13rjgdfvv428xsqixgkkkyrf6"))))
     (properties `((upstream-name . "dada2")))
     (build-system r-build-system)
     (propagated-inputs
@@ -22621,14 +22933,14 @@ fragments by exact matching.")
 (define-public r-dmrseq
   (package
     (name "r-dmrseq")
-    (version "1.20.1")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "dmrseq" version))
        (sha256
         (base32
-         "1lxrirgy42xnpdj7b2nrabbki33an8ri6j1mgxp3jn4h0a88c280"))))
+         "0z53vh5qirkyn7yw3g2m2kj6dzii96l81vc8j59n2dl7p602l9a2"))))
     (properties `((upstream-name . "dmrseq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -22667,13 +22979,13 @@ interest on transformed methylation proportions.")
 (define-public r-omicade4
   (package
     (name "r-omicade4")
-    (version "1.40.0")
+    (version "1.42.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "omicade4" version))
               (sha256
                (base32
-                "086nh0m82gjlxyg6i230wpkin4zc3a7cfla0qzvj28h0n8irkm5r"))))
+                "0i4ln95ayl1irr8sr3639x35ilysdi663kksw7g93q1ry91yav8r"))))
     (properties `((upstream-name . "omicade4")))
     (build-system r-build-system)
     (propagated-inputs (list r-ade4 r-biobase r-made4))
@@ -22686,13 +22998,13 @@ interest on transformed methylation proportions.")
 (define-public r-omnipathr
   (package
     (name "r-omnipathr")
-    (version "3.8.2")
+    (version "3.10.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "OmnipathR" version))
        (sha256
-        (base32 "13ac98jj03vkzrc1ghrs98qrfvr74wz099w26lgc7jw2yxj575as"))))
+        (base32 "1wbzb4kh7bzsvixr3vxzih9rfkpjx00f33i0yl0dqj0yixnrghwr"))))
     (properties `((upstream-name . "OmnipathR")))
     (build-system r-build-system)
     (arguments
@@ -22711,6 +23023,7 @@ interest on transformed methylation proportions.")
            r-jsonlite
            r-later
            r-logger
+           r-lubridate
            r-magrittr
            r-progress
            r-purrr
@@ -22720,6 +23033,7 @@ interest on transformed methylation proportions.")
            r-rlang
            r-rmarkdown
            r-rvest
+           r-stringi
            r-stringr
            r-tibble
            r-tidyr
@@ -22741,14 +23055,14 @@ for ligand activity prediction from transcriptomics data.")
 (define-public r-biscuiteer
   (package
     (name "r-biscuiteer")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biscuiteer" version))
        (sha256
         (base32
-         "07nak6mfw9m8ldl336sqgkl3638ibv1hxwd89hwxdrn914wz3hw3"))))
+         "1q90p14qj5plz6cbvwxq875y29in6jg7adyni5wd33pf9i4gsxzi"))))
     (properties `((upstream-name . "biscuiteer")))
     (build-system r-build-system)
     (propagated-inputs
@@ -22793,13 +23107,13 @@ estimates, etc.")
 (define-public r-tcgabiolinks
   (package
     (name "r-tcgabiolinks")
-    (version "2.28.3")
+    (version "2.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "TCGAbiolinks" version))
        (sha256
-        (base32 "1hh09ya4jg062k1ibp1cpvdrgv6gwr95ch57iycgd3cjc5g0xhii"))))
+        (base32 "1k8xiv4bmil420176ckfda2r6y0s46dk1cm8dbywav86q28bmzzx"))))
     (properties `((upstream-name . "TCGAbiolinks")))
     (build-system r-build-system)
     (propagated-inputs
@@ -22848,13 +23162,13 @@ starburst plots) in order to easily develop complete analysis pipelines.")
 (define-public r-tricycle
   (package
     (name "r-tricycle")
-    (version "1.8.0")
+    (version "1.10.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "tricycle" version))
               (sha256
                (base32
-                "1ags05rhi431jsk0kqs7rmxj853mf5c0ibfqknbwy2wmbz8p1vq6"))))
+                "1dawkp681pz9hf7fp2nag9pcfxx5rq0z4j9czlalf0sylsjbirkd"))))
     (properties `((upstream-name . "tricycle")))
     (build-system r-build-system)
     (propagated-inputs
@@ -22887,14 +23201,14 @@ embeddings and functions to build new reference.")
 (define-public r-tximeta
   (package
     (name "r-tximeta")
-    (version "1.18.3")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "tximeta" version))
        (sha256
         (base32
-         "01s8x8a3rb0a5i599pxc5miz84ssvh10b4vha79nmbhkqccffvml"))))
+         "0wn7r1dzckiq3zacvcv2w780fj9bvz1vbyzcazv2qvsicbwc4vd8"))))
     (properties `((upstream-name . "tximeta")))
     (build-system r-build-system)
     (propagated-inputs
@@ -22928,13 +23242,13 @@ reproducibility.")
 (define-public r-phyloseq
   (package
     (name "r-phyloseq")
-    (version "1.44.0")
+    (version "1.46.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "phyloseq" version))
        (sha256
-        (base32 "0rmv8f1m8ck97v991wdly3fma2rjczhi974lh7ikwx6rcx6fp9ah"))))
+        (base32 "06gnpjcniqm8i52xh9xl3nn0wm9nn9rkqd3w3fjv7ii142xypjln"))))
     (properties `((upstream-name . "phyloseq")))
     (build-system r-build-system)
     (propagated-inputs
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 508f5ea09a..3572f3d551 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1063,11 +1063,11 @@ plotnames, filenames and paths.")
       (license license:gpl3))))
 
 (define-public r-readwriter
-  (let ((commit "71454f4aa706f5d2fbe606acd95abc14224e7058")
+  (let ((commit "12d32cb6533ef4b9eab4d707d1502525c2034aee")
         (revision "1"))
     (package
       (name "r-readwriter")
-      (version (git-version "0.2.9" revision commit))
+      (version (git-version "0.3.2" revision commit))
       (source (origin
                 (method git-fetch)
                 (uri (git-reference
@@ -1076,7 +1076,7 @@ plotnames, filenames and paths.")
                 (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "0sp27smhdva2hi2x0svia2l56k8xrh7p5akn78g5b0lcvz4x3hd7"))))
+                  "1hy47g8d7zppr2i9zlkwl2yb0ii8x710hqk07h089ldx9171qxab"))))
       (properties `((upstream-name . "ReadWriter")))
       (build-system r-build-system)
       (propagated-inputs
@@ -5164,13 +5164,25 @@ software to answer ad hoc questions.")
            python-pysam
            python-pyyaml
            python-scipy
+           r-biocmanager
+           r-dplyr
+           r-genomicranges
+           r-here
+           r-openxlsx
+           r-optparse
+           r-readr
+           r-rsamtools
+           r-stringr
+           r-tidyr
+           r-upsetr
+           r-yaml
            snakemake-7))
     (native-inputs (list python-cython python-pyfakefs python-pytest))
     (home-page "https://github.com/dieterich-lab/Baltica")
     (synopsis "Integrated splice junction usage analysis")
     (description
      "This framework facilitates the execution of @dfn{differential junction
-usage} (DJU) methods. Additionally, it enables the integration of results from
+usage} (DJU) methods.  Additionally, it enables the integration of results from
 multiple DJU methods.")
     (license license:expat)))
 
@@ -10653,6 +10665,40 @@ of transcriptional heterogeneity among single cells.")
     ;; See https://github.com/hms-dbmi/scde/issues/38
     (license license:gpl2)))
 
+(define-public r-miamiplot
+  (let ((commit "beede9c5d6431b4d822aa42e064e01baeb5dd4a0")
+        (revision "1"))
+    (package
+      (name "r-miamiplot")
+      (version (git-version "1.1.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/juliedwhite/miamiplot")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "0wxxk1lk9jbf0imf59qp302ffasvs84idinkvzirs3dw9w3589n9"))))
+      (properties `((upstream-name . "miamiplot")))
+      (build-system r-build-system)
+      (propagated-inputs (list r-checkmate
+                               r-dplyr
+                               r-ggplot2
+                               r-ggrepel
+                               r-gridextra
+                               r-magrittr
+                               r-rlang))
+      (native-inputs (list r-knitr))
+      (home-page "https://github.com/juliedwhite/miamiplot")
+      (synopsis "Create a ggplot2 miami plot")
+      (description
+       "This package generates a Miami plot with centered chromosome labels.
+The output is a ggplot2 object.  Users can specify which data they want
+plotted on top vs. bottom, whether to display significance line(s), what
+colors to give chromosomes, and what points to label.")
+      (license license:gpl2))))
+
 (define-public r-millefy
   (package
     (name "r-millefy")
@@ -18796,6 +18842,73 @@ transcriptional derivatives and visualization of the resulting velocity
 patterns.")
       (license license:gpl3))))
 
+(define-public r-voltron
+  (let ((commit "5057b703479239a9aaba761f07e65d849f6111f8")
+        (revision "1"))
+    (package
+      (name "r-voltron")
+      (version (git-version "1.0.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/BIMSBbioinfo/VoltRon")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "1nximl4708a7fdwn8ysxpni3mp6dx33cphavlay7hh1pa55pnzgn"))
+                (modules '((guix build utils)))
+                ;; The tripack package is not available under a free license,
+                ;; but interp provides free implementations of "tri.mesh" and
+                ;; "neighbours".
+                (snippet
+                 '(substitute* '("DESCRIPTION" "NAMESPACE" "R/spatial.R")
+                    (("tripack") "interp")))))
+      (properties `((upstream-name . "VoltRon")))
+      (build-system r-build-system)
+      (inputs (list opencv tbb zlib))
+      (propagated-inputs (list r-anndata
+                               r-data-table
+                               r-dplyr
+                               r-ebimage
+                               r-fastdummies
+                               r-fnn
+                               r-ggforce
+                               r-ggplot2
+                               r-ggpubr
+                               r-ggrepel
+                               r-hdf5r
+                               r-htmltools
+                               r-igraph
+                               r-interp
+                               r-irlba
+                               r-magick
+                               r-matrix
+                               r-morpho
+                               r-raster
+                               r-rcpp
+                               r-reshape2
+                               r-rjson
+                               r-rlang
+                               r-s4vectors
+                               r-scales
+                               r-shiny
+                               r-shinyjs
+                               r-stringr
+                               r-terra
+                               r-umap
+                               r-xml))
+      (native-inputs (list pkg-config))
+      (home-page "https://github.com/BIMSBbioinfo/VoltRon")
+      (synopsis "VoltRon for Spatial Data Integration and Analysis")
+      (description
+       "@code{VoltRon} is a toolbox for spatial data analysis, multi-omics
+integration using spatial image registration.  @code{VoltRon} is capable of
+analyzing multiple types and modalities of spatially-aware datasets.
+@code{VoltRon} visualizes and analyzes regions of interests (ROIs), spots,
+cells and even molecules.")
+      (license license:expat))))
+
 (define-public methyldackel
   (package
     (name "methyldackel")
diff --git a/gnu/packages/bittorrent.scm b/gnu/packages/bittorrent.scm
index b357d96fbc..abf8a609e9 100644
--- a/gnu/packages/bittorrent.scm
+++ b/gnu/packages/bittorrent.scm
@@ -83,7 +83,7 @@
 (define-public transmission
   (package
     (name "transmission")
-    (version "4.0.3")
+    (version "4.0.4")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/transmission/transmission"
@@ -91,7 +91,7 @@
                                   version ".tar.xz"))
               (sha256
                (base32
-                "0njlmpcdsxwx8vwdk9dvsby51l6f6awks9d0mgvi9fs2ivaizc5n"))))
+                "19nm7f4x3zq610da5fl63vpycj4kv07np6ldm8czpgyziwqv9xqm"))))
     (build-system cmake-build-system)
     (outputs '("out"                      ; library and command-line interface
                "gui"))                    ; graphical user interface
@@ -112,8 +112,9 @@
            (replace 'check
              (lambda* (#:key tests? parallel-tests? #:allow-other-keys)
                (if tests?
-                   ;; XXX this test fails...
-                   (invoke "ctest" "-E" "usesBootstrapFile"
+                   (invoke "ctest"
+                           ;; XXX this test fails...
+                           "-E" "usesBootstrapFile"
                            "-j" (if parallel-tests?
                                     (number->string (parallel-job-count))
                                     "1"))
@@ -155,7 +156,7 @@
     (native-inputs
      (list intltool pkg-config))
     (home-page "https://transmissionbt.com/")
-    (synopsis "Fast and easy BitTorrent client")
+    (synopsis "BitTorrent client")
     (description
      "Transmission is a BitTorrent client that comes with graphical,
 textual, and Web user interfaces.  Transmission also has a daemon for
diff --git a/gnu/packages/browser-extensions.scm b/gnu/packages/browser-extensions.scm
index 252c95729d..8ae6fbf497 100644
--- a/gnu/packages/browser-extensions.scm
+++ b/gnu/packages/browser-extensions.scm
@@ -28,6 +28,7 @@
   #:use-module (gnu build chromium-extension)
   #:use-module (gnu build icecat-extension)
   #:use-module (gnu packages compression)
+  #:use-module (gnu packages password-utils)
   #:use-module (gnu packages python))
 
 (define play-to-kodi
@@ -150,3 +151,73 @@ ungoogled-chromium.")
 
 (define-public ublock-origin/icecat
   (make-icecat-extension ublock-origin "firefox"))
+
+(define-public passff-host
+  (package
+    (name "passff-host")
+    (version "1.2.3")
+    (home-page "https://github.com/passff/passff-host")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference (url home-page) (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1p18l1jh20x4v8dj64z9qjlp96fxsl5h069iynxfpbkzj6hd74yl"))))
+    (build-system copy-build-system)
+    (arguments
+     (let ((native-manifests "lib/icecat/native-messaging-hosts"))
+       (list
+        #:install-plan
+        `'(("src" ,native-manifests #:include ("passff.json" "passff.py")))
+        #:phases
+        #~(modify-phases %standard-phases
+            (add-after 'unpack 'substitute
+              (lambda _
+                (substitute* "src/passff.json"
+                  (("PLACEHOLDER")
+                   (format #f "~a/~a/passff.py" #$output #$native-manifests)))
+                (substitute* "src/passff.py"
+                  (("_VERSIONHOLDER_") #$version)
+                  (("^COMMAND = .*")
+                   (format #f "COMMAND = \"~a/bin/pass\"~%"
+                           #$(this-package-input "password-store"))))
+                (patch-shebang "src/passff.py")))))))
+    (inputs (list password-store python))
+    (synopsis "Host app for the WebExtension PassFF")
+    (description "This piece of software wraps around the zx2c4 pass shell
+command.  It has to be installed for the PassFF browser extension to work
+properly.")
+    (license license:gpl2+)))
+
+(define passff
+  (package
+    (name "passff")
+    (version "1.15")
+    (home-page "https://github.com/passff/passff")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference (url home-page) (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1gymqyqppr8k9fqv5js7f6pk6hcc47qpf51x5cy6aahsk2v1qssj"))))
+    (propagated-inputs (list passff-host))
+    (build-system copy-build-system)
+    (properties '((addon-id . "passff@invicem.pro")))
+    (arguments
+     `(#:install-plan '(("src" ,(assq-ref properties 'addon-id)))
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'substitute-placeholder
+           (lambda _
+             (substitute* "src/manifest.json"
+               (("_VERSIONHOLDER_") ,version)))))))
+    (synopsis "zx2c4 pass management extension for Mozilla Firefox")
+    (description "This extension will allow you to access your zx2c4 pass
+repository directly from your web browser.  You can choose to automatically
+fill and submit login forms if a matching password entry is found.")
+    (license license:gpl2+)))
+
+(define-public passff/icecat
+  (make-icecat-extension passff))
diff --git a/gnu/packages/ci.scm b/gnu/packages/ci.scm
index e0bf59b616..1fa5818b6d 100644
--- a/gnu/packages/ci.scm
+++ b/gnu/packages/ci.scm
@@ -59,11 +59,11 @@
   #:use-module ((guix search-paths) #:select ($SSL_CERT_DIR)))
 
 (define-public cuirass
-  (let ((commit "db6b63371159a735de74eee97c313740c998439a")
-        (revision "20"))
+  (let ((commit "eb3f539dc95de705c89b07258efe4663e76f7dab")
+        (revision "0"))
     (package
       (name "cuirass")
-      (version (git-version "1.1.0" revision commit))
+      (version "1.2.0")
       (source
        (origin
          (method git-fetch)
@@ -73,7 +73,7 @@
          (file-name (git-file-name name version))
          (sha256
           (base32
-           "16d9ylzk8mwsgppfdxyl0k2mkwll7fq17d6v09406rqkgddxg3m2"))))
+           "0rvzcsm0zwwv8rb5z0jdgc7adzzx0cin9n2hhclp5d0kqn582hny"))))
       (build-system gnu-build-system)
       (arguments
        (list #:modules `((guix build utils)
diff --git a/gnu/packages/cmake.scm b/gnu/packages/cmake.scm
index bc14286070..1592703f8d 100644
--- a/gnu/packages/cmake.scm
+++ b/gnu/packages/cmake.scm
@@ -263,6 +263,7 @@ and workspaces that can be used in the compiler environment of your choice.")
   (package
     (inherit cmake-bootstrap)
     (name "cmake-minimal")
+    (properties (alist-delete 'hidden? (package-properties cmake-bootstrap)))
     (source (origin
               (inherit (package-source cmake-bootstrap))
               ;; Purge CMakes bundled dependencies as they are no longer needed.
diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm
index d89fcaeb1e..0ce60c49de 100644
--- a/gnu/packages/cpp.scm
+++ b/gnu/packages/cpp.scm
@@ -1112,6 +1112,10 @@ portable applications targeting all major HPC platforms.  For that purpose it
 provides abstractions for both parallel execution of code and data management.
 Kokkos is designed to target complex node architectures with N-level memory
 hierarchies and multiple types of execution resources.")
+
+    ;; Code exhibits integer size mismatches when compiled on 32-bit systems.
+    (supported-systems %64bit-supported-systems)
+
     (license license:asl2.0))) ; With LLVM exception
 
 (define-public tweeny
@@ -1250,12 +1254,25 @@ Google's C++ code base.")
                                      (number->string version))
                     #$flags))))))))
 
+(define (make-static-abseil-cpp version)
+  (let ((base abseil-cpp))
+    (hidden-package
+     (package/inherit base
+       (arguments
+        (substitute-keyword-arguments (package-arguments base)
+          ((#:configure-flags flags)
+           #~(cons* "-DCMAKE_POSITION_INDEPENDENT_CODE=ON"
+                    (delete "-DBUILD_SHARED_LIBS=ON" #$flags)))))))))
+
 (define-public abseil-cpp-cxxstd17
   (abseil-cpp-for-c++-standard 17))             ;XXX: the default with GCC 11?
 
 (define-public abseil-cpp-cxxstd11
   (abseil-cpp-for-c++-standard 11))
 
+(define-public static-abseil-cpp
+  (make-static-abseil-cpp abseil-cpp))
+
 (define-public pegtl
   (package
     (name "pegtl")
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index de31f44dbd..1a5189cbca 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -305,6 +305,30 @@ are included as well.")
     ;; Any version of the GPL.
     (license license:gpl3+)))
 
+(define-public r-celestial
+  (package
+    (name "r-celestial")
+    (version "1.4.6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "celestial" version))
+       (sha256
+        (base32 "1gls0qvr8mxz79lsmk76v253f747g0cqys8p8wjmpijs8r0pyr4z"))))
+    (properties `((upstream-name . "celestial")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-nistunits r-pracma r-rann))
+    (home-page "https://cran.r-project.org/package=celestial")
+    (synopsis
+     "Collection of common astronomical conversion routines and functions")
+    (description
+     "This package contains a number of common astronomy conversion routines,
+particularly the HMS and degrees schemes, which can be fiddly to convert between
+on mass due to the textural nature of the former.  It allows users to coordinate
+match datasets quickly.  It also contains functions for various cosmological
+calculations.")
+    (license license:gpl3)))
+
 ;; The package sources include multiple non-minified JavaScript files and the
 ;; v5.1.0 variant of d3.js.  The d3.js file is not minified.
 (define-public r-chromomap
@@ -341,6 +365,61 @@ Shiny applications.")
     (license (list license:gpl3
                    license:isc)))) ;for bundled d3js
 
+(define-public r-consort
+  (package
+    (name "r-consort")
+    (version "1.2.1")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "consort" version))
+              (sha256
+               (base32
+                "03xkypy4r84mdif6m331c27haxnyi1s87vvj2f83xxw0m0s5im5j"))))
+    (properties `((upstream-name . "consort")))
+    (build-system r-build-system)
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/adayim/consort/")
+    (synopsis "Create Consort Diagrams")
+    (description
+     "To make it easy to create CONSORT diagrams for the transparent reporting of
+participant allocation in randomized, controlled clinical trials.  This is done
+by creating a standardized disposition data, and using this data as the source
+for the creation a standard CONSORT diagram.  Human effort by supplying text
+labels on the node can also be achieved.")
+    (license license:expat)))
+
+(define-public r-collapse
+  (package
+    (name "r-collapse")
+    (version "2.0.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "collapse" version))
+       (sha256
+        (base32 "16y4qxqr4k04690xn8s6c9fr3igpk34pgxygxkc41gc1na0ym37v"))))
+    (properties `((upstream-name . "collapse")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-rcpp))
+    (native-inputs (list r-knitr))
+    (home-page "https://sebkrantz.github.io/collapse/")
+    (synopsis "Advanced and fast data transformation")
+    (description
+     "This is a C/C++ based package for advanced data transformation and
+statistical computing in R that is extremely fast, class-agnostic, robust and
+programmer friendly.  Core functionality includes a rich set of S3 generic
+grouped and weighted statistical functions for vectors, matrices and data
+frames, which provide efficient low-level vectorizations, @code{OpenMP}
+multithreading, and skip missing values by default.  These are integrated with
+fast grouping and ordering algorithms (also callable from C), and efficient
+data manipulation functions.  The package also provides a flexible and
+rigorous approach to time series and panel data in R.  It further includes
+fast functions for common statistical procedures, detailed (grouped, weighted)
+summary statistics, powerful tools to work with nested data, fast data object
+conversions, functions for memory efficient R programming, and helpers to
+effectively deal with variable labels, attributes, and missing data.")
+    (license (list license:gpl2+))))
+
 (define-public r-collections
   (package
     (name "r-collections")
@@ -777,6 +856,64 @@ dumbbell charts, the ability to encircle points and coordinate-system-based
 text annotations.")
     (license license:agpl3)))
 
+(define-public r-ggbreak
+  (package
+    (name "r-ggbreak")
+    (version "0.1.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ggbreak" version))
+       (sha256
+        (base32 "14rx16v66xd0fjlywi89dq9dbw41zn7hpq14wgvf0178cxdp2fw4"))))
+    (properties `((upstream-name . "ggbreak")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-aplot r-ggfun r-ggplot2 r-ggplotify r-rlang))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/YuLab-SMU/ggbreak")
+    (synopsis "Set axis break for ggplot2")
+    (description
+     "This package provides an implementation of scale functions for setting
+axis breaks of a ggplot.")
+    (license license:artistic2.0)))
+
+(define-public r-ggdist
+  (package
+    (name "r-ggdist")
+    (version "3.3.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ggdist" version))
+       (sha256
+        (base32 "0b15b972wrllsvqqn0nc2c81fd9jl618fvqsfi50hjxwwpdach8l"))))
+    (properties `((upstream-name . "ggdist")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-cli
+                             r-distributional
+                             r-dplyr
+                             r-ggplot2
+                             r-glue
+                             r-numderiv
+                             r-quadprog
+                             r-rlang
+                             r-scales
+                             r-tibble
+                             r-tidyselect
+                             r-vctrs
+                             r-withr))
+    (native-inputs (list r-knitr))
+    (home-page "https://mjskay.github.io/ggdist/")
+    (synopsis "Visualizations of distributions and uncertainty")
+    (description
+     "This package provides primitives for visualizing distributions using
+ggplot2 that are particularly tuned for visualizing uncertainty in either a
+frequentist or Bayesian mode.  Both analytical distributions (such as
+frequentist confidence distributions or Bayesian priors) and distributions
+represented as samples (such as bootstrap distributions or Bayesian posterior
+samples) are easily visualized.")
+    (license license:gpl3+)))
+
 (define-public r-ggfittext
   (package
     (name "r-ggfittext")
@@ -1242,6 +1379,37 @@ engines that convert R Markdown into HTML pages.  Various themes and syntax
 highlight styles are supported.")
     (license license:asl2.0)))
 
+(define-public r-profmem
+  (package
+    (name "r-profmem")
+    (version "0.6.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "profmem" version))
+       (sha256
+        (base32 "0gg6ja0ifwn9jj42rw1gnyil55sl9r2y5rjb6yjcvqwd5arajp3l"))))
+    (properties `((upstream-name . "profmem")))
+    (build-system r-build-system)
+    (arguments
+     (list
+      #:phases
+      '(modify-phases %standard-phases
+         (add-before 'install 'set-HOME
+           (lambda _
+             ;; Needed for building vignettes
+             (setenv "HOME" "/tmp"))))))
+    (native-inputs
+     (list r-r-rsp r-markdown)) ;for vignettes
+    (home-page "https://github.com/HenrikBengtsson/profmem")
+    (synopsis "Simple memory profiling for R")
+    (description
+     "This package provides a simple and light-weight API for memory profiling
+of R expressions.  The profiling is built on top of R's built-in memory
+profiler @code{utils::Rprofmem()}, which records every memory allocation done
+by R (also native code).")
+    (license license:lgpl2.1+)))
+
 (define-public r-proj4
   (package
     (name "r-proj4")
@@ -1425,6 +1593,26 @@ Singularity containers.  You can execute a command inside a container, mount a
 volume or copy a file.")
     (license license:expat)))
 
+(define-public r-bench
+  (package
+    (name "r-bench")
+    (version "1.1.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "bench" version))
+       (sha256
+        (base32 "05zky7l6103gabv9y0g3qlx8sgkq1sn9yl9jd3x8834cmlh67bmz"))))
+    (properties `((upstream-name . "bench")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-glue r-pillar r-profmem r-rlang r-tibble))
+    (home-page "https://bench.r-lib.org/")
+    (synopsis "High precision timing of R expressions")
+    (description
+     "This package provides tools to accurately benchmark and analyze execution
+times for R expressions.")
+    (license license:expat)))
+
 (define-public r-benchmarkmedata
   (package
     (name "r-benchmarkmedata")
@@ -1561,13 +1749,13 @@ larger than memory.")
 (define-public r-bwstest
   (package
     (name "r-bwstest")
-    (version "0.2.2")
+    (version "0.2.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "BWStest" version))
        (sha256
-        (base32 "02amzlfprmw5pyis0dg0kg0x8xqh50a4vfdcxxmklrzik3b1vzzs"))))
+        (base32 "1chlszmshda84000jj4q5j2swflj512vfj3h97361aphzhkwri2b"))))
     (properties `((upstream-name . "BWStest")))
     (build-system r-build-system)
     (propagated-inputs (list r-memoise r-rcpp))
@@ -1584,14 +1772,14 @@ similar rank-based tests for equal probability distributions due to Neuhauser
 (define-public r-v8
   (package
     (name "r-v8")
-    (version "4.3.3")
+    (version "4.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "V8" version))
        (sha256
         (base32
-         "04x2dph917dwq6ja69yiizw808zwmm17v78j17mlksdnl6wcmm0c"))))
+         "0ilg9ihx1mp9zj8023rh3lj875vqy253v9gbn1bw61h2p47w4nv3"))))
     (properties
      `((upstream-name . "V8")
        (updater-extra-inputs . ("libnode"))))
@@ -2844,13 +3032,13 @@ excellent candidate for labeling of a polygon.")
 (define-public r-poorman
   (package
     (name "r-poorman")
-    (version "0.2.6")
+    (version "0.2.7")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "poorman" version))
               (sha256
                (base32
-                "0x1pk00ca7wjxnqfh1jphgsxcrq37s0c1nawv52yh5qgc4z0m3ij"))))
+                "1amlcbgfnm6yh7lmlzhs7aalv4mdm2ir3s2kpx33ppnz7hlii508"))))
     (properties `((upstream-name . "poorman")))
     (build-system r-build-system)
     (native-inputs (list r-knitr))
@@ -2990,6 +3178,27 @@ functions, including @code{sort}, @code{order}, and @code{match}.  The
 functions are simplified but can be faster or have other advantages.")
     (license license:gpl3)))
 
+(define-public r-matrixtests
+  (package
+    (name "r-matrixtests")
+    (version "0.2.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "matrixTests" version))
+       (sha256
+        (base32 "0d7i00cxzszfdnjm8q5b72ildic8nig6fbw7rba6acdnllpp7sza"))))
+    (properties `((upstream-name . "matrixTests")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-matrixstats))
+    (home-page "https://github.com/karoliskoncevicius/matrixTests")
+    (synopsis "Statistical hypothesis tests on rows and columns of matrices")
+    (description
+     "This package offers quick statistical hypothesis testing for matrix
+rows/columns.  The main goals are speed through vectorization, detailed and
+user-friendly output, and compatibility with tests implemented in R.")
+    (license license:gpl2)))
+
 (define-public r-matrix-utils
   (package
     (name "r-matrix-utils")
@@ -3432,6 +3641,27 @@ convenience functions useful for using CSS selectors on XML nodes.  This
 package is a port of the Python package @code{cssselect}.")
     (license license:bsd-3)))
 
+(define-public r-relations
+  (package
+    (name "r-relations")
+    (version "0.6-13")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "relations" version))
+       (sha256
+        (base32 "1nnr0kcr3whbwzi36sg7wn46jp7r0hfkvcwlybvjsjhczcvc6ngq"))))
+    (properties `((upstream-name . "relations")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-cluster r-sets r-slam))
+    (home-page "https://cran.r-project.org/package=relations")
+    (synopsis "Data structures and algorithms for relations")
+    (description
+     "This package provides data structures and algorithms for k-ary relations
+with arbitrary domains, featuring relational algebra, predicate functions, and
+fitters for consensus relations.")
+    (license license:gpl2)))
+
 (define-public r-repmis
   (package
     (name "r-repmis")
@@ -3546,6 +3776,27 @@ without affecting the current R process at all.  This package does exactly
 that.")
     (license license:expat)))
 
+(define-public r-deming
+  (package
+    (name "r-deming")
+    (version "1.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "deming" version))
+       (sha256
+        (base32 "1yx3qrbik6jpqgsi0gqgc7y2cra13qlisg2gq8rvnv57nvcvb421"))))
+    (properties `((upstream-name . "deming")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-boot))
+    (home-page "https://cran.r-project.org/package=deming")
+    (synopsis
+     "Deming, Theil-Sen, Passing-Bablock and Total Least Squares regression")
+    (description
+     "This package implements generalized Deming regression, Theil-Sen
+regression and Passing-Bablock regression functions.")
+    (license license:lgpl2.0+)))
+
 (define-public r-depmixs4
   (package
     (name "r-depmixs4")
@@ -3775,40 +4026,24 @@ Zucchini.")
 (define-public r-httpuv
   (package
     (name "r-httpuv")
-    (version "1.6.11")
+    (version "1.6.12")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "httpuv" version))
               (sha256
                (base32
-                "1xgf7q8ah9sbgbbjm9nwvry154g8i0gwfrn55npls9sihc59x9wb"))
+                "0x2y5yjj1ha99dv5c8j6pxm8fqhdcx010jl4rcw2qw20qaqp5ndi"))
               (modules '((guix build utils)))
               ;; Cannot unbundle http-parser, because it contains local
               ;; modifications.
               (snippet
                '(delete-file-recursively "src/libuv"))))
     (build-system r-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'unbundle-libuv
-           (lambda* (#:key outputs #:allow-other-keys)
-             (substitute* "src/Makevars"
-               (("PKG_LIBS = ./libuv/.libs/libuv.a")
-                "PKG_LIBS = -luv")
-               (("\\$\\(SHLIB\\): libuv/.libs/libuv.a")
-                "$(SHLIB): "))
-             (substitute* (find-files "src" "\\.cpp$|\\.h$")
-               (("\"libuv/include/uv\\.h\"")
-                "<uv.h>"))
-             ;; Fix https://github.com/rstudio/httpuv/issues/282
-             (substitute* "src/http.cpp"
-               (("uv_pipe_init\\(pLoop, &pSocket->handle\\.pipe, true\\);")
-                "uv_pipe_init(pLoop, &pSocket->handle.pipe, 0);")))))))
     (inputs
      (list libuv-for-r-httpuv zlib))
     (propagated-inputs
      (list r-later r-promises r-r6 r-rcpp))
+    (native-inputs (list pkg-config))
     (home-page "https://github.com/rstudio/httpuv")
     (synopsis "HTTP and WebSocket server library for R")
     (description
@@ -4015,15 +4250,31 @@ applications.")
 (define-public r-htmltable
   (package
     (name "r-htmltable")
-    (version "2.4.1")
+    (version "2.4.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "htmlTable" version))
        (sha256
-        (base32 "14qg65nw0bpikqs1hb1x7apzdzrnnl3ykjnks67kkp46v1skwzrs"))))
+        (base32 "039nnxnvw5l284n7w8q0hnplm0b58nwhsrpjfi5asg61f9hxv0va"))))
     (properties `((upstream-name . "htmlTable")))
     (build-system r-build-system)
+    (arguments
+     (list
+      #:modules
+      '((guix build r-build-system)
+        (guix build minify-build-system)
+        (guix build utils))
+      #:imported-modules
+      `(,@%r-build-system-modules
+        (guix build minify-build-system))
+      #:phases
+      #~(modify-phases (@ (guix build r-build-system) %standard-phases)
+          (add-after 'unpack 'replace-bundled-minified-JavaScript
+            (lambda* (#:key inputs #:allow-other-keys)
+              (minify (assoc-ref inputs "js-jquery")
+                      #:target
+                      "inst/htmlwidgets/lib/jquery/jquery.min.js"))))))
     (propagated-inputs
      (list r-checkmate
            r-htmltools
@@ -4033,7 +4284,15 @@ applications.")
            r-rstudioapi
            r-stringr))
     (native-inputs
-     (list r-knitr))
+     `(("esbuild" ,esbuild)
+       ("js-jquery"
+        ,(origin
+           (method url-fetch)
+           (uri "https://code.jquery.com/jquery-3.7.1.js")
+           (sha256
+            (base32
+             "1zicjv44sx6n83vrkd2lwnlbf7qakzh3gcfjw0lhq48b5z55ma3q"))))
+       ("r-knitr" ,r-knitr)))
     (home-page "http://gforge.se/packages/")
     (synopsis "Advanced tables for Markdown/HTML")
     (description
@@ -4296,13 +4555,13 @@ jQuery.")
 (define-public r-jqr
   (package
     (name "r-jqr")
-    (version "1.3.0")
+    (version "1.3.1")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "jqr" version))
               (sha256
                (base32
-                "0gys1b2fiafmm49mkj9iazziwql87s52rjx093ahn8g3v79amirh"))))
+                "0dlz9wwkgz06mnnmwaq4pr68x7zywp2iczfw0bjpzrgpbzkn2972"))))
     (properties `((upstream-name . "jqr")))
     (build-system r-build-system)
     (inputs (list jq))
@@ -4985,13 +5244,13 @@ in a ggplot2 plot.")
 (define-public r-mbess
   (package
     (name "r-mbess")
-    (version "4.9.2")
+    (version "4.9.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "MBESS" version))
        (sha256
-        (base32 "0cq4z7nx361rcw42jflrrdjbqs2q5973dlvhcr7i2wbkj3gzkwla"))))
+        (base32 "05ph8dwigwn0c4qg8smqhsjijvsvfawbzvm74mqpasi8qifz8nd3"))))
     (properties `((upstream-name . "MBESS")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5974,14 +6233,14 @@ functions and compiled functions callable by other packages.")
 (define-public r-rcppthread
   (package
     (name "r-rcppthread")
-    (version "2.1.5")
+    (version "2.1.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "RcppThread" version))
        (sha256
         (base32
-         "0rra7qqbq2y4bj54x76559p5ghpj3r03c4vlpg96phwafwnc2y8m"))))
+         "1997ka0dd36d79fb4crqq0ar3bgzdv4mw5hd6v2pmq7555g0qiz9"))))
     (properties `((upstream-name . "RcppThread")))
     (build-system r-build-system)
     (native-inputs (list r-r-rsp))
@@ -6713,13 +6972,13 @@ most popular ones.")
 (define-public r-sp
   (package
     (name "r-sp")
-    (version "2.1-0")
+    (version "2.1-1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "sp" version))
        (sha256
-        (base32 "03041jp74z7l5vs1yzp145w331940kj9gf52jaxdninknikhc0vk"))))
+        (base32 "0ns0n4929db2g8wjmg8nscq286df4hxrv7gr4mj8giymm3icsd1d"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-lattice))
@@ -6738,13 +6997,13 @@ print, summary, etc.")
 (define-public r-lambertw
   (package
     (name "r-lambertw")
-    (version "0.6.8")
+    (version "0.6.9")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "LambertW" version))
               (sha256
                (base32
-                "10lqsz44ndm8pl8z75j35fzd1s313q09rs9bs3lkym8d43k50pha"))))
+                "0260sa4w5i4vwxg13g3q0dmairsrbyaijr2gxlppy09nxriccwbr"))))
     (properties `((upstream-name . "LambertW")))
     (build-system r-build-system)
     (propagated-inputs (list r-ggplot2
@@ -7589,13 +7848,13 @@ variable models.")
 (define-public r-drat
   (package
     (name "r-drat")
-    (version "0.2.3")
+    (version "0.2.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "drat" version))
        (sha256
-        (base32 "191yxlj9jccakmz27g7n9izfcy19kj3fgnw4w6zl9iq66787qpm6"))))
+        (base32 "13v7dj2688ix6j9nzhvf8q9ynfihwzkppfdjkis6q1r5m4nikya3"))))
     (properties `((upstream-name . "drat")))
     (build-system r-build-system)
     (native-inputs (list r-simplermarkdown))
@@ -7753,6 +8012,33 @@ a variety of functions for the manipulation and analysis of arbitrarily
 dimensioned arrays.")
     (license license:gpl2)))
 
+(define-public r-magicaxis
+  (package
+    (name "r-magicaxis")
+    (version "2.2.14")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "magicaxis" version))
+       (sha256
+        (base32 "1gqnivn6qjmf7axdi0pff6a40clklbipcr6qvm6ivzqbqhpbcb7v"))))
+    (properties `((upstream-name . "magicaxis")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-celestial
+           r-mapproj
+           r-mass
+           r-plotrix
+           r-rann
+           r-sm))
+    (home-page "https://cran.r-project.org/package=magicaxis")
+    (synopsis "Scientific plotting with minor-tick and log minor-tick support")
+    (description
+     "This package provides functions to make useful (and pretty) plots for
+scientific plotting.  Additional plotting features are added for base plotting,
+with particular emphasis on making attractive log axis plots.")
+    (license license:gpl3)))
+
 (define-public r-rmysql
   (package
     (name "r-rmysql")
@@ -7830,25 +8116,25 @@ to access PostgreSQL database systems.")
 (define-public r-rpostgres
   (package
     (name "r-rpostgres")
-    (version "1.4.5")
+    (version "1.4.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "RPostgres" version))
        (sha256
         (base32
-         "15y732ylnq1h1hw16nh1ichnygh3l76h23m2893avpaipa689zvh"))))
+         "1ld03r9rzfxx6gzy3yn8jhzp9sp2qd9wydpxz955ggjxwdklpvnr"))))
     (properties `((upstream-name . "RPostgres")))
     (build-system r-build-system)
     (inputs (list postgresql))
     (propagated-inputs
      (list r-bit64
            r-blob
+           r-cpp11
            r-dbi
            r-hms
            r-lubridate
            r-plogr
-           r-rcpp
            r-withr))
     (native-inputs
      (list pkg-config r-knitr))
@@ -8181,14 +8467,14 @@ for certain use cases.")
 (define-public r-ggrepel
   (package
     (name "r-ggrepel")
-    (version "0.9.3")
+    (version "0.9.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ggrepel" version))
        (sha256
         (base32
-         "0p00kb1x3q0krk5g8mmwqknnjlsznqs4i7mlfq1dp17fxpia1sxr"))))
+         "0gngsx87rcqijdr684bgpnazdlz3vj4brzw0fic0jdsrf1rb9aw1"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-ggplot2 r-rcpp r-rlang r-scales r-withr))
@@ -8463,13 +8749,13 @@ distances.")
 (define-public r-useful
   (package
    (name "r-useful")
-   (version "1.2.6")
+   (version "1.2.6.1")
    (source (origin
             (method url-fetch)
             (uri (cran-uri "useful" version))
             (sha256
              (base32
-              "0n50v1q75k518sq23id14jphwla35q4sasahrnrnllwrachl67v1"))))
+              "1gb9hqvbm6pr56dfqlsgz26lan7xargfsm8jpdja18mpgli2gyvc"))))
    (properties `((upstream-name . "useful")))
    (build-system r-build-system)
    (propagated-inputs
@@ -9229,13 +9515,13 @@ script.")
 (define-public r-aricode
   (package
     (name "r-aricode")
-    (version "1.0.2")
+    (version "1.0.3")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "aricode" version))
               (sha256
                (base32
-                "1w5jnql49f0wd5h4b89l69s7qldp7qm90p4jm0j4kz9w0vvm2kjz"))))
+                "02nrw66jfpzf6dy0zy21sbdjxjc8c11iv9fkjqj5akzb7wskk9qh"))))
     (properties `((upstream-name . "aricode")))
     (build-system r-build-system)
     (propagated-inputs (list r-matrix r-rcpp))
@@ -9520,14 +9806,14 @@ packages maintained by Yihui Xie.")
 (define-public r-utf8
   (package
     (name "r-utf8")
-    (version "1.2.3")
+    (version "1.2.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "utf8" version))
        (sha256
         (base32
-         "0iv3ppy7sddzl4sm3qlghpc64k6zx5j0jzcia8xx8jhzb638da60"))))
+         "0zbv2s5dkzxim3ydyk12479m28f68mak9m50v396in4wpm5q53s1"))))
     (build-system r-build-system)
     (native-inputs
      (list r-knitr r-rmarkdown)) ; for vignettes
@@ -9585,14 +9871,14 @@ estimated from a given sample.")
 (define-public r-vctrs
   (package
     (name "r-vctrs")
-    (version "0.6.3")
+    (version "0.6.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "vctrs" version))
        (sha256
         (base32
-         "1hm5rw85ln0mk1mfmhgygnhjgs2lyc74cq12ddc41d78rl6j5p4k"))))
+         "1j01s27ybzn60p17y7k5n5dzsmjqhgjy634sv0dx4977aqiik04a"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-cli r-glue r-lifecycle r-rlang))
@@ -9713,14 +9999,14 @@ their own grammars and easily expose them in R packages.")
 (define-public r-tinytex
   (package
     (name "r-tinytex")
-    (version "0.47")
+    (version "0.48")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tinytex" version))
        (sha256
         (base32
-         "1py5i4h2vpicl79ypxw061p9byxvj703z1rh8l2shfpq7wqwhxbr"))))
+         "15bnb4fxdzapgj9ws3rfbcxwdzwbq8h5yy4d1db0m9c1lygrh2qx"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-xfun))
@@ -9795,6 +10081,43 @@ implementation of an approximate nearest neighbor search using hierarchical
 @acronym{NSW, Navigable Small World} graphs.")
     (license license:asl2.0)))
 
+(define-public r-nestedcv
+  (package
+    (name "r-nestedcv")
+    (version "0.7.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "nestedcv" version))
+       (sha256
+        (base32 "0jpg4il1niyizfq8kkk391x7anhp2s38mrfypa86skr08ca46zss"))))
+    (properties `((upstream-name . "nestedcv")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-caret
+                             r-data-table
+                             r-doparallel
+                             r-foreach
+                             r-ggplot2
+                             r-glmnet
+                             r-matrixstats
+                             r-matrixtests
+                             r-proc
+                             r-rfast
+                             r-rlang))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/myles-lewis/nestedcv")
+    (synopsis "Nested cross-validation with glmnet and caret")
+    (description
+     "This package implements nested cross-validation applied to the
+@code{glmnet} and @code{caret} packages.  With glmnet this includes
+cross-validation of elastic net alpha parameter.  A number of feature
+selection filter functions (t-test, Wilcoxon test, ANOVA, Pearson/Spearman
+correlation, random forest, ReliefF) for feature selection are provided and
+can be embedded within the outer loop of the nested CV.  Nested CV can be also
+be performed with the @code{caret} package giving access to the large number
+of prediction methods available in @code{caret}.")
+    (license license:expat)))
+
 (define-public r-network
   (package
     (name "r-network")
@@ -9817,6 +10140,27 @@ implementation of an approximate nearest neighbor search using hierarchical
 supports arbitrary vertex/edge/graph attributes.")
     (license license:gpl2+)))
 
