From ee8de7381466ad917d1d2cab49830325230b4e5c Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Sun, 26 Apr 2020 13:22:35 +0300
Subject: gnu: python-scanpy: Update to 1.4.6.

* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.4.6.
[arguments]: Add another network based test to skip.
[propagated-inputs]: Add python-tqdm.
---
 gnu/packages/bioinformatics.scm | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b9be0c1918..6c5b49e37e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13365,14 +13365,14 @@ (define-public find-circ
 (define-public python-scanpy
   (package
     (name "python-scanpy")
-    (version "1.4.5.1")
+    (version "1.4.6")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "scanpy" version))
        (sha256
         (base32
-         "14kh1ji70xxhmri5q8sgcibsidhr6f221wxrcw8a5xvibj5da17j"))))
+         "0s2b6cvaigx4wzw3850qb93sjwwxbzh22kpbp498zklc5rjpbz4l"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
@@ -13382,6 +13382,7 @@ (define-public python-scanpy
              ;; These tests require Internet access.
              (delete-file-recursively "scanpy/tests/notebooks")
              (delete-file "scanpy/tests/test_clustering.py")
+             (delete-file "scanpy/tests/test_datasets.py")
 
              ;; TODO: I can't get the plotting tests to work, even with Xvfb.
              (delete-file "scanpy/tests/test_plotting.py")
@@ -13398,8 +13399,8 @@ (define-public python-scanpy
        ("python-h5py" ,python-h5py)
        ("python-igraph" ,python-igraph)
        ("python-joblib" ,python-joblib)
-       ("python-louvain" ,python-louvain)
        ("python-legacy-api-wrap" ,python-legacy-api-wrap)
+       ("python-louvain" ,python-louvain)
        ("python-matplotlib" ,python-matplotlib)
        ("python-natsort" ,python-natsort)
        ("python-networkx" ,python-networkx)
@@ -13412,6 +13413,7 @@ (define-public python-scanpy
        ("python-seaborn" ,python-seaborn)
        ("python-statsmodels" ,python-statsmodels)
        ("python-tables" ,python-tables)
+       ("python-tqdm" ,python-tqdm)
        ("python-umap-learn" ,python-umap-learn)))
     (native-inputs
      `(("python-pytest" ,python-pytest)
-- 
cgit v1.2.3


From ca4b55882a0f6b4ba46253485afb82ec000f8fc2 Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Thu, 2 Apr 2020 14:10:40 -0400
Subject: gnu: Add rav1e.

* gnu/packages/video.scm (rav1e): New variable.
* gnu/packages/rust-apps.scm (rust-cbindgen-0.12, rust-cargo-c): New
variables.
* gnu/packages/crates-io.scm: Various new packages and upgrades.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
---
 gnu/packages/crates-io.scm | 3941 ++++++++++++++++++++++++++++++++++++++++----
 gnu/packages/rust-apps.scm |   51 +-
 gnu/packages/video.scm     |   87 +
 3 files changed, 3745 insertions(+), 334 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm
index a42661e3f8..d318a05d71 100644
--- a/gnu/packages/crates-io.scm
+++ b/gnu/packages/crates-io.scm
@@ -6,6 +6,7 @@
 ;;; Copyright © 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2019, 2020 John Soo <jsoo1@asu.edu>
 ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
+;;; Copyright © 2020 Leo Famulari <leo@famulari.name>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -40,6 +41,7 @@ (define-module (gnu packages crates-io)
   #:use-module (gnu packages python)
   #:use-module (gnu packages ssh)
   #:use-module (gnu packages tls)
+  #:use-module (gnu packages video)
   #:use-module (gnu packages version-control)
   #:use-module (gnu packages xml)
   #:use-module (gnu packages xorg))
@@ -72,8 +74,46 @@ (define-public rust-abomonation-0.7
 library in Rust.")
     (license license:expat)))
 
+(define-public rust-addr2line-0.11
+  (package
+    (name "rust-addr2line")
+    (version "0.11.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "addr2line" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0sk5g8cb2yynlcm0wcqff9l9c9ml69rqgfrrbii0ybgdc236jkhw"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:tests? #f      ; Not all test files included.
+       #:cargo-inputs
+       (("rust-rustc-demangle" ,rust-rustc-demangle-0.1)
+        ("rust-object" ,rust-object-0.17)
+        ("rust-fallible-iterator" ,rust-fallible-iterator-0.2)
+        ("rust-cpp-demangle" ,rust-cpp-demangle-0.2)
+        ("rust-gimli" ,rust-gimli-0.20)
+        ("rust-smallvec" ,rust-smallvec-1)
+        ("rust-lazycell" ,rust-lazycell-1.2))
+       #:cargo-development-inputs
+       (("rust-backtrace" ,rust-backtrace-0.3)
+        ("rust-clap" ,rust-clap-2)
+        ("rust-findshlibs" ,rust-findshlibs-0.5)
+        ("rust-memmap" ,rust-memmap-0.7)
+        ("rust-rustc-test" ,rust-rustc-test-0.3))))
+    (home-page "https://github.com/gimli-rs/addr2line")
+    (synopsis "Symbolication library written in Rust, using gimli")
+    (description
+     "This package provides a cross-platform symbolication library written in
+Rust, using gimli.")
+    (license (list license:asl2.0 license:expat))))
+
 (define-public rust-addr2line-0.9
   (package
+    (inherit rust-addr2line-0.11)
     (name "rust-addr2line")
     (version "0.9.0")
     (source
@@ -85,7 +125,6 @@ (define-public rust-addr2line-0.9
        (sha256
         (base32
          "17rlf04nx3g3rcy661v24ksnmpk6vqn680g5b5sp8lk20iih2xnx"))))
-    (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
        #:cargo-inputs
@@ -100,15 +139,9 @@ (define-public rust-addr2line-0.9
        #:cargo-development-inputs
        (("rust-backtrace" ,rust-backtrace-0.3)
         ("rust-clap" ,rust-clap-2)
-        ("rust-findshlibs" ,rust-findshlibs-0.5)
+        ;("rust-findshlibs" ,rust-findshlibs-0.4)
         ("rust-memmap" ,rust-memmap-0.7)
-        ("rust-rustc-test" ,rust-rustc-test-0.3))))
-    (home-page "https://github.com/gimli-rs/addr2line")
-    (synopsis "Symbolication library written in Rust, using gimli")
-    (description
-     "This package provides a cross-platform symbolication library written in
-Rust, using gimli.")
-    (license (list license:asl2.0 license:expat))))
+        ("rust-rustc-test" ,rust-rustc-test-0.3))))))
 
 (define-public rust-adler32-1.0
   (package
@@ -136,6 +169,34 @@ (define-public rust-adler32-1.0
     (license (list license:bsd-3
                    license:zlib))))
 
+(define-public rust-afl-0.5
+  (package
+    (name "rust-afl")
+    (version "0.5.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "afl" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0azpi917l8nhvx25n2v670nvkxkrhcwmddfi85qnr6kchmi6y946"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-rustc-version" ,rust-rustc-version-0.2)
+        ("rust-cc" ,rust-cc-1.0)
+        ("rust-xdg" ,rust-xdg-2.2)
+        ("rust-clap" ,rust-clap-2))))
+    (home-page "https://github.com/rust-fuzz/afl.rs")
+    (synopsis
+     "Fuzzing Rust code with american-fuzzy-lop")
+    (description
+     