+(define-public r-nistunits
+  (package
+    (name "r-nistunits")
+    (version "1.0.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "NISTunits" version))
+       (sha256
+        (base32 "0km9l3k9p35sb1qrhrz4ijjsdihvsp6j7cz5kh46lgf7nn6xdk7a"))))
+    (properties `((upstream-name . "NISTunits")))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/package=NISTunits")
+    (synopsis "Fundamental physical constants and unit conversions")
+    (description
+     "This package provides fundamental physical constants (quantity, value,
+uncertainty, unit) for @acronym{SI, International System of Units} and non-SI
+units, plus unit conversions based on the data from @acronym{NIST, National
+Institute of Standards and Technology}, USA.")
+    (license license:gpl3+)))
+
 (define-public r-stabs
   (package
     (name "r-stabs")
@@ -9983,15 +10327,16 @@ rules with R.")
 (define-public r-leaflet-providers
   (package
     (name "r-leaflet-providers")
-    (version "1.13.0")
+    (version "2.0.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "leaflet.providers" version))
        (sha256
-        (base32 "1jrfhqmr735maa0mr3ia7441vzd3q95msgicclzdpglmk4aqhhhh"))))
+        (base32 "0rl69bfx2l10x80rl8cppqch3fnd05sk9w29h8589jc8h3ffmkn5"))))
     (properties `((upstream-name . "leaflet.providers")))
     (build-system r-build-system)
+    (propagated-inputs (list r-htmltools))
     (home-page "https://github.com/rstudio/leaflet.providers")
     (synopsis "Leaflet map tile providers")
     (description
@@ -10532,14 +10877,14 @@ interface.")
 (define-public r-trend
   (package
     (name "r-trend")
-    (version "1.1.5")
+    (version "1.1.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "trend" version))
        (sha256
         (base32
-         "12xswr925jjbkdccjiigkr6a44jmgvzwvnizciv6rr3mnklv6n66"))))
+         "0991fp6kjk704rfg0l1m7kwbck9fj1rg27zy4llm5ikczd55w05h"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-extradistr))
@@ -11048,14 +11393,14 @@ local smoothers and many more.")
 (define-public r-radiant-data
   (package
     (name "r-radiant-data")
-    (version "1.6.1")
+    (version "1.6.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "radiant.data" version))
        (sha256
         (base32
-         "00bjq3zpxhd6yjq3jwizgiyzp2qf557ms6mhlz74d0wcm0l3vd72"))
+         "0227ry366v9kmksa4vyjmhix0jbl894gdc6gckg209wna35fn20p"))
        (modules '((guix build utils)))
        (snippet
         '(begin
@@ -12475,14 +12820,14 @@ always locate the files relative to your project root.")
 (define-public r-reticulate
   (package
     (name "r-reticulate")
-    (version "1.32.0")
+    (version "1.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "reticulate" version))
        (sha256
         (base32
-         "0r9rycwin4yv5k2n1lzybwblb8529yhw5xnl46if6yvxm3bcra9s"))))
+         "01j2dr93r5a18irwbm6hlh2v0s2rc5bl6dcmds1m64c1rli8j3cd"))))
     (build-system r-build-system)
     (arguments
      (list
@@ -12790,14 +13135,14 @@ clustering.")
 (define-public r-factominer
   (package
     (name "r-factominer")
-    (version "2.8")
+    (version "2.9")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "FactoMineR" version))
        (sha256
         (base32
-         "0lgqbw7534wadkdv7zh1y5nanl72jys070qydznmaj2cmvvqd460"))))
+         "0c2j3xid85qffsdjwndqiwihclzw6k1nkbpzcc7whhd6k79rh9l8"))))
     (properties `((upstream-name . "FactoMineR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -12863,6 +13208,30 @@ packages.  It contains also functions for simplifying some clustering analysis
 steps and provides ggplot2-based elegant data visualization.")
     (license license:gpl2)))
 
+(define-public r-fancova
+  (package
+    (name "r-fancova")
+    (version "0.6-1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "fANCOVA" version))
+       (sha256
+        (base32 "04mw0blgpwdk6wdg8llrig43psgc0vb42cbimvzbnym8v503dsn3"))))
+    (properties `((upstream-name . "fANCOVA")))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/package=fANCOVA")
+    (synopsis "Nonparametric analysis of covariance")
+    (description
+     "This package provides a collection of R functions to perform
+nonparametric analysis of covariance for regression curves or surfaces.
+Testing the equality or parallelism of nonparametric curves or surfaces is
+equivalent to analysis of variance (ANOVA) or analysis of covariance (ANCOVA)
+for one-sample functional data.  Three different testing methods are available
+in the package, including one based on L-2 distance, one based on an ANOVA
+statistic, and one based on variance estimators.")
+    (license license:gpl3)))
+
 (define-public r-fansi
   (package
     (name "r-fansi")
@@ -13086,14 +13455,14 @@ hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.")
 (define-public r-rbibutils
   (package
     (name "r-rbibutils")
-    (version "2.2.15")
+    (version "2.2.16")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rbibutils" version))
        (sha256
         (base32
-         "1kjk953xqakbxb2z8rcfcni8b9vi1m27n0ksdddil6x7q03flxb5"))))
+         "1brab8vzzf44d9rpp9k3r2ajvrs09cbwf4ak014iffzn8yx0yz4w"))))
     (properties `((upstream-name . "rbibutils")))
     (build-system r-build-system)
     (home-page "https://geobosh.github.io/rbibutils/")
@@ -13134,14 +13503,14 @@ references and Rd files.")
 (define-public r-officer
   (package
     (name "r-officer")
-    (version "0.6.2")
+    (version "0.6.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "officer" version))
        (sha256
         (base32
-         "0dfk1didy5lfh07chqfwlrdlrib7a5na65rb71ipnxlhbiwbaj09"))))
+         "0z3phawwxj4h1pwzw8lsl6pnypr77b329mg6r2qnzmj0j81585z5"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-openssl r-r6 r-ragg r-uuid r-xml2 r-zip))
@@ -13371,14 +13740,14 @@ Decomposition in R (Beaton et al 2014) <doi:10.1016/j.csda.2013.11.006>.")
 (define-public r-insight
   (package
     (name "r-insight")
-    (version "0.19.5")
+    (version "0.19.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "insight" version))
        (sha256
         (base32
-         "0794p9dbclj1d7fcka6sqm8jzqsc58hxmmsksd3hmzv0qz49yhkg"))))
+         "1gnxhszwccmvjarq47p7s09jrkhvd8zkz632ysxz6dgxfpqn9zqh"))))
     (build-system r-build-system)
     (native-inputs
      (list r-knitr))
@@ -13530,14 +13899,14 @@ functions.")
 (define-public r-flextable
   (package
     (name "r-flextable")
-    (version "0.9.3")
+    (version "0.9.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "flextable" version))
        (sha256
         (base32
-         "1jdikfiswxi63vj9xr9a24p8fv50h91pvhv3xllgwwfbs1wqyq4x"))))
+         "1dlsag1y3s7d5lp1dh2kxf1qax4r9xvxycpmxl64gkr50dk13bam"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-data-table
@@ -13608,16 +13977,16 @@ contains or can be specified by the user.")
 (define-public r-wrs2
   (package
     (name "r-wrs2")
-    (version "1.1-4")
+    (version "1.1-5")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "WRS2" version))
               (sha256
                (base32
-                "1838wy59cqd65s0bw6c24xcvx7zflypqcbgs35l9s2fj87vw2hdc"))))
+                "028xs424m879siaf3rrhzl1dacp9j7wcl5fpikyx2n0cc7anq4vq"))))
     (properties `((upstream-name . "WRS2")))
     (build-system r-build-system)
-    (propagated-inputs (list r-mass r-mc2d r-plyr r-reshape))
+    (propagated-inputs (list r-mass r-plyr r-reshape))
     (native-inputs (list r-knitr))
     (home-page "https://r-forge.r-project.org/projects/psychor/")
     (synopsis "Collection of robust statistical methods")
@@ -14161,14 +14530,14 @@ from the @code{stats} package (plus some extra parameters).")
 (define-public r-cmplot
   (package
     (name "r-cmplot")
-    (version "4.4.1")
+    (version "4.4.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "CMplot" version))
        (sha256
         (base32
-         "1y6fs3b7jps4ah0lpniq0ip3x426acql1aibx95pvfykgc2b2hvm"))))
+         "0mkjpmwpd0izczp8jgfcfxw9i4qv82aj1xyhzsxgdxnjdd7ark66"))))
     (properties `((upstream-name . "CMplot")))
     (build-system r-build-system)
     (home-page "https://github.com/YinLiLin/CMplot")
@@ -14186,14 +14555,14 @@ visualization and candidate genes around SNPs.")
 (define-public r-precrec
   (package
     (name "r-precrec")
-    (version "0.14.2")
+    (version "0.14.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "precrec" version))
        (sha256
         (base32
-         "159vxdnp7vi6na3cji1rbsr1311ciqn1aldg0nwnd6sb3hgb14w2"))))
+         "03hvp5h7fz4v2aswxim0mqgj9rdrhnk5xqz212161kpcrw6m67z8"))))
     (properties `((upstream-name . "precrec")))
     (build-system r-build-system)
     (propagated-inputs
@@ -14737,14 +15106,14 @@ used to teach mathematics, statistics, computation and modeling.")
 (define-public r-raster
   (package
     (name "r-raster")
-    (version "3.6-23")
+    (version "3.6-26")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "raster" version))
        (sha256
         (base32
-         "0ng18sfw9kmhi48j8b5bzgh2ylvf5wi2zidn66k4vqaxl5s6hidz"))))
+         "14jmpm6rlhya192ckyjlwhais6fgc16gb600wycsdba6b8i7fmy6"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-rcpp r-sp r-terra))
@@ -15373,14 +15742,14 @@ samples is large and the number of mixture components is not too large.")
 (define-public r-magick
   (package
     (name "r-magick")
-    (version "2.8.0")
+    (version "2.8.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "magick" version))
        (sha256
         (base32
-         "1al1apw9vgdl6ccm4nnpqpnya0pi2cfp62xii7dwnv7pd47m8fp8"))))
+         "13j55dwvcqbyqgx0c6vj9knqrz25pc2xz19f22b2gm0p307d3z6q"))))
     (properties
      '((updater-extra-inputs . ("imagemagick"))))
     (build-system r-build-system)
@@ -15521,13 +15890,13 @@ were influenced by the drake R package by Will Landau (2018)
 (define-public r-targets
   (package
     (name "r-targets")
-    (version "1.3.0")
+    (version "1.3.2")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "targets" version))
               (sha256
                (base32
-                "146ylh76sc5vzfgh2xp5mfpgdxvm3j9b2hzh0wqgih6d9d11n8pk"))))
+                "0zlbq658zxflz2fk9pksbjx3r5dmay4411byl33gkp3rnynvchgh"))))
     (properties `((upstream-name . "targets")))
     (build-system r-build-system)
     (propagated-inputs (list r-base64url
@@ -15697,13 +16066,13 @@ estimation problem.")
 (define-public r-quickjsr
   (package
     (name "r-quickjsr")
-    (version "1.0.6")
+    (version "1.0.7")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "QuickJSR" version))
               (sha256
                (base32
-                "1n09jivw1qvsniyap0ki5ablvkwgggh981hcs7k5wx3lp3qxxlnk"))))
+                "14wq7qymzrdbg3mhm4gk3vx1dr4yx8di8i2b10as4knnzr1w4q9i"))))
     (properties `((upstream-name . "QuickJSR")))
     (build-system r-build-system)
     (propagated-inputs (list r-jsonlite r-r6 r-rcpp))
@@ -15964,14 +16333,14 @@ the differences were not significantly different.")
 (define-public r-emmeans
   (package
     (name "r-emmeans")
-    (version "1.8.8")
+    (version "1.8.9")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "emmeans" version))
        (sha256
         (base32
-         "1v5svzcvkssf3ch10cbi0pdw2xkgdhn8i1d1cqjawwgzmq61c62j"))))
+         "1ipzs88inyif52rbifqwrfv8vwxw8fwq2hb489vgws8xznhz034a"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-estimability r-mvtnorm r-numderiv))
@@ -16233,14 +16602,14 @@ ROPE percentage and pd).")
 (define-public r-performance
   (package
     (name "r-performance")
-    (version "0.10.5")
+    (version "0.10.8")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "performance" version))
        (sha256
         (base32
-         "1bwcdz2iah6ya1p9ykbj5ybvzwlq9spv6mq3fn68cckymg0hs76r"))))
+         "0zvj0bzbqcy35jcg1s6b1wqbz7rbajzvjm74aks4j6iq4grh4d2j"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-bayestestr r-datawizard r-insight))
@@ -16259,14 +16628,14 @@ effects models and Bayesian models.")
 (define-public r-ggeffects
   (package
     (name "r-ggeffects")
-    (version "1.3.1")
+    (version "1.3.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ggeffects" version))
        (sha256
         (base32
-         "0cw9j08qqck1gbfqsfyl3nb4rgi5cwsydxazqw8ppfnjqzw3nwmp"))))
+         "1wp9q2zqygxg2ibmrwdh614sdxqhj80rx0ixbz8kxld99b37ixl7"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-insight))
@@ -18876,13 +19245,13 @@ handling.")
 (define-public r-gridpattern
   (package
     (name "r-gridpattern")
-    (version "1.1.0")
+    (version "1.1.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "gridpattern" version))
        (sha256
-        (base32 "19g8mnc5y68w9pybckmcvr56qkwbs5z9z6zhj0bxmlprwanq4f8x"))))
+        (base32 "1v7xfgbnrr4v3arr7nm0663aywn47xb89sd0rn9s9dcz7r50aa2i"))))
     (properties `((upstream-name . "gridpattern")))
     (build-system r-build-system)
     (propagated-inputs
@@ -18954,14 +19323,14 @@ PostScript pictures in R plots.")
 (define-public r-grimport2
   (package
     (name "r-grimport2")
-    (version "0.3-0")
+    (version "0.3-1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "grImport2" version))
        (sha256
         (base32
-         "04k71x2wm1wsgv5fnk8xip2q5brl9cnjp3fv2rs0kdq9jkhs6yhz"))))
+         "1lj58z6yc2p6ns27fkgh11ac90bcihi65hf62gxpsylcn5dilsi1"))))
     (properties `((upstream-name . "grImport2")))
     (build-system r-build-system)
     (propagated-inputs
@@ -19780,14 +20149,14 @@ to throw errors if they aren't in the right form.")
 (define-public r-dotcall64
   (package
     (name "r-dotcall64")
-    (version "1.0-2")
+    (version "1.1-0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "dotCall64" version))
        (sha256
         (base32
-         "1b546z9r26q4xpr17gy2wzfych52q17sxvzydpqfp9dyxf575iz0"))))
+         "1ibh2f2vcv30k1c919diw6qdmhxmvkl83k3396vy3xigbcny711l"))))
     (properties `((upstream-name . "dotCall64")))
     (build-system r-build-system)
     (native-inputs (list gfortran))
@@ -19804,18 +20173,18 @@ This makes it a convenient and fast interface to C/C++ and Fortran code.")
 (define-public r-spam
   (package
     (name "r-spam")
-    (version "2.9-1")
+    (version "2.10-0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "spam" version))
        (sha256
-        (base32 "1nvx965vxzs697k9m2l40a15bykflksn9bwa4py1p2wqg6922bn3"))))
+        (base32 "0ydc513jg7phzdqg8jp7210ayrrmxq91jafqzx8z1v0172i8d73i"))))
     (build-system r-build-system)
     (propagated-inputs
-     (list r-dotcall64))
+     (list r-dotcall64 r-rcpp))
     (native-inputs
-     (list gfortran r-knitr))
+     (list gfortran r-knitr r-r-rsp))
     (home-page "https://www.math.uzh.ch/pages/spam/")
     (synopsis "Sparse matrix algebra")
     (description
@@ -22234,14 +22603,14 @@ tessellation.")
 (define-public r-wk
   (package
     (name "r-wk")
-    (version "0.8.0")
+    (version "0.9.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "wk" version))
        (sha256
         (base32
-         "1300x3rfb4fk11mrxzs0vy6aj4nbsvd7zisvdxxhrdibmz38l1xa"))))
+         "1nmrgdp3swl34kr51hypm3azf8yhcalg5nngp70l56afsbaskyqh"))))
     (properties `((upstream-name . "wk")))
     (build-system r-build-system)
     (home-page "https://paleolimbot.github.io/wk/")
@@ -22543,13 +22912,13 @@ either PDF/EPS files.")
 (define-public r-polspline
   (package
     (name "r-polspline")
-    (version "1.1.23")
+    (version "1.1.24")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "polspline" version))
        (sha256
-        (base32 "1qa9j7s09yzi65fav27zxc1w1wxwsmgjz8a8ghy7hhi5f3gvsqw3"))))
+        (base32 "0mal78f79jl6cj02xabv9vqf88m4iiadmgiv3qliv117cxkc6hb6"))))
     (build-system r-build-system)
     (native-inputs (list gfortran))
     (home-page "https://cran.r-project.org/web/packages/polspline/")
@@ -22810,13 +23179,13 @@ SELECT or UPDATE queries to an end-point.")
 (define-public r-bookdown
   (package
     (name "r-bookdown")
-    (version "0.35")
+    (version "0.36")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "bookdown" version))
               (sha256
                (base32
-                "1fzzppwp2ri4jhl1j2122rhiniay34cccvxr559bypv5b38yjywd"))
+                "0c4pj5sg4cnz2b2kpxgr0wk1n1pf7wkn1npm76aghy4yxj29cj4y"))
               ;; TODO: there is one more file to replace:
               ;; inst/resources/gitbook/js/app.min.js
               (snippet
@@ -22932,13 +23301,13 @@ that accept short and long options.")
 (define-public r-osqp
   (package
     (name "r-osqp")
-    (version "0.6.3.1")
+    (version "0.6.3.2")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "osqp" version))
               (sha256
                (base32
-                "178vvv0yajjy02ww4brrjb4197dp7c0n8zmk1zwh44h9msnnacj3"))))
+                "0i1jh3fr8d45b7inq9s6iyqszhh18hps8jpzkm0hzgj2k8r3nm0q"))))
     (properties `((upstream-name . "osqp")))
     (build-system r-build-system)
     (propagated-inputs (list r-matrix r-r6 r-rcpp))
@@ -23023,14 +23392,14 @@ handle missing genotypes at some SNPs.")
 (define-public r-sampling
   (package
     (name "r-sampling")
-    (version "2.9")
+    (version "2.10")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "sampling" version))
        (sha256
         (base32
-         "11xis4vzn2ga8ml9xrgfgqzccvwbnabq35aidzdvpnvciybsanvz"))))
+         "0x976wblv663aidqmcif1rjv72nbxf4nzms901lmryxbq1p9gv7x"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-lpsolve r-mass))
@@ -23080,29 +23449,24 @@ the corresponding outputs (tables and graphs).")
     (properties `((upstream-name . "rJava")))
     (build-system r-build-system)
     (arguments
-     `(#:modules ((guix build utils)
-                  (guix build r-build-system)
-                  (ice-9 match))
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'set-JAVA_HOME
-           (lambda* (#:key inputs #:allow-other-keys)
-             (let ((jdk (assoc-ref inputs "jdk")))
-               (setenv "JAVA_HOME" jdk)
-               (setenv "JAVA" (which "java"))
-               (setenv "JAR" (which "jar"))
-               (setenv "JAVAC" (which "javac"))
-               (setenv "JAVAH" (which "javah"))
-               (setenv "JAVA_CPPFLAGS"
-                       (string-append "-I" jdk "/include "
-                                      "-I" jdk "/include/linux"))
-               (match (find-files (string-append jdk "/jre/lib/") "libjvm.so")
-                 ((lib) (setenv "JAVA_LIBS" lib))
-                 (_ (error "Could not find libjvm.so"))))
-             #t)))))
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'set-JAVA_HOME
+            (lambda* (#:key inputs #:allow-other-keys)
+              (let ((jdk (assoc-ref inputs "jdk")))
+                (setenv "JAVA_HOME" jdk)
+                (setenv "JAVA" (which "java"))
+                (setenv "JAR" (which "jar"))
+                (setenv "JAVAC" (which "javac"))
+                (setenv "JAVAH" (which "javah"))
+                (setenv "JAVA_CPPFLAGS"
+                        (string-append "-I" jdk "/include "
+                                       "-I" jdk "/include/linux"))
+                (setenv "JAVA_LIBS" (search-input-file inputs "/lib/libjvm.so"))))))))
     (inputs
      `(("icu4c" ,icu4c)
-       ("jdk" ,icedtea-8 "jdk")
+       ("jdk" ,openjdk11 "jdk")
        ("zlib" ,zlib)))
     (home-page "https://www.rforge.net/rJava/")
     (synopsis "Low-Level R to Java interface")
@@ -24811,14 +25175,14 @@ from SuiteSparse.")
 (define-public r-sctransform
   (package
     (name "r-sctransform")
-    (version "0.4.0")
+    (version "0.4.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "sctransform" version))
        (sha256
         (base32
-         "1cxlqscjn33rszigk7bxjj2hdsr8rxalq94fg86qwmx9jv0i1vws"))))
+         "0wgimf7qqgnnmyspn2rpb4a8hl570fv0fwh0r0r4qgjlpvwffssz"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-dplyr
@@ -25984,14 +26348,15 @@ function and interfaces to external frameworks.")
 (define-public r-covr
   (package
     (name "r-covr")
-    (version "3.6.2")
+    (version "3.6.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "covr" version))
        (sha256
-        (base32 "0ns8xbq1l21mg8p2aiqv5h306a3vpn64j6jrgzbv8iv1a7kqrrmc"))
+        (base32 "17m2zzgfghr7gzcdgim21vsl12nd4714867dcp9xfb6ili31ikn0"))
        (modules '((guix build utils)))
+       ;; TODO: still need to replace highlight.js/highlight.pack.js
        (snippet
         '(with-directory-excursion "inst/www/shared"
            (for-each delete-file
@@ -26081,14 +26446,14 @@ both R code and compiled C/C++/FORTRAN code.")
 (define-public r-systemfonts
   (package
     (name "r-systemfonts")
-    (version "1.0.4")
+    (version "1.0.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "systemfonts" version))
        (sha256
         (base32
-         "1h44bal845jp7ya8i7ff1kz1n3wklkb00jk6hb9lgwa2p5snqxpg"))))
+         "08sqw5izpwhawcjkcyscvslz914skwfi0s68rdwrqwwkh8fzn3w4"))))
     (properties `((upstream-name . "systemfonts")))
     (build-system r-build-system)
     (propagated-inputs
@@ -26136,14 +26501,14 @@ emphasize hidden group structures in networks or focus on specific nodes.")
 (define-public r-terra
   (package
     (name "r-terra")
-    (version "1.7-46")
+    (version "1.7-55")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "terra" version))
        (sha256
         (base32
-         "0jpni25g9rhsqh71pgr2d3221r9xacsw3kz5qqnifj0jz5g3wyh1"))))
+         "1v1if9ypmra02ngg4r8qg1hldmxan8lyyhgq3j969glihpyvs03h"))))
     (properties `((upstream-name . "terra")))
     (build-system r-build-system)
     (inputs
@@ -26455,13 +26820,13 @@ to ODEs by numerical differencing.")
 (define-public r-pmcmrplus
   (package
     (name "r-pmcmrplus")
-    (version "1.9.7")
+    (version "1.9.8")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "PMCMRplus" version))
        (sha256
-        (base32 "06i5vsf8hpzv0c8v156072xbqpxk1wf2iami7mnsjfp9xjjjzbhx"))))
+        (base32 "1wqx5nikhpjsqnn7lgb2zy949sxmq7n3phlaix70as0zky534scg"))))
     (properties `((upstream-name . "PMCMRplus")))
     (build-system r-build-system)
     (inputs (list gmp))
@@ -26872,14 +27237,14 @@ cell free DNA} (cfDNA).")
 (define-public r-rintrojs
   (package
     (name "r-rintrojs")
-    (version "0.3.2")
+    (version "0.3.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rintrojs" version))
        (sha256
         (base32
-         "19lpq421hrs1wc9bnimbwxx35p8bbzil3x1h9l28gjayn4djmjsh"))
+         "1fy5lz9d9njs4yrnwrrn0n1fn0chccgi1gzn4qz4g6adr3v35rgw"))
        (snippet
         '(delete-file "inst/javascript/introjs/intro.min.js"))))
     (properties `((upstream-name . "rintrojs")))
@@ -27994,14 +28359,14 @@ transcription, ...")
 (define-public r-seewave
   (package
     (name "r-seewave")
-    (version "2.2.2")
+    (version "2.2.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "seewave" version))
        (sha256
         (base32
-         "12r09cirqzpg0lki304kfrdvxhdjpvsficba8inmnr4qzpfw7s5a"))))
+         "13c48sn453yp4j0ap8slnnr2gfhlxasz926p2pazkrg817w7m28z"))))
     (properties `((upstream-name . "seewave")))
     (build-system r-build-system)
     (inputs
@@ -28897,14 +29262,14 @@ API; see the package vignette for details.")
 (define-public r-actuar
   (package
     (name "r-actuar")
-    (version "3.3-2")
+    (version "3.3-3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "actuar" version))
        (sha256
         (base32
-         "0ys7kqqbx9g2mhsn243z9vj7qkdd69d3jy1vin9v8bknwimgdxvb"))))
+         "0ji5p19vqnr3i3vfrql2qndhzcjnr57jrh0szil6gaz6bm56afc4"))))
     (properties `((upstream-name . "actuar")))
     (build-system r-build-system)
     (propagated-inputs (list r-expint))
@@ -29125,14 +29490,14 @@ done.")
 (define-public r-adagio
   (package
     (name "r-adagio")
-    (version "0.8.5")
+    (version "0.9.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "adagio" version))
        (sha256
         (base32
-         "0icwr3cark67jyg9zzqwyv9q4fs0j0xgb5i7nkwv9s7y5dlldl0b"))))
+         "100mqwlzqml154d0hk7spi4sbwx9y3gh06vkls49kca2q1kf99qz"))))
     (properties `((upstream-name . "adagio")))
     (build-system r-build-system)
     (propagated-inputs
@@ -30306,14 +30671,14 @@ programming} (OOP) using R Reference Class.")
 (define-public r-proxyc
   (package
     (name "r-proxyc")
-    (version "0.3.3")
+    (version "0.3.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "proxyC" version))
        (sha256
         (base32
-         "00p3604ny6qax5rr1865c27hfp90v2vga0xcrp3bb81xcfadl99y"))))
+         "1skq5cxd0kh2pccfg4h9bis4wbqb6zm04q4iwfa6dqml6hyiv7gk"))))
     (properties `((upstream-name . "proxyC")))
     (build-system r-build-system)
     (native-inputs (list r-knitr))
@@ -31518,14 +31883,14 @@ techniques to average Bayesian predictive distributions.")
 (define-public r-rstan
   (package
     (name "r-rstan")
-    (version "2.26.23")
+    (version "2.32.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rstan" version))
        (sha256
         (base32
-         "08hdwrpxbxp2wdnfk2jj2xsdgl7q9nbalz5wgwmy0m878swxxzci"))))
+         "17alp92kj9mnlkzplk7zd83sv2zi2h7yc44fx5f7nz3dpwd9x7d2"))))
     (properties `((upstream-name . "rstan")))
     (build-system r-build-system)
     (arguments
@@ -32474,18 +32839,18 @@ estimation.")
 (define-public r-optimx
   (package
     (name "r-optimx")
-    (version "2023-8.13")
+    (version "2023-10.21")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "optimx" version))
        (sha256
         (base32
-         "00w8h450gs8vf0raghjg2818xzj4gz5jr3hwk9m9zc5k3rwmcf8n"))))
+         "1da4daxgk4kbq1n2mn72482c3j96wba0xf4mzffgasn20ib2swqd"))))
     (properties `((upstream-name . "optimx")))
     (build-system r-build-system)
     (propagated-inputs (list r-nloptr r-numderiv r-pracma))
-    (native-inputs (list r-knitr))
+    (native-inputs (list r-r-rsp))
     (home-page "https://cran.r-project.org/web/packages/optimx/")
     (synopsis "Expanded replacement and extension of the optim function")
     (description
@@ -32579,14 +32944,14 @@ including means, variances, intervals, and highest density regions.")
 (define-public r-posterior
   (package
     (name "r-posterior")
-    (version "1.4.1")
+    (version "1.5.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "posterior" version))
        (sha256
         (base32
-         "1lsqpczf8ll8m1a99kwmxdjm8wpavlqw88qha82s3438ipx5729b"))))
+         "1pp233ddrs116w1rmp3khhmibjf6l021b1x79k6z48g3r9zk042a"))))
     (properties `((upstream-name . "posterior")))
     (build-system r-build-system)
     (propagated-inputs
@@ -33356,13 +33721,13 @@ diagonals.  This package allows you to compute the tensor product of arrays.")
 (define-public r-spatstat-explore
   (package
     (name "r-spatstat-explore")
-    (version "3.2-3")
+    (version "3.2-5")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "spatstat.explore" version))
               (sha256
                (base32
-                "18zhpspq07rcnpmnkc82hzjvjp39fsb06g73gin4x5bwzbi22kgr"))))
+                "053wl87whmkkqp058lwzlwv0wydddizsni9m94f6kxgl5ahia1sc"))))
     (properties `((upstream-name . "spatstat.explore")))
     (build-system r-build-system)
     (propagated-inputs
@@ -33396,13 +33761,13 @@ Kolmogorov-Smirnov, ANOVA) are also supported.")
 (define-public r-spatstat-model
   (package
     (name "r-spatstat-model")
-    (version "3.2-6")
+    (version "3.2-8")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "spatstat.model" version))
               (sha256
                (base32
-                "1lvs6ns4hna7w6b0nvzsx2rw699ampdm8jmxdzlfpk4hla2lf7wq"))))
+                "1x03fy921rq8dyr6jkpwnx7pf7fc5593mvnl8r1gz3sypnmp6p4d"))))
     (properties `((upstream-name . "spatstat.model")))
     (build-system r-build-system)
     (propagated-inputs
@@ -33440,14 +33805,14 @@ Kolmogorov-Smirnov, ANOVA) are also supported.")
 (define-public r-spatstat-utils
   (package
     (name "r-spatstat-utils")
-    (version "3.0-3")
+    (version "3.0-4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "spatstat.utils" version))
        (sha256
         (base32
-         "0j6w9b479qqah2vzbq31v1xa6rjql8a85hdlahqhwqd9j1scd03s"))))
+         "1i1w1ys29s22jfjvliqnbw3zi6zar8bxxz3r8za182p2w0wqwhax"))))
     (properties
      `((upstream-name . "spatstat.utils")))
     (build-system r-build-system)
@@ -33461,14 +33826,14 @@ which may also be useful for other purposes.")
 (define-public r-spatstat-sparse
   (package
     (name "r-spatstat-sparse")
-    (version "3.0-2")
+    (version "3.0-3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "spatstat.sparse" version))
        (sha256
         (base32
-         "1gnlgz11dv66b41kdyyzm8nhkhhi4yajlcr2g52h2lfxlryb5g2h"))))
+         "0scdk3ns4nl1v1avbggnsinfpvl4i8391qy3x1iwxvkimr14xg3b"))))
     (properties
      `((upstream-name . "spatstat.sparse")))
     (build-system r-build-system)
@@ -33485,14 +33850,14 @@ matrix calculations that are common in statistics, such as quadratic forms.")
 (define-public r-spatstat-data
   (package
     (name "r-spatstat-data")
-    (version "3.0-1")
+    (version "3.0-3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "spatstat.data" version))
        (sha256
         (base32
-         "002kvli3n9cppaar7q062dm4fapdgkyf1daq5zscxsanwcflpswf"))))
+         "0fxd266rza07s73fj1n4rd4i7x1bv1ll36iikxzjhnlh3vjc0hkn"))))
     (properties `((upstream-name . "spatstat.data")))
     (build-system r-build-system)
     (propagated-inputs
@@ -33507,14 +33872,14 @@ package.")
 (define-public r-spatstat-geom
   (package
     (name "r-spatstat-geom")
-    (version "3.2-5")
+    (version "3.2-7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "spatstat.geom" version))
        (sha256
         (base32
-         "13xlp88yfp61kl0c3vaqs7lrckkc4ixpp0mpf89h5ggmjyf57nxx"))))
+         "13k85918zd2n64mxjwlgzd986zvs3is8vg06k9i195yymfrik65y"))))
     (properties `((upstream-name . "spatstat.geom")))
     (build-system r-build-system)
     (propagated-inputs
@@ -33563,14 +33928,14 @@ user-level code from spatstat, except for the code for linear networks.")
 (define-public r-spatstat-linnet
   (package
     (name "r-spatstat-linnet")
-    (version "3.1-1")
+    (version "3.1-3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "spatstat.linnet" version))
        (sha256
         (base32
-         "0adha3bi1a250p8wm7agqdmwzznd6blsfg0km11n25ad8y2r5q0c"))))
+         "1ybjl5ccp9r5ilbihwzk93zcm46pbpldn3nfbfpdw458xh894r3q"))))
     (properties
      `((upstream-name . "spatstat.linnet")))
     (build-system r-build-system)
@@ -33593,13 +33958,13 @@ for spatial data on a linear network.")
 (define-public r-spatstat-random
   (package
     (name "r-spatstat-random")
-    (version "3.1-6")
+    (version "3.2-1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "spatstat.random" version))
        (sha256
-        (base32 "0vrx0mxzcd6yr6rzn9jk2wj5d2l7yn0ij1n58yb3hw2g7nasad06"))))
+        (base32 "1p1imyqrpvdhsc24pq3mvdg9n29h6q8zlawdyahqiymynyp22m4j"))))
     (properties `((upstream-name . "spatstat.random")))
     (build-system r-build-system)
     (propagated-inputs (list r-spatstat-data r-spatstat-geom r-spatstat-utils))
@@ -33621,14 +33986,14 @@ sampler).")
 (define-public r-spatstat
   (package
     (name "r-spatstat")
-    (version "3.0-6")
+    (version "3.0-7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "spatstat" version))
        (sha256
         (base32
-         "0vlpa5a1b5s27lgxkq65iixrsbbj0x4zahg0sfsak0ackj8ks577"))))
+         "1h6fnri3ma5kgzkwv4lr2i2jvsx8sg4am3rgzb29h7l89x59yxrk"))))
     (properties `((upstream-name . "spatstat")))
     (build-system r-build-system)
     (propagated-inputs
@@ -33750,18 +34115,18 @@ aggregation for comparing different implementations in order to provide a
 (define-public r-rfast
   (package
     (name "r-rfast")
-    (version "2.0.8")
+    (version "2.0.9")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "Rfast" version))
        (sha256
         (base32
-         "1c64j8hg6id4ri3m32aa1r0qyn09kl3dvl865dzf43qdb3qcichv"))))
+         "12jl5kqjn571zcqh4n351d7nx86b3jh46ds8krqz92f0z6fjmkzz"))))
     (properties `((upstream-name . "Rfast")))
     (build-system r-build-system)
     (propagated-inputs
-     (list r-rcpp r-rcpparmadillo r-rcppziggurat))
+     (list r-rcpp r-rcpparmadillo r-rcppparallel r-rcppziggurat))
     (home-page "https://github.com/RfastOfficial/Rfast")
     (synopsis "Collection of efficient and fast R functions")
     (description
@@ -34690,14 +35055,14 @@ different palettes and includes both diverging and sequential types.")
 (define-public r-slider
   (package
     (name "r-slider")
-    (version "0.3.0")
+    (version "0.3.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "slider" version))
        (sha256
         (base32
-         "18gw0bxpbb00qcafmyv2avyj83s710hrj10x998ch9qbbyx1fsmw"))))
+         "1c19lk0ddh5qh0jzx7178l314zyygmlpmbvn7670bcmdbxwjc2i0"))))
     (properties `((upstream-name . "slider")))
     (build-system r-build-system)
     (propagated-inputs
@@ -34938,14 +35303,14 @@ results.")
 (define-public r-tidyposterior
   (package
     (name "r-tidyposterior")
-    (version "1.0.0")
+    (version "1.0.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tidyposterior" version))
        (sha256
         (base32
-         "19cyyhh417i5xcchb8kq3iycaf4y7aznr7y9r004h2k2vk3svc86"))))
+         "1yi0pihglp683dmfg0bn9lnb0qsl2xprj3al65v642rcfzrr7h4h"))))
     (properties `((upstream-name . "tidyposterior")))
     (build-system r-build-system)
     (propagated-inputs
@@ -35636,25 +36001,28 @@ data to rasters.  It speeds up plotting of data with millions of points.")
 (define-public r-seuratobject
   (package
     (name "r-seuratobject")
-    (version "4.1.4")
+    (version "5.0.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "SeuratObject" version))
        (sha256
         (base32
-         "1vqhad76hnr0l47klg56fniah4cvpzbkkl0j1cn9cp3rv6d69rvl"))))
+         "0wlr53cswq7a7zzzzkif82iy4xrrd2afz093b265kjlq4qxmzn9d"))))
     (properties `((upstream-name . "SeuratObject")))
     (build-system r-build-system)
     (propagated-inputs
      (list r-future
            r-future-apply
+           r-generics
+           r-lifecycle
            r-matrix
            r-progressr
            r-rcpp
            r-rcppeigen
            r-rlang
-           r-sp))
+           r-sp
+           r-spam))
     (home-page "https://satijalab.org/seurat")
     (synopsis "Data structures for single cell data")
     (description
@@ -36795,14 +37163,14 @@ clusterings as resolution increases.")
 (define-public r-textshaping
   (package
     (name "r-textshaping")
-    (version "0.3.6")
+    (version "0.3.7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "textshaping" version))
        (sha256
         (base32
-         "1niaj1dh09rqrg9hrh98ddnc0f2nkyq9iizv24lcwm9gjs3w1ql0"))))
+         "0hpcjz66ykji89g2lzpp6hfkz10388py8vn2ss08n4xl3yz4v4ps"))))
     (properties `((upstream-name . "textshaping")))
     (build-system r-build-system)
     (inputs
@@ -36823,14 +37191,14 @@ the font tool-set provided by the @code{systemfonts} package.")
 (define-public r-ragg
   (package
     (name "r-ragg")
-    (version "1.2.5")
+    (version "1.2.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ragg" version))
        (sha256
         (base32
-         "1yd89p4f2b7r2n1kl6lybbgd04kqvlf14zgmp7pxw770w1slsvwk"))))
+         "1izpw02b8kq6pm37kvxp9pbd9srvfp5bzfjg27j9hbmm794xq50h"))))
     (properties `((upstream-name . "ragg")))
     (build-system r-build-system)
     (inputs
@@ -37013,14 +37381,14 @@ visualized at any level of the experiment's design.")
 (define-public r-qdapregex
   (package
     (name "r-qdapregex")
-    (version "0.7.5")
+    (version "0.7.8")
     (source
       (origin
         (method url-fetch)
         (uri (cran-uri "qdapRegex" version))
         (sha256
           (base32
-            "1hdilycwrvi0q6cx7k8vg87bamm2xsafjkya5x4smxysm5k1r4qb"))))
+            "1pf1cz03i6sn83d1aaj4cv4jfavs6k81nn5sy7b0aw4i1hpkyiwz"))))
     (properties `((upstream-name . "qdapRegex")))
     (build-system r-build-system)
     (propagated-inputs (list r-stringi))
@@ -37292,13 +37660,13 @@ user streams, and to parse the output into data frames.")
 (define-public r-strex
   (package
     (name "r-strex")
-    (version "1.6.0")
+    (version "1.6.1")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "strex" version))
               (sha256
                (base32
-                "1fxg07n8cjvvgpbzqhyx5ma5bv6vax1yw0rbfdqfzr79v6k5x3n7"))))
+                "1vz5zrvf052bg2y48yvkci4hciknvyw5gpbvnklgyny5lzlqvyiq"))))
     (properties `((upstream-name . "strex")))
     (build-system r-build-system)
     (propagated-inputs
@@ -37626,18 +37994,18 @@ supply the workflow to create thematic maps.  This package also facilitates
 (define-public r-rworldmap
   (package
     (name "r-rworldmap")
-    (version "1.3-6")
+    (version "1.3-8")
     (source
       (origin
         (method url-fetch)
         (uri (cran-uri "rworldmap" version))
         (sha256
           (base32
-            "1q1h0n9qr0m5pdx10swrh9ddsvdj8kv5nqngrf3lnx9rg9iwivjk"))))
+            "007avjl7jhllybp82illrn8v38a85j6xbzk5pvykfx8ayx4wc3m6"))))
     (properties `((upstream-name . "rworldmap")))
     (build-system r-build-system)
     (propagated-inputs
-      (list r-fields r-maptools r-sp))
+      (list r-fields r-raster r-sp r-terra))
     (home-page
       "https://github.com/AndySouth/rworldmap/")
     (synopsis "Mapping Global Data")
@@ -37648,14 +38016,14 @@ supply the workflow to create thematic maps.  This package also facilitates
 (define-public r-rtweet
   (package
     (name "r-rtweet")
-    (version "1.1.0")
+    (version "1.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rtweet" version))
        (sha256
         (base32
-         "0dq6ckf2mp6wm6y8xzjby21s356760fmck1m8nsnv5gz8lhy6dhg"))))
+         "18ynravc5vz7ywm1n7ww48gx06dndcishl6lq8nqajxsjwiphq3r"))))
     (properties `((upstream-name . "rtweet")))
     (build-system r-build-system)
     (propagated-inputs
@@ -38149,17 +38517,18 @@ utility operations.")
 (define-public r-rsq
   (package
     (name "r-rsq")
-    (version "2.5")
+    (version "2.6")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "rsq" version))
               (sha256
                (base32
-                "1r628srxhhf7b51lnj4qrzgbqajkm0ls47a9rzjkvmfq4ax5i73f"))))
+                "01b9rl2ng1sq0ibpfsf50agkwh01pfpw354vvgdjd0lzh9dxmsgp"))))
     (properties `((upstream-name . "rsq")))
     (build-system r-build-system)
     (propagated-inputs
-     (list r-deriv
+     (list r-deming
+           r-deriv
            r-lme4
            r-mass
            r-matrix
@@ -38836,14 +39205,14 @@ fully reproducible.")
 (define-public r-paws-common
   (package
     (name "r-paws-common")
-    (version "0.6.1")
+    (version "0.6.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "paws.common" version))
        (sha256
         (base32
-         "0haw72885xmzl6rmb8vlkqwnxh7iq5cr89d852j2vk56sxjxv1y5"))))
+         "1jgls5fks9s8m616qs6b7hvv0wf7nhzajyds15hnlasqwg387h3d"))))
     (properties `((upstream-name . "paws.common")))
     (build-system r-build-system)
     (propagated-inputs
diff --git a/gnu/packages/crates-gtk.scm b/gnu/packages/crates-gtk.scm
index 3c6f833145..266a513dc2 100644
--- a/gnu/packages/crates-gtk.scm
+++ b/gnu/packages/crates-gtk.scm
@@ -3,6 +3,7 @@
 ;;; Copyright © 2020, 2021 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;; Copyright © 2022 Petr Hodina <phodina@protonmail.com>
 ;;; Copyright © 2022 Aleksandr Vityazev <avityazev@posteo.org>
+;;; Copyright © 2023 Steve George <steve@futurile.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -29,6 +30,7 @@
   #:use-module (gnu packages crates-graphics)
   #:use-module (gnu packages glib)
   #:use-module (gnu packages gnome)
+  #:use-module (gnu packages gstreamer)
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages webkit))
@@ -1709,6 +1711,255 @@
        (("rust-shell-words" ,rust-shell-words-0.1)
         ("rust-tempfile" ,rust-tempfile-3))))))
 
+(define-public rust-gstreamer-0.18
+  (package
+    (name "rust-gstreamer")
+    (version "0.18.8")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "gstreamer" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0mjlnw9917j3wwij8225bjp54k7408lxqjjnh6r6wksyryx66qyn"))))
+    (build-system cargo-build-system)
+    (arguments
+     (list #:tests? #f  ; https://github.com/gtk-rs/gtk3-rs/issues/768
+           #:cargo-inputs `(("rust-bitflags" ,rust-bitflags-1)
+                            ("rust-cfg-if" ,rust-cfg-if-1)
+                            ("rust-futures-channel" ,rust-futures-channel-0.3)
+                            ("rust-futures-core" ,rust-futures-core-0.3)
+                            ("rust-futures-util" ,rust-futures-util-0.3)
+                            ("rust-glib" ,rust-glib-0.15)
+                            ("rust-gstreamer-sys" ,rust-gstreamer-sys-0.18)
+                            ("rust-libc" ,rust-libc-0.2)
+                            ("rust-muldiv" ,rust-muldiv-1)
+                            ("rust-num-integer" ,rust-num-integer-0.1)
+                            ("rust-num-rational" ,rust-num-rational-0.4)
+                            ("rust-once-cell" ,rust-once-cell-1)
+                            ("rust-option-operations" ,rust-option-operations-0.4)
+                            ("rust-paste" ,rust-paste-1)
+                            ("rust-pretty-hex" ,rust-pretty-hex-0.3)
+                            ("rust-serde" ,rust-serde-1)
+                            ("rust-serde-bytes" ,rust-serde-bytes-0.11)
+                            ("rust-thiserror" ,rust-thiserror-1))
+           #:cargo-development-inputs
+            `(("rust-futures-executor" ,rust-futures-executor-0.3)
+              ("rust-gir-format-check" ,rust-gir-format-check-0.1)
+              ("rust-ron" ,rust-ron-0.7)
+              ("rust-serde-json" ,rust-serde-json-1))))
+    (native-inputs (list pkg-config))
+    (inputs (list glib gstreamer))
+    (home-page "https://gstreamer.freedesktop.org")
+    (synopsis "Rust bindings for GStreamer")
+    (description "Rust bindings for GStreamer.")
+    (license (list license:expat license:asl2.0))))
+
+(define-public rust-gstreamer-app-0.18
+  (package
+    (name "rust-gstreamer-app")
+    (version "0.18.7")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (crate-uri "gstreamer-app" version))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32 "115nykpdvfccyzvfi73qkhn061f6rdyhcaj9ajnw2ik5pimdyjk6"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:tests? #f  ; https://github.com/gtk-rs/gtk3-rs/issues/768
+       #:cargo-inputs (("rust-bitflags" ,rust-bitflags-1)
+                       ("rust-futures-core" ,rust-futures-core-0.3)
+                       ("rust-futures-sink" ,rust-futures-sink-0.3)
+                       ("rust-glib" ,rust-glib-0.15)
+                       ("rust-gstreamer" ,rust-gstreamer-0.18)
+                       ("rust-gstreamer-app-sys" ,rust-gstreamer-app-sys-0.18)
+                       ("rust-gstreamer-base" ,rust-gstreamer-base-0.18)
+                       ("rust-libc" ,rust-libc-0.2)
+                       ("rust-once-cell" ,rust-once-cell-1))
+       #:cargo-development-inputs (("rust-futures-executor" ,rust-futures-executor-0.3)
+                                   ("rust-futures-util" ,rust-futures-util-0.3)
+                                   ("rust-gir-format-check" ,rust-gir-format-check-0.1))))
+    (native-inputs (list pkg-config))
+    (inputs (list glib gstreamer gst-plugins-base))
+    (home-page "https://gstreamer.freedesktop.org")
+    (synopsis "Rust bindings for GStreamer App library")
+    (description "Rust bindings for the GStreamer App library.")
+    (license (list license:expat license:asl2.0))))
+
+(define-public rust-gstreamer-app-sys-0.18
+  (package
+    (name "rust-gstreamer-app-sys")
+    (version "0.18.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (crate-uri "gstreamer-app-sys" version))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32 "1fsgdb3b23s45xc7s06xw96x7avza0jpyj02x1fkw6vk3pr03d63"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs (("rust-glib-sys" ,rust-glib-sys-0.15)
+                       ("rust-gstreamer-base-sys" ,rust-gstreamer-base-sys-0.18)
+                       ("rust-gstreamer-sys" ,rust-gstreamer-sys-0.18)
+                       ("rust-libc" ,rust-libc-0.2)
+                       ("rust-system-deps" ,rust-system-deps-6))
+       #:cargo-development-inputs (("rust-shell-words" ,rust-shell-words-1)
+                                   ("rust-tempfile" ,rust-tempfile-3))))
+    (native-inputs (list pkg-config))
+    (inputs (list glib gstreamer gst-plugins-base))
+    (home-page "https://gstreamer.freedesktop.org")
+    (synopsis "FFI bindings to libgstapp-1.0")
+    (description "FFI bindings to libgstapp-1.0, part of Gstreamer.")
+    (license license:expat)))
+
+(define-public rust-gstreamer-audio-0.18
+  (package
+    (name "rust-gstreamer-audio")
+    (version "0.18.7")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (crate-uri "gstreamer-audio" version))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32 "0zl0bj03rz19qlrm50w7i5sagh0i0p5d8gr7ig1k6k5yd7k47sww"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:tests? #f  ; https://github.com/gtk-rs/gtk3-rs/issues/768
+       #:cargo-inputs (("rust-array-init" ,rust-array-init-2)
+                       ("rust-bitflags" ,rust-bitflags-1)
+                       ("rust-cfg-if" ,rust-cfg-if-1)
+                       ("rust-glib" ,rust-glib-0.15)
+                       ("rust-gstreamer" ,rust-gstreamer-0.18)
+                       ("rust-gstreamer-audio-sys" ,rust-gstreamer-audio-sys-0.18)
+                       ("rust-gstreamer-base" ,rust-gstreamer-base-0.18)
+                       ("rust-libc" ,rust-libc-0.2)
+                       ("rust-once-cell" ,rust-once-cell-1))
+       #:cargo-development-inputs (("rust-gir-format-check" ,rust-gir-format-check-0.1)
+                                   ("rust-itertools" ,rust-itertools-0.10))))
+    (native-inputs (list pkg-config))
+    (inputs (list glib gstreamer gst-plugins-base))
+    (home-page "https://gstreamer.freedesktop.org")
+    (synopsis "Rust bindings for the GStreamer Audio library")
+    (description "Rust bindings for the GStreamer Audio library.")
+    (license (list license:expat license:asl2.0))))
+
+(define-public rust-gstreamer-audio-sys-0.18
+  (package
+    (name "rust-gstreamer-audio-sys")
+    (version "0.18.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (crate-uri "gstreamer-audio-sys" version))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32 "0z3xryblh75xp08xyw3m6jfz9azarcvl06dd3psc0n65agxmhhm3"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-test-flags
+       (list "--release" "--"
+             "--skip=cross_validate_constants_with_c")
+       #:cargo-inputs (("rust-glib-sys" ,rust-glib-sys-0.15)
+                       ("rust-gobject-sys" ,rust-gobject-sys-0.15)
+                       ("rust-gstreamer-base-sys" ,rust-gstreamer-base-sys-0.18)
+                       ("rust-gstreamer-sys" ,rust-gstreamer-sys-0.18)
+                       ("rust-libc" ,rust-libc-0.2)
+                       ("rust-system-deps" ,rust-system-deps-6))
+       #:cargo-development-inputs (("rust-shell-words" ,rust-shell-words-1)
+                                   ("rust-tempfile" ,rust-tempfile-3))))
+    (native-inputs (list pkg-config))
+    (inputs (list glib gstreamer gst-plugins-base))
+    (home-page "https://gstreamer.freedesktop.org")
+    (synopsis "FFI bindings to libgstaudio-1.0")
+    (description "FFI bindings to libgstaudio, part of Gstreamer.")
+    (license license:expat)))
+
+(define-public rust-gstreamer-base-0.18
+  (package
+    (name "rust-gstreamer-base")
+    (version "0.18.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (crate-uri "gstreamer-base" version))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32 "0gw6sr75h01y3j6lpxhc7p1frvkba9a4imyyb2ppqh42cprkakr2"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:tests? #f  ; https://github.com/gtk-rs/gtk3-rs/issues/768
+       #:cargo-inputs (("rust-bitflags" ,rust-bitflags-1)
+                       ("rust-cfg-if" ,rust-cfg-if-1)
+                       ("rust-glib" ,rust-glib-0.15)
+                       ("rust-gstreamer" ,rust-gstreamer-0.18)
+                       ("rust-gstreamer-base-sys" ,rust-gstreamer-base-sys-0.18)
+                       ("rust-libc" ,rust-libc-0.2))
+       #:cargo-development-inputs (("rust-gir-format-check" ,rust-gir-format-check-0.1))))
+    (native-inputs (list pkg-config))
+    (inputs (list glib gstreamer))
+    (home-page "https://gstreamer.freedesktop.org")
+    (synopsis "Rust bindings for GStreamer Base library")
+    (description "Rust bindings for GStreamer Base library.")
+    (license (list license:expat license:asl2.0))))
+
+(define-public rust-gstreamer-base-sys-0.18
+  (package
+    (name "rust-gstreamer-base-sys")
+    (version "0.18.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (crate-uri "gstreamer-base-sys" version))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32 "13h79fcn3b9bkg7h8j0vxc1zryp92shbvvk6gkx723il7hy4k0x0"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs (("rust-glib-sys" ,rust-glib-sys-0.15)
+                       ("rust-gobject-sys" ,rust-gobject-sys-0.15)
+                       ("rust-gstreamer-sys" ,rust-gstreamer-sys-0.18)
+                       ("rust-libc" ,rust-libc-0.2)
+                       ("rust-system-deps" ,rust-system-deps-6))
+       #:cargo-development-inputs (("rust-shell-words" ,rust-shell-words-1)
+                                   ("rust-tempfile" ,rust-tempfile-3))))
+    (native-inputs (list pkg-config))
+    (inputs (list glib gstreamer))
+    (home-page "https://gstreamer.freedesktop.org")
+    (synopsis "FFI bindings to libgstbase-1.0")
+    (description "FFI bindings to libgstbase-1.0, part of GStreamer.")
+    (license license:expat)))
+
+(define-public rust-gstreamer-sys-0.18
+  (package
+    (name "rust-gstreamer-sys")
+    (version "0.18.0")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "gstreamer-sys" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1qikgp5m3xj41fbfyfl6ckb5i8dxadfvlvj5bf8girn2sdjpllg3"))))
+    (build-system cargo-build-system)
+    (arguments
+     (list #:cargo-inputs `(("rust-glib-sys" ,rust-glib-sys-0.15)
+                            ("rust-gobject-sys" ,rust-gobject-sys-0.15)
+                            ("rust-libc" ,rust-libc-0.2)
+                            ("rust-system-deps" ,rust-system-deps-6))
+           #:cargo-development-inputs `(("rust-shell-words" ,rust-shell-words-1)
+                                        ("rust-tempfile" ,rust-tempfile-3))))
+    (native-inputs (list pkg-config))
+    (inputs (list glib gstreamer))
+    (home-page "https://gstreamer.freedesktop.org")
+    (synopsis "FFI bindings to libgstreamer-1.0")
+    (description
+     "Foreign Function Interface (FFI) bindings to libgstreamer-1.0.")
+    (license license:expat)))
+
 (define-public rust-gtk-0.14
   (package
     (name "rust-gtk")
diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm
index 1fba8641a8..fc26147157 100644
--- a/gnu/packages/crates-io.scm
+++ b/gnu/packages/crates-io.scm
@@ -59,6 +59,7 @@
   #:use-module (guix utils)
   #:use-module (gnu packages)
   #:use-module (gnu packages admin)
+  #:use-module (gnu packages audio)
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages avahi)
   #:use-module (gnu packages bash)
@@ -81,6 +82,7 @@
   #:use-module (gnu packages linux)
   #:use-module (gnu packages llvm)
   #:use-module (gnu packages mail)
+  #:use-module (gnu packages mp3)
   #:use-module (gnu packages multiprecision)
   #:use-module (gnu packages nettle)
   #:use-module (gnu packages pcre)
@@ -2788,6 +2790,28 @@ using AES-NI for high performance.")
         ("rust-rand" ,rust-rand-0.3)
         ("rust-rustc-serialize" ,rust-rustc-serialize-0.3))))))
 
+(define-public rust-al-sys-0.6
+  (package
+    (name "rust-al-sys")
+    (version "0.6.1")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "al-sys" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "08whlcfrhn4gqi4nbglkdqv5ysdpnvnlsqg51q34q9hh9l7rp3gz"))))
+    (build-system cargo-build-system)
+    (arguments
+     (list #:cargo-inputs
+           `(("rust-cmake" ,rust-cmake-0.1)
+             ("rust-libloading" ,rust-libloading-0.5)
+             ("rust-rental" ,rust-rental-0.5))))
+    (home-page "https://github.com/jpernst/alto")
+    (synopsis "Raw bindings for OpenAL 1.1")
+    (description "Rust bindings for OpenAL, this crate contains FFI elements.")
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-alacritty-config-0.1
   (package
     (name "rust-alacritty-config")
@@ -3070,6 +3094,125 @@ be used with the stdlib.")
     (description "Mirror of Rust's allocator API.")
     (license (list license:expat license:asl2.0))))
 
+(define-public rust-alsa-0.7
+  (package
+    (name "rust-alsa")
+    (version "0.7.1")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "alsa" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0iwbdgb6lr81iji9sr4f91mys24pia5avnkgbkv8kxzhvkc2lmp2"))))
+    (build-system cargo-build-system)
+    (arguments
+     (list #:cargo-test-flags `(list "--release"
+                                     ;; Not the doc tests.
+                                     "--lib" "--bins" "--tests"
+                                     "--"
+                                     ;; These try to use the audio interface
+                                     "--skip=pcm::drop"
+                                     "--skip=pcm::info_from_default"
+                                     "--skip=pcm::playback_to_default"
+                                     "--skip=pcm::record_from_default"
+                                     "--skip=seq::print_seqs"
+                                     "--skip=seq::seq_loopback"
+                                     "--skip=seq::seq_portsubscribeiter"
+                                     "--skip=seq::seq_subscribe")
+           #:cargo-inputs `(("rust-alsa-sys" ,rust-alsa-sys-0.3)
+                            ("rust-bitflags" ,rust-bitflags-1)
+                            ("rust-libc" ,rust-libc-0.2)
+                            ("rust-nix" ,rust-nix-0.24))))
+    (native-inputs (list pkg-config alsa-lib))
+    (home-page "https://github.com/diwic/alsa-rs")
+    (synopsis "Thin and safe wrapper around ALSA")
+    (description
+     "A thin and safe wrapper around ALSA.  Provides APIs for
+many parts of ALSA including audio playback, audio recording, HCtl API, raw
+MIDI and MIDI sequencer.")
+    (license license:expat)))
+
+(define-public rust-alsa-0.6
+  (package
+    (inherit rust-alsa-0.7)
+    (name "rust-alsa")
+    (version "0.6.0")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "alsa" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0szx8finhqbffh08fp3bgh4ywz0b572vcdyh4hwyhrfgw8pza5ar"))))
+    (arguments
+     (list #:cargo-test-flags `(list "--release"
+                                     ;; Not the doc tests.
+                                     "--lib" "--bins" "--tests"
+                                     "--"
+                                     ;; These try to use the audio interface
+                                     "--skip=pcm::drop"
+                                     "--skip=pcm::info_from_default"
+                                     "--skip=pcm::playback_to_default"
+                                     "--skip=pcm::record_from_default"
+                                     "--skip=seq::print_seqs"
+                                     "--skip=seq::seq_loopback"
+                                     "--skip=seq::seq_portsubscribeiter"
+                                     "--skip=seq::seq_subscribe")
+           #:cargo-inputs `(("rust-alsa-sys" ,rust-alsa-sys-0.3)
+                            ("rust-bitflags" ,rust-bitflags-1)
+                            ("rust-libc" ,rust-libc-0.2)
+                            ("rust-nix" ,rust-nix-0.23))))))
+
+(define-public rust-alsa-sys-0.3
+  (package
+    (name "rust-alsa-sys")
+    (version "0.3.1")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "alsa-sys" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "09qmmnpmlcj23zcgx2xsi4phcgm5i02g9xaf801y7i067mkfx3yv"))))
+    (build-system cargo-build-system)
+    (arguments
+     (list #:tests? #f  ; doc tests fail
+           #:cargo-inputs `(("rust-libc" ,rust-libc-0.2)
+                            ("rust-pkg-config" ,rust-pkg-config-0.3))))
+    (native-inputs (list pkg-config alsa-lib))
+    (home-page "https://github.com/diwic/alsa-sys")
+    (synopsis "FFI bindings for the ALSA sound API")
+    (description
+     "FFI bindings for the ALSA sound API.  This package contains
+the code to interact with the underlying operating system ALSA interface.")
+    (license license:expat)))
+
+(define-public rust-alto-3
+  (package
+    (name "rust-alto")
+    (version "3.0.4")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "alto" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1rgsdmh346s3rwhzqacjc6nz7jap4dd72c1gfmkaq9sgzh9fhnyp"))))
+    (build-system cargo-build-system)
+    (arguments
+     (list #:tests? #f  ; Not all files included.
+           #:cargo-inputs
+           `(("rust-al-sys" ,rust-al-sys-0.6)
+             ("rust-lazy-static" ,rust-lazy-static-0.2)
+             ("rust-parking-lot" ,rust-parking-lot-0.4))))
+    (home-page "https://github.com/jpernst/alto")
+    (synopsis
+     "Idiomatic Rust bindings for OpenAL 1.1 and extensions (including EFX)")
+    (description
+     "Rust bindings for OpenAL 1.1 and extensions (including EFX).")
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-always-assert-0.1
   (package
     (name "rust-always-assert")
@@ -3946,6 +4089,26 @@ initializing large arrays (greater than 32 elements), or arrays of types which
 do not implement the copy or default traits.")
     (license (list license:expat license:asl2.0))))
 
+(define-public rust-array-init-2
+  (package
+    (name "rust-array-init")
+    (version "2.1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (crate-uri "array-init" version))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32 "1z0bh6grrkxlbknq3xyipp42rasngi806y92fiddyb2n99lvfqix"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/Manishearth/array-init/")
+    (synopsis "Safe wrapper for initializing fixed-size arrays")
+    (description
+     "A crate that removes the need to fill an array before running
+initialisers.  Provides an init closure that's called for each element of the
+array.")
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-array-macro-1
   (package
     (name "rust-array-macro")
@@ -4316,6 +4479,33 @@ the abi_stable and structural crates.")
         ("rust-serde-derive" ,rust-serde-derive-1)
         ("rust-syn" ,rust-syn-1))))))
 
+(define-public rust-asio-sys-0.2
+  (package
+    (name "rust-asio-sys")
+    (version "0.2.1")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "asio-sys" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "16lbavksj2aasadyxbdnbrll6a1m8cwl4skbxgbvr1ma2wpwv82c"))))
+    (build-system cargo-build-system)
+    (arguments
+     (list #:skip-build? #t
+           #:cargo-inputs `(("rust-bindgen" ,rust-bindgen-0.56)
+                            ("rust-cc" ,rust-cc-1)
+                            ("rust-num-derive" ,rust-num-derive-0.3)
+                            ("rust-num-traits" ,rust-num-traits-0.2)
+                            ("rust-once-cell" ,rust-once-cell-1)
+                            ("rust-walkdir" ,rust-walkdir-2))))
+    (home-page "https://github.com/RustAudio/cpal/")
+    (synopsis
+     "Low-level interface and binding generation for the Steinberg ASIO SDK")
+    (description
+     "Low-level interface and binding generation for the Steinberg ASIO SDK.")
+    (license license:asl2.0)))
+
 (define-public rust-askama-escape-0.10
   (package
     (name "rust-askama-escape")
@@ -7328,6 +7518,41 @@ bindings to C and C++ libraries.")
     (inputs
      (list clang))))
 
+(define-public rust-bindgen-0.56
+  (package
+    (inherit rust-bindgen-0.57)
+    (name "rust-bindgen")
+    (version "0.56.0")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "bindgen" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0fajmgk2064ca1z9iq1jjkji63qwwz38z3d67kv6xdy0xgdpk8rd"))))
+    (arguments
+     (list #:cargo-test-flags ``("--release" "--"
+                                 "--skip=test::commandline_multiple_headers")
+           #:cargo-inputs `(("rust-bitflags" ,rust-bitflags-1)
+                            ("rust-cexpr" ,rust-cexpr-0.4)
+                            ("rust-clang-sys" ,rust-clang-sys-1)
+                            ("rust-clap" ,rust-clap-2)
+                            ("rust-env-logger" ,rust-env-logger-0.8)
+                            ("rust-lazy-static" ,rust-lazy-static-1)
+                            ("rust-lazycell" ,rust-lazycell-1)
+                            ("rust-log" ,rust-log-0.4)
+                            ("rust-peeking-take-while" ,rust-peeking-take-while-0.1)
+                            ("rust-proc-macro2" ,rust-proc-macro2-1)
+                            ("rust-quote" ,rust-quote-1)
+                            ("rust-regex" ,rust-regex-1)
+                            ("rust-rustc-hash" ,rust-rustc-hash-1)
+                            ("rust-shlex" ,rust-shlex-0.1)
+                            ("rust-which" ,rust-which-3))
+           #:cargo-development-inputs `(("rust-clap" ,rust-clap-2)
+                                        ("rust-diff" ,rust-diff-0.1)
+                                        ("rust-shlex" ,rust-shlex-0.1))))
+    (inputs (list clang))))
+
 (define-public rust-bindgen-0.55
   (package
     (inherit rust-bindgen-0.57)
@@ -12418,6 +12643,25 @@ usage.")
     (description "This package provides Rust bindings for libclang.")
     (license license:asl2.0)))
 
+(define-public rust-claxon-0.4
+  (package
+    (name "rust-claxon")
+    (version "0.4.3")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "claxon" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1206mxvw833ysg10029apcsjjwly8zmsvksgza5cm7ma4ikzbysb"))))
+    (build-system cargo-build-system)
+    (arguments
+     (list #:skip-build? #t)) ; Cut the dependency graph.
+    (home-page "https://github.com/ruuda/claxon#readme")
+    (synopsis "FLAC decoding library")
+    (description "This package provides a FLAC decoding library.")
+    (license license:asl2.0)))
+
 (define-public rust-cipher-0.4
   (package
     (name "rust-cipher")
@@ -15362,6 +15606,50 @@ contents of the OS-level clipboard.")
 numbers using the CORDIC method.")
     (license license:bsd-3)))
 
+(define-public rust-coreaudio-rs-0.10
+  (package
+    (name "rust-coreaudio-rs")
+    (version "0.10.0")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "coreaudio-rs" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "125d4zr3n363ybga4629p41ym7iqjfb2alnwrc1zj7zyxch4p28i"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t ; Only builds for macos or ios.
+       #:cargo-inputs (("rust-bitflags" ,rust-bitflags-1)
+                       ("rust-coreaudio-sys" ,rust-coreaudio-sys-0.2))))
+    (home-page "https://github.com/RustAudio/coreaudio-rs")
+    (synopsis "Rust interface for Apple's CoreAudio API")
+    (description
+     "This package provides a rust interface for Apple's CoreAudio API.")
+    (license (list license:expat license:asl2.0))))
+
+(define-public rust-coreaudio-sys-0.2
+  (package
+    (name "rust-coreaudio-sys")
+    (version "0.2.12")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "coreaudio-sys" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "091b4sq3kl8n4dy86l4mxq9vjzsn8w8b51xzfcpxwjkciqjv4d7h"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t ; Only builds for macos or ios.
+       #:cargo-inputs (("rust-bindgen" ,rust-bindgen-0.64))))
+    (home-page "https://github.com/RustAudio/coreaudio-sys")
+    (synopsis
+     "Bindings for Apple's CoreAudio frameworks generated via rust-bindgen")
+    (description
+     "Bindings for Apple's CoreAudio frameworks generated via rust-bindgen.")
+    (license license:expat)))
+
 (define-public rust-core-extensions-1
   (package
     (name "rust-core-extensions")
@@ -15864,6 +16152,63 @@ intrinsics.")
      "This package provides a counts the number of live instances of types.")
     (license (list license:expat license:asl2.0))))
 
+(define-public rust-cpal-0.13
+  (package
+    (name "rust-cpal")
+    (version "0.13.5")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "cpal" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32 "05j11vz8rw19gqqvpd48i7wvm6j77v8fwx5lwhlkckqjllv7h4bl"))
+        (snippet
+         #~(begin (use-modules (guix build utils))
+                  ;; Force cpal-0.13.5 to accept any version of jack, so
+                  ;; that other packages like librespot-playback can use
+                  ;; the one they want.
+                  (substitute* "Cargo.toml.orig"
+                    (("(jack = \\{ version = \").*(\", optional.*)" _ jack optional)
+                     (string-append jack "*" optional))
+                    ;; Remove path for asio-sys, use packaged crate.
+                    ((", path =.*,") ","))
+                  (copy-file "Cargo.toml.orig" "Cargo.toml")))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs (("rust-alsa" ,rust-alsa-0.6)
+                       ("rust-asio-sys" ,rust-asio-sys-0.2)
+                       ("rust-core-foundation-sys" ,rust-core-foundation-sys-0.8)
+                       ("rust-coreaudio-rs" ,rust-coreaudio-rs-0.10)
+                       ("rust-jack" ,rust-jack-0.8)
+                       ("rust-jni" ,rust-jni-0.19)
+                       ("rust-js-sys" ,rust-js-sys-0.3)
+                       ("rust-lazy-static" ,rust-lazy-static-1)
+                       ("rust-libc" ,rust-libc-0.2)
+                       ("rust-mach" ,rust-mach-0.3)
+                       ("rust-ndk" ,rust-ndk-0.6)
+                       ("rust-ndk-glue" ,rust-ndk-glue-0.6)
+                       ("rust-nix" ,rust-nix-0.23)
+                       ("rust-num-traits" ,rust-num-traits-0.2)
+                       ("rust-oboe" ,rust-oboe-0.4)
+                       ("rust-parking-lot" ,rust-parking-lot-0.11)
+                       ("rust-stdweb" ,rust-stdweb-0.1)
+                       ("rust-thiserror" ,rust-thiserror-1)
+                       ("rust-wasm-bindgen" ,rust-wasm-bindgen-0.2)
+                       ("rust-web-sys" ,rust-web-sys-0.3)
+                       ("rust-winapi" ,rust-winapi-0.3))
+       #:cargo-development-inputs (("rust-anyhow" ,rust-anyhow-1)
+                                   ("rust-clap" ,rust-clap-3)
+                                   ("rust-hound" ,rust-hound-3)
+                                   ("rust-ringbuf" ,rust-ringbuf-0.2))))
+    (native-inputs (list pkg-config))
+    (inputs (list alsa-lib))
+    (home-page "https://github.com/rustaudio/cpal")
+    (synopsis "Low-level cross-platform audio I/O library in pure Rust")
+    (description "Low-level cross-platform audio I/O library in pure Rust.
+Supports Linux through either JACK or ALSA.")
+    (license license:asl2.0)))
+
 (define-public rust-cpp-demangle-0.4
   (package
     (name "rust-cpp-demangle")
@@ -17245,6 +17590,34 @@ abstractions around common WinAPI calls.")
 number ``crunching``.")
     (license license:expat)))
 
+(define-public rust-rodio-0.15
+  (package
+    (name "rust-rodio")
+    (version "0.15.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (crate-uri "rodio" version))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32 "07kkrx0hxfcqgkpg0lrh9355bj1rl0k65nwsk3qwdri6yvlkj2gc"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs (("rust-claxon" ,rust-claxon-0.4)
+                       ("rust-cpal" ,rust-cpal-0.13)
+                       ("rust-hound" ,rust-hound-3)
+                       ("rust-lewton" ,rust-lewton-0.10)
+                       ("rust-minimp3" ,rust-minimp3-0.5)
+                       ("rust-symphonia" ,rust-symphonia-0.4))
+       #:cargo-development-inputs (("rust-quickcheck" ,rust-quickcheck-0.9))))
+    (native-inputs (list pkg-config))
+    (inputs (list alsa-lib))
+    (home-page "https://github.com/RustAudio/rodio")
+    (synopsis "Pure Rust audio playback library")
+    (description "Audio playback library written in pure Rust that supports
+many formats including AAC, FLAC, MP3, MP4 and WAV.")
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-roxmltree-0.14
   (package
     (name "rust-roxmltree")
@@ -25249,6 +25622,31 @@ Atom, RSS 2.0, RSS 1.0, RSS 0.x and JSON Feed")
      "This package provides a simple, efficient logging system for Rust.")
     (license license:expat)))
 
+(define-public rust-fetch-unroll-0.3
+  (package
+    (name "rust-fetch-unroll")
+    (version "0.3.0")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "fetch_unroll" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1l3cf8fhcrw354hdmjf03f5v4bxgn2wkjna8n0fn8bgplh8b3666"))))
+    (build-system cargo-build-system)
+    (arguments
+     (list #:tests? #f  ; Tries to connect to github.com
+           #:cargo-inputs `(("rust-libflate" ,rust-libflate-1)
+                            ("rust-tar" ,rust-tar-0.4)
+                            ("rust-ureq" ,rust-ureq-2))))
+    ; perl required for building rust-ring
+    (inputs (list perl))
+    (home-page "https://github.com/katyo/fetch_unroll")
+    (synopsis "Simple utilities for fetching and unrolling .tar.gz archives")
+    (description
+     "Simple utilities for fetching and unrolling .tar.gz archives.")
+    (license license:asl2.0)))
+
 (define-public rust-fever-api-0.2
   (package
     (name "rust-fever-api")
@@ -31539,6 +31937,25 @@ Hash-based Message Authentication Code algorithm} for SHA1.")
        (("rust-libc" ,rust-libc-0.2)
         ("rust-winutil" ,rust-winutil-0.1))))))
 
+(define-public rust-hound-3
+  (package
+    (name "rust-hound")
+    (version "3.5.1")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "hound" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0kw5yybfc7hdwxwm6d3m3h4ms52fkw0n0zch35drb52ci2xsmbb2"))))
+    (build-system cargo-build-system)
+    (arguments
+     (list #:skip-build? #t)) ; Cut the dependency graph.
+    (home-page "https://github.com/ruuda/hound")
+    (synopsis "Wav encoding and decoding library")
+    (description "This package provides a wav encoding and decoding library.")
+    (license license:asl2.0)))
+
 (define-public rust-html5ever-0.26
   (package
     (name "rust-html5ever")
@@ -34854,6 +35271,101 @@ format.")
     (description "This package provides a simple ivf muxer.")
     (license license:bsd-2)))
 
+(define-public rust-jack-0.10
+  (package
+    (name "rust-jack")
+    (version "0.10.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (crate-uri "jack" version))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32 "0djs3j0icxbzbivhj73vgjrvjw6ncpfak2vyxjcbn4wvl9ajcwnf"))))
+    (build-system cargo-build-system)
+    (arguments
+     (list #:tests? #f
+           #:cargo-inputs
+           `(("rust-bitflags" ,rust-bitflags-1)
+             ("rust-jack-sys" ,rust-jack-sys-0.4)
+             ("rust-lazy-static" ,rust-lazy-static-1)
+             ("rust-libc" ,rust-libc-0.2)
+             ("rust-log" ,rust-log-0.4))
+           #:cargo-development-inputs
+           `(("rust-crossbeam-channel" ,rust-crossbeam-channel-0.5))))
+    (native-inputs (list pkg-config))
+    (inputs (list jack-2))
+    (home-page "https://github.com/RustAudio/rust-jack")
+    (synopsis "Real time audio and midi with JACK")
+    (description "Real time audio and midi with JACK.")
+    (license license:expat)))
+
+(define-public rust-jack-0.8
+  (package
+    (inherit rust-jack-0.10)
+    (name "rust-jack")
+    (version "0.8.4")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "jack" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0lz10s0n2gy128m65pf96is9ip00vfgvnkfja0y9ydmv24pw2ajx"))))
+    (arguments
+     (list #:tests? #f
+           #:cargo-inputs `(("rust-bitflags" ,rust-bitflags-1)
+                            ("rust-jack-sys" ,rust-jack-sys-0.2)
+                            ("rust-lazy-static" ,rust-lazy-static-1)
+                            ("rust-libc" ,rust-libc-0.2)
+                            ("rust-log" ,rust-log-0.4)
+                            ("rust-crossbeam-channel" ,rust-crossbeam-channel-0.5))))))
+
+(define-public rust-jack-sys-0.4
+  (package
+    (name "rust-jack-sys")
+    (version "0.4.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (crate-uri "jack-sys" version))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32 "17vaq4i8q5nx39rjqx9sixqn1xraf1vxs3bmrf618v8nzxchbmz9"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:tests? #f      ; cannot find value `library` in this scope
+       #:cargo-inputs (("rust-bitflags" ,rust-bitflags-1)
+                       ("rust-lazy-static" ,rust-lazy-static-1)
+                       ("rust-libc" ,rust-libc-0.2)
+                       ("rust-libloading" ,rust-libloading-0.7)
+        ("rust-pkg-config" ,rust-pkg-config-0.3))))
+    (native-inputs (list pkg-config))
+    (inputs (list jack-2))
+    (home-page "https://github.com/RustAudio/rust-jack/tree/main/jack-sys")
+    (synopsis "Low-level binding to the JACK audio API")
+    (description "Low-level binding to the JACK audio API.")
+    (license (list license:expat license:asl2.0))))
+
+(define-public rust-jack-sys-0.2
+  (package
+    (inherit rust-jack-sys-0.4)
+    (name "rust-jack-sys")
+    (version "0.2.3")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "jack-sys" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1h9c9za19nyr1prx77gkia18ia93f73lpyjdiyrvmhhbs79g54bv"))))
+    (build-system cargo-build-system)
+    (arguments
+     (list #:cargo-inputs `(("rust-lazy-static" ,rust-lazy-static-1)
+                            ("rust-libc" ,rust-libc-0.2)
+                            ("rust-libloading" ,rust-libloading-0.6)
+                            ("rust-pkg-config" ,rust-pkg-config-0.3))))))
+
 (define-public rust-javascriptcore-rs-sys-0.2
   (package
     (name "rust-javascriptcore-rs-sys")
@@ -36078,6 +36590,34 @@ requires non-const function calls to be computed.")
 sending emails from Rust applications.")
     (license license:expat)))
 
+(define-public rust-lewton-0.10
+  (package
+    (name "rust-lewton")
+    (version "0.10.2")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "lewton" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0c60fn004awg5c3cvx82d6na2pirf0qdz9w3b93mbcdakbglhyvp"))))
+    (build-system cargo-build-system)
+    (arguments
+     (list #:cargo-inputs
+           `(("rust-byteorder" ,rust-byteorder-1)
+             ("rust-futures" ,rust-futures-0.1)
+             ("rust-ogg" ,rust-ogg-0.8)
+             ("rust-tinyvec" ,rust-tinyvec-1)
+             ("rust-tokio-io" ,rust-tokio-io-0.1))
+           #:cargo-development-inputs
+           `(("rust-alto" ,rust-alto-3)
+             ("rust-ogg" ,rust-ogg-0.8))))
+    (home-page "https://github.com/RustAudio/lewton")
+    (synopsis "Pure Rust Vorbis decoder")
+    (description "A pure Rust Vorbis decoder.  Vorbis is a free and open
+source audio format.")
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-lexical-core-0.8
   (package
     (name "rust-lexical-core")
@@ -37082,21 +37622,17 @@ file.
 @end itemize")
     (license license:gpl2+)))
 
-;; https://github.com/jnqnfe/pulse-binding-rust/blob/c788a8069f455f864d2ba5f0aa5f62e6648dfd26/pulse-sys/build.rs
-;; fix location of pulseaudio
 (define-public rust-libpulse-binding-2
   (package
     (name "rust-libpulse-binding")
-    (version "2.23.1")
+    (version "2.28.1")
     (source
      (origin
        (method url-fetch)
        (uri (crate-uri "libpulse-binding" version))
-       (file-name
-        (string-append name "-" version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
        (sha256
-        (base32
-         "1qx85j489mmad9cvw5k71271l3qy4s8a5qq8a9wac6cfi4viz5fv"))))
+        (base32 "1zza12f22wf1qs6h71lq1i73aj3kmv3036hqc7qci063vyi5fdgd"))))
     (build-system cargo-build-system)
     (arguments
      `(#:cargo-inputs
@@ -37109,7 +37645,7 @@ file.
        #:phases
        (modify-phases %standard-phases
          (add-before 'check 'set-HOME
-           (lambda _ (setenv "HOME" "/tmp") #t)))))
+           (lambda _ (setenv "HOME" "/tmp"))))))
     (native-inputs
      (list pkg-config))
     (inputs
@@ -37121,19 +37657,67 @@ file.
 library.")
     (license (list license:expat license:asl2.0))))
 
+(define-public rust-libpulse-simple-binding-2
+  (package
+    (name "rust-libpulse-simple-binding")
+    (version "2.28.1")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "libpulse-simple-binding" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                 "139hiksmxrmj8zcdqvswgjnwl1rivh915vg6cl92asizydl6pz85"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs (("rust-libpulse-binding" ,rust-libpulse-binding-2)
+                       ("rust-libpulse-simple-sys" ,rust-libpulse-simple-sys-1)
+                       ("rust-libpulse-sys" ,rust-libpulse-sys-1))
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'check 'set-HOME
+           (lambda _ (setenv "HOME" "/tmp"))))))
+    (native-inputs (list pkg-config))
+    (inputs (list pulseaudio))
+    (home-page "https://github.com/jnqnfe/pulse-binding-rust")
+    (synopsis "Rust language bindings for PulseAudio's libpulse-simple library")
+    (description
+     "A Rust language binding for the PulseAudio libpulse-simple library.")
+    (license (list license:expat license:asl2.0))))
+
+(define-public rust-libpulse-simple-sys-1
+  (package
+    (name "rust-libpulse-simple-sys")
+    (version "1.21.1")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "libpulse-simple-sys" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32 "0lj13ibdwf69ghy1zlldxq5vsyxi1h13wqpvvh79z2wx36s16rpa"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs (("rust-libpulse-sys" ,rust-libpulse-sys-1)
+                       ("rust-pkg-config" ,rust-pkg-config-0.3))))
+    (native-inputs (list pkg-config))
+    (inputs (list pulseaudio))
+    (home-page "https://github.com/jnqnfe/pulse-binding-rust")
+    (synopsis "FFI indings for PulseAudio's libpulse-simple system library")
+    (description
+     "FFI bindings for the PulseAudio libpulse-simple system library.")
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-libpulse-sys-1
   (package
     (name "rust-libpulse-sys")
-    (version "1.18.0")
+    (version "1.21.0")
     (source
      (origin
        (method url-fetch)
        (uri (crate-uri "libpulse-sys" version))
-       (file-name
-        (string-append name "-" version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
        (sha256
-        (base32
-         "10msfr8f951v86ag0fl2bsm4a3siq2r7hz9bqhhg7i234s1yj5yg"))))
+        (base32 "16vs0qk6xadckb5qxlrhg0f4jn2zakfd7xih1lk1fb7lzc8f26dw"))))
     (build-system cargo-build-system)
     (arguments
      `(#:cargo-inputs
@@ -37368,6 +37952,54 @@ Spotify.  This package contains the discovery logic.")
 Spotify.  This package contains the metadata logic.")
     (license license:expat)))
 
+(define-public rust-librespot-playback-0.4
+  (package
+    (name "rust-librespot-playback")
+    (version "0.4.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (crate-uri "librespot-playback" version))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32 "1dygnzldvkv1qpagr9nl62hmqh0xfcf4lsva37j0xxy7pjws142i"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-alsa" ,rust-alsa-0.6)
+        ("rust-byteorder" ,rust-byteorder-1)
+        ("rust-cpal" ,rust-cpal-0.13)
+        ("rust-futures-executor" ,rust-futures-executor-0.3)
+        ("rust-futures-util" ,rust-futures-util-0.3)
+        ("rust-glib" ,rust-glib-0.15)
+        ("rust-gstreamer" ,rust-gstreamer-0.18)
+        ("rust-gstreamer-app" ,rust-gstreamer-app-0.18)
+        ("rust-gstreamer-audio" ,rust-gstreamer-audio-0.18)
+        ("rust-jack" ,rust-jack-0.10)
+        ("rust-lewton" ,rust-lewton-0.10)
+        ("rust-libpulse-binding" ,rust-libpulse-binding-2)
+        ("rust-libpulse-simple-binding" ,rust-libpulse-simple-binding-2)
+        ("rust-librespot-audio" ,rust-librespot-audio-0.4)
+        ("rust-librespot-core" ,rust-librespot-core-0.4)
+        ("rust-librespot-metadata" ,rust-librespot-metadata-0.4)
+        ("rust-log" ,rust-log-0.4)
+        ("rust-ogg" ,rust-ogg-0.8)
+        ("rust-parking-lot" ,rust-parking-lot-0.12)
+        ("rust-portaudio-rs" ,rust-portaudio-rs-0.3)
+        ("rust-rand" ,rust-rand-0.8)
+        ("rust-rand-distr" ,rust-rand-distr-0.4)
+        ("rust-rodio" ,rust-rodio-0.15)
+        ("rust-sdl2" ,rust-sdl2-0.35)
+        ("rust-shell-words" ,rust-shell-words-1)
+        ("rust-thiserror" ,rust-thiserror-1)
+        ("rust-tokio" ,rust-tokio-1)
+        ("rust-zerocopy" ,rust-zerocopy-0.6))))
+    (home-page "https://github.com/librespot-org/librespot")
+    (synopsis "Audio playback for Librespot")
+    (description "Audio playback for Librespot, an open source client
+library for Spotify.")
+    (license license:expat)))
+
 (define-public rust-librespot-protocol-0.4
   (package
     (name "rust-librespot-protocol")
@@ -40867,6 +41499,53 @@ efficient round-trip float parsing. Minimal-lexical implements a correct, fast
 float parser.")
     (license (list license:expat license:asl2.0))))
 
+(define-public rust-minimp3-0.5
+  (package
+    (name "rust-minimp3")
+    (version "0.5.1")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "minimp3" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0wj3nzj1swnvwsk3a4a3hkfj1d21jsi7babi40wlrxzbbzvkhm4q"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:tests? #f  ; no method named `next_frame_future` found for struct `Decoder`
+       #:cargo-inputs (("rust-minimp3-sys" ,rust-minimp3-sys-0.3)
+                       ("rust-slice-deque" ,rust-slice-deque-0.3)
+                       ("rust-thiserror" ,rust-thiserror-1)
+                       ("rust-tokio" ,rust-tokio-1))
+       #:cargo-development-inputs (("rust-futures" ,rust-futures-0.3)
+                                   ("rust-tokio" ,rust-tokio-1))))
+    (home-page "https://github.com/germangb/minimp3-rs")
+    (synopsis "Rust bindings for the minimp3 library")
+    (description "Rust bindings for the minimp3 library.")
+    (license license:expat)))
+
+(define-public rust-minimp3-sys-0.3
+  (package
+    (name "rust-minimp3-sys")
+    (version "0.3.2")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "minimp3-sys" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "144vmf3s89kad0smjprzigcp2c9r5dm95n4ydilrbp399irp6772"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:tests? #f      ; Not all files included.
+       #:cargo-inputs (("rust-cc" ,rust-cc-1))))
+    (native-inputs (list pkg-config))
+    (inputs (list minimp3))
+    (home-page "https://github.com/germangb/minimp3-rs")
+    (synopsis "Rust bindings for the minimp3 library")
+    (description "Rust bindings for the minimp3 library.")
+    (license license:expat)))
+
 (define-public rust-miniz-oxide-0.7
   (package
     (name "rust-miniz-oxide")
@@ -41453,6 +42132,27 @@ select the mock struct at compile time.  Used with the Mockall crate.")
     (description "mp4 is a Rust library to read and write ISO-MP4 files.")
     (license license:expat)))
 
+(define-public rust-muldiv-1
+  (package
+    (name "rust-muldiv")
+    (version "1.0.1")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "muldiv" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1c6ljsp41n8ijsx7zicwfm135drgyhcms12668ivvsbm1r98frwm"))))
+    (build-system cargo-build-system)
+    (arguments
+     (list #:cargo-inputs `(("rust-quickcheck" ,rust-quickcheck-1))))
+    (home-page "https://github.com/sdroege/rust-muldiv")
+    (synopsis "Trait for numeric types to combine multiplication and division")
+    (description
+     "This package provides a trait for numeric types to perform combined
+multiplication and division with overflow protection.")
+    (license license:expat)))
+
 (define-public rust-multimap-0.8
   (package
     (name "rust-multimap")
@@ -42631,6 +43331,28 @@ general elements and for numerics.")
      "This package provides safe Rust bindings to the Android NDK.")
     (license (list license:expat license:asl2.0))))
 
+(define-public rust-ndk-0.6
+  (package
+    (inherit rust-ndk-0.7)
+    (name "rust-ndk")
+    (version "0.6.0")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "ndk" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1m1dfjw35qpys1hr4qib6mm3zacd01k439l7cx5f7phd0dzcfci0"))))
+    (arguments
+     `(#:skip-build? #t     ; Android only
+       #:cargo-inputs (("rust-bitflags" ,rust-bitflags-1)
+                       ("rust-jni" ,rust-jni-0.18)
+                       ("rust-jni-glue" ,rust-jni-glue-0.0)
+                       ("rust-jni-sys" ,rust-jni-sys-0.3)
+                       ("rust-ndk-sys" ,rust-ndk-sys-0.3)
+                       ("rust-num-enum" ,rust-num-enum-0.5)
+                       ("rust-thiserror" ,rust-thiserror-1))))))
+
 (define-public rust-ndk-0.5
   (package
     (inherit rust-ndk-0.7)
@@ -42696,35 +43418,56 @@ general elements and for numerics.")
      "This package provides handles for accessing Android APIs.")
     (license (list license:expat license:asl2.0))))
 
-(define-public rust-ndk-glue-0.5
+(define-public rust-ndk-glue-0.6
   (package
     (name "rust-ndk-glue")
-    (version "0.5.2")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (crate-uri "ndk-glue" version))
-       (file-name (string-append name "-" version ".tar.gz"))
-       (sha256
-        (base32 "1m44jh4f9sirs757ikc8sracg6dzw77h9l4bw9vm8s1dly7fw6y7"))))
+    (version "0.6.2")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "ndk-glue" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0pz6cdmmlzsb2jhrfvkma5d5vw2i331dlghqnkk2c0l6hdxll30d"))))
     (build-system cargo-build-system)
     (arguments
-     `(#:skip-build? #true              ;XXX: Android only
-       #:cargo-inputs
-       (("rust-android-logger" ,rust-android-logger-0.10)
-        ("rust-lazy-static" ,rust-lazy-static-1)
-        ("rust-libc" ,rust-libc-0.2)
-        ("rust-log" ,rust-log-0.4)
-        ("rust-ndk" ,rust-ndk-0.5)
-        ("rust-ndk-context" ,rust-ndk-context-0.1)
-        ("rust-ndk-macro" ,rust-ndk-macro-0.3)
-        ("rust-ndk-sys" ,rust-ndk-sys-0.2))))
-    (home-page "https://github.com/rust-windowing/android-ndk-rs")
+     (list #:skip-build? #t ;XXX: Android only
+           #:cargo-inputs `(("rust-android-logger" ,rust-android-logger-0.10)
+                            ("rust-lazy-static" ,rust-lazy-static-1)
+                            ("rust-libc" ,rust-libc-0.2)
+                            ("rust-log" ,rust-log-0.4)
+                            ("rust-ndk" ,rust-ndk-0.6)
+                            ("rust-ndk-context" ,rust-ndk-context-0.1)
+                            ("rust-ndk-macro" ,rust-ndk-macro-0.3)
+                            ("rust-ndk-sys" ,rust-ndk-sys-0.3))))
+    (home-page "https://github.com/rust-mobile/ndk")
     (synopsis "Startup code for Android binaries")
-    (description
-     "This package provides startup code for Android binaries.")
+    (description "This package provides startup code for Android binaries.")
     (license (list license:expat license:asl2.0))))
 
+(define-public rust-ndk-glue-0.5
+  (package
+    (inherit rust-ndk-glue-0.6)
+    (name "rust-ndk-glue")
+    (version "0.5.2")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "ndk-glue" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1m44jh4f9sirs757ikc8sracg6dzw77h9l4bw9vm8s1dly7fw6y7"))))
+    (arguments
+     (list #:skip-build? #t ;XXX: Android only
+           #:cargo-inputs `(("rust-android-logger" ,rust-android-logger-0.10)
+                            ("rust-lazy-static" ,rust-lazy-static-1)
+                            ("rust-libc" ,rust-libc-0.2)
+                            ("rust-log" ,rust-log-0.4)
+                            ("rust-ndk" ,rust-ndk-0.5)
+                            ("rust-ndk-context" ,rust-ndk-context-0.1)
+                            ("rust-ndk-macro" ,rust-ndk-macro-0.3)
+                            ("rust-ndk-sys" ,rust-ndk-sys-0.2))))))
+
 (define-public rust-ndk-glue-0.2
   (package
     (inherit rust-ndk-glue-0.5)
@@ -42812,6 +43555,19 @@ general elements and for numerics.")
     (description "This package provides FFI bindings for the Android NDK.")
     (license (list license:expat license:asl2.0))))
 
+(define-public rust-ndk-sys-0.3
+  (package
+    (inherit rust-ndk-sys-0.4)
+    (name "rust-ndk-sys")
+    (version "0.3.0")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "ndk-sys" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "15zsq4p6k5asf4mc0rknd8cz9wxrwvi50qdspgf87qcfgkknlnkf"))))))
+
 (define-public rust-ndk-sys-0.2
   (package
     (inherit rust-ndk-sys-0.4)
@@ -45912,6 +46668,57 @@ file formats.")
         ("rust-rustc-std-workspace-core" ,rust-rustc-std-workspace-core-1)
         ("rust-wasmparser" ,rust-wasmparser-0.57))))))
 
+(define-public rust-oboe-0.4
+  (package
+    (name "rust-oboe")
+    (version "0.4.6")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "oboe" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1hd5626s8qkpgrl2alwz73i8rh1rzifbxj6pxz7zp82gicskrxi7"))))
+    (build-system cargo-build-system)
+    (arguments
+     (list #:skip-build? #t ; requires Android libs
+           #:cargo-inputs `(("rust-jni" ,rust-jni-0.19)
+                            ("rust-ndk" ,rust-ndk-0.6)
+                            ("rust-ndk-context" ,rust-ndk-context-0.1)
+                            ("rust-num-derive" ,rust-num-derive-0.3)
+                            ("rust-num-traits" ,rust-num-traits-0.2)
+                            ("rust-oboe-sys" ,rust-oboe-sys-0.4))))
+    (home-page "https://github.com/katyo/oboe-rs")
+    (synopsis
+     "Safe interface for oboe an android library for low latency audio IO")
+    (description
+     "Safe interface for oboe an android library for low latency audio IO.")
+    (license license:asl2.0)))
+
+(define-public rust-oboe-sys-0.4
+  (package
+    (name "rust-oboe-sys")
+    (version "0.4.5")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "oboe-sys" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1gcl494yy880h2gfgsbdd32g2h0s1n94v58j5hil9mrf6yvsnw1k"))))
+    (build-system cargo-build-system)
+    (arguments
+     (list #:skip-build? #t ; requires Android libs
+           #:cargo-inputs `(("rust-bindgen" ,rust-bindgen-0.59)
+                            ("rust-cc" ,rust-cc-1)
+                            ("rust-fetch-unroll" ,rust-fetch-unroll-0.3))))
+    (home-page "https://github.com/katyo/oboe-rs")
+    (synopsis
+     "Unsafe bindings for oboe an android library for low latency audio IO")
+    (description
+     "Unsafe bindings for oboe an android library for low latency audio IO.")
+    (license license:asl2.0)))
+
 (define-public rust-odds-0.3
   (package
     (name "rust-odds")
@@ -45970,6 +46777,32 @@ Things in odds may move to more appropriate crates if we find them.")
         ("rust-memchr" ,rust-memchr-2)
         ("rust-quickcheck" ,rust-quickcheck-0.4))))))
 
+(define-public rust-ogg-0.8
+  (package
+    (name "rust-ogg")
+    (version "0.8.0")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "ogg" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0vjxmqcv9252aj8byy70iy2krqfjknfcxg11lcyikj11pzlb8lb9"))))
+    (build-system cargo-build-system)
+    (arguments
+     (list #:cargo-inputs
+           `(("rust-byteorder" ,rust-byteorder-1)
+             ("rust-bytes" ,rust-bytes-0.4)
+             ("rust-futures" ,rust-futures-0.1)
+             ("rust-tokio-io" ,rust-tokio-io-0.1))
+           #:cargo-development-inputs
+           `(("rust-rand" ,rust-rand-0.3))))
+    (home-page "https://github.com/RustAudio/ogg")
+    (synopsis "Ogg container decoder and encoder written in pure Rust")
+    (description "An Ogg decoder and encoder.  Implements the xiph.org Ogg
+spec in pure Rust.")
+    (license license:expat)))
+
 (define-public rust-oid-registry-0.6
   (package
     (name "rust-oid-registry")
@@ -46521,6 +47354,27 @@ system for OpenSSL.")
     (description "Extends `Option` with additional operations")
     (license license:mpl2.0)))
 
+(define-public rust-option-operations-0.4
+  (package
+    (name "rust-option-operations")
+    (version "0.4.1")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "option-operations" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "18jhy5sc56gwdvqc3asr6az685zc9zkgv8p8n69s94bcj6bibc22"))))
+    (build-system cargo-build-system)
+    (arguments
+     (list #:cargo-inputs `(("rust-paste" ,rust-paste-1))))
+    (home-page "https://github.com/fengalin/option-operations")
+    (synopsis "Improved arithmetic operations when dealing with Rust Options")
+    (description
+     "Traits and auto-implementations to improve arithmetic operations
+usability when dealing with Rust Options.")
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-option-set-0.2
   (package
     (name "rust-option-set")
@@ -47181,6 +48035,22 @@ owner with them.  This can sometimes be useful because Rust borrowing rules
 normally prevent moving a type that has been borrowed from.")
     (license license:expat)))
 
+(define-public rust-owning-ref-0.3
+  (package
+    (inherit rust-owning-ref-0.4)
+    (name "rust-owning-ref")
+    (version "0.3.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (crate-uri "owning-ref" version))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32 "0dqgf5hwbmvkf2ffbik5xmhvaqvqi6iklhwk9x47n0wycd0lzy6d"))))
+    (arguments
+     (list #:cargo-inputs
+           `(("rust-stable-deref-trait" ,rust-stable-deref-trait-1))))))
+
 (define-public rust-p256-0.13
   (package
     (name "rust-p256")
@@ -47858,6 +48728,26 @@ synchronization primitives.")
         ("rust-rand" ,rust-rand-0.4)
         ("rust-rustc-version" ,rust-rustc-version-0.2))))))
 
+(define-public rust-parking-lot-0.4
+  (package
+    (inherit rust-parking-lot-0.9)
+    (name "rust-parking-lot")
+    (version "0.4.8")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "parking-lot" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0ph0kv3dfcxpjbi83wkzammqb7lm95j8in7w7hz17hgkjxdqz78l"))))
+    (build-system cargo-build-system)
+    (arguments
+     (list #:cargo-inputs
+           `(("rust-parking-lot-core" ,rust-parking-lot-core-0.2)
+             ("rust-owning-ref" ,rust-owning-ref-0.3))
+           #:cargo-development-inputs
+           `(("rust-rand" ,rust-rand-0.3))))))
+
 (define-public rust-parking-lot-core-0.9
   (package
     (name "rust-parking-lot-core")
@@ -48032,6 +48922,28 @@ synchronization primitives.")
         ("rust-winapi" ,rust-winapi-0.3)
         ("rust-rustc-version" ,rust-rustc-version-0.2))))))
 
+(define-public rust-parking-lot-core-0.2
+  (package
+    (inherit rust-parking-lot-core-0.6)
+    (name "rust-parking-lot-core")
+    (version "0.2.14")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "parking-lot-core" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1yip8m6npxb87ilnn0q774psp1zd0vgv66fcjkkvr9rlyz6aicad"))))
+    (arguments
+     (list #:cargo-inputs
+           `(("rust-backtrace" ,rust-backtrace-0.3)
+             ("rust-libc" ,rust-libc-0.2)
+             ("rust-petgraph" ,rust-petgraph-0.4)
+             ("rust-rand" ,rust-rand-0.4)
+             ("rust-smallvec" ,rust-smallvec-0.6)
+             ("rust-thread-id" ,rust-thread-id-3)
+             ("rust-winapi" ,rust-winapi-0.3))))))
+
 (define-public rust-parquet-5
   (package
     (name "rust-parquet")
@@ -51268,6 +52180,53 @@ overloading without macros in Rust.")
 128-bit atomics, atomic float, etc.")
     (license (list license:asl2.0 license:expat))))
 
+(define-public rust-portaudio-rs-0.3
+  (package
+    (name "rust-portaudio-rs")
+    (version "0.3.2")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "portaudio-rs" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0qnmc7amk0fzbcs985ixv0k4955f0fmpkhrl9ps9pk3cz7pvbdnd"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs (("rust-bitflags" ,rust-bitflags-1)
+                       ("rust-libc" ,rust-libc-0.2)
+                       ("rust-portaudio-sys" ,rust-portaudio-sys-0.1))))
+    (native-inputs (list pkg-config))
+    (inputs (list portaudio alsa-lib))
+    (home-page "https://github.com/RustAudio/rust-portaudio")
+    (synopsis "Rust bindings for PortAudio a cross-platfomr audio library")
+    (description "Rusting bindings for PortAudio an open source, cross-platform
+audio I/O library.")
+    (license license:expat)))
+
+(define-public rust-portaudio-sys-0.1
+  (package
+    (name "rust-portaudio-sys")
+    (version "0.1.1")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "portaudio-sys" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1xdpywirpr1kqkbak7hnny62gmsc93qgc3ij3j2zskrvjpxa952i"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs (("rust-libc" ,rust-libc-0.2)
+                       ("rust-pkg-config" ,rust-pkg-config-0.3))))
+    (native-inputs (list pkg-config))
+    (inputs (list portaudio alsa-lib))
+    (home-page "https://github.com/RustAudio/rust-portaudio")
+    (synopsis "Bindings for PortAudio a cross-platform audio library")
+    (description "Bindings for PortAudio an open source, cross-platform audio
+I/O library.")
+    (license license:expat)))
+
 (define-public rust-postgres-0.19
   (package
     (name "rust-postgres")
@@ -51857,6 +52816,25 @@ replacements, adding colorful diffs.")
      "This package provides a minimal `syn` syntax tree pretty-printer.")
     (license (list license:expat license:asl2.0))))
 
+(define-public rust-pretty-hex-0.3
+  (package
+    (name "rust-pretty-hex")
+    (version "0.3.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (crate-uri "pretty-hex" version))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32 "1mf8xvlfri4impj2paj4azx7hxh7l0i38cjyib1hiikwvlqhiyn6"))))
+    (build-system cargo-build-system)
+    (arguments
+     (list #:cargo-development-inputs `(("rust-heapless" ,rust-heapless-0.5))))
+    (home-page "https://github.com/wolandr/pretty-hex")
+    (synopsis "Prettified output of hexadecimal byte slices")
+    (description "Pretty hex dump of byte slices in the common style.")
+    (license license:expat)))
+
 (define-public rust-prettytable-rs-0.8
   (package
     (name "rust-prettytable-rs")
@@ -56713,6 +57691,55 @@ crate unless you're working on a regex implementation.")
 Rust.")
     (license license:expat)))
 
+(define-public rust-rental-0.5
+  (package
+    (name "rust-rental")
+    (version "0.5.6")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "rental" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0bhzz2pfbg0yaw8p1l31bggq4jn077wslf6ifhj22vf3r8mgx2fc"))))
+    (build-system cargo-build-system)
+    (arguments
+     (list #:tests? #f  ; cannot move out of `foo` because it is borrowed
+           #:cargo-inputs
+           `(("rust-rental-impl" ,rust-rental-impl-0.5)
+             ("rust-stable-deref-trait" ,rust-stable-deref-trait-1))))
+    (home-page "https://github.com/jpernst/rental")
+    (synopsis "Macro to generate safe self-referential structs")
+    (description
+     "A macro to generate safe self-referential structs, plus
+premade types for common use-cases.  This crate is frozen and should be
+avoided if possible.")
+    (license (list license:expat license:asl2.0))))
+
+(define-public rust-rental-impl-0.5
+  (package
+    (name "rust-rental-impl")
+    (version "0.5.5")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "rental-impl" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1pj0qgmvwwsfwyjqyjxzikkwbwc3vj7hm3hdykr47dy5inbnhpj7"))))
+    (build-system cargo-build-system)
+    (arguments
+     (list #:skip-build? #f
+           #:cargo-inputs
+           `(("rust-proc-macro2" ,rust-proc-macro2-1)
+             ("rust-quote" ,rust-quote-1)
+             ("rust-syn" ,rust-syn-1))))
+    (home-page "https://github.com/jpernst/rental")
+    (synopsis "Implementation details of the rust-rental crate")
+    (description "Implementation details for the rust-rental crate.
+Should not be used directly.")
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-reopen-0.3
   (package
     (name "rust-reopen")
@@ -57230,6 +58257,28 @@ Digital Signature Algorithm} (ECDSA).")
                  (lambda _
                    (invoke "python" "make_curve25519_tables.py")))))))))))
 
+(define-public rust-ringbuf-0.2
+  (package
+    (name "rust-ringbuf")
+    (version "0.2.6")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "ringbuf" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1wxd2sb5b0kjwc5mcv8qrmzl0spfs0agznrxain3xhrr769g6q3c"))))
+    (build-system cargo-build-system)
+    (arguments
+     (list #:cargo-inputs `(("rust-cache-padded" ,rust-cache-padded-1))))
+    (home-page "https://github.com/agerasev/ringbuf")
+    (synopsis
+     "Lock-free SPSC FIFO ring buffer with direct access to inner data")
+    (description
+     "Lock-free @acronym{SPSC, Single Producer Single Consumer} @acronym{FIFO,
+First In First Out} ring buffer with direct access to inner data.")
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-ripemd-0.1
   (package
     (name "rust-ripemd")
@@ -65753,23 +66802,22 @@ implementations.")
      "Rust FFI bindings to the SLEEF Vectorized Math Library.")
     (license (list license:asl2.0 license:expat))))
 
-(define-public rust-slice-deque-0.2
+(define-public rust-slice-deque-0.3
   (package
     (name "rust-slice-deque")
-    (version "0.2.4")
+    (version "0.3.0")
     (source
      (origin
        (method url-fetch)
        (uri (crate-uri "slice-deque" version))
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
-        (base32 "1mq78l0vfwabnyanb85amgzakfhdaxx455yq6cszd5zmynagbpgz"))))
+        (base32 "098gvqjw52qw4gac567c9hx3y6hw9al7hjqb5mnvmvydh3i6xvri"))))
     (build-system cargo-build-system)
     (arguments
-     `(#:skip-build? #t
-       #:cargo-inputs
+     `(#:cargo-inputs
        (("rust-libc" ,rust-libc-0.2)
-        ("rust-mach" ,rust-mach-0.2)
+        ("rust-mach" ,rust-mach-0.3)
         ("rust-winapi" ,rust-winapi-0.3))))
     (home-page "https://github.com/gnzlbg/slice_deque")
     (synopsis "Double-ended queue that Deref's into a slice")
@@ -65777,6 +66825,25 @@ implementations.")
      "This package provides a double-ended queue that Deref's into a slice.")
     (license (list license:expat license:asl2.0))))
 
+(define-public rust-slice-deque-0.2
+  (package
+    (inherit rust-slice-deque-0.3)
+    (name "rust-slice-deque")
+    (version "0.2.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (crate-uri "slice-deque" version))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32 "1mq78l0vfwabnyanb85amgzakfhdaxx455yq6cszd5zmynagbpgz"))))
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-libc" ,rust-libc-0.2)
+        ("rust-mach" ,rust-mach-0.2)
+        ("rust-winapi" ,rust-winapi-0.3))))))
+
 (define-public rust-slog-2
   (package
     (name "rust-slog")
@@ -67709,6 +68776,24 @@ on verbosity specified")
 Web.")
     (license (list license:expat license:asl2.0))))
 
+(define-public rust-stdweb-0.1
+  (package
+    (inherit rust-stdweb-0.4)
+    (name "rust-stdweb")
+    (version "0.1.3")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "stdweb" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0gjk7ch31a3kgdc39kj4zqinf10yqaf717wanh9kwwbbwg430m7g"))))
+    (arguments
+     (list #:skip-build? #t
+           #:cargo-inputs `(("rust-clippy" ,rust-clippy-0.0)
+                            ("rust-serde" ,rust-serde-1)
+                            ("rust-serde-json" ,rust-serde-json-1))))))
+
 (define-public rust-stdweb-derive-0.5
   (package
     (name "rust-stdweb-derive")
@@ -69316,6 +70401,305 @@ executed by swayipc.")
 interface")
    (license license:expat)))
 
+(define-public rust-symphonia-0.4
+  (package
+    (name "rust-symphonia")
+    (version "0.4.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (crate-uri "symphonia" version))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32 "1dx4v5libbksi4rd6b9290nci3h8xqyakymhxd72yybyl25g7rd7"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs (("rust-lazy-static" ,rust-lazy-static-1)
+                       ("rust-symphonia-bundle-flac" ,rust-symphonia-bundle-flac-0.4)
+                       ("rust-symphonia-bundle-mp3" ,rust-symphonia-bundle-mp3-0.4)
+                       ("rust-symphonia-codec-aac" ,rust-symphonia-codec-aac-0.4)
+                       ("rust-symphonia-codec-pcm" ,rust-symphonia-codec-pcm-0.4)
+                       ("rust-symphonia-codec-vorbis" ,rust-symphonia-codec-vorbis-0.4)
+                       ("rust-symphonia-core" ,rust-symphonia-core-0.4)
+                       ("rust-symphonia-format-isomp4" ,rust-symphonia-format-isomp4-0.4)
+                       ("rust-symphonia-format-ogg" ,rust-symphonia-format-ogg-0.4)
+                       ("rust-symphonia-format-wav" ,rust-symphonia-format-wav-0.4)
+                       ("rust-symphonia-metadata" ,rust-symphonia-metadata-0.4))))
+    (home-page "https://github.com/pdeljanov/Symphonia")
+    (synopsis
+     "Symphonia is a pure Rust media container and audio decoding library")
+    (description
+     "Symphonia is a pure Rust media container and audio decoding library
+that supports a wide range of audio formats.")
+    (license license:mpl2.0)))
+
+(define-public rust-symphonia-bundle-flac-0.4
+  (package
+    (name "rust-symphonia-bundle-flac")
+    (version "0.4.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (crate-uri "symphonia-bundle-flac" version))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32 "00jxn9izfg1g07srhgglpqgadmzwsr88sqnnxw3mskpvyl958vhi"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs (("rust-log" ,rust-log-0.4)
+                       ("rust-symphonia-core" ,rust-symphonia-core-0.4)
+                       ("rust-symphonia-metadata" ,rust-symphonia-metadata-0.4)
+                       ("rust-symphonia-utils-xiph" ,rust-symphonia-utils-xiph-0.4))))
+    (home-page "https://github.com/pdeljanov/Symphonia")
+    (synopsis "FLAC demuxer and decoder for the Symphonia library")
+    (description
+     "Symphonia is a pure Rust audio decoding and media demuxing library
+supporting a wide range of audio formats.  This package contains a FLAC demuxer
+and decoder.")
+    (license license:mpl2.0)))
+
+(define-public rust-symphonia-core-0.4
+  (package
+    (name "rust-symphonia-core")
+    (version "0.4.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (crate-uri "symphonia-core" version))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32 "1j84q4a9p9qa23976spxap9s6ns3fm6fzrfz65n6cjhgpsbmw4zs"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs (("rust-arrayvec" ,rust-arrayvec-0.7)
+                       ("rust-bitflags" ,rust-bitflags-1)
+                       ("rust-bytemuck" ,rust-bytemuck-1)
+                       ("rust-lazy-static" ,rust-lazy-static-1)
+                       ("rust-log" ,rust-log-0.4))))
+    (home-page "https://github.com/pdeljanov/Symphonia")
+    (synopsis "Shared elements for Symphonia a Rust audio library")
+    (description
+     "Symphonia is a pure Rust audio decoding and media demuxing
+library supporting a wide range of audio formats.  This package contains
+shared structs, traits, and features.")
+    (license license:mpl2.0)))
+
+(define-public rust-symphonia-metadata-0.4
+  (package
+    (name "rust-symphonia-metadata")
+    (version "0.4.0")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "symphonia-metadata" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "06lvwy24kirc84r6d23ncad544525fsb6gna0plqz3d1mffmjq2j"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs (("rust-encoding-rs" ,rust-encoding-rs-0.8)
+                       ("rust-lazy-static" ,rust-lazy-static-1)
+                       ("rust-log" ,rust-log-0.4)
+                       ("rust-symphonia-core" ,rust-symphonia-core-0.4))))
+    (home-page "https://github.com/pdeljanov/Symphonia")
+    (synopsis "Multimedia tag and metadata readers for the Symphonia library")
+    (description "Symphonia is a pure Rust audio decoding and media demuxing
+library supporting a wide range of audio formats.  This package contains
+multimedia tag and metadata readers.")
+    (license license:mpl2.0)))
+
+(define-public rust-symphonia-bundle-mp3-0.4
+  (package
+    (name "rust-symphonia-bundle-mp3")
+    (version "0.4.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (crate-uri "symphonia-bundle-mp3" version))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32 "14074njhgrcgh2p5iryrd68mgdzcxf9v7p8xfm8ldkhylv29fkgc"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs (("rust-bitflags" ,rust-bitflags-1)
+                       ("rust-lazy-static" ,rust-lazy-static-1)
+                       ("rust-log" ,rust-log-0.4)
+                       ("rust-symphonia-core" ,rust-symphonia-core-0.4)
+                       ("rust-symphonia-metadata" ,rust-symphonia-metadata-0.4))))
+    (home-page "https://github.com/pdeljanov/Symphonia")
+    (synopsis "MP1, MP2, and MP3 demuxers and decoders written in pure Rust")
+    (description
+     "Symphonia is a pure Rust audio decoding and media demuxing library
+supporting a wide range of aduio formats.  This package contains support for
+MP1, MP2 and MP3.")
+    (license license:mpl2.0)))
+
+(define-public rust-symphonia-codec-aac-0.4
+  (package
+    (name "rust-symphonia-codec-aac")
+    (version "0.4.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (crate-uri "symphonia-codec-aac" version))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32 "13smaxgb1jadl4jyay7hixqgwaiqrjvsvmzdvlbdzdxrgsrplgdx"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs (("rust-lazy-static" ,rust-lazy-static-1)
+                       ("rust-log" ,rust-log-0.4)
+                       ("rust-symphonia-core" ,rust-symphonia-core-0.4))))
+    (home-page "https://github.com/pdeljanov/Symphonia")
+    (synopsis "Pure Rust AAC decoder from Symphonia")
+    (description
+     "Symphonia is a pure Rust audio decoding and media demuxing library
+that supports a wide range of audio formats.  This package contains an AAC
+decoder.")
+    (license license:mpl2.0)))
+
+(define-public rust-symphonia-codec-pcm-0.4
+  (package
+    (name "rust-symphonia-codec-pcm")
+    (version "0.4.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (crate-uri "symphonia-codec-pcm" version))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32 "1is49qjnfy541zpgzz498hnpz0nsq7i4nfky2133b6aqhxrm87ds"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs (("rust-log" ,rust-log-0.4)
+                       ("rust-symphonia-core" ,rust-symphonia-core-0.4))))
+    (home-page "https://github.com/pdeljanov/Symphonia")
+    (synopsis "Pure Rust PCM audio decoder, part of Symphonia")
+    (description
+     "Symphonia is a pure Rust audio decoding and media demuxing library
+that supports a wide range of audio formats.  This package contains a
+@acronym{PCM, Pulse-Code Modulation} audio decoder.")
+    (license license:mpl2.0)))
+
+(define-public rust-symphonia-codec-vorbis-0.4
+  (package
+    (name "rust-symphonia-codec-vorbis")
+    (version "0.4.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (crate-uri "symphonia-codec-vorbis" version))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32 "1yj1si92fnnzdfkw27cq324h6y1s958s8r2hl0szpvvqh1sdd7m2"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs (("rust-log" ,rust-log-0.4)
+                       ("rust-symphonia-core" ,rust-symphonia-core-0.4)
+                       ("rust-symphonia-utils-xiph" ,rust-symphonia-utils-xiph-0.4))))
+    (home-page "https://github.com/pdeljanov/Symphonia")
+    (synopsis "Pure Rust Vorbis decoder, part of the Symphonia project")
+    (description
+     "Symphonia is a pure Rust audio decoding and media demuxing library
+that supports a wide range of audio formats.  This package is a Vorbis
+decoder.")
+    (license license:mpl2.0)))
+
+(define-public rust-symphonia-format-isomp4-0.4
+  (package
+    (name "rust-symphonia-format-isomp4")
+    (version "0.4.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (crate-uri "symphonia-format-isomp4" version))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32 "1dap5yh286j74sybjsam378v1jxkpdl3hvvm81sipv7725vkmvpy"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs (("rust-encoding-rs" ,rust-encoding-rs-0.8)
+                       ("rust-log" ,rust-log-0.4)
+                       ("rust-symphonia-core" ,rust-symphonia-core-0.4)
+                       ("rust-symphonia-metadata" ,rust-symphonia-metadata-0.4))))
+    (home-page "https://github.com/pdeljanov/Symphonia")
+    (synopsis "Rust ISO/MP4 demuxer from the Symphonia project")
+    (description
+     "Symphonia is a pure Rust audio decoding and media demuxing library
+that supports a wide range of audio formats.  This package contains an
+ISO/MP4 demuxer.")
+    (license license:mpl2.0)))
+
+(define-public rust-symphonia-format-ogg-0.4
+  (package
+    (name "rust-symphonia-format-ogg")
+    (version "0.4.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (crate-uri "symphonia-format-ogg" version))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32 "06d5327m4yk8a6yq7zzyiv2sbkwnjq28dz9cagndz6m7i1r3bcnp"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs (("rust-log" ,rust-log-0.4)
+                       ("rust-symphonia-core" ,rust-symphonia-core-0.4)
+                       ("rust-symphonia-metadata" ,rust-symphonia-metadata-0.4)
+                       ("rust-symphonia-utils-xiph" ,rust-symphonia-utils-xiph-0.4))))
+    (home-page "https://github.com/pdeljanov/Symphonia")
+    (synopsis "Pure Rust OGG demuxer, part of Symphonia")
+    (description
+     "Symphonia is a pure Rust decoding and media demuxing library that
+supports a wide range of audio formats.  This package is an OGG demuxer.")
+    (license license:mpl2.0)))
+
+(define-public rust-symphonia-format-wav-0.4
+  (package
+    (name "rust-symphonia-format-wav")
+    (version "0.4.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (crate-uri "symphonia-format-wav" version))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32 "1b8x213s44xis4pb1ibnqr1a20hsxf3phm527dvadpi0nkjsb7vd"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs (("rust-log" ,rust-log-0.4)
+                       ("rust-symphonia-core" ,rust-symphonia-core-0.4)
+                       ("rust-symphonia-metadata" ,rust-symphonia-metadata-0.4))))
+    (home-page "https://github.com/pdeljanov/Symphonia")
+    (synopsis "Rust WAV demuxer from the Symphonia project")
+    (description
+     "Symphonia is a pure Rust decoding and media demuxing library that
+supports a wide range of audio formats.  This package is a WAV demuxer.")
+    (license license:mpl2.0)))
+
+(define-public rust-symphonia-utils-xiph-0.4
+  (package
+    (name "rust-symphonia-utils-xiph")
+    (version "0.4.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (crate-uri "symphonia-utils-xiph" version))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32 "1sg1y7s607rk1akrrzyhdsqimiwwaw440jzr1cp89zs8d5n04dva"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs (("rust-symphonia-core" ,rust-symphonia-core-0.4)
+                       ("rust-symphonia-metadata" ,rust-symphonia-metadata-0.4))))
+    (home-page "https://github.com/pdeljanov/Symphonia")
+    (synopsis "Xiph codecs and formats for Rust's Symphonia")
+    (description
+     "Symphonia is a pure Rust audio decoding and media demuxing
+library that supports a wide range of audio formats.  This package contains Xiph
+codecs and formats.")
+    (license license:mpl2.0)))
+
 (define-public rust-syn-2
   (package
     (name "rust-syn")
diff --git a/gnu/packages/cups.scm b/gnu/packages/cups.scm
index 647b89dc03..731091ea7d 100644
--- a/gnu/packages/cups.scm
+++ b/gnu/packages/cups.scm
@@ -8,6 +8,7 @@
 ;;; Copyright © 2017–2022 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2020 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2021, 2023 Maxim Cournoyer <maxim.cournoyer@gmail.com>
+;;; Copyright © 2023 Zheng Junjie <873216071@qq.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -204,8 +205,11 @@ driver is known to work with these printers:
                     (find-files (string-append #$output
                                                "/lib/cups/filter"))))))))
     (native-inputs
-     (list `(,glib "bin")               ; for gdbus-codegen
-           pkg-config))
+     (append (if (%current-target-system)
+                 (list cups-minimal)
+                 '())
+             (list `(,glib "bin")               ; for gdbus-codegen
+                   pkg-config)))
     (inputs
      (list avahi
            fontconfig
@@ -315,7 +319,10 @@ filters for the PDF-centric printing workflow introduced by OpenPrinting.")
                      ;; to a missing font.  Substitute the last observed count.
                      (("(\\$count != )33" _ prefix)
                       (string-append prefix "39"))))))))
-    (native-inputs (list config pkg-config))
+    (native-inputs (cons* config pkg-config
+                          (if (%current-target-system)
+                              (list this-package)
+                              '())))
     (inputs (list zlib gnutls))
     (home-page "https://openprinting.github.io/cups")
     (synopsis "The Common Unix Printing System")
@@ -522,6 +529,7 @@ should only be used as part of the Guix cups-pk-helper service.")
               (sha256
                (base32
                 "0ihv9ddjrjx5bdf8pwc2fvljkpfzq4qi9r2awm8dgky053v0bk7p"))
+              (patches (search-patches "hplip-usb-timeout.patch"))
               (modules '((guix build utils)))
               (snippet
                '(begin
diff --git a/gnu/packages/curl.scm b/gnu/packages/curl.scm
index 02803833e6..9f06f35495 100644
--- a/gnu/packages/curl.scm
+++ b/gnu/packages/curl.scm
@@ -405,7 +405,7 @@ asynchronously via cURL in C++.")
 (define-public curlie
   (package
     (name "curlie")
-    (version "1.6.9")
+    (version "1.7.2")
     (source
      (origin
        (method git-fetch)
@@ -415,7 +415,7 @@ asynchronously via cURL in C++.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "1b94wfliivfq06i5sf664nhmp3v1k0lpz33cv9lyk6s59awb2hnw"))))
+         "04gwd9sqpykappnzyw9icgn5253cx1vwpr2h1fg7sgkyq3fjmsv0"))))
     (build-system go-build-system)
     (arguments
      `(#:import-path "github.com/rs/curlie"))
diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index e25b88941a..3eeee9fadf 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -61,6 +61,7 @@
 ;;; Copyright © 2021, 2022 jgart <jgart@dismail.de>
 ;;; Copyright © 2023 Felix Gruber <felgru@posteo.ne
 ;;; Copyright © 2023 Munyoki Kilyungi <me@bonfacemunyoki.com>
+;;; Copyright © 2023 Giacomo Leidi <goodoldpaul@autistici.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -2973,14 +2974,16 @@ can autogenerate peewee models using @code{pwiz}, a model generator.")
 (define-public python-pypika-tortoise
   (package
     (name "python-pypika-tortoise")
-    (version "0.1.5")
+    (version "0.1.6")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pypika-tortoise" version))
        (sha256
-        (base32 "0j20574s2yrq8d7fav3816vj1nfpihkm2mj8jzh2ank4zixp8brf"))))
-    (build-system python-build-system)
+        (base32 "0dmzpsnlqjjz0vm0r9xjk69xfsm235bpnk3jccr8ww4s8y7qc0nq"))))
+    (build-system pyproject-build-system)
+    (native-inputs
+     (list poetry))
     (home-page "https://github.com/tortoise/pypika-tortoise")
     (synopsis "Pypika fork for tortoise-orm")
     (description "Pypika-tortoise is a fork of pypika which has been
@@ -3075,20 +3078,25 @@ of PyMySQL.  @code{aiomysql} tries to preserve the same API as the
 (define-public python-tortoise-orm
   (package
     (name "python-tortoise-orm")
-    (version "0.19.1")
+    (version "0.20.0")
     (source
      (origin
-       (method url-fetch)
-       (uri (pypi-uri "tortoise-orm" version))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/tortoise/tortoise-orm")
+             (commit version)))
+       (file-name (git-file-name name version))
        (sha256
-        (base32 "17yk71dlx5ai98i6ivqgsplkwivdxackz9jfn6z42bpcdgbpiwhg"))))
-    (build-system python-build-system)
+        (base32 "19rgyvs2y9gn27x71y7djdz6rb6bszgvprv55q1hr4266wy6g999"))))
+    (build-system pyproject-build-system)
     ;; The test suite relies on asynctest, which is abandoned and doesn't
     ;; support Python >= 3.8.
     (arguments '(#:tests? #f))
+    (native-inputs
+     (list poetry))
     (propagated-inputs
      (list python-aiomysql
-           python-aiosqlite
+           python-aiosqlite-0.17
            python-asyncmy
            python-asyncpg
            python-ciso8601
@@ -3106,6 +3114,48 @@ engraved in its design that you are working not with just tables, you work
 with relational data.")
     (license license:asl2.0)))
 
+(define-public aerich
+  (package
+    (name "aerich")
+    (version "0.7.2")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/tortoise/aerich")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "0pcy945bg890p12s7cyw0mg7hxwsxyy570j600sbf7kwj2d3lilg"))))
+    (build-system pyproject-build-system)
+    (native-inputs
+     (list poetry
+           python-bandit
+           python-cryptography
+           python-isort
+           python-pydantic
+           python-pytest
+           python-pytest-asyncio
+           python-pytest-mock
+           python-pytest-xdist))
+    (propagated-inputs
+     (list python-asyncmy
+           python-asyncpg
+           python-click
+           python-ddlparse
+           python-dictdiffer
+           python-tomlkit
+           python-tortoise-orm))
+    (home-page "https://github.com/tortoise/aerich")
+    (synopsis "Database migrations tool for Tortoise @acronym{ORM, Object Relational
+Mapper}")
+    (description
+     "This package provides @code{aerich}, a Python database migrations tool
+for Tortoise @acronym{ORM, Object Relational Mapper}.  It can be used both
+programmatically or as a standalone CLI application.")
+    (license license:asl2.0)))
+
 (define-public sqlcipher
   (package
     (name "sqlcipher")
@@ -3778,6 +3828,33 @@ async versions of all the standard connection and cursor methods, and context
 managers for automatically closing connections.")
     (license license:expat)))
 
+(define-public python-aiosqlite-0.17
+  (package
+    (inherit python-aiosqlite)
+    (version "0.17.0")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/omnilib/aiosqlite")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name (package-name python-aiosqlite)
+                                        version))
+              (sha256
+               (base32
+                "1agh7b9g7rgryvb8flph85i8m80ai1rinpljxzlsrs0s0y616qgg"))))
+    (build-system pyproject-build-system)
+    (arguments
+     '(#:phases (modify-phases %standard-phases
+                  (replace 'check
+                    (lambda* (#:key tests? #:allow-other-keys)
+                      (if tests?
+                          (invoke "python" "-m" "unittest" "aiosqlite.tests")
+                          (format #t "test suite not run~%")))))))
+    (propagated-inputs
+     (list python-typing-extensions))
+    (native-inputs
+     (list python-flit-core python-aiounittest))))
+
 (define-public python-databases
   (package
     (name "python-databases")
diff --git a/gnu/packages/dezyne.scm b/gnu/packages/dezyne.scm
index db3523ac3e..5e84875a42 100644
--- a/gnu/packages/dezyne.scm
+++ b/gnu/packages/dezyne.scm
@@ -32,14 +32,14 @@
 (define-public dezyne
   (package
     (name "dezyne")
-    (version "2.17.6")
+    (version "2.17.7")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://dezyne.org/download/dezyne/"
                            name "-" version ".tar.gz"))
        (sha256
-        (base32 "0z019yyvf1ac1l95j29wlayi2gmwa9sjqg31a4r89za1bijmk19k"))))
+        (base32 "09w2rl2ghm8z6fv3iflxnikcj2q98119imvlgvkmkhch5cplx7ny"))))
     (inputs (list bash-minimal
                   guile-3.0-latest
                   guile-json-4
diff --git a/gnu/packages/diffoscope.scm b/gnu/packages/diffoscope.scm
index 1b8b77d7a4..5ab54de0e9 100644
--- a/gnu/packages/diffoscope.scm
+++ b/gnu/packages/diffoscope.scm
@@ -74,7 +74,7 @@
 (define-public diffoscope
   (package
     (name "diffoscope")
-    (version "250")
+    (version "251")
     (source
      (origin
        (method git-fetch)
@@ -83,7 +83,7 @@
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "12cdsgxlva1gcry16w9x44ji9asar1n8p9q6rv2jd1gr9fi6l0sz"))))
+        (base32 "1200kzwqyw2m298z8rfbiiziprz4s1n176z42xyziwc6mbx8m09z"))))
     (build-system python-build-system)
     (arguments
      (list
diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm
index 7112a65181..07a9d4cbe7 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -95,7 +95,7 @@
 ;;; Copyright © 2021 Alexey Abramov <levenson@mmer.org>
 ;;; Copyright © 2021 Xinglu Chen <public@yoctocell.xyz>
 ;;; Copyright © 2021, 2022 Stefan Reichör <stefan@xsteve.at>
-;;; Copyright © 2021, 2022 Simon Tournier <zimon.toutoune@gmail.com>
+;;; Copyright © 2021, 2022, 2023 Simon Tournier <zimon.toutoune@gmail.com>
 ;;; Copyright © 2021 Eugene Klimov <lipklim@mailbox.org>
 ;;; Copyright © 2021 Zheng Junjie <873216071@qq.com>
 ;;; Copyright © 2021 David Dashyan <mail@davie.li>
@@ -795,6 +795,35 @@ configuration language which makes it trivial to write your own themes.")
 Common Lisp or Smalltalk, but for Emacs Lisp.")
       (license license:gpl3+))))
 
+(define-public emacs-treebundel
+  (package
+    (name "emacs-treebundel")
+    (version "0.1.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/purplg/treebundel")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1hk2xnjsr85in48h02xbzi8lsccp36li2bp9v9j0r8qn1bis2vv9"))))
+    (build-system emacs-build-system)
+    (propagated-inputs
+     (list emacs-compat))
+    (home-page "https://github.com/purplg/treebundel")
+    (synopsis "Bundle related git-worktrees together")
+    (description
+     "This package is used for bundling related git-worktrees from multiple
+repositories together.  This helps switch quickly between repositories and
+ensure you're on the correct branch.  When you're done with your changes, you
+can use the repositories in the workspace and know which ones were modified to
+simplify the process of getting the changes merged in together.  Additionally,
+git metadata is shared between all projects.  You can stash, pop, and pull
+changes in from the same repository in other workspaces thanks to the power of
+git-worktrees.")
+    (license license:expat)))
+
 (define-public emacs-tree-inspector
   (let ((commit "bbb8d2dfe84fbf857fcc1579de5a1324b09a877e"))
     (package
@@ -1730,6 +1759,27 @@ leveraging built-in functionality.")
 purpose finder.")
       (license license:gpl3+))))
 
+(define-public emacs-pacfiles-mode
+  (package
+    (name "emacs-pacfiles-mode")
+    (version "1.2")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/UndeadKernel/pacfiles-mode")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1d61s846r9ncmyx97f44r8i3p1ikgi4bab8k7xk868lja96y2ij7"))))
+    (build-system emacs-build-system)
+    (home-page "https://github.com/UndeadKernel/pacfiles-mode")
+    (synopsis "ArchLinux's pacnew and pacsave merging tool")
+    (description
+     "This Emacs major mode helps manage @file{.pacnew} and @file{.pacsave}
+files left by ArchLinux's pacman.")
+    (license license:expat)))
+
 (define-public emacs-minions
   (package
     (name "emacs-minions")
@@ -4547,6 +4597,30 @@ popup for completion candidates when using @code{emacs-corfu}.  It can
 be regarded as @code{emacs-company-quickhelp} for @code{emacs-corfu}.")
     (license license:gpl3+)))
 
+(define-public emacs-corfu-candidate-overlay
+  (package
+    (name "emacs-corfu-candidate-overlay")
+    (version "1.5")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://code.bsdgeek.org/adam/corfu-candidate-overlay")
+             (commit "265438b16155e899d82a869aebca16105665c998")))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "0i36g2i7435pby32vcapv4ydmp6rqn0r51qm91wqyzan1f3n3qck"))))
+    (build-system emacs-build-system)
+    (propagated-inputs (list emacs-corfu))
+    (license license:gpl3)
+    (home-page "https://code.bsdgeek.org/adam/corfu-candidate-overlay")
+    (synopsis "Show first Corfu's completion candidate in an overlay while
+ typing")
+    (description
+     "Simple corfu as-you-type auto-suggestion candidate overlay with a visual
+ indication of whether there are many or exactly one candidate available.")))
+
 (define-public emacs-cape
   (package
     (name "emacs-cape")
@@ -5068,6 +5142,30 @@ This buffer is typically shown as a sidebar (Emacs vertically splits the
 window).")
       (license license:gpl3+))))
 
+(define-public emacs-imenu-anywhere
+  (package
+    (name "emacs-imenu-anywhere")
+    (version "1.1.6")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/vspinu/imenu-anywhere")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0lbwfhcl40ayxskvmsvdrg8p63qp086xpzw61bqk4b3fxndxl04h"))))
+    (build-system emacs-build-system)
+    (home-page "https://github.com/vspinu/imenu-anywhere")
+    (synopsis
+     "Imenu tag selection across buffers with the same mode/project")
+    (description
+     "This Emacs package provides navigation for imenu tags across all buffers
+that satisfy a filtering criteria.  Available criteria are all buffers with
+the same major mode, same project buffers, and user-defined list of friendly
+mode buffers.")
+    (license license:gpl3+)))
+
 (define-public emacs-mmm-mode
   (package
     (name "emacs-mmm-mode")
@@ -9895,68 +9993,71 @@ in @code{html-mode}.")
     (license license:gpl3+)))
 
 (define-public emacs-slime
-  (package
-    (name "emacs-slime")
-    (version "2.28")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://github.com/slime/slime")
-             (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "1acmm4w1mv1qzpnkgc4wyiilbx8l0dk16sx8wv815ri5ks289rll"))))
-    (build-system emacs-build-system)
-    (arguments
-     (list
-      #:include #~(cons* "\\.lisp$" "\\.asd$"
-                         "contrib"
-                         "lib/hyperspec.el"
-                         %default-include)
-      #:exclude #~(list "^slime-tests.el" "^contrib/test/"
-                        "^contrib/Makefile$" "^contrib/README.md$")
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-before 'install 'configure
-            (lambda* _
-              (emacs-substitute-variables "slime.el"
-                ("inferior-lisp-program" "sbcl"))))
-          (add-before 'install 'install-doc
-            (lambda _
-              (let ((info-dir (string-append #$output "/share/info"))
-                    (doc-dir (string-append #$output "/share/doc/"
-                                            #$name "-" #$version))
-                    (doc-files '("doc/slime-refcard.pdf"
-                                 "README.md" "NEWS" "PROBLEMS"
-                                 "CONTRIBUTING.md")))
-                (with-directory-excursion "doc"
-                  (substitute* "Makefile"
-                    (("infodir=/usr/local/info")
-                     (string-append "infodir=" info-dir)))
-                  (invoke "make" "html/index.html")
-                  (invoke "make" "slime.info")
-                  (install-file "slime.info" info-dir)
-                  (copy-recursively "html" (string-append doc-dir "/html")))
-                (for-each (lambda (f)
-                            (install-file f doc-dir)
-                            (delete-file f))
-                          doc-files)
-                (delete-file-recursively "doc")))))))
-    (propagated-inputs
-     (list emacs-macrostep))
-    (native-inputs
-     (list texinfo))
-    (home-page "https://github.com/slime/slime")
-    (synopsis "Superior Lisp Interaction Mode for Emacs")
-    (description
-     "SLIME extends Emacs with support for interactive programming in
+  ;; Update together with sbcl-slime-swank.
+  (let ((commit "0cc2e736112a0bc2a048ef6efd11dd67e3fbf7ad")
+        (revision "0"))
+    (package
+      (name "emacs-slime")
+      (version (git-version "2.28" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/slime/slime")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "0iq9r4007rrnabj290y79i926x2m4j20j6b0x701pkywz926sn02"))))
+      (build-system emacs-build-system)
+      (arguments
+       (list
+        #:include #~(cons* "\\.lisp$" "\\.asd$"
+                           "contrib"
+                           "lib/hyperspec.el"
+                           %default-include)
+        #:exclude #~(list "^slime-tests.el" "^contrib/test/"
+                          "^contrib/Makefile$" "^contrib/README.md$")
+        #:phases
+        #~(modify-phases %standard-phases
+            (add-before 'install 'configure
+              (lambda* _
+                (emacs-substitute-variables "slime.el"
+                  ("inferior-lisp-program" "sbcl"))))
+            (add-before 'install 'install-doc
+              (lambda _
+                (let ((info-dir (string-append #$output "/share/info"))
+                      (doc-dir (string-append #$output "/share/doc/"
+                                              #$name "-" #$version))
+                      (doc-files '("doc/slime-refcard.pdf"
+                                   "README.md" "NEWS" "PROBLEMS"
+                                   "CONTRIBUTING.md")))
+                  (with-directory-excursion "doc"
+                    (substitute* "Makefile"
+                      (("infodir=/usr/local/info")
+                       (string-append "infodir=" info-dir)))
+                    (invoke "make" "html/index.html")
+                    (invoke "make" "slime.info")
+                    (install-file "slime.info" info-dir)
+                    (copy-recursively "html" (string-append doc-dir "/html")))
+                  (for-each (lambda (f)
+                              (install-file f doc-dir)
+                              (delete-file f))
+                            doc-files)
+                  (delete-file-recursively "doc")))))))
+      (propagated-inputs
+       (list emacs-macrostep))
+      (native-inputs
+       (list texinfo))
+      (home-page "https://github.com/slime/slime")
+      (synopsis "Superior Lisp Interaction Mode for Emacs")
+      (description
+       "SLIME extends Emacs with support for interactive programming in
 Common Lisp.  The features are centered around @command{slime-mode},
 an Emacs minor mode that complements the standard @command{lisp-mode}.
 While lisp-mode supports editing Lisp source files, @command{slime-mode}
 adds support for interacting with a running Common Lisp process
 for compilation, debugging, documentation lookup, and so on.")
-    (license (list license:gpl2+ license:public-domain))))
+      (license (list license:gpl2+ license:public-domain)))))
 
 (define-public emacs-popup
   (package
@@ -13016,7 +13117,7 @@ allowing unprefixed keys to insert their respective characters as expected.")
 (define-public emacs-clojure-mode
   (package
     (name "emacs-clojure-mode")
-    (version "5.17.0")
+    (version "5.18.0")
     (source
      (origin
        (method git-fetch)
@@ -13025,7 +13126,7 @@ allowing unprefixed keys to insert their respective characters as expected.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0knx3y53z0dn49xisa78bac55vhhkwxs2iw3jvalx41wfwvkirxc"))))
+        (base32 "0g4x587fpzcj9y59k8sb1g7c6yvga9gjs8ximpmar7d8jq2cv5qa"))))
     (build-system emacs-build-system)
     (native-inputs
      (list emacs-buttercup emacs-dash emacs-paredit emacs-s))
@@ -13068,7 +13169,7 @@ Clojure projects from templates.")
 (define-public emacs-clj-refactor
   (package
     (name "emacs-clj-refactor")
-    (version "3.9.4")
+    (version "3.10.0")
     (source
      (origin
        (method git-fetch)
@@ -13077,7 +13178,7 @@ Clojure projects from templates.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1j9pkkpnbvyl9p45dycngdiq2kyj6bmyb709pdxj3nar2d8ryl1h"))))
+        (base32 "100ngpgvff0xvw1h5krvh40sa3ympl241imwskcv62yk29m9z411"))))
     (build-system emacs-build-system)
     (propagated-inputs
      (list emacs-cider
@@ -13484,30 +13585,44 @@ E-Prime forbids the use of the \"to be\" form to strengthen your writing.")
       (license license:gpl3+))))
 
 (define-public emacs-julia-mode
+  ;; Last release was in March 2020.
+  (let ((commit "7a8c868e0d3e51ba4a2c621ee22ca9599e0e4bbb")
+        (revision "0"))
     (package
       (name "emacs-julia-mode")
-      (version "0.4")
+      (version (git-version "0.4" revision commit))
       (source
        (origin
          (method git-fetch)
          (uri (git-reference
                (url "https://github.com/JuliaEditorSupport/julia-emacs")
-               (commit version)))
+               (commit commit)))
          (file-name (git-file-name name version))
          (sha256
           (base32
-           "1w131jb9mhvyjxa0p93iwfhzidgbcs6b8i6jg79yisqb9wchik99"))))
+           "0xwd4kq69ray6bk8hwjxnqf7myc3mn36chc2l9jn7a0x1f8x6k10"))))
       (build-system emacs-build-system)
       (arguments
-       `(#:tests? #t
-         #:test-command '("emacs" "--batch"
-                          "-l" "julia-mode-tests.el"
-                          "-f" "ert-run-tests-batch-and-exit")))
+       (list
+        #:tests? #t
+        #:test-command #~(list "emacs" "--batch"
+                               "-l" "julia-mode-tests.el"
+                               "-f" "ert-run-tests-batch-and-exit")
+        #:phases
+        #~(modify-phases %standard-phases
+            (add-before 'check 'fix-test
+              (lambda _
+                (substitute* "julia-mode-tests.el"
+                  ;; The test started failing with Emacs 29; see
+                  ;; <https://github.com/JuliaEditorSupport/julia-emacs/issues/199>
+                  ;; and discrepancy reported <https://issues.guix.gnu.org/66763>.
+                  (("julia--test-end-of-defun-nested-2.*" all)
+                   (string-append all "  :expected-result :failed\n"))))))))
       (home-page "https://github.com/JuliaEditorSupport/julia-emacs")
       (synopsis "Major mode for Julia")
       (description "This Emacs package provides a mode for the Julia
 programming language.")
-      (license license:expat)))
+      (license license:expat))))
 
 (define-public emacs-julia-repl
   (package
@@ -15219,7 +15334,7 @@ implementation.")
 (define-public emacs-cider
   (package
     (name "emacs-cider")
-    (version "1.7.0")
+    (version "1.9.0")
     (source
      (origin
        (method git-fetch)
@@ -15228,10 +15343,11 @@ implementation.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0jqjgygdvny1vhjbx7k0l492fhamwndsjcbb2mccwp9j47k4qar9"))))
+        (base32 "0sjscbi3qgwn3wcpq5lz7k4gam69h0svh8wbhxcbskr9ys1rmysp"))))
     (build-system emacs-build-system)
     (arguments
-     '(#:exclude                        ;don't exclude 'cider-test.el'
+     '(#:include (cons* "^lein\\.sh$" "^clojure\\.sh$" %default-include)
+       #:exclude                        ;don't exclude 'cider-test.el'
        '("^\\.dir-locals\\.el$" "^test/")
        #:phases
        ;; XXX: file "test/cider-tests.el" contains a bogus "/bin/command"
@@ -16398,8 +16514,6 @@ programming and reproducible research.")
          (add-after 'unpack 'enter-source-directory
            (lambda _
              (chdir "lisp"))))))
-    (native-inputs
-     (list emacs-cider))
     (propagated-inputs
      (list emacs-org))
     (home-page "https://git.sr.ht/~bzg/org-contrib")
@@ -18858,7 +18972,7 @@ It should enable you to implement low-level X11 applications.")
 (define-public emacs-exwm
   (package
     (name "emacs-exwm")
-    (version "0.27")
+    (version "0.28")
     (synopsis "Emacs X window manager")
     (source
      (origin
@@ -18866,7 +18980,7 @@ It should enable you to implement low-level X11 applications.")
        (uri (string-append "https://elpa.gnu.org/packages/"
                            "exwm-" version ".tar"))
        (sha256
-        (base32 "094k33clmxhnab0wniyrs48sdz28kna2g6fmkhsd7n20nmhhc4sn"))))
+        (base32 "00h5awqazk807zxvb02a9dp8gd5ifi3y1kcwmr1czk6kdmkjx32l"))))
     (build-system emacs-build-system)
     (propagated-inputs
      (list emacs-xelb))
@@ -28172,6 +28286,27 @@ editors to read the file format and adhere to defined styles.  EditorConfig
 files are easily readable and they work nicely with version control systems.")
     (license license:gpl3+)))
 
+(define-public emacs-nerd-icons
+  (package
+    (name "emacs-nerd-icons")
+    (version "0.1.0")
+    (home-page "https://github.com/rainstormstudio/nerd-icons.el")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference (url home-page) (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "0ggj6lm02m7nb5gxnqs2v2lkxsclml6kq176vam9qyg1fsm7yvdw"))))
+    (build-system emacs-build-system)
+    (arguments
+     (list #:include #~(cons "^data\\/" %default-include)))
+    (synopsis "Library for easily using nerd font icons inside Emacs")
+    (description "Nerd-icons an alternative to all-the-icons.  It works on both
+GUI and terminal, and requires a nerd font installed on your system.")
+    (license license:gpl3+)))
+
 (define-public emacs-all-the-icons
   (package
     (name "emacs-all-the-icons")
@@ -32854,7 +32989,7 @@ simple but powerful Org contents.")
       (source (origin
                 (method git-fetch)
                 (uri (git-reference
-                      (url "https://gitlab.com/nsavage/ox-rss")
+                      (url "https://github.com/BenedictHW/ox-rss")
                       (commit commit)))
                 (file-name (git-file-name name version))
                 (sha256
@@ -32918,7 +33053,7 @@ time.")
 (define-public emacs-mastodon
   (package
     (name "emacs-mastodon")
-    (version "1.0.6")
+    (version "1.0.13")
     (source
      (origin
        (method git-fetch)
@@ -32927,7 +33062,7 @@ time.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1z5lmzxhindxa0f6qi6z361k9smqcz68alr6w6jbmwg279qmk8jj"))))
+        (base32 "143wmg9jhdi79y1gdi0y9xxpp8vyn7qbhvaysq1sf7g1h0jskxc2"))))
     (build-system emacs-build-system)
     (arguments
      (list
@@ -33980,7 +34115,7 @@ contributed packages to Telega.")))
 (define-public emacs-doom-modeline
   (package
     (name "emacs-doom-modeline")
-    (version "3.4.0")
+    (version "4.0.1")
     (source
      (origin
        (method git-fetch)
@@ -33988,14 +34123,14 @@ contributed packages to Telega.")))
              (url "https://github.com/seagle0128/doom-modeline")
              (commit (string-append "v" version))))
        (sha256
-        (base32 "1z5cqn33v7sjihs05ycz1yzi5wcg90yn3cy09qj9g5g8pjs8qdki"))
+        (base32 "0pwfmj01cqij84dig5qj86n7f4cva5mdjqahr0061byrlv9xrpzb"))
        (file-name (git-file-name name version))))
     (build-system emacs-build-system)
     (arguments
      `(#:test-command '("ert-runner")))
     (native-inputs (list emacs-ert-runner))
     (propagated-inputs
-     (list emacs-all-the-icons emacs-compat emacs-dash emacs-shrink-path))
+     (list emacs-nerd-icons emacs-compat emacs-shrink-path))
     (synopsis "Fancy and fast mode-line inspired by minimalism design")
     (description "Doom modeline is a complete modeline for GNU Emacs inspired
 by the Doom theme collection.  This modeline features support for mode-specific
@@ -35899,6 +36034,26 @@ should replace it.  However, if you call them again immediately after, they
 restore that occurrence of the placeholder and move to the next.")
       (license license:gpl3+))))
 
+(define-public emacs-pddl-mode
+  (package
+    (name "emacs-pddl-mode")
+    (version "0.100")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/emacsmirror/pddl-mode")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1zq5a0sv8am1c1gxky80dsi39gqsgnwbasv3nw4993r3ccz180r8"))))
+    (build-system emacs-build-system)
+    (home-page "https://github.com/emacsmirror/pddl-mode")
+    (synopsis "Emacs mode for PDDL files")
+    (description "This package provides a major mode for browsing and editing
+PDDL files with syntax highlighting, templates, auto-completion, and more.")
+    (license license:gpl2+)))
+
 (define-public emacs-plantuml-mode
   (package
     (name "emacs-plantuml-mode")
diff --git a/gnu/packages/emulators.scm b/gnu/packages/emulators.scm
index 0cb947c58a..0729feb071 100644
--- a/gnu/packages/emulators.scm
+++ b/gnu/packages/emulators.scm
@@ -1431,7 +1431,7 @@ as RetroArch.")
 (define-public retroarch
   (package
     (name "retroarch")
-    (version "1.15.0")
+    (version "1.16.0.3")
     (source
      (origin
        (method git-fetch)
@@ -1440,7 +1440,7 @@ as RetroArch.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1ii31mc7wfd386rzyxqk8nmx5a13f9iqz47991z4zx0d8gqcchzg"))))
+        (base32 "1nvvd78hx1s73nif7g02pqms29b9v072mxnld0vmsh78236qngq5"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f                      ; no tests
@@ -1471,26 +1471,36 @@ as RetroArch.")
                  ;; Non-free software are available through the core updater,
                  ;; disable it.  See <https://issues.guix.gnu.org/38360>.
                  "--disable-update_cores"
-                 "--disable-builtinzlib")))))))
+                 "--disable-builtinmbedtls"
+                 "--disable-builtinbearssl"
+                 "--disable-builtinzlib"
+                 "--disable-builtinflac"
+                 "--disable-builtinglslang")))))))
     (inputs
-     `(("alsa-lib" ,alsa-lib)
-       ("ffmpeg" ,ffmpeg-4)
-       ("freetype" ,freetype)
-       ("libxinerama" ,libxinerama)
-       ("libxkbcommon" ,libxkbcommon)
-       ("libxml2" ,libxml2)
-       ("libxrandr" ,libxrandr)
-       ("libxv" ,libxv)
-       ("mesa" ,mesa)
-       ("openal" ,openal)
-       ("pulseaudio" ,pulseaudio)
-       ("python" ,python)
-       ("qtbase" ,qtbase-5)
-       ("sdl" ,sdl2)
-       ("udev" ,eudev)
-       ("vulkan-loader" ,vulkan-loader)
-       ("wayland" ,wayland)
-       ("zlib" ,zlib)))
+     (list alsa-lib
+           eudev
+           ffmpeg
+           flac
+           freetype
+           glslang
+           libxinerama
+           libxkbcommon
+           libxml2
+           libxrandr
+           libxv
+           mbedtls-apache
+           mesa
+           openal
+           openssl
+           pulseaudio
+           python
+           qtbase-5
+           sdl2
+           spirv-headers
+           spirv-tools
+           vulkan-loader
+           wayland
+           zlib))
     (native-inputs
      (list pkg-config wayland-protocols which))
     (native-search-paths
diff --git a/gnu/packages/firmware.scm b/gnu/packages/firmware.scm
index a674421157..294bbea184 100644
--- a/gnu/packages/firmware.scm
+++ b/gnu/packages/firmware.scm
@@ -10,6 +10,7 @@
 ;;; Copyright © 2021 Petr Hodina <phodina@protonmail.com>
 ;;; Copyright © 2022, 2023 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;; Copyright © 2023 Foundation Devices, Inc. <hello@foundationdevices.com>
+;;; Copyright © 2023 Zheng Junjie <873216071@qq.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -174,6 +175,8 @@ Linux-libre.")
                     (guix build gnu-build-system)
                     (guix build utils))
          #:tests? #f                    ; no tests
+         #:make-flags `(,(string-append "PREFIX=" (assoc-ref %outputs "out"))
+                        ,(string-append "CC=" ,(cc-for-target)))
          #:phases
          (let ((subdirs '("assembler" "disassembler")))
            (modify-phases %standard-phases
@@ -181,24 +184,19 @@ Linux-libre.")
              (add-before 'build 'patch-/bin/true
                (lambda _
                  (substitute* (find-files "." "Makefile")
-                   (("/bin/true") ":"))
-                 #t))
+                   (("/bin/true") ":"))))
              (replace 'build
-               (lambda _
+               (lambda* (#:key (make-flags '()) #:allow-other-keys)
                  (for-each (lambda (dir)
-                             (invoke "make" "-C" dir "CC=gcc"))
-                           subdirs)
-                 #t))
+                             (apply invoke "make" "-C" dir make-flags))
+                           subdirs)))
              (replace 'install
-               (lambda* (#:key outputs #:allow-other-keys)
+               (lambda* (#:key outputs (make-flags '()) #:allow-other-keys)
                  (let ((out (assoc-ref outputs "out")))
                    (mkdir-p (string-append out "/bin"))
                    (for-each (lambda (dir)
-                               (invoke "make" "-C" dir
-                                       (string-append "PREFIX=" out)
-                                       "install"))
-                             subdirs)
-                   #t)))))))
+                               (apply invoke "make" "-C" dir "install" make-flags))
+                             subdirs))))))))
       (home-page
        "https://bues.ch/cms/hacking/misc.html#linux_b43_driver_firmware_tools")
       (synopsis "Collection of tools for the b43 wireless driver")
@@ -397,6 +395,7 @@ broadband modem as found, for example, on PinePhone.")
       #:test-target "tests"
       #:make-flags
       #~(list (string-append "CC=" #$(cc-for-target))
+              (string-append "STRIP=" #$(strip-for-target))
               (string-append "DESTDIR=" #$output))
       #:phases
       #~(modify-phases %standard-phases
diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm
index eb1d74d1e1..1d9abd9705 100644
--- a/gnu/packages/game-development.scm
+++ b/gnu/packages/game-development.scm
@@ -2055,7 +2055,7 @@ scripted in a Python-like language.")
 (define-public godot
   (package
     (name "godot")
-    (version "4.1.1")
+    (version "4.1.2")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -2064,7 +2064,7 @@ scripted in a Python-like language.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1byy4zdsj8nq54rhmij7kl0mdh4zv3c056y6c7rjy17bqjq2n8fh"))
+                "1zm07rknpjkvyxpiscqsx5hi4gc5wi647jlhillxdf85b36s6q9j"))
               (modules '((guix build utils)
                          (ice-9 ftw)
                          (srfi srfi-1)))
diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm
index 2387ad3fc6..8313c02754 100644
--- a/gnu/packages/games.scm
+++ b/gnu/packages/games.scm
@@ -1071,10 +1071,10 @@ want what you have.")
     (license license:cc-by-sa3.0)))
 
 (define-public cockatrice
-  (let ((release-date "2021-01-26"))
+  (let ((release-date "2023-09-14"))
     (package
       (name "cockatrice")
-      (version "2.8.0")
+      (version "2.9.0")
       (source
        (origin
          (method git-fetch)
@@ -1084,7 +1084,7 @@ want what you have.")
          (file-name (git-file-name name version))
          (sha256
           (base32
-           "0q8ffcklb2b7hcqhy3d2f9kz9aw22pp04pc9y4sslyqmf17pwnz9"))
+           "1jhn6pprd3j8m312mm8nlb9hwcchg3qkks5rw0x7d22alk922dlv"))
          (modules '((guix build utils)))
          (snippet
           ;; Strip image URLs as they point towards non-free web services
@@ -6926,7 +6926,7 @@ fish.  The whole game is accompanied by quiet, comforting music.")
 (define-public crawl
   (package
     (name "crawl")
-    (version "0.29.1")
+    (version "0.30.1")
     (source
      (origin
        (method git-fetch)
@@ -6935,7 +6935,7 @@ fish.  The whole game is accompanied by quiet, comforting music.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "17bl8hdv2z3mpdfmd5gnwg3r1p9dqjbisiql24pxs1d33qcw0h7x"))
+        (base32 "1rlp8z1n7ziv7aaa3fb4h4nnq24pfz1m23a99c1ra582fh0yx1pl"))
        (patches (search-patches "crawl-upgrade-saves.patch"))))
     (build-system gnu-build-system)
     (inputs
@@ -7324,7 +7324,7 @@ Crowther & Woods, its original authors, in 1995.  It has been known as
 (define-public tome4
   (package
     (name "tome4")
-    (version "1.7.4")
+    (version "1.7.6")
     (synopsis "Single-player, RPG roguelike game set in the world of Eyal")
     (source
      (origin
@@ -7332,104 +7332,104 @@ Crowther & Woods, its original authors, in 1995.  It has been known as
        (uri (string-append "https://te4.org/dl/t-engine/t-engine4-src-"
                            version ".tar.bz2"))
        (sha256
-        (base32 "197jmd99l3w3sig32pvdlq9fcgdjjx7g9csy08kz174cyhrlyly3"))
+        (base32 "0338lirc4jbmq29449bw8c6src8b91yn9x14w2nxr31zh00fm7cq"))
        (modules '((guix build utils)))))
     (build-system gnu-build-system)
     (native-inputs
      (list unzip))
     (inputs
-     `(("sdl-union" ,(sdl-union (list sdl2 sdl2-image sdl2-mixer sdl2-ttf)))
-       ("glu" ,glu)
-       ("premake4" ,premake4)
-       ("openal" ,openal)
-       ("vorbis" ,libvorbis)
-       ("luajit" ,luajit)))
+     (list glu
+           libvorbis
+           luajit
+           openal
+           premake4
+           (sdl-union (list sdl2 sdl2-image sdl2-mixer sdl2-ttf))))
     (arguments
-     `(#:make-flags
-       (list (string-append "CC=" ,(cc-for-target))
-             "config=release")
-       ;; XXX: Building in parallel occasionally causes this build failure:
-       ;;   ../src/luajit2/src/host/buildvm.c:73:10: fatal error: buildvm_arch.h:
-       ;;   No such file or directory
-       #:parallel-build? #f
-       #:phases (modify-phases %standard-phases
-                  (delete 'bootstrap)
-                  (replace 'configure
-                    (lambda _
-                      (invoke "premake4" "gmake")))
-                  (add-after 'set-paths 'set-sdl-paths
-                    (lambda* (#:key inputs #:allow-other-keys)
-                      (setenv "CPATH"
-                              (string-append
-                               (search-input-directory inputs "/include/SDL2")
-                               ":" (or (getenv "CPATH") "")))))
-                  (delete 'check)
-                  ;; premake doesn't provide install target
-                  (replace 'install
-                    (lambda* (#:key inputs outputs #:allow-other-keys)
-                      (let* ((out (assoc-ref outputs "out"))
-                             (usr (string-append out "/usr"))
-                             (bin (string-append out "/bin"))
-                             (licenses (string-append out "/share/licenses"))
-                             (documents (string-append out "/share/doc"))
-                             (pixmaps (string-append out "/share/pixmaps"))
-                             (icon "te4-icon.png")
-                             (data (string-append out "/share/" ,name))
-                             (applications (string-append
-                                            out "/share/applications"))
-                             (unzip (string-append
-                                     (assoc-ref inputs "unzip") "/bin/unzip"))
-                             (wrapper (string-append bin "/" ,name)))
-                        ;; icon
-                        (mkdir-p pixmaps)
-                        (invoke unzip "-j"
-                                (string-append
-                                 "game/engines/te4-" ,version ".teae")
-                                (string-append
-                                 "data/gfx/" icon) "-d" pixmaps)
-                        ;; game executable
-                        (install-file "t-engine" data)
-                        (mkdir-p bin)
-                        (with-output-to-file wrapper
-                          (lambda ()
-                            (display
-                             (string-append
-                              "#!/bin/sh\n"
-                              ;; No bootstrap code found,
-                              ;; defaulting to working directory
-                              ;; for engine code!
-                              "cd " data "\n"
-                              "exec -a tome4 ./t-engine \"$@\"\n"))))
-                        (chmod wrapper #o555)
-                        ;; licenses
-                        (for-each (lambda (file)
-                                    (install-file file licenses))
-                                  '("COPYING" "COPYING-MEDIA"))
-                        ;; documents
-                        (for-each (lambda (file)
-                                    (install-file file documents))
-                                  '("CONTRIBUTING" "CREDITS"))
-                        ;; data
-                        (copy-recursively "bootstrap" (string-append
-                                                       data "/bootstrap"))
-                        (copy-recursively "game" (string-append data "/game"))
-                        ;; launcher
-                        (mkdir-p applications)
-                        (make-desktop-entry-file
-                         (string-append applications "/" ,name ".desktop")
-                         #:name "ToME4"
-                         #:comment ,synopsis
-                         #:exec ,name
-                         #:icon icon
-                         #:categories '("Game" "RolePlaying"))))))))
+     (list
+      #:tests? #false                   ;no test
+      #:make-flags
+      #~(list (string-append "CC=" #$(cc-for-target))
+              "config=release")
+      ;; XXX: Building in parallel occasionally causes this build failure:
+      ;;   ../src/luajit2/src/host/buildvm.c:73:10: fatal error: buildvm_arch.h:
+      ;;   No such file or directory
+      #:parallel-build? #f
+      #:phases
+      #~(modify-phases %standard-phases
+          (delete 'bootstrap)
+          (replace 'configure
+            (lambda _
+              (invoke "premake4" "gmake")))
+          (add-after 'set-paths 'set-sdl-paths
+            (lambda* (#:key inputs #:allow-other-keys)
+              (setenv "CPATH"
+                      (string-append
+                       (search-input-directory inputs "/include/SDL2")
+                       ":" (or (getenv "CPATH") "")))))
+          ;; premake doesn't provide install target
+          (replace 'install
+            (lambda* (#:key inputs outputs #:allow-other-keys)
+              (let* ((out (assoc-ref outputs "out"))
+                     (usr (string-append out "/usr"))
+                     (bin (string-append out "/bin"))
+                     (licenses (string-append out "/share/licenses"))
+                     (documents (string-append out "/share/doc"))
+                     (pixmaps (string-append out "/share/pixmaps"))
+                     (icon "te4-icon.png")
+                     (data (string-append out "/share/" #$name))
+                     (applications (string-append
+                                    out "/share/applications"))
+                     (unzip (string-append
+                             (assoc-ref inputs "unzip") "/bin/unzip"))
+                     (wrapper (string-append bin "/" #$name)))
+                ;; icon
+                (mkdir-p pixmaps)
+                (invoke unzip "-j"
+                        (string-append
+                         "game/engines/te4-" #$version ".teae")
+                        (string-append
+                         "data/gfx/" icon) "-d" pixmaps)
+                ;; game executable
+                (install-file "t-engine" data)
+                (mkdir-p bin)
+                (with-output-to-file wrapper
+                  (lambda ()
+                    (display
+                     (string-append
+                      "#!/bin/sh\n"
+                      ;; No bootstrap code found,
+                      ;; defaulting to working directory
+                      ;; for engine code!
+                      "cd " data "\n"
+                      "exec -a tome4 ./t-engine \"$@\"\n"))))
+                (chmod wrapper #o555)
+                ;; licenses
+                (for-each (lambda (file)
+                            (install-file file licenses))
+                          '("COPYING" "COPYING-MEDIA"))
+                ;; documents
+                (for-each (lambda (file)
+                            (install-file file documents))
+                          '("CONTRIBUTING" "CREDITS"))
+                ;; data
+                (copy-recursively "bootstrap" (string-append
+                                               data "/bootstrap"))
+                (copy-recursively "game" (string-append data "/game"))
+                ;; launcher
+                (mkdir-p applications)
+                (make-desktop-entry-file
+                 (string-append applications "/" #$name ".desktop")
+                 #:name "ToME4"
+                 #:comment #$synopsis
+                 #:exec #$name
+                 #:icon icon
+                 #:categories '("Game" "RolePlaying"))))))))
     (home-page "https://te4.org")
     (description "Tales of Maj’Eyal (ToME) RPG, featuring tactical turn-based
 combat and advanced character building.  Play as one of many unique races and
 classes in the lore-filled world of Eyal, exploring random dungeons, facing
 challenging battles, and developing characters with your own tailored mix of
-abilities and powers.  With a modern graphical and customisable interface,
-intuitive mouse control, streamlined mechanics and deep, challenging combat,
-Tales of Maj’Eyal offers engaging roguelike gameplay for the 21st century.")
+abilities and powers.")
     (license license:gpl3+)))
 
 (define-public quakespasm
@@ -10366,6 +10366,55 @@ ChessX.")
       (home-page "https://stockfishchess.org/")
       (license license:gpl3+))))
 
+(define-public moonfish
+  (let ((commit "4f8829009e8c26e6a878261e0bc4c7e7617ef6b6")
+        (revision "1"))
+    (package
+      (name "moonfish")
+      (version (git-version "0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://git.sr.ht/~zamfofex/moonfish")
+                      (commit commit)))
+                (sha256
+                 (base32
+                  "1ksg42x9cyn3pbfryy9raqb355k47cqcisascpy157c3cgdr2z60"))
+                (file-name (git-file-name name version))))
+      (build-system gnu-build-system)
+      (arguments
+       (list
+        #:make-flags
+        #~(list (string-append "CC=" #$(cc-for-target)))
+        #:tests? #f                     ;no check target
+        #:phases
+        #~(modify-phases %standard-phases
+            (delete 'configure)         ;no configure script
+            (replace 'install           ;no 'install' target
+              (lambda _
+                (let* ((out-bin (string-append #$output "/bin"))
+                       (tools-bin (string-append #$output:tools "/bin"))
+                       (tool (string-append tools-bin "/moonfish-")))
+                  (mkdir-p out-bin)
+                  (mkdir-p tools-bin)
+                  (copy-file "moonfish"
+                             (string-append out-bin "/moonfish"))
+                  (copy-file "play"
+                             (string-append tool "play"))
+                  (copy-file "lichess"
+                             (string-append tool "lichess"))
+                  (copy-file "analyse"
+                             (string-append tool "analyse"))))))))
+      (inputs (list bearssl cjson))
+      (outputs '("out" "tools"))
+      (home-page "https://git.sr.ht/~zamfofex/moonfish")
+      (synopsis "Simple chess engine written in C")
+      (description
+       "moonfish is a toy UCI chess engine made for fun.  It is inspired by
+sunfish, but is written in C rather than Python.  It also has TUI tools for
+using any UCI engine and also to connect UCI engines to Lichess.")
+      (license license:agpl3+))))
+
 (define-public barrage
   (package
     (name "barrage")
diff --git a/gnu/packages/gcc.scm b/gnu/packages/gcc.scm
index 04926e6385..e352cff5f9 100644
--- a/gnu/packages/gcc.scm
+++ b/gnu/packages/gcc.scm
@@ -706,17 +706,16 @@ It also includes runtime support libraries for these languages.")
 (define-public gcc-10
   (package
    (inherit gcc-8)
-   (version "10.4.0")
+   (version "10.5.0")
    (source (origin
             (method url-fetch)
             (uri (string-append "mirror://gnu/gcc/gcc-"
                                 version "/gcc-" version ".tar.xz"))
             (sha256
              (base32
-              "1wg4xdizkksmwi66mvv2v4pk3ja8x64m7v9gzhykzd3wrmdpsaf9"))
+              "1h87lcfaga0ydsf4pkhwlnjr8mky5ix8npbv6iy3jvzlzm1ra415"))
             (patches (search-patches "gcc-9-strmov-store-file-names.patch"
-                                     "gcc-5.0-libvtv-runpath.patch"
-                                     "gcc-10-tree-sra-union-handling.patch"))
+                                     "gcc-5.0-libvtv-runpath.patch"))
             (modules '((guix build utils)))
             (snippet gcc-canadian-cross-objdump-snippet)))
    (properties
@@ -1059,7 +1058,6 @@ as the 'native-search-paths' field."
                  (package-outputs gcc)
                  (delete "lib" (package-outputs gcc))))
     (native-search-paths search-paths)
-    (properties (alist-delete 'hidden? (package-properties gcc)))
     (arguments
      (substitute-keyword-arguments (package-arguments gcc)
        ((#:modules modules %gnu-build-system-modules)
@@ -1079,7 +1077,9 @@ as the 'native-search-paths' field."
                 (for-each
                  delete-file
                  (find-files (string-append (assoc-ref outputs "out") "/bin")
-                             ".*(c\\+\\+|cpp|g\\+\\+|gcov|gcc|lto)(-.*)?$"))))))))))
+                             ".*(c\\+\\+|cpp|g\\+\\+|gcov|gcc|lto)(-.*)?$"))))))))
+    (properties `((upstream-name . "gcc")
+                  ,@(alist-delete 'hidden? (package-properties gcc))))))
 
 (define %generic-search-paths
   ;; This is the language-neutral search path for GCC.  Entries in $CPATH are
@@ -1224,15 +1224,22 @@ provides the GNU compiler for the Go programming language."))
               ;; a cyclic dependency.  <http://debbugs.gnu.org/18101>
               #:separate-lib-output? #f))
 
+;; Provides go-1.14.6
 (define-public gccgo-10
   (make-gccgo gcc-10))
 
+;; Provides go-1.16.5
 (define-public gccgo-11
   (make-gccgo gcc-11))
 
+;; Provides go-1.18
 (define-public gccgo-12
   (make-gccgo gcc-12))
 
+;; Provides go-1.18
+(define-public gccgo-13
+  (make-gccgo gcc-13))
+
 (define %objc-search-paths
   (list (search-path-specification
          (variable "OBJC_INCLUDE_PATH")
diff --git a/gnu/packages/gnuzilla.scm b/gnu/packages/gnuzilla.scm
index 8e56b0af63..dc129ff498 100644
--- a/gnu/packages/gnuzilla.scm
+++ b/gnu/packages/gnuzilla.scm
@@ -547,9 +547,9 @@ variable defined below.  It requires guile-json to be installed."
 ;; XXXX: Workaround 'snippet' limitations.
 (define computed-origin-method (@@ (guix packages) computed-origin-method))
 
-(define %icecat-base-version "115.3.1")
+(define %icecat-base-version "115.4.0")
 (define %icecat-version (string-append %icecat-base-version "-guix0-preview1"))
-(define %icecat-build-id "20230928000000") ;must be of the form YYYYMMDDhhmmss
+(define %icecat-build-id "20231024000000") ;must be of the form YYYYMMDDhhmmss
 
 ;; 'icecat-source' is a "computed" origin that generates an IceCat tarball
 ;; from the corresponding upstream Firefox ESR tarball, using the 'makeicecat'
@@ -569,12 +569,12 @@ variable defined below.  It requires guile-json to be installed."
                   "firefox-" upstream-firefox-version ".source.tar.xz"))
             (sha256
              (base32
-              "0lqymabkhxpdhmgz81if8za1hdakh8nlm4cmsir4y1fa95p2bnkx"))))
+              "0ndf8b6qj0f178k5yq9s9mjgj9csb62f0igy74dzj28vlgrxn7y3"))))
 
          ;; The upstream-icecat-base-version may be older than the
          ;; %icecat-base-version.
-         (upstream-icecat-base-version "115.3.1")
-         (gnuzilla-commit "1b0f0ba84716023657dd7dff72cb408e35380a60")
+         (upstream-icecat-base-version "115.4.0")
+         (gnuzilla-commit "5b2ce0c4cefc73f996f260edfac368ecc3d86b24")
          (gnuzilla-source
           (origin
             (method git-fetch)
@@ -586,7 +586,7 @@ variable defined below.  It requires guile-json to be installed."
                                       (string-take gnuzilla-commit 8)))
             (sha256
              (base32
-              "0kvdyg2kzjabldqa10any5ad8r06pcybamvfnkn7nwcvd86g8s0v"))))
+              "13a0rv6b2vcf2mv7bfbb0rlx08pi0bz29dig0xrfdy3m1p39apla"))))
 
          ;; 'search-patch' returns either a valid file name or #f, so wrap it
          ;; in 'assume-valid-file-name' to avoid 'local-file' warnings.
diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm
index b32e379e47..9c707e5414 100644
--- a/gnu/packages/golang.scm
+++ b/gnu/packages/golang.scm
@@ -10826,7 +10826,7 @@ additions.")
 (define-public go-github-com-hjson-hjson-go
   (package
     (name "go-github-com-hjson-hjson-go")
-    (version "3.1.0")
+    (version "4.3.1")
     (source
      (origin
        (method git-fetch)
@@ -10836,7 +10836,7 @@ additions.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "1dfdiahimg6z9idg8jiqxwnlwjnmasbjccx8gnag49cz4yfqskaz"))))
+         "138vmbnrwzxf64cia27k407clrydvs2jx927dlv6ziydiqyvy7m3"))))
     (build-system go-build-system)
     (arguments
      '(#:import-path "github.com/hjson/hjson-go"))
diff --git a/gnu/packages/guile-xyz.scm b/gnu/packages/guile-xyz.scm
index 982eebacba..2a13c3e44a 100644
--- a/gnu/packages/guile-xyz.scm
+++ b/gnu/packages/guile-xyz.scm
@@ -46,6 +46,7 @@
 ;;; Copyright © 2022, 2023 Zheng Junjie <873216071@qq.com>
 ;;; Copyright © 2022 Evgeny Pisemsky <evgeny@pisemsky.com>
 ;;; Copyright © 2022 jgart <jgart@dismail.de>
+;;; Copyright © 2023 Andrew Tropin <andrew@trop.in>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -119,6 +120,7 @@
   #:use-module (gnu packages tex)
   #:use-module (gnu packages texinfo)
   #:use-module (gnu packages tls)
+  #:use-module (gnu packages tree-sitter)
   #:use-module (gnu packages version-control)
   #:use-module (gnu packages webkit)
   #:use-module (gnu packages xdisorg)
@@ -728,7 +730,7 @@ you send to a FIFO file.")
 (define-public guile-dsv
   (package
     (name "guile-dsv")
-    (version "0.7.0")
+    (version "0.7.1")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -737,7 +739,7 @@ you send to a FIFO file.")
               (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
-                "0shrzmbh6x3n3xzpcijkxk3f73z6m1i50zgc2dnnccwf4j1c78p2"))))
+                "18v8snh45ibh13mvihhajs226yflxpl6v09wqndyfj1da8cdmkzk"))))
     (build-system gnu-build-system)
     (native-inputs (list autoconf
                          automake
@@ -757,6 +759,7 @@ you send to a FIFO file.")
        #:imported-modules ((guix build guile-build-system)
                            ,@%gnu-build-system-modules)
        #:phases (modify-phases %standard-phases
+                  (delete 'strip)
                   (add-after 'install 'wrap-program
                     (lambda* (#:key inputs outputs #:allow-other-keys)
                       (let* ((out (assoc-ref outputs "out"))
@@ -1401,8 +1404,8 @@ the Guile compiler tower to generate the DSL from AWS JSON specifications.")
       (license license:gpl3+))))
 
 (define-public guile-simple-zmq
-  (let ((commit "ff0b39aec9312517fb48681564e261bd000aaf63")
-        (revision "10"))
+  (let ((commit "d25d1865e3378d93c44e2b4f5246a70b078a489d")
+        (revision "11"))
     (package
       (name "guile-simple-zmq")
       (version (git-version "0.0.0" revision commit))
@@ -1414,7 +1417,7 @@ the Guile compiler tower to generate the DSL from AWS JSON specifications.")
                (commit commit)))
          (sha256
           (base32
-           "0qfnljap1cxkfsydadarvhcw4p6cgayxzbhqr6r1y0as0m8250q3"))
+           "1aq1s0f0z5g6qsv9jqr0663qv4rwxd9j1pmg1g8v6rl09xb8g8lp"))
          (file-name (git-file-name name version))))
       (build-system gnu-build-system)
       (arguments
@@ -4587,6 +4590,52 @@ models and also supports a rich set of boolean query operators.")
 according to Bitorrent BEP003.")
     (license license:gpl3+)))
 
+(define-public guile-ts
+  (package
+    (name "guile-ts")
+    (version "0.1.0")
+    (source (origin (method git-fetch)
+                    (uri (git-reference
+                          (url
+                           "https://github.com/Z572/guile-ts")
+                          (commit (string-append "v" version))))
+                    (file-name (git-file-name name version))
+                    (sha256
+                     (base32
+                      "0xmq2d3mv921m0g1hqw6bjzh4m622g2c7pal11ks7vjn0m8d4bxj"))))
+    (build-system gnu-build-system)
+    (arguments
+     (list #:make-flags #~(list "GUILE_AUTO_COMPILE=0")
+           #:phases
+           #~(modify-phases %standard-phases
+               (add-after 'unpack 'set-extension-path
+                 (lambda* (#:key outputs #:allow-other-keys)
+                   (substitute*
+                       (find-files "." ".*\\.scm")
+                     (("\\(load-extension \"libguile_ts\" *\"(.*)\"\\)" _ o)
+                      (string-append
+                       (object->string
+                        `(or (false-if-exception
+                              (load-extension "libguile_ts" ,o))
+                             (load-extension
+                              ,(string-append
+                                #$output
+                                "/lib/libguile_ts.so")
+                              ,o)))))))))))
+    (native-inputs
+     (list autoconf automake libtool texinfo pkg-config guile-3.0))
+    (inputs
+     (list guile-3.0 tree-sitter))
+    (native-search-paths
+     (list (search-path-specification
+            (variable "TREE_SITTER_GRAMMAR_PATH")
+            (files '("lib/tree-sitter")))))
+    (synopsis "Guile bindings to the Tree-sitter parsing library")
+    (description "This package provides Guile bindings to the Tree-sitter
+parsing library.")
+    (home-page "https://github.com/Z572/guile-ts")
+    (license license:gpl3+)))
+
 (define-public guile-irc
   (let ((commit "7d08ce6fdcb87ac668c5d3bfd5584247805507bb")
         (revision "1"))
@@ -5292,7 +5341,7 @@ locations.")
 (define-public guile-netlink
   (package
     (name "guile-netlink")
-    (version "1.2")
+    (version "1.2.1")
     (source
      (origin
        (method git-fetch)
@@ -5302,7 +5351,7 @@ locations.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "06ls830nrshzi2j532di5vdf03fp8cy1275ll4ms93x1hv2g8dk0"))))
+         "181drjshcz7pi5zwydwd702h7v8p1nh50q6slsw9q372k2bzyl4a"))))
     (build-system gnu-build-system)
     (inputs
      (list guile-3.0))
diff --git a/gnu/packages/ipfs.scm b/gnu/packages/ipfs.scm
index ac12aea002..a4c0613e40 100644
--- a/gnu/packages/ipfs.scm
+++ b/gnu/packages/ipfs.scm
@@ -219,10 +219,10 @@ powerful and simple.")
 written in Go.")
     (license license:expat)))
 
-(define-public go-ipfs
+(define-public kubo
   (package
-    (name "go-ipfs")
-    (version "0.14.0")
+    (name "kubo")
+    (version "0.15.0")
     (source
      (origin
        (method url-fetch/tarbomb)
@@ -230,7 +230,7 @@ written in Go.")
              "https://dist.ipfs.io/kubo/v" version
              "/kubo-source.tar.gz"))
        (sha256
-        (base32 "0n7nfiymh6knj3h672gdrb24g9vz9j15x3vn6aml2nk7pv9dsy7p"))
+        (base32 "0ss5k8xnzn9qk977dni5ja89yygcysdw7r3mdk67cac2dpa9hhqs"))
        (file-name (string-append name "-" version "-source"))
        (modules '((guix build utils)))
        (snippet '(for-each delete-file-recursively
@@ -368,3 +368,6 @@ like a single bittorrent swarm, exchanging git objects.  IPFS provides an
 interface as simple as the HTTP web, but with permanence built in.  You can
 also mount the world at @code{/ipfs}.")
     (license license:expat)))
+
+(define-public go-ipfs
+  (deprecated-package "go-ipfs" kubo))
diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index 9445c37b67..f482c4c16d 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -13450,7 +13450,7 @@ network protocols, and core version control algorithms.")
 (define-public abcl
   (package
     (name "abcl")
-    (version "1.9.0")
+    (version "1.9.2")
     (source
      (origin
        (method url-fetch)
@@ -13458,7 +13458,7 @@ network protocols, and core version control algorithms.")
                            version "/abcl-src-" version ".tar.gz"))
        (sha256
         (base32
-         "0scqq5c7201xhp0g6i4y3m2nrk6l5any1nisiscbsd48ya25qax1"))
+         "0f0xpi47pfgz36y15krggshk2qdd2zxdkg5xwnamvng2hn7lnbsf"))
        (patches
         (search-patches
          "abcl-fix-build-xml.patch"))))
diff --git a/gnu/packages/jupyter.scm b/gnu/packages/jupyter.scm
index 9337197cb2..87854afd72 100644
--- a/gnu/packages/jupyter.scm
+++ b/gnu/packages/jupyter.scm
@@ -410,6 +410,54 @@ endpoints—to Jupyter web applications.")
 are interactive HTML widgets for Jupyter notebooks and the IPython kernel.")
     (license license:bsd-3)))
 
+(define-public python-jupyterlite-core
+  (package
+    (name "python-jupyterlite-core")
+    (version "0.1.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "jupyterlite_core" version))
+       (sha256
+        (base32 "18ysrqlsh7a31sknfnng419r7wpx9nfj59lxxd6zl1kcj6wazh34"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs (list python-doit python-importlib-metadata
+                             python-jupyter-core))
+    (native-inputs (list python-ansi2html
+                         python-hatchling
+                         python-pytest-console-scripts
+                         python-pytest-cov
+                         python-pytest-xdist
+                         python-tornado-6))
+    (home-page "https://github.com/jupyterlite/jupyterlite")
+    (synopsis "Core functionality for building JupyterLite websites")
+    (description "The jupyterlite-core package provides the core functionality
+for building JupyterLite websites, the jupyter-lite CLI, and extension points
+for authoring custom addons.")
+    (license license:bsd-3)))
+
+(define-public python-jupyterlite-sphinx
+  (package
+    (name "python-jupyterlite-sphinx")
+    (version "0.9.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "jupyterlite_sphinx" version))
+       (sha256
+        (base32 "05h7zrvsx0xzxlddsqfz1fxdgld66yhn6nxfp4jz20wbx6csrr4v"))))
+    (build-system pyproject-build-system)
+    (arguments (list #:tests? #false))  ;there are none
+    (propagated-inputs (list python-docutils python-jupyter-server
+                             python-jupyterlab-server python-jupyterlite-core
+                             python-sphinx))
+    (native-inputs (list python-hatchling))
+    (home-page "https://github.com/jupyterlite/jupyterlite")
+    (synopsis "Sphinx extension for deploying JupyterLite")
+    (description "This package provides a Sphinx extension for deploying
+@code{JupyterLite}.")
+    (license license:bsd-3)))
+
 (define-public python-jupyter-server-mathjax
   (package
     (name "python-jupyter-server-mathjax")
diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 560ba6c637..e5b2642da6 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -493,17 +493,17 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
 ;; The current "stable" kernels. That is, the most recently released major
 ;; versions that are still supported upstream.
 
-(define-public linux-libre-6.5-version "6.5.7")
+(define-public linux-libre-6.5-version "6.5.9")
 (define-public linux-libre-6.5-gnu-revision "gnu")
 (define deblob-scripts-6.5
   (linux-libre-deblob-scripts
    linux-libre-6.5-version
    linux-libre-6.5-gnu-revision
    (base32 "01mm6v67bcrhgm97axsw46x0iix9im7hmlb765f3bkjhwklpxdy7")
-   (base32 "132ps1jprxw6kqyscsar38fn7s12kg416mfhz7w702f4ajgq1ndi")))
+   (base32 "066z5lw5vrfayhv23hpfcm6fh6b7zmn2v13kfv1g3z3jl1wblhfh")))
 (define-public linux-libre-6.5-pristine-source
   (let ((version linux-libre-6.5-version)
-        (hash (base32 "135v3y2vgc83dca4xi7q52wqi4dkfal74k1y73jwzj85h12fl28d")))
+        (hash (base32 "1mcg0lpxr832mwyqlbn0s5gssvsk2nn2xhq9w0qbymizf5j2yrn6")))
    (make-linux-libre-source version
                             (%upstream-linux-source version hash)
                             deblob-scripts-6.5)))
@@ -511,7 +511,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
 ;; The "longterm" kernels — the older releases with long-term upstream support.
 ;; Here are the support timelines:
 ;; <https://www.kernel.org/category/releases.html>
-(define-public linux-libre-6.1-version "6.1.58")
+(define-public linux-libre-6.1-version "6.1.60")
 (define-public linux-libre-6.1-gnu-revision "gnu")
 (define deblob-scripts-6.1
   (linux-libre-deblob-scripts
@@ -521,12 +521,12 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
    (base32 "1c73516nbhnz0cxjz38b5794dxygb8sznv9idiibw7ablmjbhd11")))
 (define-public linux-libre-6.1-pristine-source
   (let ((version linux-libre-6.1-version)
-        (hash (base32 "1b913ina3rcw4dx2s7n37kynv8rqsmrqa2ialsib6h7nsb9px66f")))
+        (hash (base32 "02pvymr1dgd36mp7yikxqqv0sfrpwi1grnvxvx6jbbx6wmx0wljq")))
    (make-linux-libre-source version
                             (%upstream-linux-source version hash)
                             deblob-scripts-6.1)))
 
-(define-public linux-libre-5.15-version "5.15.135")
+(define-public linux-libre-5.15-version "5.15.137")
 (define-public linux-libre-5.15-gnu-revision "gnu")
 (define deblob-scripts-5.15
   (linux-libre-deblob-scripts
@@ -536,12 +536,12 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
    (base32 "1c3lm0j401lv2lk39dmr4mlf5ic173snm7cc0cckl6czyvxr5ysy")))
 (define-public linux-libre-5.15-pristine-source
   (let ((version linux-libre-5.15-version)
-        (hash (base32 "0w3i8jvzqvfnlarcvg89k1144ln96fszv16lzrn16zr3kri5x0ql")))
+        (hash (base32 "1xxjbxldrhmnh2q6rykpxyfbj8xqgl82q30n8sfavrzr14bb4jcp")))
    (make-linux-libre-source version
                             (%upstream-linux-source version hash)
                             deblob-scripts-5.15)))
 
-(define-public linux-libre-5.10-version "5.10.198")
+(define-public linux-libre-5.10-version "5.10.199")
 (define-public linux-libre-5.10-gnu-revision "gnu1")
 (define deblob-scripts-5.10
   (linux-libre-deblob-scripts
@@ -551,12 +551,12 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
    (base32 "0nnp46mn32yk436swd2qh34igmzinfgkwvbzp3lqyy45f06hbc2j")))
 (define-public linux-libre-5.10-pristine-source
   (let ((version linux-libre-5.10-version)
-        (hash (base32 "01gsw96anw44nh8ii3zipp6vh61m1n8yf0bv2fzznr23k771y51b")))
+        (hash (base32 "1h944syk7n6c4j1djlx19n77alzwbxcdza77c9ykicgfynhpgsm0")))
    (make-linux-libre-source version
                             (%upstream-linux-source version hash)
                             deblob-scripts-5.10)))
 
-(define-public linux-libre-5.4-version "5.4.258")
+(define-public linux-libre-5.4-version "5.4.259")
 (define-public linux-libre-5.4-gnu-revision "gnu1")
 (define deblob-scripts-5.4
   (linux-libre-deblob-scripts
@@ -566,12 +566,12 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
    (base32 "0sw67b2pk3lng4y67diqqnhxaggnp3nbkx8dxc5fs27rinfxr4m1")))
 (define-public linux-libre-5.4-pristine-source
   (let ((version linux-libre-5.4-version)
-        (hash (base32 "0gk2xav1ng565l1qsqlr8ja6m4j5g8rfj66vad1fmdd1lwaihw1r")))
+        (hash (base32 "195v4fidavzm637glj6580006mrcaygnbj4za874imb62bxf9rpz")))
    (make-linux-libre-source version
                             (%upstream-linux-source version hash)
                             deblob-scripts-5.4)))
 
-(define-public linux-libre-4.19-version "4.19.296")
+(define-public linux-libre-4.19-version "4.19.297")
 (define-public linux-libre-4.19-gnu-revision "gnu1")
 (define deblob-scripts-4.19
   (linux-libre-deblob-scripts
@@ -581,12 +581,12 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
    (base32 "1425mhkfxn18vxn05bb4h3li7x1jl7l1hf1zi8xhnqv3wa31h9wl")))
 (define-public linux-libre-4.19-pristine-source
   (let ((version linux-libre-4.19-version)
-        (hash (base32 "1bk051canr4fb00j6x9ff2wam2f20whw4h4z767x2cn2kmv6cqb3")))
+        (hash (base32 "0c9xxqgv2i36hrr06dwz7f3idc04xpv0a5pxg08xdh03cnyf12cx")))
     (make-linux-libre-source version
                              (%upstream-linux-source version hash)
                              deblob-scripts-4.19)))
 
-(define-public linux-libre-4.14-version "4.14.327")
+(define-public linux-libre-4.14-version "4.14.328")
 (define-public linux-libre-4.14-gnu-revision "gnu1")
 (define deblob-scripts-4.14
   (linux-libre-deblob-scripts
@@ -596,7 +596,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
    (base32 "1faagsj4i31z2bp83hflx3q9vrddjnn37a3ah2b47iaplva7z1nd")))
 (define-public linux-libre-4.14-pristine-source
   (let ((version linux-libre-4.14-version)
-        (hash (base32 "0nharfyxlr17yan86zrhlbq7idm0g3zvvvmy2zbw7m9dhgc8bw5z")))
+        (hash (base32 "1igcpvnhwwrczfdsafmszvi0456k7f6j4cgpfw6v6afw09p95d8x")))
     (make-linux-libre-source version
                              (%upstream-linux-source version hash)
                              deblob-scripts-4.14)))
@@ -3673,7 +3673,7 @@ processes currently causing I/O.")
 (define-public iotop
   (package
     (name "iotop")
-    (version "1.23")
+    (version "1.25")
     (source
      (origin
        (method git-fetch)
@@ -3682,7 +3682,7 @@ processes currently causing I/O.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1i5m2w0jzxzxn2xvragygidw35p87skjs6bfjakrz6bd96sxhd70"))))
+        (base32 "0h8fb7zzqszdrybk9zzzqqkiz78i8z2zr0f2nj84jja6visdd2v4"))))
     (build-system gnu-build-system)
     (arguments
      (list #:make-flags
diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm
index 3bf9ebcbe2..0aaa3c8446 100644
--- a/gnu/packages/lisp-xyz.scm
+++ b/gnu/packages/lisp-xyz.scm
@@ -3610,76 +3610,51 @@ writing code that contains string literals that contain code themselves.")
   (sbcl-package->ecl-package sbcl-pythonic-string-reader))
 
 (define-public sbcl-slime-swank
-  (package
-    (name "sbcl-slime-swank")
-    (version "2.28")
-    (source
-     (origin
-       (file-name (git-file-name "cl-slime-swank" version))
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://github.com/slime/slime/")
-             (commit (string-append "v" version))))
-       (sha256
-        (base32 "1acmm4w1mv1qzpnkgc4wyiilbx8l0dk16sx8wv815ri5ks289rll"))
-       (modules '((guix build utils)))
+  (let ((commit "0cc2e736112a0bc2a048ef6efd11dd67e3fbf7ad")
+        (revision "0"))
+    (package
+      (name "sbcl-slime-swank")
+      (version (git-version "2.28" revision commit))
+      (source
+       (origin
+         (file-name (git-file-name "cl-slime-swank" version))
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/slime/slime/")
+               (commit commit)))
+         (sha256
+          (base32 "0iq9r4007rrnabj290y79i926x2m4j20j6b0x701pkywz926sn02"))
+         (modules '((guix build utils)))
          (snippet
           ;; The doc folder drags `gawk' into the closure.  Doc is already
           ;; provided by emacs-slime.
           `(begin
              (delete-file-recursively "doc")
              #t))))
-    (build-system asdf-build-system/sbcl)
-    (arguments
-     '(#:asd-systems '("swank")
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'set-fasl-directory
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let* ((out (assoc-ref outputs "out"))
-                    (lib-dir (string-append out "/lib/common-lisp/"
-                                            (%lisp-type)
-                                            "/slime-swank/")))
-               ;; Use the ASDF registry instead of Swank's default that places
-               ;; the .fasl files in ~/.slime.
-               (substitute* "swank.asd"
-                 (("\\(load \\(asdf::component-pathname f\\)\\)" all)
-                  (string-append
-                   all "\n"
-                   "(setf (symbol-value"
-                   "(read-from-string \"swank-loader::*fasl-directory*\"))"
-                   "\"" lib-dir "\")")))
+      (build-system asdf-build-system/sbcl)
+      (arguments
+       '(#:asd-systems '("swank" "swank/exts")
+         #:phases
+         (modify-phases %standard-phases
+           (add-after 'unpack 'set-fasl-directory
+             (lambda* (#:key outputs #:allow-other-keys)
                (substitute* "swank-loader.lisp"
                  (("\\(probe-file fasl\\)" all)
                   ;; Do not try to delete Guix store files.
                   (string-append
                    all "\n"
                    " (not (equal (subseq (pathname-directory fasl) 1 3)"
-                   " '(\"gnu\" \"store\"))) ; XXX: GUIX PATCH")))))))))
-    (home-page "https://github.com/slime/slime")
-    (synopsis "Common Lisp Swank server")
-    (description
-     "This is only useful if you want to start a Swank server in a Lisp
+                   " '(\"gnu\" \"store\"))) ; XXX: GUIX PATCH"))))))))
+      (home-page "https://github.com/slime/slime")
+      (synopsis "Common Lisp Swank server")
+      (description
+       "This is only useful if you want to start a Swank server in a Lisp
 processes that doesn't run under Emacs.  Lisp processes created by
 @command{M-x slime} automatically start the server.")
-    (license (list license:gpl2+ license:public-domain))))
+      (license (list license:gpl2+ license:public-domain)))))
 
 (define-public cl-slime-swank
-  (let ((pkg (sbcl-package->cl-source-package sbcl-slime-swank)))
-    (package
-      (inherit pkg)
-      (arguments
-       (substitute-keyword-arguments (package-arguments pkg)
-         ((#:phases phases)
-          `(modify-phases ,phases
-             (add-after 'install 'revert-asd-patch
-               ;; We do not want to include the Guix patch in the cl- package
-               ;; since it would include the sbcl- package in the closure.
-               (lambda* (#:key outputs #:allow-other-keys)
-                 (let* ((out (assoc-ref outputs "out"))
-                        (source-path (string-append out "/share/common-lisp/source/")))
-                   (substitute* (string-append source-path "/cl-slime-swank/swank.asd")
-                     ((".*fasl-directory.*") ""))))))))))))
+  (sbcl-package->cl-source-package sbcl-slime-swank))
 
 (define-public ecl-slime-swank
   (sbcl-package->ecl-package sbcl-slime-swank))
diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index c54a9b4b3a..15004f449e 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -1439,7 +1439,7 @@ executable Common Lisp image.  It is similar to cl-launch and hu.dwim.build.")
 (define-public eisl
   (package
     (name "eisl")
-    (version "3.00")
+    (version "3.50")
     (source
      (origin
        (method git-fetch)
@@ -1448,7 +1448,7 @@ executable Common Lisp image.  It is similar to cl-launch and hu.dwim.build.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0nppbzfdx4cjy72b4n0yk177i7063a0nhsrs9b1y45y4avbrbl00"))))
+        (base32 "18alxwpvkcjfm63bc5kp6nn8351fl0p0ccxc8j9a7nb3fmg4fvyb"))))
     (build-system gnu-build-system)
     (inputs
      (list bash-minimal freeglut gdbm libiconv ncurses tcl tk))
diff --git a/gnu/packages/llvm.scm b/gnu/packages/llvm.scm
index cd551f4e02..5d779b87cc 100644
--- a/gnu/packages/llvm.scm
+++ b/gnu/packages/llvm.scm
@@ -3,7 +3,7 @@
 ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2015, 2017, 2018, 2019, 2020, 2021 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2016 Dennis Mungai <dmngaie@gmail.com>
-;;; Copyright © 2016, 2018, 2019, 2020, 2021 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2016, 2018, 2019, 2020, 2021, 2023 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2017 Roel Janssen <roel@gnu.org>
 ;;; Copyright © 2018–2022 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
@@ -1970,25 +1970,27 @@ requirements according to version 1.1 of the OpenCL specification.")
     (build-system python-build-system)
     (outputs '("out"))
     (arguments
-     '(#:phases (modify-phases %standard-phases
-                  (add-before 'build 'change-directory
-                    (lambda _
-                      (chdir "bindings/python")))
-                  (add-before 'build 'create-setup-py
-                    (lambda _
-                      ;; Generate a basic "setup.py", enough so it can be
-                      ;; built and installed.
-                      (with-output-to-file "setup.py"
-                        (lambda ()
-                          (display "from setuptools import setup
-setup(name=\"clang\", packages=[\"clang\"])\n")))))
-                  (add-before 'build 'set-libclang-file-name
-                    (lambda* (#:key inputs #:allow-other-keys)
-                      ;; Record the absolute file name of libclang.so.
-                      (let ((libclang (search-input-file inputs
-                                                         "/lib/libclang.so")))
-                        (substitute* "clang/cindex.py"
-                          (("libclang\\.so") libclang))))))))
+     (list
+      #:phases #~(modify-phases %standard-phases
+                   (add-before 'build 'change-directory
+                     (lambda _
+                       (chdir "bindings/python")))
+                   (add-before 'build 'create-setup-py
+                     (lambda _
+                       ;; Generate a basic "setup.py", enough so it can be
+                       ;; built and installed.
+                       (with-output-to-file "setup.py"
+                         (lambda ()
+                           (format #true "from setuptools import setup
+setup(name=\"clang\", version=\"~a\", packages=[\"clang\"])\n"
+                                   #$(package-version this-package))))))
+                   (add-before 'build 'set-libclang-file-name
+                     (lambda* (#:key inputs #:allow-other-keys)
+                       ;; Record the absolute file name of libclang.so.
+                       (let ((libclang (search-input-file inputs
+                                                          "/lib/libclang.so")))
+                         (substitute* "clang/cindex.py"
+                           (("libclang\\.so") libclang))))))))
     (inputs (list clang))
     (synopsis "Python bindings to libclang")))
 
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 16781b7aa1..a84377e1eb 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -151,6 +151,42 @@ representations and sentence classification.")
     (inputs (list fasttext))
     (native-inputs (list pybind11))))
 
+(define-public python-funsor
+  (package
+    (name "python-funsor")
+    (version "0.4.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "funsor" version))
+       (sha256
+        (base32 "0cgysij0dix0fikyz2x4f8jvaskm5s5a04s07chzaz2dw1fpxdq8"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs (list python-makefun python-multipledispatch
+                             python-numpy python-opt-einsum
+                             python-typing-extensions))
+    (native-inputs (list python-black
+                         python-flake8
+                         python-isort
+                         python-nbsphinx
+                         python-pandas
+                         python-pillow
+                         python-pyro-api
+                         python-pytest
+                         python-pytest-xdist
+                         python-requests
+                         python-scipy
+                         python-sphinx
+                         python-sphinx-gallery
+                         python-sphinx-rtd-theme
+                         python-torchvision))
+    (home-page "https://github.com/pyro-ppl/funsor")
+    (synopsis "Tensor-like library for functions and distributions")
+    (description
+     "This package provides a tensor-like library for functions and
+distributions.")
+    (license license:asl2.0)))
+
 (define-public fann
   ;; The last release is >100 commits behind, so we package from git.
   (let ((commit "d71d54788bee56ba4cf7522801270152da5209d7"))
@@ -260,6 +296,42 @@ classification.")
      (list python))
     (synopsis "Python bindings of libSVM")))
 
+(define-public python-ml-collections
+  (package
+    (name "python-ml-collections")
+    (version "0.1.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "ml_collections" version))
+       (sha256
+        (base32 "1k38psfzqsqnl99fl578bd07zdmvfkja61r3sgjs2fj3xircrvrz"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (replace 'check
+            (lambda* (#:key tests? #:allow-other-keys)
+              (when tests?
+                ;; TODO: we can't seem to run the config_flags tests, because
+                ;; the installed Python files conflict with those from the
+                ;; source directory, resulting in constants to be defined more
+                ;; than once.
+                (invoke "pytest" "ml_collections/config_dict/tests"
+                        ;; This one fails because we're testing the __main__
+                        ;; class, not config_dict_test.
+                        "-k" "not testJSONConversionBestEffort")))))))
+    (propagated-inputs
+     (list python-absl-py python-contextlib2 python-pyyaml python-six))
+    (native-inputs (list python-mock python-pytest))
+    (home-page "https://github.com/google/ml_collections")
+    (synopsis "Python collections designed for Machine Learning usecases")
+    (description
+     "ML Collections is a library of Python collections designed for Machine
+Learning usecases.")
+    (license license:asl2.0)))
+
 (define-public ghmm
   ;; The latest release candidate is several years and a couple of fixes have
   ;; been published since.  This is why we download the sources from the SVN
@@ -1672,7 +1744,7 @@ for k-neighbor-graph construction and approximate nearest neighbor search.")
 (define-public python-opentsne
   (package
     (name "python-opentsne")
-    (version "0.7.1")
+    (version "1.0.0")
     (source
      (origin
        (method git-fetch) ; no tests in PyPI release
@@ -1681,7 +1753,7 @@ for k-neighbor-graph construction and approximate nearest neighbor search.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "12wp98mh67v6v683yi7wbv8zhpafrfz21z349bww4wgi2q7bl3il"))))
+        (base32 "05qzpq1zjs42bl0z8girfwcj3nfxs1a99c5525vp3589sglk351g"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
@@ -2030,13 +2102,13 @@ discrete, and conditional dimensions.")
 (define-public python-deepxde
   (package
     (name "python-deepxde")
-    (version "1.9.3")
+    (version "1.10.0")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "DeepXDE" version))
               (sha256
                (base32
-                "1zw2gqssc0s3maf4gdjckxmzx1d3036hbp1iir26kd08hxj93vzs"))))
+                "0fdxrjrm7l19yx6n8vaklxlhwzx0bw9n08vp8idikzdifybz5gij"))))
     (build-system pyproject-build-system)
     (arguments
      (list #:tests? #f                  ; there are no tests
diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm
index ac8cff93d4..5047a2f18d 100644
--- a/gnu/packages/mail.scm
+++ b/gnu/packages/mail.scm
@@ -118,6 +118,7 @@
   #:use-module (gnu packages icu4c)
   #:use-module (gnu packages kerberos)
   #:use-module (gnu packages language)
+  #:use-module (gnu packages libbsd)
   #:use-module (gnu packages libcanberra)
   #:use-module (gnu packages libevent)
   #:use-module (gnu packages libffi)
@@ -1837,14 +1838,14 @@ addons which can add many functionalities to the base client.")
 (define-public msmtp
   (package
     (name "msmtp")
-    (version "1.8.24")
+    (version "1.8.25")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://marlam.de/msmtp/releases"
                            "/msmtp-" version ".tar.xz"))
        (sha256
-        (base32 "0nda218iz72pvh6v10s2qlihp1mdxzir6yb4hqdxc5xbmaql8rmx"))))
+        (base32 "0f6pa8kdlfingw6yf61dshnxgygx5v6ykcmnn3h6zllpnfxivzid"))))
     (build-system gnu-build-system)
     (inputs
      (list libsecret gnutls zlib gsasl))
@@ -3183,26 +3184,32 @@ from the Cyrus IMAP project.")
 (define-public opensmtpd
   (package
     (name "opensmtpd")
-    (version "7.3.0p2")
+    (version "7.4.0p0")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://www.opensmtpd.org/archives/"
                            "opensmtpd-" version ".tar.gz"))
        (sha256
-        (base32 "0kjs5cxbh9lq51b8p20hxmiah61cfm8yzkcwpw9005cdp72zpkgw"))))
+        (base32 "0x731hi7i01mxaz07p1l5q3gwmyl422h404yc61ya4aa8g1wr0f1"))))
     (build-system gnu-build-system)
     (inputs
+     ;; OpenSMTPd bundled (a subset of) libasr and libtls, which we use.  See
+     ;; https://www.mail-archive.com/misc@opensmtpd.org/msg05909.html for why.
      (list bdb
+           libbsd          ;https://github.com/OpenSMTPD/OpenSMTPD/issues/1233
            libevent
            libressl
            linux-pam
            zlib))
     (native-inputs
-     (list bison groff))               ; for man pages
+     (list bison
+           groff                        ;for man pages
+           pkg-config))
     (arguments
      `(#:configure-flags
        (list "--localstatedir=/var"
+             "--with-libbsd"
              ;; This is the default only if it exists at build time—it doesn't.
              "--with-path-socket=/var/run"
              "--with-path-CAfile=/etc/ssl/certs/ca-certificates.crt"
diff --git a/gnu/packages/markup.scm b/gnu/packages/markup.scm
index ad2d74f742..6ee7bebf57 100644
--- a/gnu/packages/markup.scm
+++ b/gnu/packages/markup.scm
@@ -391,7 +391,7 @@ CommonMark C library libcmark.  It closely follows the original API.")
   (package
     (inherit cmark)
     (name "cmark-gfm")
-    (version "0.29.0.gfm.2")
+    (version "0.29.0.gfm.13")
     (home-page "https://github.com/github/cmark-gfm")
     (source (origin
               (method git-fetch)
@@ -399,16 +399,15 @@ CommonMark C library libcmark.  It closely follows the original API.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0vz6zs3m22k7jzfj4782lahciwfjlbi4m3qz5crsmssip3rwdy7h"))))
+                "1apy9i76rgs0bmgdlpjszv0fpqhlap2s12m68wvnsv8j3fsqc90y"))))
     (arguments
-     '(#:test-target "test"
-       #:phases (modify-phases %standard-phases
-                  (add-after 'install 'install-config
-                    (lambda* (#:key outputs #:allow-other-keys)
-                      (let ((out (assoc-ref outputs "out")))
-                        ;; XXX: cmark-gfm-core-extensions.h includes this file.
-                        (install-file "src/config.h"
-                                      (string-append out "/include"))))))))
+     (list #:test-target "test"
+           #:phases #~(modify-phases %standard-phases
+                        (add-after 'install 'install-config
+                          (lambda _
+                            ;; XXX: cmark-gfm-core-extensions.h includes this file.
+                            (install-file "src/config.h"
+                                          (string-append #$output "/include")))))))
     (synopsis "GitHub flavored CommonMark")
     (description
      "This package is a fork of @code{cmark}, with GitHub-specific Markdown
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 1c8a7f1865..8e4ebb4587 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -1302,14 +1302,14 @@ in the terminal or with an external viewer.")
 (define-public gnuplot
   (package
     (name "gnuplot")
-    (version "5.4.8")
+    (version "5.4.9")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://sourceforge/gnuplot/gnuplot/"
                                   version "/gnuplot-"
                                   version ".tar.gz"))
        (sha256
-        (base32 "1kzmj4yyxvlxqzqbrw6sx6dnvhj1zzqnciyb8ryzy6mdrb3pj4lk"))))
+        (base32 "15vabi30s4ln4vi82csx4nvfms3ik8704rk0prcm9h1xylhs0a53"))))
     (build-system gnu-build-system)
     (native-inputs
      (list pkg-config (texlive-updmap.cfg)))
@@ -1317,7 +1317,8 @@ in the terminal or with an external viewer.")
      (list cairo gd lua pango readline))
     (arguments
      (list #:configure-flags
-           #~(list (string-append "--with-texdir=" #$output
+           #~(list "--with-qt=no"
+                   (string-append "--with-texdir=" #$output
                                   "/texmf-local/tex/latex/gnuplot"))
            ;; Plot on a dumb terminal during tests.
            #:make-flags #~'("GNUTERM=dumb")))
@@ -3180,6 +3181,54 @@ This is the certified version of the Open Cascade Technology (OCCT) library.")
 supports the propositional fragment of PDDL2.2.")
     (license license:gpl3+)))
 
+(define-public popf
+  (package
+    (name "popf")
+    (version "0.0.15")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/fmrico/popf")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1i1am3h6japn8fgapi5s5mnyrm31a05jkjhzgk48cd2n42c5060v"))))
+    (build-system cmake-build-system)
+    (arguments
+     (list
+      #:tests? #f                       ; no tests
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'fix-cmake
+            (lambda* (#:key inputs #:allow-other-keys)
+              (substitute* (find-files "." "CMakeLists\\.txt")
+                (("/usr/local/opt/flex/include")
+                 (dirname (search-input-file inputs "include/FlexLexer.h"))))
+              (substitute* "CMakeLists.txt"
+                (("find_package\\(ament_cmake REQUIRED\\)") "")
+                (("ament_.*") "")
+                (("(RUNTIME DESTINATION) .*" all dst)
+                 (string-append dst " libexec/${PROJECT_NAME}")))))
+          (add-after 'install 'symlink
+            (lambda* (#:key outputs #:allow-other-keys)
+              (let ((out (assoc-ref outputs "out")))
+                (mkdir-p (string-append out "/bin"))
+                (for-each (lambda (link)
+                            (symlink
+                             (string-append out "/libexec/popf/" (cdr link))
+                             (string-append out "/bin/" (car link))))
+                          '(("popf" . "popf") ("VAL" . "validate")))))))))
+    (inputs (list cbc flex))
+    (native-inputs (list flex bison perl))
+    (home-page "https://github.com/fmrico/popf")
+    (synopsis "Forward-chaining temporal planner")
+    (description "This package contains an implementation of the @acronym{POPF,
+Partial Order Planning Forwards} planner described in @cite{Forward-Chaining
+Partial Order Planning}, that has been updated to compile with newer C++
+compilers.")
+    (license license:gpl2+)))
+
 (define-public gmsh
   (package
     (name "gmsh")
@@ -8519,15 +8568,15 @@ management via the GIMPS project's Primenet server.")
 (define-public nauty
   (package
     (name "nauty")
-    (version "2.7r4")
+    (version "2.8.6")
     (source
      (origin
        (method url-fetch)
        (uri (string-append
              "https://pallini.di.uniroma1.it/"
-             "nauty" (string-join (string-split version #\.) "") ".tar.gz"))
+             "nauty" (string-join (string-split version #\.) "_") ".tar.gz"))
        (sha256
-        (base32 "19j8i10cgnqavphj0p7kq939azxckj9ayjpjr6sg76g2dxdch45q"))))
+        (base32 "1yp6wpz2drq0viww8px1vl4pw919nq3xgxrmrrdhycx8bhi9ikpj"))))
     (build-system gnu-build-system)
     (outputs '("out" "lib"))
     (arguments
@@ -8536,37 +8585,11 @@ management via the GIMPS project's Primenet server.")
       #:configure-flags #~(list "--enable-generic") ;prevent -march-native
       #:phases
       #~(modify-phases %standard-phases
-          ;; Default make target does not build all available
-          ;; executables.  Create them now.
-          (add-after 'build 'build-extra-programs
-            (lambda _
-              (for-each (lambda (target) (invoke "make" target))
-                        '("blisstog" "bliss2dre" "checks6" "sumlines"))))
-          ;; Upstream does not provide any install target.
-          (replace 'install
+          (add-after 'unpack 'normalize-pkgconfig-files-location
             (lambda _
-              (let* ((bin (string-append #$output "/bin"))
-                     (doc (string-append #$output "/share/doc/nauty/"))
-                     (include (string-append #$output:lib "/include/nauty"))
-                     (lib (string-append #$output:lib "/lib/nauty")))
-                (for-each (lambda (f) (install-file f bin))
-                          '("addedgeg"  "amtog" "assembleg" "biplabg" "blisstog"
-                            "bliss2dre" "catg" "checks6" "complg" "converseg"
-                            "copyg" "countg" "cubhamg" "deledgeg" "delptg"
-                            "directg"  "dreadnaut" "dretodot" "dretog" "genbg"
-                            "genbgL" "geng" "genquarticg" "genrang" "genspecialg"
-                            "gentourng" "gentreeg" "hamheuristic" "labelg"
-                            "linegraphg" "listg" "multig" "newedgeg" "pickg"
-                            "planarg" "ranlabg" "shortg" "showg" "subdivideg"
-                            "sumlines" "twohamg" "underlyingg" "vcolg"
-                            "watercluster2" "NRswitchg"))
-                (for-each (lambda (f) (install-file f include))
-                          (find-files "." "\\.h$"))
-                (for-each (lambda (f) (install-file f lib))
-                          (find-files "." "\\.a$"))
-                (for-each (lambda (f) (install-file f doc))
-                          (append '("formats.txt" "README" "schreier.txt")
-                              (find-files "." "\\.pdf$")))))))))
+              (substitute* "makefile.in"
+                (("^(pkgconfigexecdir=).*" _ prefix)
+                 (string-append prefix "${libdir}/pkgconfig\n"))))))))
     (inputs
      (list gmp))                        ;for sumlines
     (home-page "https://pallini.di.uniroma1.it/")
diff --git a/gnu/packages/mpd.scm b/gnu/packages/mpd.scm
index 0edc056472..0e762144a1 100644
--- a/gnu/packages/mpd.scm
+++ b/gnu/packages/mpd.scm
@@ -622,7 +622,7 @@ mpdevil loads all tags and covers on demand.")
 (define-public mympd
   (package
     (name "mympd")
-    (version "12.1.0")
+    (version "12.1.1")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -631,7 +631,7 @@ mpdevil loads all tags and covers on demand.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0vmnfwkajgm1dmm34z0zk74j5wzlwcwk45aalfzc5pqlkcy6c4z5"))))
+                "1bal31xmdmq46bi0qmia07sqcwy695vcz5y5hxwkz71rcfywbsf9"))))
     (build-system cmake-build-system)
     (arguments
      (list
diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index fff0cab749..b8f3a1d93b 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -40,7 +40,7 @@
 ;;; Copyright © 2021 Frank Pursel <frank.pursel@gmail.com>
 ;;; Copyright © 2021 Rovanion Luckey <rovanion.luckey@gmail.com>
 ;;; Copyright © 2021 Justin Veilleux <terramorpha@cock.li>
-;;; Copyright © 2021, 2022 Felix Gruber <felgru@posteo.net>
+;;; Copyright © 2021, 2022, 2023 Felix Gruber <felgru@posteo.net>
 ;;; Copyright © 2021 Simon Streit <simon@netpanic.org>
 ;;; Copyright © 2021 Xinglu Chen <public@yoctocell.xyz>
 ;;; Copyright © 2021 Thomas Albers Raviola <thomas@thomaslabs.org>
@@ -553,7 +553,7 @@ you create custom user interfaces for your MIDI hardware.")
 (define-public strawberry
   (package
     (name "strawberry")
-    (version "1.0.18")
+    (version "1.0.21")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -562,7 +562,7 @@ you create custom user interfaces for your MIDI hardware.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1knijckphq2jxrz8nmv4cb64zl1rz3bjyq5ipac09hnj2gvv5rmw"))
+                "1ibs7x7i1zz2r13wg238c5bhr1j4x8vl7hvjg01vdl5hfrh2gk1i"))
               (modules '((guix build utils)
                          (ice-9 regex)))
               (snippet
@@ -619,6 +619,7 @@ you create custom user interfaces for your MIDI hardware.")
            gst-plugins-good
            icu4c
            libcdio
+           libebur128
            libmtp
            protobuf
            pulseaudio
@@ -3780,7 +3781,7 @@ event-based scripts for scrobbling, notifications, etc.")
 (define-public picard
   (package
     (name "picard")
-    (version "2.9.2")
+    (version "2.10")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -3788,7 +3789,7 @@ event-based scripts for scrobbling, notifications, etc.")
                     "picard/picard-" version ".tar.gz"))
               (sha256
                (base32
-                "1gd4mypqcmpf8xnil1kqfv56znqg9pllvsj7fx8nq8jqaaw9cy6g"))))
+                "0f9rvif9m83jhal9n9x8kks17c0cgcipi1hjqmki7a296lz175ss"))))
     (build-system python-build-system)
     (arguments
      (list
@@ -6790,7 +6791,7 @@ plugin support, JACK support and chord assistance.")
 (define-public dragonfly-reverb
   (package
     (name "dragonfly-reverb")
-    (version "3.2.5")
+    (version "3.2.10")
     (source
      (origin
        (method git-fetch)
@@ -6802,7 +6803,7 @@ plugin support, JACK support and chord assistance.")
          (recursive? #t)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "14kia9wjs0nqfx4psnr3vf4x6hihkf80gb0mjzmdnnnk4cnrdydm"))))
+        (base32 "11i2k888m3zj4gz9si4y5mach8dwdq3yksbvjn1syrbwj99phwk1"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f                      ; no check target
diff --git a/gnu/packages/parallel.scm b/gnu/packages/parallel.scm
index df7b498d1f..2ec87e751a 100644
--- a/gnu/packages/parallel.scm
+++ b/gnu/packages/parallel.scm
@@ -64,14 +64,14 @@
 (define-public parallel
   (package
     (name "parallel")
-    (version "20230922")
+    (version "20231022")
     (source
      (origin
       (method url-fetch)
       (uri (string-append "mirror://gnu/parallel/parallel-"
                           version ".tar.bz2"))
       (sha256
-       (base32 "0qz0pzy6icgdr6ak0gszzlxqm4s0w514ayyg2d8gcpayvlb78i0i"))
+       (base32 "1316ydijavz41078c99mbrbaddnshspbs8nsbm5qlyah317vkwlk"))
       (snippet
        '(begin
           (use-modules (guix build utils))
diff --git a/gnu/packages/password-utils.scm b/gnu/packages/password-utils.scm
index 9558da1dee..385bd64985 100644
--- a/gnu/packages/password-utils.scm
+++ b/gnu/packages/password-utils.scm
@@ -678,7 +678,7 @@ any X11 window.")
            (lambda* (#:key inputs outputs #:allow-other-keys)
              (let* ((out (assoc-ref outputs "out"))
                     (requisites '("getopt" "git" "gpg" "qrencode" "sed"
-                                  "tree" "which" "wl-copy" "xclip"))
+                                  "tail" "tree" "which" "wl-copy" "xclip"))
                     (path (map (lambda (pkg)
                                  (dirname (search-input-file
                                            inputs (string-append "/bin/" pkg))))
@@ -699,7 +699,8 @@ any X11 window.")
             (separator #f)             ;single entry
             (files '("lib/password-store/extensions")))))
     (inputs
-     (list dmenu
+     (list coreutils
+           dmenu
            util-linux
            git
            gnupg
diff --git a/gnu/packages/patches/hplip-usb-timeout.patch b/gnu/packages/patches/hplip-usb-timeout.patch
new file mode 100644
index 0000000000..b98ed1cc78
--- /dev/null
+++ b/gnu/packages/patches/hplip-usb-timeout.patch
@@ -0,0 +1,24 @@
+# Source: <https://bugs.launchpad.net/hplip/+bug/1922404>
+
+--- a/config_usb_printer.py
++++ b/config_usb_printer.py
+@@ -28,6 +28,7 @@
+ # Std Lib
+ import sys
+ import os
++import time
+ 
+ # Local
+ from base.g import *
+@@ -181,9 +182,10 @@
+        # ******************************* RUNNING FIRMWARE DOWNLOAD TO DEVICE FOR SUPPORTED PRINTER'S
+        fw_download_req = mq.get('fw-download', False)
+        if fw_download_req:
+-           fw_cmd = "hp-firmware -y3 -s %s"%param
++           fw_cmd = "hp-firmware -n -y3 -s %s"%param
+            log.info(fw_cmd)
+            fw_sts, fw_out = utils.run(fw_cmd)
++           time.sleep(5)
+            if fw_sts == 0:
+                log.debug("Firmware downloaded to %s "%device_uri)
+            else:
diff --git a/gnu/packages/patches/online-judge-tools.patch b/gnu/packages/patches/online-judge-tools.patch
new file mode 100644
index 0000000000..9e016d7104
--- /dev/null
+++ b/gnu/packages/patches/online-judge-tools.patch
@@ -0,0 +1,62 @@
+Skip failing tests and an assertion.  The skipped tests require network
+connections.
+
+--- a/tests/command_download.py
++++ b/tests/command_download.py
+@@ -90,6 +90,7 @@ class DownloadTest(unittest.TestCase):
+     def snippet_call_download_failure(self, *args, **kwargs):
+         tests.command_download.snippet_call_download_failure(self, *args, **kwargs)
+ 
++    @unittest.skip("Disabled by Guix")
+     def test_call_download_atcoder_abc114_c(self):
+         self.snippet_call_download('https://atcoder.jp/contests/abc114/tasks/abc114_c', [
+             {
+@@ -106,6 +107,7 @@ class DownloadTest(unittest.TestCase):
+             },
+         ], type='json')
+ 
++    @unittest.skip("Disabled by Guix")
+     def test_call_download_atcoder_abc003_4(self):
+         self.snippet_call_download('https://atcoder.jp/contests/abc003/tasks/abc003_4', [
+             {
+@@ -126,9 +128,11 @@ class DownloadTest(unittest.TestCase):
+             },
+         ], type='json')
+ 
++    @unittest.skip("Disabled by Guix")
+     def test_call_download_invalid_url(self):
+         self.snippet_call_download_failure('http://abc001.contest.atcoder.jp/tasks/abc001_100')
+ 
++    @unittest.skip("Disabled by Guix")
+     def test_call_download_413(self):
+         # This task is not supported.
+         self.snippet_call_download_failure('https://chokudai001.contest.atcoder.jp/tasks/chokudai_001_a')
+@@ -141,13 +145,16 @@ class DownloadInvalidTest(unittest.TestCase):
+     def snippet_call_download_twice(self, *args, **kwargs):
+         tests.command_download.snippet_call_download_twice(self, *args, **kwargs)
+ 
++    @unittest.skip("Disabled by Guix")
+     def test_call_download_invalid(self):
+         self.snippet_call_download_failure('https://not_exist_contest.jp/tasks/001_a')
+ 
++    @unittest.skip("Disabled by Guix")
+     def test_call_download_no_sample_found(self):
+         self.snippet_call_download_failure('https://atcoder.jp/contests/tenka1-2013-quala/tasks/tenka1_2013_qualA_a')
+         self.snippet_call_download_failure('https://open.kattis.com/problems/hello')
+ 
++    @unittest.skip("Disabled by Guix")
+     def test_call_download_twice(self):
+         self.snippet_call_download_twice('https://atcoder.jp/contests/abc114/tasks/abc114_c', 'https://atcoder.jp/contests/abc003/tasks/abc003_4', [
+             {
+
+--- a/tests/command_test.py
++++ b/tests/command_test.py
+@@ -1319,7 +1319,7 @@ class TestTest(unittest.TestCase):
+         timer = threading.Timer(1.0, send_keyboard_interrupt)
+         timer.start()
+         result = tests.utils.run_in_sandbox(args=['-v', 'test', '-c', tests.utils.python_c("import time; time.sleep(10)  # {}".format(marker_for_callee)), 'test/{}-1.in'.format(marker_for_caller)], files=files)
+-        self.assertNotEqual(result['proc'].returncode, 0)
++        # self.assertNotEqual(result['proc'].returncode, 0)
+ 
+         # check there are no processes whose command-line arguments contains the marker word
+         for cmdline in pathlib.Path('/proc').glob('*/cmdline'):
diff --git a/gnu/packages/patches/python-online-judge-api-client-tests.patch b/gnu/packages/patches/python-online-judge-api-client-tests.patch
new file mode 100644
index 0000000000..f999828ab3
--- /dev/null
+++ b/gnu/packages/patches/python-online-judge-api-client-tests.patch
@@ -0,0 +1,429 @@
+Skip tests which requires network connections.
+
+--- a/tests/dispatch.py
++++ b/tests/dispatch.py
+@@ -4,6 +4,7 @@ from onlinejudge import dispatch, service
+ 
+ 
+ class DispatchAtCoderTest(unittest.TestCase):
++    @unittest.skip("Disabled by Guix")
+     def test_problem_from_url(self):
+         problem = dispatch.problem_from_url('https://atcoder.jp/contests/arc001/tasks/arc001_1')
+         self.assertIsInstance(problem, service.atcoder.AtCoderProblem)
+
+--- a/tests/service_anarchygolf.py
++++ b/tests/service_anarchygolf.py
+@@ -10,6 +10,7 @@ class AnarchyGolfServiceTest(unittest.TestCase):
+         self.assertIsInstance(AnarchyGolfService.from_url('http://golf.shinh.org/p.rb?Indent+Space+Alignment'), AnarchyGolfService)
+ 
+ 
++@unittest.skip("Disabled by Guix")
+ class AnarchyGolfProblemTest(unittest.TestCase):
+     def test_download_sample_cases(self):
+         self.assertEqual(AnarchyGolfProblem.from_url('http://golf.shinh.org/p.rb?last+non+zero').download_sample_cases(), [
+
+--- a/tests/service_aoj.py
++++ b/tests/service_aoj.py
+@@ -20,6 +20,7 @@ class AOJProblemTest(unittest.TestCase):
+         self.assertEqual(AOJProblem.from_url('https://onlinejudge.u-aizu.ac.jp/challenges/sources/JAG/Spring/2394?year=2011').problem_id, '2394')
+         self.assertIsNone(AOJProblem.from_url('https://onlinejudge.u-aizu.ac.jp/services/room.html#RitsCamp19Day2/problems/A'))
+ 
++    @unittest.skip("Disabled by Guix")
+     def test_download_sample_cases(self):
+         self.assertEqual(AOJProblem.from_url('http://judge.u-aizu.ac.jp/onlinejudge/description.jsp?id=DSL_1_A').download_sample_cases(), [
+             TestCase(name='sample-1', input_name='1', input_data=b'5 12\n0 1 4\n0 2 3\n1 1 2\n1 3 4\n1 1 4\n1 3 2\n0 1 3\n1 2 4\n1 3 0\n0 0 4\n1 0 2\n1 3 0\n', output_name='1', output_data=b'0\n0\n1\n1\n1\n0\n1\n1\n'),
+@@ -39,6 +40,7 @@ class AOJProblemTest(unittest.TestCase):
+             TestCase(name='sample-1', input_name='1', input_data=b'4\n0 0\n10 0\n10 10\n0 10\n3\n0 0\n1 0\n0 1\n0\n', output_name='1', output_data=b'Case 1: 14.142135624\nCase 2: 1.41421356\n'),
+         ])
+ 
++    @unittest.skip("Disabled by Guix")
+     def test_download_sample_cases_not_registered(self):
+         # see: https://github.com/kmyk/online-judge-tools/issues/207
+         self.assertEqual(AOJProblem.from_url('https://onlinejudge.u-aizu.ac.jp/challenges/sources/ICPC/Regional/1399').download_sample_cases(), [
+@@ -57,11 +59,13 @@ class AOJArenaProblemTest(unittest.TestCase):
+         self.assertEqual(AOJArenaProblem.from_url('https://onlinejudge.u-aizu.ac.jp/services/room.html#ACPC2018Day2/problems/d').alphabet, 'D')
+         self.assertIsNone(AOJArenaProblem.from_url('http://judge.u-aizu.ac.jp/onlinejudge/description.jsp?id=DSL_1_A'))
+ 
++    @unittest.skip("Disabled by Guix")
+     def test_download_sample_cases(self):
+         self.assertEqual(AOJArenaProblem.from_url('https://onlinejudge.u-aizu.ac.jp/services/room.html#yupro/problems/A').download_sample_cases(), [
+             TestCase(name='sample-1', input_name='1', input_data=b'koukyoukoukokukikou\nabrakadabra\nacmicpc\njapaque\nhelloworld\n#\n', output_name='1', output_data=b'0\n2\n4\n5\n7\n'),
+         ])
+ 
++    @unittest.skip("Disabled by Guix")
+     def test_download_sample_cases_not_registered(self):
+         # see: https://github.com/kmyk/online-judge-tools/issues/207
+         self.assertEqual(AOJArenaProblem.from_url('https://onlinejudge.u-aizu.ac.jp/services/room.html#RitsCamp18Day3/problems/B').download_sample_cases(), [
+
+--- a/tests/service_atcoder.py
++++ b/tests/service_atcoder.py
+@@ -15,6 +15,7 @@ class AtCoderSerivceTest(unittest.TestCase):
+         self.assertIsInstance(AtCoderService.from_url('https://atcoder.jp/contests/agc001/submissions/806160'), AtCoderService)
+         self.assertIsNone(AtCoderService.from_url('https://codeforces.com/'))
+ 
++    @unittest.skip("Disabled by Guix")
+     def test_iterate_contests(self):
+         contests = list(AtCoderService().iterate_contests())
+         contest_ids = [contest.contest_id for contest in contests]
+@@ -37,6 +38,7 @@ class AtCoderContestTest(unittest.TestCase):
+         self.assertEqual(AtCoderContest.from_url('https://atcoder.jp/contests/agc030').contest_id, 'agc030')
+         self.assertIsNone(AtCoderContest.from_url('https://atcoder.jp/contests/'))
+ 
++    @unittest.skip("Disabled by Guix")
+     def test_load_details(self):
+         contest = AtCoderContest.from_url('https://atcoder.jp/contests/keyence2019')
+         self.assertEqual(contest.download_data(lang='en').name, 'KEYENCE Programming Contest 2019')
+@@ -62,10 +64,12 @@ class AtCoderContestTest(unittest.TestCase):
+         self.assertEqual(data.rated_range, '-')
+         self.assertEqual(data.penalty.total_seconds(), 5 * 60)
+ 
++    @unittest.skip("Disabled by Guix")
+     def test_get_penalty_a_singular_form(self):
+         contest = AtCoderContest.from_url('https://atcoder.jp/contests/chokudai_S002')
+         self.assertEqual(contest.download_data().penalty.total_seconds(), 60)  # Penalty is written as "1 minute", not  "1 minutes"
+ 
++    @unittest.skip("Disabled by Guix")
+     def test_list_problems(self):
+         contest = AtCoderContest.from_url('https://atcoder.jp/contests/agc028')
+         problems = contest.list_problems()
+@@ -79,6 +83,7 @@ class AtCoderContestTest(unittest.TestCase):
+         self.assertEqual(problems[6].download_data().alphabet, 'F2')
+         self.assertEqual(problems[6].problem_id, 'agc028_f2')
+ 
++    @unittest.skip("Disabled by Guix")
+     def test_list_problems_with_float_values(self):
+         """
+         .. seealso:
+@@ -92,6 +97,7 @@ class AtCoderContestTest(unittest.TestCase):
+         self.assertEqual(problems[1].download_data().time_limit_msec, 5252)
+         self.assertEqual(problems[1].download_data().memory_limit_byte, 512 * 1000 * 1000)
+ 
++    @unittest.skip("Disabled by Guix")
+     def test_list_problems_time_limit_is_less_than_msec(self):
+         contest = AtCoderContest.from_url('https://atcoder.jp/contests/joi2019ho')
+         problems = contest.list_problems()
+@@ -101,12 +107,14 @@ class AtCoderContestTest(unittest.TestCase):
+         self.assertEqual(problems[3].download_data().time_limit_msec, 1000)
+         self.assertEqual(problems[4].download_data().time_limit_msec, 2000)
+ 
++    @unittest.skip("Disabled by Guix")
+     def test_list_problems_memory_limit_is_zero(self):
+         contest = AtCoderContest.from_url('https://atcoder.jp/contests/future-contest-2019-final-open')
+         problems = contest.list_problems()
+         self.assertEqual(problems[0].download_data().memory_limit_byte, 1024 * 1000 * 1000)  # 1024 MB
+         self.assertEqual(problems[1].download_data().memory_limit_byte, 0)  # 0 KB
+ 
++    @unittest.skip("Disabled by Guix")
+     def test_iterate_submissions(self):
+         contest = AtCoderContest.from_url('https://atcoder.jp/contests/code-festival-2014-exhibition-open')
+         submissions = list(contest.iterate_submissions())
+@@ -114,6 +122,7 @@ class AtCoderContestTest(unittest.TestCase):
+         self.assertEqual(submissions[0].get_url(), 'https://atcoder.jp/contests/code-festival-2014-exhibition-open/submissions/272697')
+         self.assertEqual(submissions[1].get_url(), 'https://atcoder.jp/contests/code-festival-2014-exhibition-open/submissions/272700')
+ 
++    @unittest.skip("Disabled by Guix")
+     def test_get_contest_without_penalty(self):
+         contest = AtCoderContest.from_url('https://atcoder.jp/contests/otemae2019')
+         self.assertEqual(contest.download_data(lang='ja').name, '大手前プロコン 2019')
+@@ -154,6 +163,7 @@ class AtCoderProblemTest(unittest.TestCase):
+         self.assertEqual(AtCoderProblem.from_url('https://kupc2014.contest.atcoder.jp/tasks/kupc2014_d'), AtCoderProblem.from_url('https://atcoder.jp/contests/kupc2014/tasks/kupc2014_d'))
+         self.assertNotEqual(AtCoderProblem.from_url('https://kupc2014.contest.atcoder.jp/tasks/kupc2014_d'), AtCoderProblem.from_url('https://atcoder.jp/contests/agc030/tasks/agc030_c'))
+ 
++    @unittest.skip("Disabled by Guix")
+     def test_load_details(self):
+         problem = AtCoderProblem.from_url('https://atcoder.jp/contests/abc118/tasks/abc118_a')
+         data = problem.download_data()
+@@ -163,14 +173,17 @@ class AtCoderProblemTest(unittest.TestCase):
+         self.assertEqual(data.memory_limit_byte, 1024 * 1000 * 1000)
+         self.assertEqual(data.score, 100)
+ 
++    @unittest.skip("Disabled by Guix")
+     def test_get_alphabet(self):
+         self.assertEqual(AtCoderProblem.from_url('https://atcoder.jp/contests/agc028/tasks/agc028_f').download_data().alphabet, 'F')
+         self.assertEqual(AtCoderProblem.from_url('https://atcoder.jp/contests/agc028/tasks/agc028_f2').download_data().alphabet, 'F2')
+ 
++    @unittest.skip("Disabled by Guix")
+     def test_get_score(self):
+         self.assertEqual(AtCoderProblem.from_url('https://atcoder.jp/contests/future-contest-2018-final/tasks/future_contest_2018_final_a').download_data().score, 50000000)
+         self.assertEqual(AtCoderProblem.from_url('https://atcoder.jp/contests/abc001/tasks/abc001_4').download_data().score, None)
+ 
++    @unittest.skip("Disabled by Guix")
+     def test_get_score_latex(self):
+         """
+         .. seealso::
+@@ -179,13 +192,16 @@ class AtCoderProblemTest(unittest.TestCase):
+ 
+         self.assertIsNone(AtCoderProblem.from_url('https://atcoder.jp/contests/wupc2019/tasks/wupc2019_a').download_data().score)
+ 
++    @unittest.skip("Disabled by Guix")
+     def test_get_time_limit_is_less_than_msec(self):
+         self.assertEqual(AtCoderProblem.from_url('https://atcoder.jp/contests/joi2019ho/tasks/joi2019ho_c').download_data().time_limit_msec, 500)
+         self.assertEqual(AtCoderProblem.from_url('https://atcoder.jp/contests/future-contest-2019-qual/tasks/future_contest_2019_qual_b').download_data().time_limit_msec, 0)
+ 
++    @unittest.skip("Disabled by Guix")
+     def test_get_memory_limit_is_zero(self):
+         self.assertEqual(AtCoderProblem.from_url('https://atcoder.jp/contests/future-contest-2019-qual/tasks/future_contest_2019_qual_b').download_data().memory_limit_byte, 0)
+ 
++    @unittest.skip("Disabled by Guix")
+     def test_iterate_submissions(self):
+         problem = AtCoderProblem.from_url('https://atcoder.jp/contests/abc119/tasks/abc119_c')
+         submissions = problem.iterate_submissions()
+@@ -204,6 +220,7 @@ class AtCoderSubmissionTest(unittest.TestCase):
+ 
+ 
+ class AtCoderProblemDataTest(unittest.TestCase):
++    @unittest.skip("Disabled by Guix")
+     def test_from_html_very_old(self):
+         url = 'https://atcoder.jp/contests/utpc2011/tasks/utpc2011_1'
+         resp = requests.get(url)
+@@ -225,6 +242,7 @@ class AtCoderProblemDataTest(unittest.TestCase):
+         self.assertEqual(data.score, None)
+         self.assertEqual(data.time_limit_msec, 1 * 1000)
+ 
++    @unittest.skip("Disabled by Guix")
+     def test_from_html_old(self):
+         url = 'https://atcoder.jp/contests/abc003/tasks/abc003_4'
+         resp = requests.get(url)
+@@ -247,6 +265,7 @@ class AtCoderProblemDataTest(unittest.TestCase):
+         self.assertEqual(data.score, None)
+         self.assertEqual(data.time_limit_msec, 2 * 1000)
+ 
++    @unittest.skip("Disabled by Guix")
+     def test_from_html_standard(self):
+         url = 'https://atcoder.jp/contests/abc114/tasks/abc114_d'
+         resp = requests.get(url)
+@@ -268,6 +287,7 @@ class AtCoderProblemDataTest(unittest.TestCase):
+         self.assertEqual(data.score, 400)
+         self.assertEqual(data.time_limit_msec, 2 * 1000)
+ 
++    @unittest.skip("Disabled by Guix")
+     def test_from_html_with_empty_output(self):
+         url = 'https://atcoder.jp/contests/agc036/tasks/agc036_b'
+         resp = requests.get(url)
+@@ -290,6 +310,7 @@ class AtCoderProblemDataTest(unittest.TestCase):
+         self.assertEqual(data.score, 700)
+         self.assertEqual(data.time_limit_msec, 2 * 1000)
+ 
++    @unittest.skip("Disabled by Guix")
+     def test_from_html_without_sample_cases(self):
+         url = 'https://atcoder.jp/contests/tenka1-2013-quala/tasks/tenka1_2013_qualA_a'
+         resp = requests.get(url)
+@@ -307,6 +328,7 @@ class AtCoderProblemDataTest(unittest.TestCase):
+         self.assertEqual(data.score, None)
+         self.assertEqual(data.time_limit_msec, 2 * 1000)
+ 
++    @unittest.skip("Disabled by Guix")
+     def test_from_html_issue_414(self):
+         url = 'https://atcoder.jp/contests/fuka5/tasks/fuka_graphcut'
+         resp = requests.get(url)
+@@ -399,6 +421,7 @@ class AtCoderProblemDataTest(unittest.TestCase):
+         self.assertEqual(data.score, None)
+         self.assertEqual(data.time_limit_msec, 5 * 1000)
+ 
++    @unittest.skip("Disabled by Guix")
+     def test_download_sample_cases_pre_without_prettyprint_insection(self):
+         # see: https://github.com/kmyk/online-judge-tools/issues/625
+         self.assertEqual(AtCoderProblem.from_url('https://atcoder.jp/contests/tdpc/tasks/tdpc_fibonacci').download_sample_cases(), [
+@@ -406,6 +429,7 @@ class AtCoderProblemDataTest(unittest.TestCase):
+             TestCase(name='sample-2', input_name='Sample Input 2', input_data=b'3 10\n', output_name='Sample Output 2', output_data=b'105\n'),
+         ])
+ 
++    @unittest.skip("Disabled by Guix")
+     def test_download_sample_cases_s8pc_broken_html(self):
+         # see: https://github.com/kmyk/online-judge-tools/issues/615
+         self.assertEqual(AtCoderProblem.from_url('https://atcoder.jp/contests/s8pc-4/tasks/s8pc_4_d').download_sample_cases(), [
+@@ -427,6 +451,7 @@ class AtCoderProblemDataTest(unittest.TestCase):
+ 
+ 
+ class AtCoderProblemGetInputFormatTest(unittest.TestCase):
++    @unittest.skip("Disabled by Guix")
+     def test_normal(self):
+         """
+         .. code-block:: html
+@@ -456,6 +481,7 @@ class AtCoderProblemGetInputFormatTest(unittest.TestCase):
+ 
+         self.assertEqual(AtCoderProblem.from_url('https://beta.atcoder.jp/contests/arc083/tasks/arc083_a').download_data().input_format, '<var>A</var> <var>B</var> <var>C</var> <var>D</var> <var>E</var> <var>F</var>\r\n')
+ 
++    @unittest.skip("Disabled by Guix")
+     def test_old_problem(self):
+         """
+         :note: https://github.com/kmyk/online-judge-tools/issues/380
+@@ -475,6 +501,7 @@ class AtCoderProblemGetInputFormatTest(unittest.TestCase):
+         self.assertEqual(AtCoderProblem.from_url('https://atcoder.jp/contests/arc002/tasks/arc002_3').download_data().input_format, '\r\n<var>N</var>\r\n<var>c_{1}c_{2}...c_{N}</var>\r\n')
+         self.assertEqual(AtCoderProblem.from_url('https://atcoder.jp/contests/arc034/tasks/arc034_4').download_data().input_format, '\r\n<var>A</var> <var>B</var> <var>C</var>\r\n<var>a_1</var> <var>a_2</var> .. <var>a_A</var>\r\n<var>b_1</var> <var>b_2</var> .. <var>b_B</var>\r\n')
+ 
++    @unittest.skip("Disabled by Guix")
+     def test_dwacon_problem(self):
+         """
+         :note: https://github.com/kmyk/online-judge-tools/issues/142
+@@ -493,9 +520,11 @@ class AtCoderProblemGetInputFormatTest(unittest.TestCase):
+         self.assertEqual(AtCoderProblem.from_url('https://atcoder.jp/contests/dwacon2018-final/tasks/dwacon2018_final_a').download_data().input_format, '\r\n<var>H</var> <var>M</var> <var>S</var>\r\n<var>C_1</var> <var>C_2</var>\r\n')
+         self.assertEqual(AtCoderProblem.from_url('https://atcoder.jp/contests/dwacon2018-final/tasks/dwacon2018_final_b').download_data().input_format, '\r\n<var>N</var> <var>K</var>\r\n<var>v_1</var> <var>...</var> <var>v_N</var>\r\n')
+ 
++    @unittest.skip("Disabled by Guix")
+     def test_problem_without_input(self):
+         self.assertIsNone(AtCoderProblem.from_url('https://atcoder.jp/contests/tenka1-2013-quala/tasks/tenka1_2013_qualA_a').download_data().input_format)
+ 
++    @unittest.skip("Disabled by Guix")
+     def test_problem_without_input_format(self):
+         self.assertIsNone(AtCoderProblem.from_url('https://atcoder.jp/contests/joi2006ho/tasks/joi2006ho_a').download_data().input_format)
+ 
+--- a/tests/service_codechef.py
++++ b/tests/service_codechef.py
+@@ -15,6 +15,7 @@ class CodeChefProblemTest(unittest.TestCase):
+         self.assertEqual(CodeChefProblem.from_url('https://www.codechef.com/COOK113A/problems/DAND').contest_id, 'COOK113A')
+         self.assertEqual(CodeChefProblem.from_url('https://www.codechef.com/COOK113A/problems/DAND').problem_id, 'DAND')
+ 
++    @unittest.skip("Disabled by Guix")
+     def test_download_samples_chfgcd(self):
+         url = 'https://www.codechef.com/COOK131B/problems/CHFGCD'
+         expected = [
+
+--- a/tests/service_codeforces.py
++++ b/tests/service_codeforces.py
+@@ -25,6 +25,7 @@ class CodeforcesContestTest(unittest.TestCase):
+         self.assertEqual(CodeforcesContest.from_url('http://m3.codeforces.com/contest/1333').get_url(), CodeforcesContest.from_url('https://codeforces.com/contest/1333').get_url())
+         self.assertIsNone(CodeforcesContest.from_url('http://m4.codeforces.com/contest/1333'))
+ 
++    @unittest.skip("Disabled by Guix")
+     def test_list_problems_data(self):
+         contest = CodeforcesContest.from_url('https://codeforces.com/contest/1157')
+         problems = contest.list_problem_data()
+@@ -38,6 +39,7 @@ class CodeforcesContestTest(unittest.TestCase):
+         self.assertEqual(problems[6].tags, ['constructive algorithms', 'dp', 'greedy', 'two pointers'])
+         self.assertEqual(problems[7].tags, ['brute force', 'constructive algorithms'])
+ 
++    @unittest.skip("Disabled by Guix")
+     def test_list_problems(self):
+         contest = CodeforcesContest.from_url('https://codeforces.com/contest/1157')
+         problems = contest.list_problems()
+@@ -46,6 +48,7 @@ class CodeforcesContestTest(unittest.TestCase):
+         self.assertEqual(problems[6].get_url(), 'https://codeforces.com/contest/1157/problem/F')
+         self.assertEqual(problems[7].download_data().tags, ['brute force', 'constructive algorithms'])
+ 
++    @unittest.skip("Disabled by Guix")
+     def test_download_data(self):
+         contest = CodeforcesContest.from_url('http://codeforces.com/contest/1200')
+         data = contest.download_data()
+@@ -85,6 +88,7 @@ class CodeforcesProblemTest(unittest.TestCase):
+         self.assertEqual(CodeforcesProblem.from_url('https://codeforces.com/contest/1133/problem/F1').index, 'F1')
+         self.assertEqual(CodeforcesProblem.from_url('https://codeforces.com/contest/1133/problem/F2').index, 'F2')
+ 
++    @unittest.skip("Disabled by Guix")
+     def test_download_problem(self):
+         problem = CodeforcesProblem.from_url('http://codeforces.com/contest/1205/problem/D')
+         data = problem.download_data()
+
+--- a/tests/service_google.py
++++ b/tests/service_google.py
+@@ -42,6 +42,7 @@ class GoogleCodeJamProblemTest(unittest.TestCase):
+         self.assertEqual(problem.contest_id, '8404486')
+         self.assertEqual(problem.problem_id, 'p0')
+ 
++    @unittest.skip("Disabled by Guix")
+     def test_download_samples_codejam(self):
+         problem = GoogleCodeJamProblem.from_url('https://codingcompetitions.withgoogle.com/codejam/round/000000000019fd27/000000000020993c')
+         sample_input = textwrap.dedent("""\
+@@ -76,6 +77,7 @@ class GoogleCodeJamProblemTest(unittest.TestCase):
+             ),
+         ])
+ 
++    @unittest.skip("Disabled by Guix")
+     def test_download_samples_kickstart(self):
+         problem = GoogleCodeJamProblem.from_url('https://codingcompetitions.withgoogle.com/kickstart/round/000000000019ffc7/00000000001d3f56')
+         sample_input = textwrap.dedent("""\
+@@ -102,6 +104,7 @@ class GoogleCodeJamProblemTest(unittest.TestCase):
+             ),
+         ])
+ 
++    @unittest.skip("Disabled by Guix")
+     def test_download_multiple_samples(self):
+         problem = GoogleCodeJamProblem.from_url('https://codingcompetitions.withgoogle.com/kickstart/round/000000000019ffc7/00000000001d3ff3')
+         sample_input1 = textwrap.dedent("""\
+
+--- a/tests/service_library_checker.py
++++ b/tests/service_library_checker.py
+@@ -29,13 +29,13 @@ class LibraryCheckerProblemTest(unittest.TestCase):
+     def test_from_url(self):
+         self.assertEqual(LibraryCheckerProblem.from_url('https://judge.yosupo.jp/problem/point_add_range_sum').problem_id, 'point_add_range_sum')
+ 
+-    @unittest.skipIf(os.name == 'nt', "Library Checker is not supported on Windows")
++    @unittest.skip("Disabled by Guix")
+     def test_download_samples(self):
+         self.assertEqual(LibraryCheckerProblem.from_url('https://judge.yosupo.jp/problem/unionfind').download_sample_cases(), [
+             TestCase(name='example_00', input_name='example_00.in', input_data=b'4 7\n1 0 1\n0 0 1\n0 2 3\n1 0 1\n1 1 2\n0 0 2\n1 1 3\n', output_name='example_00.out', output_data=b'0\n1\n0\n1\n'),
+         ])
+ 
+-    @unittest.skipIf(os.name == 'nt', "Library Checker is not supported on Windows")
++    @unittest.skip("Disabled by Guix")
+     def test_pull_repository(self):
+         # reset
+         LibraryCheckerService.is_repository_updated = False
+
+--- a/tests/service_spoj.py
++++ b/tests/service_spoj.py
+@@ -14,11 +14,13 @@ class SPOJProblemTest(unittest.TestCase):
+     def test_from_url(self):
+         self.assertEqual(SPOJProblem.from_url('https://www.spoj.com/problems/ACARGO/').problem_id, 'ACARGO')
+ 
++    @unittest.skip("Disabled by Guix")
+     def test_download_samples(self):
+         self.assertEqual(SPOJProblem.from_url('https://www.spoj.com/problems/ACARGO/').download_sample_cases(), [
+             TestCase(name='sample-1', input_name='Sample Input:', input_data=b'3 5\n0\n1\n3\n2 3\n0\n1\n5 20\n2\n7\n12\n9\n13\n0 0\n', output_name='Sample Output:', output_data=b'1\n0\n10\n'),
+         ])
+ 
++    @unittest.skip("Disabled by Guix")
+     def test_download_samples_todo(self):
+         # No samples found.
+         self.assertFalse(SPOJProblem.from_url('https://www.spoj.com/problems/MKLABELS/').download_sample_cases())
+
+--- a/tests/service_yukicoder.py
++++ b/tests/service_yukicoder.py
+@@ -20,6 +20,7 @@ class YukicoderProblemTest(unittest.TestCase):
+         self.assertEqual(YukicoderProblem.from_url('http://yukicoder.me/problems/no/123/').problem_no, 123)
+         self.assertEqual(YukicoderProblem.from_url('http://yukicoder.me/problems/123').problem_id, 123)
+ 
++    @unittest.skip("Disabled by Guix")
+     def test_download_sample_cases(self):
+         self.assertEqual(YukicoderProblem.from_url('http://yukicoder.me/problems/no/9000').download_sample_cases(), [
+             TestCase(name='sample-1', input_name='サンプル1 入力', input_data=b'yukicoder\n', output_name='サンプル1 出力', output_data=b'Hello World!\n'),
+@@ -45,6 +46,7 @@ class YukicoderProblemTest(unittest.TestCase):
+             TestCase(name='sample-4', input_name='サンプル4 入力', input_data=b'\n', output_name='サンプル4 出力', output_data=b'1\n'),
+         ])
+ 
++    @unittest.skip("Disabled by Guix")
+     def test_download_sample_cases_issue_355(self):
+         # see https://github.com/kmyk/online-judge-tools/issues/355
+         self.assertEqual(YukicoderProblem.from_url('https://yukicoder.me/problems/no/649').download_sample_cases(), [
+@@ -54,6 +56,7 @@ class YukicoderProblemTest(unittest.TestCase):
+             TestCase(name='sample-4', input_name='サンプル4 入力', input_data=b'1 1\n2\n', output_name='サンプル4 出力', output_data=b'-1\n'),
+         ])
+ 
++    @unittest.skip("Disabled by Guix")
+     def test_download_sample_cases_issue_192(self):
+         # see https://github.com/kmyk/online-judge-tools/issues/192
+         self.assertEqual(YukicoderProblem.from_url('https://yukicoder.me/problems/no/750').download_sample_cases(), [
+@@ -133,6 +136,7 @@ class YukicoderContestTest(unittest.TestCase):
+         self.assertEqual(YukicoderContest.from_url('https://yukicoder.me/contests/276').contest_id, 276)
+         self.assertEqual(YukicoderContest.from_url('http://yukicoder.me/contests/276/all').contest_id, 276)
+ 
++    @unittest.skip("Disabled by Guix")
+     def test_list_problems(self):
+         self.assertEqual(YukicoderContest.from_url('https://yukicoder.me/contests/276').list_problems(), [
+             YukicoderProblem(problem_id=4401),
+@@ -145,6 +149,7 @@ class YukicoderContestTest(unittest.TestCase):
+ 
+ 
+ class YukicoderProblemGetInputFormatTest(unittest.TestCase):
++    @unittest.skip("Disabled by Guix")
+     def test_normal(self):
+         self.assertEqual(YukicoderProblem.from_url('https://yukicoder.me/problems/no/1').get_input_format(), '\\(N\\)\n\\(C\\)\n\\(V\\)\n\\(S_1\\ S_2\\ S_3\\ \\dots\\ S_V\\)\n\\(T_1\\ T_2\\ T_3\\ \\dots\\ T_V\\)\n\\(Y_1\\ Y_2\\ Y_3\\ \\dots\\ Y_V\\)\n\\(M_1\\ M_2\\ M_3\\ \\dots\\ M_V\\)\n')
+         self.assertEqual(YukicoderProblem.from_url('https://yukicoder.me/problems/no/2').get_input_format(), 'N\n')
+@@ -154,6 +159,7 @@ class YukicoderProblemGetInputFormatTest(unittest.TestCase):
+         self.assertEqual(YukicoderProblem.from_url('https://yukicoder.me/problems/no/512').get_input_format(), '$X$ $Y$\n$N$\n$A_1$ $\\cdots$ $A_N$\n')
+         self.assertEqual(YukicoderProblem.from_url('https://yukicoder.me/problems/no/777').get_input_format(), '$N$\n$A_1$ $B_1$ $C_1$\n$A_2$ $B_2$ $C_2$\n…\n$A_N$ $B_N$ $C_N$\n')
+ 
++    @unittest.skip("Disabled by Guix")
+     def test_problem_without_input(self):
+         self.assertIsNone(YukicoderProblem.from_url('https://yukicoder.me/problems/no/3003').get_input_format())
+ 
\ No newline at end of file
diff --git a/gnu/packages/patches/python-pycrypto-CVE-2013-7459.patch b/gnu/packages/patches/python-pycrypto-CVE-2013-7459.patch
deleted file mode 100644
index 3570b94e9b..0000000000
--- a/gnu/packages/patches/python-pycrypto-CVE-2013-7459.patch
+++ /dev/null
@@ -1,97 +0,0 @@
-Fix CVE-2013-7459:
-
-https://github.com/dlitz/pycrypto/issues/176
-https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2013-7459
-
-Copied from Debian:
-
-https://anonscm.debian.org/cgit/collab-maint/python-crypto.git/commit/?id=0de2243837ed369a086f15c50cca2be85bdfab9d
-
-Debian adapts this upstream commit:
-
-https://github.com/dlitz/pycrypto/commit/8dbe0dc3eea5c689d4f76b37b93fe216cf1f00d4
-
-From 8dbe0dc3eea5c689d4f76b37b93fe216cf1f00d4 Mon Sep 17 00:00:00 2001
-From: Legrandin <helderijs@gmail.com>
-Date: Sun, 22 Dec 2013 22:24:46 +0100
-Subject: [PATCH] Throw exception when IV is used with ECB or CTR
-
-The IV parameter is currently ignored when initializing
-a cipher in ECB or CTR mode.
-
-For CTR mode, it is confusing: it takes some time to see
-that a different parameter is needed (the counter).
-
-For ECB mode, it is outright dangerous.
-
-This patch forces an exception to be raised.
----
- lib/Crypto/SelfTest/Cipher/common.py | 31 +++++++++++++++++++++++--------
- src/block_template.c                 | 11 +++++++++++
- 2 files changed, 34 insertions(+), 8 deletions(-)
-
---- a/lib/Crypto/SelfTest/Cipher/common.py
-+++ b/lib/Crypto/SelfTest/Cipher/common.py
-@@ -239,19 +239,34 @@ class RoundtripTest(unittest.TestCase):
-         return """%s .decrypt() output of .encrypt() should not be garbled""" % (self.module_name,)
- 
-     def runTest(self):
--        for mode in (self.module.MODE_ECB, self.module.MODE_CBC, self.module.MODE_CFB, self.module.MODE_OFB, self.module.MODE_OPENPGP):
-+
-+        ## ECB mode
-+        mode = self.module.MODE_ECB
-+        encryption_cipher = self.module.new(a2b_hex(self.key), mode)
-+        ciphertext = encryption_cipher.encrypt(self.plaintext)
-+        decryption_cipher = self.module.new(a2b_hex(self.key), mode)
-+        decrypted_plaintext = decryption_cipher.decrypt(ciphertext)
-+        self.assertEqual(self.plaintext, decrypted_plaintext)
-+
-+        ## OPENPGP mode
-+        mode = self.module.MODE_OPENPGP
-+        encryption_cipher = self.module.new(a2b_hex(self.key), mode, self.iv)
-+        eiv_ciphertext = encryption_cipher.encrypt(self.plaintext)
-+        eiv = eiv_ciphertext[:self.module.block_size+2]
-+        ciphertext = eiv_ciphertext[self.module.block_size+2:]
-+        decryption_cipher = self.module.new(a2b_hex(self.key), mode, eiv)
-+        decrypted_plaintext = decryption_cipher.decrypt(ciphertext)
-+        self.assertEqual(self.plaintext, decrypted_plaintext)
-+
-+        ## All other non-AEAD modes (but CTR)
-+        for mode in (self.module.MODE_CBC, self.module.MODE_CFB, self.module.MODE_OFB):
-             encryption_cipher = self.module.new(a2b_hex(self.key), mode, self.iv)
-             ciphertext = encryption_cipher.encrypt(self.plaintext)
--            
--            if mode != self.module.MODE_OPENPGP:
--                decryption_cipher = self.module.new(a2b_hex(self.key), mode, self.iv)
--            else:
--                eiv = ciphertext[:self.module.block_size+2]
--                ciphertext = ciphertext[self.module.block_size+2:]
--                decryption_cipher = self.module.new(a2b_hex(self.key), mode, eiv)
-+            decryption_cipher = self.module.new(a2b_hex(self.key), mode, self.iv)
-             decrypted_plaintext = decryption_cipher.decrypt(ciphertext)
-             self.assertEqual(self.plaintext, decrypted_plaintext)
- 
-+
- class PGPTest(unittest.TestCase):
-     def __init__(self, module, params):
-         unittest.TestCase.__init__(self)
---- a/src/block_template.c
-+++ b/src/block_template.c
-@@ -170,6 +170,17 @@ ALGnew(PyObject *self, PyObject *args, P
- 				"Key cannot be the null string");
- 		return NULL;
- 	}
-+	if (IVlen != 0 && mode == MODE_ECB)
-+	{
-+		PyErr_Format(PyExc_ValueError, "ECB mode does not use IV");
-+		return NULL;
-+	}
-+	if (IVlen != 0 && mode == MODE_CTR)
-+	{
-+		PyErr_Format(PyExc_ValueError,
-+			"CTR mode needs counter parameter, not IV");
-+		return NULL;
-+	}
- 	if (IVlen != BLOCK_SIZE && mode != MODE_ECB && mode != MODE_CTR)
- 	{
- 		PyErr_Format(PyExc_ValueError,
diff --git a/gnu/packages/patches/python-pycrypto-time-clock.patch b/gnu/packages/patches/python-pycrypto-time-clock.patch
deleted file mode 100644
index 9b7a8232a2..0000000000
--- a/gnu/packages/patches/python-pycrypto-time-clock.patch
+++ /dev/null
@@ -1,23 +0,0 @@
-Drop use of the deprecated time.clock which was removed in Python 3.8.
-
-Adapted from upstream pull request:
-
-https://github.com/dlitz/pycrypto/pull/296
-
-diff --git a/lib/Crypto/Random/_UserFriendlyRNG.py b/lib/Crypto/Random/_UserFriendlyRNG.py
---- a/lib/Crypto/Random/_UserFriendlyRNG.py
-+++ b/lib/Crypto/Random/_UserFriendlyRNG.py
-@@ -73,8 +73,11 @@ class _EntropyCollector(object):
-         t = time.time()
-         self._time_es.feed(struct.pack("@I", int(2**30 * (t - floor(t)))))
- 
--        # Add the fractional part of time.clock()
--        t = time.clock()
-+        # Add the fractional part of time.process_time()
-+        try:
-+           t = time.process_time()
-+        except AttributeError:
-+           t = time.clock()
-         self._clock_es.feed(struct.pack("@I", int(2**30 * (t - floor(t)))))
- 
- 
diff --git a/gnu/packages/pdf.scm b/gnu/packages/pdf.scm
index 378655a70f..a2c0118455 100644
--- a/gnu/packages/pdf.scm
+++ b/gnu/packages/pdf.scm
@@ -824,14 +824,14 @@ and based on PDF specification 1.7.")
 (define-public mupdf
   (package
     (name "mupdf")
-    (version "1.23.3")
+    (version "1.23.4")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://mupdf.com/downloads/archive/"
-                           "mupdf-" version "-source.tar.gz"))
+                           "mupdf-" version "-source.tar.lz"))
        (sha256
-        (base32 "1b8ajj5xmi2p9c92l8fd46amfshmxdw6zcg1hqajg8y0kd0ady8y"))
+        (base32 "0068swdrlq9q7pkg3dxn4rschxm5j37pd4vz0cb2pcry75rdmxpc"))
        (modules '((guix build utils)
                   (ice-9 ftw)
                   (srfi srfi-1)))
@@ -1003,7 +1003,7 @@ using a stylus.")
 (define-public xournalpp
   (package
     (name "xournalpp")
-    (version "1.2.1")
+    (version "1.2.2")
     (source
      (origin
        (method git-fetch)
@@ -1012,7 +1012,7 @@ using a stylus.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "18slm517yazysvd0ii0gi7kg4hzyf17d86w2bflgfaz9ccclswbn"))))
+        (base32 "1svmdj43z1shm3wnkrdrq1h6rba843mp4x4d8jmxsx7kwiiz9l78"))))
     (build-system cmake-build-system)
     (arguments
      (list
diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index 0ccae07093..630c4ea97e 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2019, 2021, 2022 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2019, 2021, 2022, 2023 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2019, 2020, 2021 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2019, 2020, 2021, 2022, 2023 Maxim Cournoyer <maxim.cournoyer@gmail.com>
@@ -59,6 +59,24 @@
   #:use-module (guix packages)
   #:use-module (guix utils))
 
+(define-public python-assertpy
+  (package
+    (name "python-assertpy")
+    (version "1.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "assertpy" version))
+       (sha256
+        (base32 "0cs8xya465wvb9dw0kdl7cvkxwrslhbma66y44r1mmsajcll7imc"))))
+    (build-system pyproject-build-system)
+    (home-page "https://github.com/assertpy/assertpy")
+    (synopsis "Simple assertion library for unit testing")
+    (description
+     "This package provides a simple assertion library for unit testing in
+Python with a fluent API.")
+    (license license:bsd-3)))
+
 (define-public python-tappy
   (package
     (name "python-tappy")
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index efddd060a4..4063797a30 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -810,7 +810,7 @@ functions and around einops with an API and features adapted to xarray.")
 (define-public python-pytensor
   (package
     (name "python-pytensor")
-    (version "2.14.2")
+    (version "2.17.3")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -819,7 +819,7 @@ functions and around einops with an API and features adapted to xarray.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1428l1v7yrnls8875xjx1svn48cmz0q83sv7sg0xdqghkfnyi7xx"))))
+                "1694apl8gjdrl6hrfly9yixmfimmmh51vacxmxx63nn4k5qnsgbg"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -2030,6 +2030,33 @@ Out-of-Core DataFrames (similar to Pandas), to visualize and explore big
 tabular datasets.  This package provides the core modules of Vaex.")
     (license license:expat)))
 
+(define-public python-salib
+  (package
+    (name "python-salib")
+    (version "1.4.7")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/SALib/SALib")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "18xfyzircsx2q2lmfc9lxb6xvkxicnc83qzghd7df1jsprr5ymch"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs (list python-matplotlib
+                             python-multiprocess
+                             python-numpy
+                             python-pandas
+                             python-scipy))
+    (native-inputs (list python-hatchling python-pytest python-pytest-cov))
+    (home-page "https://salib.readthedocs.io/en/latest/")
+    (synopsis "Tools for global sensitivity analysis")
+    (description "SALib provides tools for global sensitivity analysis.  It
+contains Sobol', Morris, FAST, DGSM, PAWN, HDMR, Moment Independent and
+fractional factorial methods.")
+    (license license:expat)))
+
 (define-public python-pylems
   (package
     (name "python-pylems")
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 65c23cb318..6001e7e6eb 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -63,7 +63,7 @@
 ;;; Copyright © 2019, 2020 Alex Griffin <a@ajgrf.com>
 ;;; Copyright © 2019, 2020, 2021, 2022, 2023 Pierre Langlois <pierre.langlois@gmx.com>
 ;;; Copyright © 2019 Jacob MacDonald <jaccarmac@gmail.com>
-;;; Copyright © 2019, 2020, 2021 Giacomo Leidi <goodoldpaul@autistici.org>
+;;; Copyright © 2019-2021, 2023 Giacomo Leidi <goodoldpaul@autistici.org>
 ;;; Copyright © 2019 Wiktor Żelazny <wzelazny@vurv.cz>
 ;;; Copyright © 2019, 2020, 2021, 2022 Tanguy Le Carrour <tanguy@bioneland.org>
 ;;; Copyright © 2019, 2021-2023 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
@@ -139,6 +139,7 @@
 ;;; Copyright © 2023 Dominik Delgado Steuter <d@delgado.nrw>
 ;;; Copyright © 2023 Ivan Vilata-i-Balaguer <ivan@selidor.net>
 ;;; Copyright © 2023 Ontje Lünsdorf <ontje.luensdorf@dlr.de>
+;;; Copyright © 2023 gemmaro <gemmaro.dev@gmail.com>
 ;;; Copyright © 2023 Parnikkapore <poomklao@yahoo.com>
 ;;; Copyright © 2023 Foundation Devices, Inc. <hello@foundationdevices.com>
 ;;; Copyright © c4droid <c4droid@foxmail.com>
@@ -4881,6 +4882,30 @@ between Julian dates and Gregorian dates.")
 compare, diff, and patch JSON and JSON-like structures in Python.")
    (license license:expat)))
 
+(define-public python-ddlparse
+  (package
+    (name "python-ddlparse")
+    (version "1.10.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "ddlparse" version))
+       (sha256
+        (base32 "1nh8m6rxslwk05daxshxmgk41qfp18yynydba49b13l4m8dnh634"))))
+    (build-system pyproject-build-system)
+    (native-inputs
+     (list python-codecov
+           python-coveralls
+           python-pytest
+           python-pytest-cov
+           python-tox))
+    (propagated-inputs (list python-pyparsing))
+    (home-page "https://github.com/shinichi-takii/ddlparse")
+    (synopsis "Parses and converts DDL to BigQuery JSON schema")
+    (description "This package provides @{ddlparse}, a Python library to parse
+and convert DDL to BigQuery JSON schema.")
+    (license license:bsd-3)))
+
 (define-public python-jsonschema
   (package
     (name "python-jsonschema")
@@ -5819,14 +5844,17 @@ flexibility and power of the Python language.")
 (define-public python-dm-tree
   (package
     (name "python-dm-tree")
-    (version "0.1.7")
+    (version "0.1.8")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "dm-tree" version))
               (sha256
-               (base32 "0apxfxgmqh22qpk92zmmf3acqkavhwxz78lnwz026a5rlnncizih"))))
-    (build-system python-build-system)
-    (inputs (list pybind11 abseil-cpp python))
+               (base32 "0c4l9gpaqd7j34qwnpjibv53j9sm0nyl0wcy8dvh76772jxspjhg"))))
+    (build-system pyproject-build-system)
+    ;; We link the static abseil libraries here to avoid problems in
+    ;; downstream libraries using potentially different variants of
+    ;; abseil-cpp.  This is also what's done in the upstream CMake build.
+    (inputs (list pybind11 static-abseil-cpp python))
     (propagated-inputs (list python-wheel
                              python-absl-py
                              python-attrs
@@ -5867,13 +5895,15 @@ flexibility and power of the Python language.")
                       (string-append "-Wl," "-rpath=" python "/lib")
                       "-fno-semantic-interposition"
                       "build/temp/tree/tree.o"
+                      "-Wl,--whole-archive"
                       "-L" (string-append python "/lib")
-                      "-L" (string-append abseil-cpp "/lib")
-                      "-l" "absl_int128"
-                      "-l" "absl_raw_hash_set"
-                      "-l" "absl_raw_logging_internal"
-                      "-l" "absl_strings"
-                      "-l" "absl_throw_delegate"
+                      (string-append abseil-cpp "/lib/libabsl_int128.a")
+                      (string-append abseil-cpp "/lib/libabsl_raw_hash_set.a")
+                      (string-append abseil-cpp "/lib/libabsl_raw_logging_internal.a")
+                      (string-append abseil-cpp "/lib/libabsl_strings.a")
+                      (string-append abseil-cpp "/lib/libabsl_strings_internal.a")
+                      (string-append abseil-cpp "/lib/libabsl_throw_delegate.a")
+                      "-Wl,--no-whole-archive"
                       "-o" "build/lib/tree/_tree.so")))))))
     (home-page "https://github.com/deepmind/tree")
     (synopsis "Work with nested data structures in Python")
@@ -13467,6 +13497,24 @@ provided that can be used to do various manipulations with LilyPond files.")
 should be stored on various operating systems.")
     (license license:expat)))
 
+(define-public python-google-pasta
+  (package
+    (name "python-google-pasta")
+    (version "0.2.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "google-pasta" version))
+       (sha256
+        (base32 "0vm1r1jlaiagj0l9yf7j6zn9w3733dr2169911c0svgrr3gwiwn9"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs (list python-six))
+    (home-page "https://github.com/google/pasta")
+    (synopsis "pasta is an AST-based Python refactoring library")
+    (description "This package provides \"pasta\", an AST-based Python
+refactoring library.")
+    (license license:asl2.0)))
+
 (define-public python-gorilla
   (package
     (name "python-gorilla")
@@ -13745,22 +13793,6 @@ similar to the Python standard library's @code{json} module.")
 includes dependency resolution logic.")
     (license license:isc)))
 
-;;; This older version is required by ansible-core.
-(define-public python-resolvelib-0.5
-  (package/inherit python-resolvelib
-    (name "python-resolvelib")
-    (version "0.5.4")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://github.com/sarugaku/resolvelib")
-             (commit version)))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32
-         "0697y330sqhiclk25v151qxg7aixzpj434lbg5qib0qlna5zg9la"))))))
-
 (define-public python-commonmark
   (package
     (name "python-commonmark")
@@ -24523,6 +24555,102 @@ in Python.  You can simply type pybtex instead of bibtex.")
 time-based (TOTP) passwords.")
     (license license:expat)))
 
+(define-public python-online-judge-api-client
+  (package
+    (name "python-online-judge-api-client")
+    (version "10.10.1")
+    ;; Source distributions are not uploaded to PyPI.
+    ;; https://pypi.org/project/online-judge-api-client/10.10.1/#files
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/online-judge-tools/api-client")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0yjqhh44va5nawd9rpqcjyf0g7rjlkvn7s90fmwmwjyqvy6lhjiz"))
+              (patches (search-patches
+                        "python-online-judge-api-client-tests.patch"))))
+    (build-system python-build-system)
+    (arguments
+     (list #:phases #~(modify-phases %standard-phases
+                        ;; These tests require network connections
+                        (add-after 'unpack 'remove-failing-test
+                          (lambda _
+                            (for-each delete-file
+                                      '("tests/get_contest_atcoder.py"
+                                        "tests/get_contest_atcoder_problems.py"
+                                        "tests/get_contest_codechef.py"
+                                        "tests/get_contest_codeforces.py"
+                                        "tests/get_contest_yukicoder.py"
+                                        "tests/get_problem_anarchygolf.py"
+                                        "tests/get_problem_aoj.py"
+                                        "tests/get_problem_atcoder.py"
+                                        "tests/get_problem_codechef.py"
+                                        "tests/get_problem_codeforces.py"
+                                        "tests/get_problem_csacademy.py"
+                                        "tests/get_problem_facebook.py"
+                                        "tests/get_problem_hackerrank.py"
+                                        "tests/get_problem_kattis.py"
+                                        "tests/get_problem_library_checker.py"
+                                        "tests/get_problem_poj.py"
+                                        "tests/get_problem_topcoder.py"
+                                        "tests/get_problem_toph.py"
+                                        "tests/get_problem_yukicoder.py"
+                                        "tests/login_service.py")) #t)))))
+    (propagated-inputs (list python-appdirs
+                             python-beautifulsoup4
+                             python-colorlog
+                             python-lxml
+                             python-requests
+                             python-toml
+                             python-jsonschema))
+    (home-page "https://github.com/online-judge-tools/api-client")
+    (synopsis "API client for various online judges")
+    (description
+     "This is an API client for various online judges, used as the backend
+library of @code{oj} command.  You can use the Python
+library (@code{onlinejudge} module) and the command-line
+interface (@command{oj-api} command) which talks JSON compatible with
+jmerle/competitive-companion.")
+    (license license:expat)))
+
+(define-public online-judge-tools
+  (package
+    (name "online-judge-tools")
+    (version "11.5.1")
+    ;; Source distributions are not uploaded to PyPI.
+    ;; https://pypi.org/project/online-judge-tools/11.5.1/#files
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/online-judge-tools/oj")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0zkzmmjgjb6lyrzq1ip54cpnp7al9a7mcyjyi5vx58bvnx3q0c6m"))
+              (patches (search-patches "online-judge-tools.patch"))))
+    (build-system python-build-system)
+    (arguments
+     (list #:phases #~(modify-phases %standard-phases
+                        ;; These tests require network connections
+                        (add-after 'unpack 'remove-failing-test
+                          (lambda _
+                            (delete-file "tests/command_version.py") #t)))))
+    (inputs (list time))
+    (propagated-inputs (list python-online-judge-api-client python-colorama
+                             python-requests))
+    (home-page "https://github.com/online-judge-tools/oj")
+    (synopsis "Command to help solving problems on various online judges")
+    (description
+     "@command{oj} is a command line tool to help solving problems on
+various online judges.  This command automates downloading sample
+cases, generating additional test cases, testing for your code, and
+submitting it.")
+    (license license:expat)))
+
 (define-public python-parso
   (package
     (name "python-parso")
@@ -28912,7 +29040,7 @@ accessor layer.")
 (define-public pyzo
   (package
     (name "pyzo")
-    (version "4.12.8")
+    (version "4.13.3")
     (source
      (origin
        (method git-fetch)
@@ -28922,7 +29050,7 @@ accessor layer.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "036snpv6j63bv9z9mbq317qb43zwsj1m8vljra3c0kiakahp7cc3"))))
+         "1m0mrp20wjvy804214f4zzlbaqrakam0g3qr562yn2mjcgfba554"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
@@ -29883,26 +30011,48 @@ applications with variable CPU loads).")
 (define-public python-versioneer
   (package
     (name "python-versioneer")
-    (version "0.21")
+    (version "0.29")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "versioneer" version))
        (sha256
         (base32
-         "084fglxafbzvf1vbkzfajvs9qwnvjwwn8pxql9nrlpyipv5xpwk4"))
+         "0cap4cjckxp9mlkprqayfs77k3pn5iwpr2riacdxc4bjhnwq7cjs"))
        (patches (search-patches "python-versioneer-guix-support.patch"))))
-    (build-system python-build-system)
-    (home-page
-     "https://github.com/python-versioneer/python-versioneer")
-    (synopsis
-     "Version-string management for VCS-controlled trees")
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (replace 'check
+            (lambda* (#:key tests? #:allow-other-keys)
+              (when tests?
+                ;; Taken from tox.ini.
+                (invoke "python" "setup.py" "make_versioneer")
+                (invoke "python" "-m" "unittest" "discover" "test")
+                (invoke "python" "test/git/test_git.py" "-v")
+                ;; Some invocation tests require the network.
+                ;;(invoke "python" "test/git/test_invocations.py" "-v")
+                (invoke "python" "setup.py" "make_long_version_py_git")
+                (invoke "pyflakes" "setup.py" "versioneer.py" "git_version.py")
+                (invoke "python" "test/run_pyflakes_src.py")
+                (invoke "pyflakes" "test")
+                (invoke "flake8" "git_version.py" "versioneer.py")
+                (invoke "pycodestyle" "--max-line-length=88"
+                        "git_version.py" "versioneer.py")))))))
+    (native-inputs
+     (list git python-flake8 python-pycodestyle python-pyflakes))
+    (propagated-inputs
+     (list python-tomli))
+    (home-page "https://github.com/python-versioneer/python-versioneer")
+    (synopsis "Version-string management for VCS-controlled trees")
     (description
      "@code{versioneer} is a tool for managing a recorded version number in
 distutils-based python projects.  The goal is to remove the tedious and
 error-prone \"update the embedded version string\" step from your release
 process.")
-    (license license:public-domain)))
+    (license license:unlicense)))
 
 (define-public python-gamera
   (package
diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm
index a85762c352..17589b584c 100644
--- a/gnu/packages/radio.scm
+++ b/gnu/packages/radio.scm
@@ -1200,7 +1200,7 @@ satellites.")
 (define-public gqrx
   (package
     (name "gqrx")
-    (version "2.17.2")
+    (version "2.17.3")
     (source
      (origin
        (method git-fetch)
@@ -1209,7 +1209,7 @@ satellites.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1psfbwdgac4wkl6vjdk092rmwbd7228l0d3l5p9ab48d6vyrn2kp"))))
+        (base32 "00pasp13gqglixl0iy9jb242vx1kczgpinjs3d8a1cl8yv5w6xkl"))))
     (build-system qt-build-system)
     (native-inputs
      (list pkg-config))
diff --git a/gnu/packages/rust-apps.scm b/gnu/packages/rust-apps.scm
index 4a4247751b..a06447143a 100644
--- a/gnu/packages/rust-apps.scm
+++ b/gnu/packages/rust-apps.scm
@@ -1370,35 +1370,45 @@ rebase.")
      "This package provides a tool for generating C/C++ bindings to Rust code.")
     (license license:mpl2.0)))
 
-(define-public rust-cbindgen-0.24
+(define-public rust-cbindgen-0.26
   (package
     (inherit rust-cbindgen)
     (name "rust-cbindgen")
+    (version "0.26.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (crate-uri "cbindgen" version))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32 "0jdbxmn5h5nlr4bifx85gny309djv5djs9q78fa1d7sj0wdw2sys"))))
+    (arguments
+     `(#:cargo-inputs (("rust-clap" ,rust-clap-3)
+                       ("rust-heck" ,rust-heck-0.4)
+                       ("rust-indexmap" ,rust-indexmap-1)
+                       ("rust-log" ,rust-log-0.4)
+                       ("rust-proc-macro2" ,rust-proc-macro2-1)
+                       ("rust-quote" ,rust-quote-1)
+                       ("rust-serde" ,rust-serde-1)
+                       ("rust-serde-json" ,rust-serde-json-1)
+                       ("rust-syn" ,rust-syn-1)
+                       ("rust-tempfile" ,rust-tempfile-3)
+                       ("rust-toml" ,rust-toml-0.5))
+       #:cargo-development-inputs (("rust-serial-test" ,rust-serial-test-0.5))))
+    (native-inputs (list python-cython))))
+
+(define-public rust-cbindgen-0.24
+  (package
+    (inherit rust-cbindgen-0.26)
+    (name "rust-cbindgen")
     (version "0.24.3")
     (source (origin
-             (method url-fetch)
-             (uri (crate-uri "cbindgen" version))
-             (file-name (string-append name "-" version ".tar.gz"))
-             (sha256
-              (base32
-               "1yqxqsz2d0cppd8zwihk2139g5gy38wqgl9snj6rnk8gyvnqsdd6"))))
-    (arguments
-     `(#:cargo-inputs
-       (("rust-clap" ,rust-clap-3)
-        ("rust-heck" ,rust-heck-0.4)
-        ("rust-indexmap" ,rust-indexmap-1)
-        ("rust-log" ,rust-log-0.4)
-        ("rust-proc-macro2" ,rust-proc-macro2-1)
-        ("rust-quote" ,rust-quote-1)
-        ("rust-serde" ,rust-serde-1)
-        ("rust-serde-json" ,rust-serde-json-1)
-        ("rust-syn" ,rust-syn-1)
-        ("rust-tempfile" ,rust-tempfile-3)
-        ("rust-toml" ,rust-toml-0.5))
-        #:cargo-development-inputs
-        (("rust-serial-test" ,rust-serial-test-0.5))))
-    (native-inputs
-     (list python-cython))))
+              (method url-fetch)
+              (uri (crate-uri "cbindgen" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1yqxqsz2d0cppd8zwihk2139g5gy38wqgl9snj6rnk8gyvnqsdd6"))))))
 
 (define-public rust-cbindgen-0.23
   (package
diff --git a/gnu/packages/sdl.scm b/gnu/packages/sdl.scm
index 11aa5e1602..a4ee654097 100644
--- a/gnu/packages/sdl.scm
+++ b/gnu/packages/sdl.scm
@@ -14,6 +14,7 @@
 ;;; Copyright © 2020 Timotej Lazar <timotej.lazar@araneo.si>
 ;;; Copyright © 2020 Oleg Pykhalov <go.wigust@gmail.com>
 ;;; Copyright © 2022 Maxim Cournoyer <maxim.cournoyer@gmail.com>
+;;; Copyright © 2023 Evgeny Pisemsky <evgeny@pisemsky.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -41,6 +42,7 @@
   #:use-module (guix download)
   #:use-module (guix git-download)
   #:use-module (guix utils)
+  #:use-module (guix build-system copy)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system trivial)
   #:use-module (gnu packages audio)
@@ -563,6 +565,31 @@ directory.")
        (prepend harfbuzz freetype)))
     (properties '((upstream-name . "SDL2_ttf")))))
 
+(define-public sdl2-gamecontrollerdb
+  (let ((commit "6f3c4edcb5a2e2ed090ca8af40d2c0f00dcd77f6")
+        (revision "0"))
+    (package
+      (name "sdl2-gamecontrollerdb")
+      (version (git-version "0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/gabomdq/SDL_GameControllerDB")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "1gciqc8qm2qgcjj5s9jpclznznsp6awl4ldrnj7g01chkcx0l6a3"))))
+      (build-system copy-build-system)
+      (arguments
+       '(#:install-plan '(("gamecontrollerdb.txt" "share/sdl2/"))))
+      (home-page "https://github.com/gabomdq/SDL_GameControllerDB")
+      (synopsis "SDL2 game controller database")
+      (description
+       "This package provides a community sourced database of game controller
+mappings intended for the use with SDL2's game controller functionality.")
+      (license license:zlib))))
+
 (define-public guile-sdl
   (package
     (name "guile-sdl")
diff --git a/gnu/packages/sphinx.scm b/gnu/packages/sphinx.scm
index a7c437d6b4..eee1f1c4a8 100644
--- a/gnu/packages/sphinx.scm
+++ b/gnu/packages/sphinx.scm
@@ -49,6 +49,7 @@
   #:use-module (gnu packages graphviz)
   #:use-module (gnu packages image)
   #:use-module (gnu packages imagemagick)
+  #:use-module (gnu packages jupyter)
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-build)
   #:use-module (gnu packages python-check)
@@ -528,35 +529,42 @@ Sphinx documentation into your web application.  It provides tools to
 integrate Sphinx documents in web templates and to handle searches.")
     (license license:bsd-3)))
 
-
 (define-public python-sphinx-gallery
   (package
     (name "python-sphinx-gallery")
-    (version "0.10.1")
+    (version "0.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "sphinx-gallery" version))
        (sha256
-        (base32 "1r07sa34511fbnwi2s32q00qdyv5d23d05imyfgnh2ivhfq34gwm"))))
-    (build-system python-build-system)
+        (base32 "1hj380d5bjhbzxmhjw8f8b71jy1wk8crad0g3n750m990fphljia"))))
+    (build-system pyproject-build-system)
     (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-before 'check 'writable-files-for-tests
+     (list
+      #:test-flags
+      '(list "--pyargs" "sphinx_gallery" "-k"
+             (string-append
+              ;; These tests require online data.
+              "not test_embed_code_links_get_data"
+              " and not test_run_sphinx"
+              ;; Requires webp support
+              " and not test_image_formats"
+              ;; Needs graphviz
+              " and not test_rebuild"
+              ;; Fails because we've deleted an example file, so the numbers
+              ;; don't match.
+              " and not test_junit"
+              ;; AssertionError.
+              " and not test_embed_links_and_styles"))
+      #:phases
+      '(modify-phases %standard-phases
+         ;; TODO: Our version of matplotlib does not support webp.
+         (add-after 'unpack 'delete-webp-example
            (lambda _
-             (for-each make-file-writable (find-files "."))))
-         (replace 'check
-           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
-             (when tests?
-               (add-installed-pythonpath inputs outputs)
-               (invoke "python" "-m" "pytest" "--pyargs" "sphinx_gallery" "-k"
-                       (string-append
-                        ;; These tests require online data.
-                        "not test_embed_code_links_get_data"
-                        " and not test_run_sphinx"
-                        ;; AssertionError.
-                        " and not test_embed_links_and_styles"))))))))
+             (delete-file "sphinx_gallery/tests/tinybuild/examples/plot_webp.py"))))))
+    (propagated-inputs
+     (list python-jupyterlite-sphinx))
     (native-inputs
      (list python-joblib
            python-matplotlib
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 557b63aeae..d15732c839 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -652,13 +652,13 @@ estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995)
 (define-public r-lattice
   (package
     (name "r-lattice")
-    (version "0.21-9")
+    (version "0.22-5")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "lattice" version))
               (sha256
                (base32
-                "0ak9k6s6drd1a25m7mwzb426ms92a2p3ps04h2pacifwnk74ca59"))))
+                "1wd5dlxi0hd4l08g999y3xnxnaq06gwvflcqr9ym0cx131gbw7xs"))))
     (build-system r-build-system)
     (home-page "https://lattice.r-forge.r-project.org/")
     (synopsis "High-level data visualization system")
@@ -757,14 +757,14 @@ single hidden layer, and for multinomial log-linear models.")
 (define-public r-rpart
   (package
     (name "r-rpart")
-    (version "4.1.19")
+    (version "4.1.21")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rpart" version))
        (sha256
         (base32
-         "0rcm4hk2k0ag9qmb0f933yqrq8jpnclwrzp6825swgsqnp83wwpy"))))
+         "0av28n5as53qrxm41hcrwv59qdv7gfli668q32z0a5r1bdkiqz77"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/rpart")
     (synopsis "Recursive partitioning and regression trees")
@@ -1252,13 +1252,13 @@ using just two functions: melt and dcast (or acast).")
 (define-public r-ggplot2
   (package
     (name "r-ggplot2")
-    (version "3.4.3")
+    (version "3.4.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ggplot2" version))
        (sha256
-        (base32 "0hx5j47y2fxrcg4fxavyn5jjycpwkmsiqsjh6kj7nwp7dg79mqjw"))))
+        (base32 "0iiywrzv8j0npasvzgkxwhw0zqisf4xmpx06jl0lsq1ybl3fqxid"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-cli
@@ -1268,10 +1268,10 @@ using just two functions: melt and dcast (or acast).")
            r-lifecycle
            r-mass
            r-mgcv
-           r-tibble
            r-rlang
            r-scales
            r-svglite ; Needed for 'ggsave'
+           r-tibble
            r-vctrs
            r-withr))
     (native-inputs
@@ -1316,19 +1316,19 @@ agnes cluster diagrams.")
 (define-public r-gdtools
   (package
     (name "r-gdtools")
-    (version "0.3.3")
+    (version "0.3.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "gdtools" version))
        (sha256
         (base32
-         "10rlx1ciyvh0ayic03kckv360idl9s1zyc2ar5lisns786c1hnns"))))
+         "00mak9js1s05j5bmkda24nl2z023jsyg8zc60nm4h2xs7w1l7mxa"))))
     (build-system r-build-system)
     (native-inputs
      (list pkg-config))
     (inputs
-     (list cairo fontconfig freetype))
+     (list cairo fontconfig freetype zlib))
     (propagated-inputs
      (list r-curl
            r-fontquiver
@@ -1534,13 +1534,13 @@ data derived from /etc/mime.types in UNIX-type systems.")
 (define-public r-markdown
   (package
     (name "r-markdown")
-    (version "1.9")
+    (version "1.11")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "markdown" version))
               (sha256
                (base32
-                "0201v3spgl8a5c5xkddac5a3z9zh8d0nm9yg6alyhhj4cjwmgibh"))))
+                "052zrb6bnr6k3p9pmm3vfh3g7z20g6pjvphjdiqyjb4mb9sn3z27"))))
     (build-system r-build-system)
     ;; Skip check phase because the tests require the r-knitr package to be
     ;; installed. This prevents installation failures. Knitr normally
@@ -1578,13 +1578,13 @@ emitter (http://pyyaml.org/wiki/LibYAML) for R.")
 (define-public r-knitr
   (package
     (name "r-knitr")
-    (version "1.44")
+    (version "1.45")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "knitr" version))
               (sha256
                (base32
-                "015ylljvx0q2himch4k813021nvh0l7p5x3aqdkj3w0ax8x8k3ki"))))
+                "1yw4fnzm8lvh6kpcdlvr1fahz7421h5mmaris58zlgn57fjxwbpf"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-evaluate r-highr r-xfun r-yaml))
@@ -1866,14 +1866,14 @@ database.")
 (define-public r-dbplyr
   (package
     (name "r-dbplyr")
-    (version "2.3.4")
+    (version "2.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "dbplyr" version))
        (sha256
         (base32
-         "1b6y1jhf5ix4vry165vwid5nqm0d99q61vxak6aw3vfkj379vgk9"))))
+         "1rzi8112fi0bx2fj0j5ak9bfgqgjk5k5dv66qrb890gsf5bz6m4i"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-blob
@@ -2182,7 +2182,7 @@ comparison and diagnostics.")
 (define-public python-pymc
   (package
     (name "python-pymc")
-    (version "5.7.2")
+    (version "5.9.1")
     (source (origin
               (method git-fetch)        ; no tests in PyPI
               (uri (git-reference
@@ -2191,7 +2191,7 @@ comparison and diagnostics.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1r3lxpfc782f0wphdqfgsskbz52i0gwgrmxb65307k6cqia69s3r"))))
+                "1y90xa85q38zwsi69q5bv95vyjg3jp1hs0z18sg5jyi17irgw8x7"))))
     (build-system pyproject-build-system)
     (arguments
      (list #:tests? #f ; tests are too computationally intensive
@@ -2317,6 +2317,29 @@ uncertainties and are backed by strong theoretical guarantees thanks to
 conformal prediction methods intervals.")
     (license license:bsd-3)))
 
+(define-public python-emcee
+  (package
+    (name "python-emcee")
+    (version "3.1.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "emcee" version))
+       (sha256
+        (base32 "1vbz67cwzig28dlndkm6g246p1vcvj6yy2w65z8cdyffigf1j3lf"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs (list python-numpy))
+    (native-inputs (list python-coverage
+                         python-pytest
+                         python-pytest-cov
+                         python-setuptools-scm))
+    (home-page "https://emcee.readthedocs.io/en/stable/")
+    (synopsis "Ensemble sampling toolkit for MCMC")
+    (description
+     "@code{emcee} is a Python implementation of the affine-invariant ensemble
+sampler for Markov chain Monte Carlo (MCMC).")
+    (license license:expat)))
+
 (define-public python-statsmodels
   (package
     (name "python-statsmodels")
@@ -2374,7 +2397,7 @@ inference for statistical models.")
 (define-public python-openturns
   (package
     (name "python-openturns")
-    (version "1.21")
+    (version "1.21.1")
     (source
      (origin
        (method git-fetch)
@@ -2383,7 +2406,7 @@ inference for statistical models.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "05lbx8npvvk7jyakvfpgi9ggdp6cnzwv2hjmjrkji2s42axv0q6d"))))
+        (base32 "147pyh7j5nqp9bl9hfikcfzqj5qp95an0qrna9g5qq07md13c3if"))))
     (build-system cmake-build-system)
     (arguments
      (list
@@ -2615,14 +2638,14 @@ R version.")
 (define-public r-checkmate
   (package
     (name "r-checkmate")
-    (version "2.2.0")
+    (version "2.3.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "checkmate" version))
        (sha256
         (base32
-         "064i6l0n4w4jncpnk5wnj6sxak0jirdz757iirglcxg8ayq19v4n"))))
+         "1m41idv7iwq6mby8dyvsbljj5jkyhj65k7caz2na17a83s2inwl8"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-backports))
@@ -2966,13 +2989,13 @@ tools to simplify the devolpment of R packages.")
 (define-public r-withr
   (package
     (name "r-withr")
-    (version "2.5.1")
+    (version "2.5.2")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "withr" version))
               (sha256
                (base32
-                "1kndhxl0fxn40v9yx0iglilani3ym3ywbjf6zbg1pnb52ncf0nm9"))))
+                "01a27nqlrrf1pws57hi9631f3aj33a9dashd640m5nlgf9nzmdnm"))))
     (build-system r-build-system)
     (native-inputs
      (list r-knitr))
@@ -3317,13 +3340,13 @@ a column in data frame.")
 (define-public r-rsqlite
   (package
     (name "r-rsqlite")
-    (version "2.3.1")
+    (version "2.3.2")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "RSQLite" version))
               (sha256
                (base32
-                "1jil3wgfh1asfb9c4cr9qyr74wb9f87r7sa03kj187201hb3xlly"))))
+                "09vbx3akqws8a07ai6qbp3jn1w05qsmazl79wl2dyvvjpzs8b62x"))))
     (properties `((upstream-name . "RSQLite")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3332,8 +3355,8 @@ a column in data frame.")
            r-cpp11
            r-dbi
            r-memoise
-           r-plogr
-           r-pkgconfig))
+           r-pkgconfig
+           r-plogr))
     (native-inputs
      (list r-knitr))
     (home-page "https://github.com/rstats-db/RSQLite")
@@ -4711,13 +4734,13 @@ features present in other programming languages.")
 (define-public r-plotly
   (package
     (name "r-plotly")
-    (version "4.10.2")
+    (version "4.10.3")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "plotly" version))
               (sha256
                (base32
-                "0y2jiyfx895f15wcpizybssic4draw1vgvqz2b7f82z73319m01b"))
+                "13sxmanx2xck8dn0prn2fplgx4bafb7h2kk2wjmci21h8hk6qylb"))
               (modules '((guix build utils)))
               (snippet
                '(with-directory-excursion "inst/htmlwidgets/lib/"
@@ -4964,7 +4987,12 @@ from within R.")
           (add-after 'mkdist 'no-mtune
             (lambda _
               (substitute* "src/Makevars"
-                (("-mtune=native") "")))))))
+                (("-mtune=native") ""))))
+          (add-after 'no-mtune 'use-c++11
+            (lambda _
+              (substitute* "src/Makevars"
+                (("-DUSE_BLAS_LIB" m)
+                 (string-append m " -std=c++11"))))))))
     (native-inputs
      (list hevea
            perl
@@ -5164,17 +5192,15 @@ tests for whether a value is missing, empty or contains only @code{NA} and
 (define-public r-gdata
   (package
     (name "r-gdata")
-    (version "2.19.0")
+    (version "3.0.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "gdata" version))
        (sha256
         (base32
-         "1lv3cz990f7m2bfcf62fjm6wz6zd2ycrci06b7mfd0xmcn3bwifi"))))
+         "0zxi0634dkgczw7gicj8r6mhb83cpkxhsy2iivz0b9v52y9bjmm4"))))
     (build-system r-build-system)
-    (inputs
-     (list perl))
     (propagated-inputs
      (list r-gtools))
     (home-page "https://cran.r-project.org/web/packages/gdata")
@@ -5189,7 +5215,6 @@ including:
 @item character vector operations
 @item factor manipulation
 @item obtaining information about R objects
-@item manipulating MS-Excel formatted files
 @item generating fixed-width format files
 @item extricating components of date and time objects
 @item operations on columns of data frames
@@ -5703,14 +5728,14 @@ and resampling-based inference.")
 (define-public r-prabclus
   (package
     (name "r-prabclus")
-    (version "2.3-2")
+    (version "2.3-3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "prabclus" version))
        (sha256
         (base32
-         "0hg4d7y1w18jpgvw10z8833bbbcnlkwiasx0wh6iwa2pnnybq8gl"))))
+         "1haq8dvvi21fdnzl7ykm28sif5nv9pybir96vrqfcmy3k8500p80"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-mass r-mclust))
@@ -7171,14 +7196,14 @@ or eta squared effect size.")
 (define-public r-logspline
   (package
     (name "r-logspline")
-    (version "2.1.20")
+    (version "2.1.21")
     (source
       (origin
         (method url-fetch)
         (uri (cran-uri "logspline" version))
         (sha256
           (base32
-            "1nsrgz9sh9qg2fj0x7k48lqhpgzq1z78jfz89ckzp5xm4r8lpgcb"))))
+            "0xqbk3h28gkx3haj7hdg314616x673cmg9ia148g0q9j3zqkqflf"))))
     (properties `((upstream-name . "logspline")))
     (build-system r-build-system)
     (native-inputs (list gfortran))
diff --git a/gnu/packages/syncthing.scm b/gnu/packages/syncthing.scm
index 1709840211..2b8a37b518 100644
--- a/gnu/packages/syncthing.scm
+++ b/gnu/packages/syncthing.scm
@@ -44,7 +44,7 @@
 (define-public syncthing
   (package
     (name "syncthing")
-    (version "1.24.0")
+    (version "1.25.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/syncthing/syncthing"
@@ -52,7 +52,7 @@
                                   "/syncthing-source-v" version ".tar.gz"))
               (sha256
                (base32
-                "13v04slf231hd3rywyan0n7yyc94s34wfwnmwz8sfw4vgxk5k52a"))))
+                "18cyg0wnf34xi964fxvzxgcq6z0pbirk0k4z82w1cqi3f3l9jlg2"))))
     (build-system go-build-system)
     ;; The primary Syncthing executable goes to "out", while the auxiliary
     ;; server programs and utility tools go to "utils".  This reduces the size
diff --git a/gnu/packages/telephony.scm b/gnu/packages/telephony.scm
index ef4baff81f..fb239f1ba8 100644
--- a/gnu/packages/telephony.scm
+++ b/gnu/packages/telephony.scm
@@ -6,7 +6,7 @@
 ;;; Copyright © 2016 Lukas Gradl <lgradl@openmailbox.org>
 ;;; Copyright © 2016 Francesco Frassinelli <fraph24@gmail.com>
 ;;; Copyright © 2016, 2017 Nikita <nikita@n0.is>
-;;; Copyright © 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2017, 2018, 2023 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2017, 2018, 2021 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2017 Adonay Felipe Nogueira <https://libreplanet.org/wiki/User:Adfeno> <adfeno@hyperbola.info>
 ;;; Copyright © 2018 Jovany Leandro G.C <bit4bit@riseup.net>
@@ -903,7 +903,7 @@ telephony functionality into custom Telegram clients.")
 (define-public coturn
   (package
     (name "coturn")
-    (version "4.6.1")
+    (version "4.6.2")
     (source
      (origin
        (method git-fetch)
@@ -912,7 +912,7 @@ telephony functionality into custom Telegram clients.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "04d3c2lxc496zxx3nzqr9fskm2w57kqijdfq3wsa0yp2dp28yjkj"))))
+        (base32 "16rr8666spi84qcc8l2qga42hpskjmvrpj1w58jbanxnpsijv8h4"))))
     (inputs
      (list openssl
            sqlite
diff --git a/gnu/packages/terminals.scm b/gnu/packages/terminals.scm
index c5cecfa6db..adb5e223e7 100644
--- a/gnu/packages/terminals.scm
+++ b/gnu/packages/terminals.scm
@@ -37,6 +37,7 @@
 ;;; Copyright © 2023 Aaron Covrig <aaron.covrig.us@ieee.org>
 ;;; Copyright © 2023 Foundation Devices, Inc. <hello@foundationdevices.com>
 ;;; Copyright © 2023 Zheng Junjie <873216071@qq.com>
+;;; Copyright © 2023 Jaeme Sifat <jaeme@runbox.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -230,7 +231,7 @@ managers.")
 (define-public asciinema
   (package
     (name "asciinema")
-    (version "2.3.0")
+    (version "2.4.0")
     (source
      (origin
        (method git-fetch)
@@ -239,7 +240,7 @@ managers.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0mqn12h51nqdmn1ya7hw1l2z2893937dqq4b1zh32y6bazd807fl"))))
+        (base32 "0qhf4sc5fl81rpq3rgzy7qcch620dh12scvsbdfczfbyjb10ps2i"))))
     (build-system pyproject-build-system)
     (arguments
      (list #:phases
@@ -834,33 +835,34 @@ eye-candy, customizable, and reasonably lightweight.")
 (define-public foot
   (package
     (name "foot")
-    (version "1.15.3")
+    (version "1.16.2")
     (home-page "https://codeberg.org/dnkl/foot")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference (url home-page) (commit version)))
-              (file-name (git-file-name name version))
-              (sha256
-               (base32
-                "1a224i2i7qk170kf2rzyxqcv3lnx9f548lwa37jgjr7i339x4zwf"))))
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url home-page)
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "00wac8li1ac8ncmnlqvz3xnr5pi8gj4v3v341n0h2zzaayv9ngw5"))))
     (build-system meson-build-system)
     (arguments
-     `(;; Using a "release" build is recommended both for performance, and
-       ;; also to address a GCC 10 issue when doing PGO builds.
-       #:build-type "release"
-       ;; Enable LTO as recommended by INSTALL.md.
-       #:configure-flags '("-Db_lto=true")))
-    (native-inputs
-     (list ncurses ;for 'tic'
-           pkg-config scdoc wayland-protocols))
+     (list
+      ;; Using a "release" build is recommended both for performance, and
+      ;; also to address a GCC 10 issue when doing PGO builds.
+      #:build-type "release"
+      ;; Enable LTO as recommended by INSTALL.md.
+      #:configure-flags #~'("-Db_lto=true")))
+    (native-inputs (list ncurses ;for 'tic'
+                         pkg-config scdoc wayland-protocols))
     (native-search-paths
      ;; FIXME: This should only be located in 'ncurses'.  Nonetheless it is
      ;; provided for usability reasons.  See <https://bugs.gnu.org/22138>.
      (list (search-path-specification
             (variable "TERMINFO_DIRS")
             (files '("share/terminfo")))))
-    (inputs
-     (list fcft libxkbcommon wayland))
+    (inputs (list fcft libxkbcommon wayland))
     (synopsis "Wayland-native terminal emulator")
     (description
      "@command{foot} is a terminal emulator for systems using the Wayland
diff --git a/gnu/packages/tls.scm b/gnu/packages/tls.scm
index d62c00dcff..6a0aaf7f14 100644
--- a/gnu/packages/tls.scm
+++ b/gnu/packages/tls.scm
@@ -318,7 +318,20 @@ required structures.")
               (patches (search-patches "gnutls-skip-trust-store-test.patch"))
               (sha256
                (base32
-                "1742jiigwsfhx7nj5rz7dwqr8d46npsph6b68j7siar0mqarx2xs"))))))
+                "1742jiigwsfhx7nj5rz7dwqr8d46npsph6b68j7siar0mqarx2xs"))))
+    (arguments
+     (if (target-hurd?)
+         ;; Fix reference to undefined 'PATH_MAX'.  This is fixed in GnuTLS
+         ;; commit 3b6ec1e01de4e96d36276dfe34ee9e183f285264.
+         (substitute-keyword-arguments (package-arguments gnutls)
+           ((#:phases phases #~%standard-phases)
+            #~(modify-phases #$phases
+                (add-after 'unpack 'set-path-max
+                  (lambda _
+                    (substitute* "lib/pathbuf.h"
+                      (("^#define GNUTLS_PATH_MAX PATH_MAX")
+                       "#define GNUTLS_PATH_MAX 8192\n")))))))
+         (package-arguments gnutls)))))
 
 (define-public gnutls/dane
   ;; GnuTLS with build libgnutls-dane, implementing DNS-based
diff --git a/gnu/packages/tor.scm b/gnu/packages/tor.scm
index 1eb62a950e..562054ede4 100644
--- a/gnu/packages/tor.scm
+++ b/gnu/packages/tor.scm
@@ -63,14 +63,14 @@
 (define-public tor
   (package
     (name "tor")
-    (version "0.4.8.6")
+    (version "0.4.8.7")
     (source (origin
              (method url-fetch)
              (uri (string-append "https://dist.torproject.org/tor-"
                                  version ".tar.gz"))
              (sha256
               (base32
-               "122h6l3nh8xrpzkmn4alsbz30jw8nxivwnhgnp97qv7nr9gqjbam"))))
+               "14blalf96240dg6crpmgyf2bdcj109dyx47h0w6a0a6vfjf2n3dj"))))
     (build-system gnu-build-system)
     (arguments
      (list #:configure-flags
diff --git a/gnu/packages/upnp.scm b/gnu/packages/upnp.scm
index 1602136e29..400e6656d1 100644
--- a/gnu/packages/upnp.scm
+++ b/gnu/packages/upnp.scm
@@ -6,6 +6,7 @@
 ;;; Copyright © 2019 Jens Mølgaard <jens@zete.tk>
 ;;; Copyright © 2020 Jan Wielkiewicz <tona_kosmicznego_smiecia@interia.pl>
 ;;; Copyright © 2021 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2023 Ricardo Wurmus <rekado@elephly.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -25,17 +26,27 @@
 (define-module (gnu packages upnp)
   #:use-module (gnu packages)
   #:use-module (gnu packages autotools)
+  #:use-module (gnu packages check)
   #:use-module (gnu packages compression)
+  #:use-module (gnu packages curl)
+  #:use-module (gnu packages file)
   #:use-module (gnu packages gettext)
   #:use-module (gnu packages image)
+  #:use-module (gnu packages javascript)
+  #:use-module (gnu packages linux)
+  #:use-module (gnu packages logging)
   #:use-module (gnu packages mp3)
   #:use-module (gnu packages photo)
   #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages pretty-print)
   #:use-module (gnu packages python)
   #:use-module (gnu packages sqlite)
   #:use-module (gnu packages video)
   #:use-module (gnu packages xiph)
+  #:use-module (gnu packages xml)
+  #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
+  #:use-module (guix gexp)
   #:use-module (guix utils)
   #:use-module (guix download)
   #:use-module (guix git-download)
@@ -162,3 +173,48 @@ and others.")
 server, which serves multimedia content to compatible clients on the network.
 It aims to be fully compliant with DLNA and UPnP-AV standards.")
     (license license:gpl2)))
+
+(define-public gerbera
+  (package
+    (name "gerbera")
+    (version "1.12.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/gerbera/gerbera")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1jz3jpg6ja9vi5zykcdh410r07ysrn6g0kzyj0v7d3689jxp94lg"))))
+    (build-system cmake-build-system)
+    (arguments
+     (list
+      #:configure-flags
+      #~(list "-DWITH_SYSTEMD=NO"
+              "-DWITH_AVCODEC=YES"
+              "-DWITH_TESTS=YES")))
+    (inputs
+     (list curl
+           duktape
+           ffmpeg
+           file
+           fmt
+           libebml
+           libexif
+           libmatroska
+           libupnp
+           pugixml
+           spdlog
+           sqlite
+           taglib
+           `(,util-linux "lib")
+           zlib))
+    (native-inputs
+     (list googletest pkg-config))
+    (home-page "https://gerbera.io/")
+    (synopsis "UPnP media server")
+    (description "Gerbera is a UPnP media server which allows you to stream
+your digital media through your home network and consume it on a variety of
+UPnP compatible devices.")
+    (license license:gpl2)))
diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm
index b4dd7c27ae..a6dfec06bf 100644
--- a/gnu/packages/video.scm
+++ b/gnu/packages/video.scm
@@ -1940,6 +1940,81 @@ thumbnailer uses ffmpeg to decode frames from the video files, so supported
 videoformats depend on the configuration flags of ffmpeg.")
     (license license:gpl2+)))
 
+(define-public ffmpeg-progress-yield
+  (package
+    (name "ffmpeg-progress-yield")
+    (version "0.7.8")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "ffmpeg-progress-yield" version))
+              (sha256
+               (base32
+                "07j6m8p8z8ybl75h0d4xzjl1pvkfzr0i73siysqcgrrahdgsxrls"))))
+    (build-system pyproject-build-system)
+    (arguments
+     ;; Not sure if the test file actually does anything.
+     (list #:phases #~(modify-phases %standard-phases
+                        (replace 'check
+                          (lambda* (#:key tests? #:allow-other-keys)
+                            (when tests?
+                              (invoke "python" "test/test.py"))))
+                        (add-after 'wrap 'wrap-program
+                          ;; Wrap ffmpeg on the executable.
+                          (lambda* (#:key inputs outputs #:allow-other-keys)
+                            (let ((fpy "bin/ffmpeg-progress-yield")
+                                  (ffm "bin/ffmpeg"))
+                              (wrap-program (search-input-file outputs fpy)
+                                `("PATH" ":" prefix
+                                  (,(search-input-file inputs ffm))))))))))
+    (inputs (list bash-minimal ffmpeg))
+    (home-page "https://github.com/slhck/ffmpeg-progress-yield")
+    (synopsis "Run an ffmpeg command with progress")
+    (description "This package allows an ffmpeg command to run with progress.
+It is usually a complement to @code{ffmpeg-normalize}.")
+    (license license:expat)))
+
+(define-public ffmpeg-normalize
+  (package
+    (name "ffmpeg-normalize")
+    (version "1.27.7")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "ffmpeg-normalize" version))
+              (sha256
+               (base32
+                "0idqqgsr3p840vx2x3idn851qwghjdbm6v4yrq2kprppyfvglni7"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list #:phases
+           #~(modify-phases %standard-phases
+               (replace 'check
+                 (lambda* (#:key tests? #:allow-other-keys)
+                   (when tests?
+                     (invoke "python" "-m" "pytest"
+                             "test/test.py"))))
+               (add-after 'wrap 'wrap-ffmpeg
+                 ;; Wrap ffmpeg on the executable.
+                 (lambda* (#:key inputs outputs #:allow-other-keys)
+                   (let ((ffn (search-input-file outputs
+                                                 "bin/ffmpeg-normalize"))
+                         (ffm (search-input-file inputs "bin/ffmpeg")))
+                     (wrap-program ffn
+                       `("FFMPEG_PATH" = (,ffm)))))))))
+    (native-inputs (list python-pytest))
+    (inputs (list bash-minimal ffmpeg))
+    (propagated-inputs (list ffmpeg-progress-yield
+                             python-colorama
+                             python-colorlog
+                             python-tqdm))
+    (home-page "https://github.com/slhck/ffmpeg-normalize")
+    (synopsis "Normalize audio via ffmpeg")
+    (description "This program normalizes media files to a certain loudness
+level using the EBU R128 loudness normalization procedure.  It can also
+perform RMS-based normalization (where the mean is lifted or attenuated),
+or peak normalization to a certain target level.  Batch processing of several
+input files is possible, including video files.")
+    (license license:expat)))
+
 (define-public vlc
   (package
     (name "vlc")
diff --git a/gnu/packages/vim.scm b/gnu/packages/vim.scm
index d2ea9b7ae1..c2ed7b9249 100644
--- a/gnu/packages/vim.scm
+++ b/gnu/packages/vim.scm
@@ -719,7 +719,7 @@ are detected, the user is notified.")))
 (define-public neovim
   (package
     (name "neovim")
-    (version "0.9.1")
+    (version "0.9.4")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -728,7 +728,7 @@ are detected, the user is notified.")))
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "18dsl9fjcqvcqffny6jmcxwx5a7d13aykn310hbgghny8l11rw3c"))))
+                "0wj1p5x88s58f22crdyzwlfiqgnwlqdkbw4wxllf0v5hg16gbnhp"))))
     (build-system cmake-build-system)
     (arguments
      (list #:modules
diff --git a/gnu/packages/web-browsers.scm b/gnu/packages/web-browsers.scm
index 5ffe54bd78..d1372c2243 100644
--- a/gnu/packages/web-browsers.scm
+++ b/gnu/packages/web-browsers.scm
@@ -586,7 +586,7 @@ driven and does not detract you from your daily work.")
 (define-public nyxt
   (package
     (name "nyxt")
-    (version "3.9.0")
+    (version "3.9.1")
     (source
      (origin
        (method git-fetch)
@@ -595,7 +595,7 @@ driven and does not detract you from your daily work.")
              (commit version)))
        (sha256
         (base32
-         "1nbj3nv9bb6gngkd3xdcz5wxpb9j3yh8gcskrb7hbbj4849h16kd"))
+         "1x7ia43yh024hwwsh2a6g2daznkzgjlisnxvjfcb9sgvfqfa368i"))
        (file-name (git-file-name "nyxt" version))
        (modules '((guix build utils)))
        (snippet
diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index b46286c690..66d09700db 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -278,14 +278,14 @@
 (define-public httpd
   (package
     (name "httpd")
-    (version "2.4.57")
+    (version "2.4.58")
     (source (origin
              (method url-fetch)
              (uri (string-append "mirror://apache/httpd/httpd-"
                                  version ".tar.bz2"))
              (sha256
               (base32
-               "0ajdz5f2w9nbmqydip2mv9m4xlnc4swmw7mqzgnrbq4mxr5bik6v"))))
+               "1id45r2ccgkbjm9i998997ch32lvicpyynyx8x6aa4420wmdf5ps"))))
     (build-system gnu-build-system)
     (native-inputs (list `(,pcre "bin")))       ;for 'pcre-config'
     (inputs (list apr apr-util openssl perl)) ; needed to run bin/apxs
@@ -448,7 +448,7 @@ replacing them with data URIs.")
 (define-public monolith
   (package
     (name "monolith")
-    (version "2.6.1")
+    (version "2.7.0")
     (source
      (origin
        (method git-fetch)
@@ -457,23 +457,24 @@ replacing them with data URIs.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1pj4wnsw5a4ys79sqw68ib6zimaqlkplb89x6yncg949a6hj8516"))))
+        (base32 "0ccwjsp8gdgp0wafc3zvlfmx3f58axc1k1ac80qha3g60xccqn56"))))
     (build-system cargo-build-system)
     (arguments
      `(#:cargo-inputs
        (("rust-atty" ,rust-atty-0.2)
         ("rust-base64" ,rust-base64-0.13)
         ("rust-chrono" ,rust-chrono-0.4)
-        ("rust-clap" ,rust-clap-2)
-        ("rust-cssparser" ,rust-cssparser-0.28)
+        ("rust-clap" ,rust-clap-3)
+        ("rust-cssparser" ,rust-cssparser-0.29)
         ("rust-encoding-rs" ,rust-encoding-rs-0.8)
         ("rust-html5ever" ,rust-html5ever-0.24)
+        ("rust-percent-encoding" ,rust-percent-encoding-2)
         ("rust-regex" ,rust-regex-1)
         ("rust-reqwest" ,rust-reqwest-0.11)
-        ("rust-sha2" ,rust-sha2-0.9)
+        ("rust-sha2" ,rust-sha2-0.10)
         ("rust-url" ,rust-url-2))
        #:cargo-development-inputs
-       (("rust-assert-cmd" ,rust-assert-cmd-1))))
+       (("rust-assert-cmd" ,rust-assert-cmd-2))))
     (native-inputs
      (list pkg-config))
     (inputs
@@ -1003,7 +1004,7 @@ similar to live activity monitoring provided with NGINX plus.")
 (define-public lighttpd
   (package
     (name "lighttpd")
-    (version "1.4.71")
+    (version "1.4.72")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://download.lighttpd.net/lighttpd/"
@@ -1011,7 +1012,7 @@ similar to live activity monitoring provided with NGINX plus.")
                                   "lighttpd-" version ".tar.xz"))
               (sha256
                (base32
-                "1b5g4l9q84sjfwx9x1d7bqp9n5j0wkaj8cyzak1zv5h3l9fr3dmq"))))
+                "1v2m9vavrg3ibbl0kfq3rjlnqicbrlrkqih1iisa0m5pd56xxjpp"))))
     (build-system gnu-build-system)
     (arguments
      (list #:configure-flags
@@ -7958,6 +7959,7 @@ derivation by David Revoy from the original MonsterID by Andreas Gohr.")
   (package
     (name "nghttp2")
     (version "1.49.0")
+    (replacement nghttp2-1.57)
     (source
      (origin
        (method url-fetch)
@@ -8068,6 +8070,19 @@ compressed JSON header blocks.
                    (("print \\(ver >= '3\\.8'\\)")
                     "print (tuple(map(int, ver.split('.'))) >= (3,8))")))))))))))
 
+(define-public nghttp2-1.57
+  (package
+    (inherit nghttp2)
+    (version "1.57.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/nghttp2/nghttp2/"
+                                  "releases/download/v" version "/"
+                                  "nghttp2-" version ".tar.xz"))
+              (sha256
+               (base32
+                "0n598w7w8rqdqiay2fad3a11253hibakan5c4vjkpx09648v044j"))))))
+
 (define-public hpcguix-web
   (package
     (name "hpcguix-web")
diff --git a/gnu/packages/wine.scm b/gnu/packages/wine.scm
index 3822165f7f..400f0e7607 100644
--- a/gnu/packages/wine.scm
+++ b/gnu/packages/wine.scm
@@ -79,7 +79,7 @@
 (define-public wine-minimal
   (package
     (name "wine-minimal")
-    (version "8.16")
+    (version "8.18")
     (source
      (origin
        (method url-fetch)
@@ -91,7 +91,8 @@
               (string-append "https://dl.winehq.org/wine/source/" dir
                              "wine-" version ".tar.xz")))
        (sha256
-        (base32 "1zgkqflqgl2y3a90f2nvcc1vhzr9ni0lps276553j8zgbqvnd0hn"))))
+        (base32 "1nv06awb3hv26v64nqnks9yiz7w368scxznj77vxa3zpmhafzyih"))))
+    (properties '((upstream-name . "wine")))
     (build-system gnu-build-system)
     (native-inputs (list bison flex))
     (inputs `())
diff --git a/gnu/packages/wm.scm b/gnu/packages/wm.scm
index 8576d0297d..c3a6b31c84 100644
--- a/gnu/packages/wm.scm
+++ b/gnu/packages/wm.scm
@@ -1988,7 +1988,7 @@ core/thread.")
 (define-public wlr-randr
   (package
     (name "wlr-randr")
-    (version "0.3.0")
+    (version "0.3.1")
     (source
      (origin
        (method git-fetch)
@@ -1997,7 +1997,7 @@ core/thread.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0cj24fb6s7n8nphvhrp8ldrivjdcrjw64i5v9rsfb6z80q4qg548"))))
+        (base32 "13mya6j5z7cwg2a973y28ya8w36kxhj0fgj8bk9z6yf2w0ryr5xv"))))
     (build-system meson-build-system)
     (inputs (list wayland))
     (native-inputs (list pkg-config))
@@ -2943,7 +2943,7 @@ read and write, and compatible with JSON.")
 (define-public labwc
   (package
     (name "labwc")
-    (version "0.6.4")
+    (version "0.6.5")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -2952,13 +2952,14 @@ read and write, and compatible with JSON.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "00ajr7s8qywdfa9vhlfc02p1wwdcqaaa09pm1im9w6mrvb904lzh"))))
+                "04401k1i6b9s2v6mbhw5llla8fdpkhmgz826iva246iqch9z20lx"))))
     (build-system meson-build-system)
     (native-inputs
      (list pkg-config gettext-minimal scdoc))
     (inputs
      (list cairo
            glib
+           librsvg
            libxcb
            libxml2
            pango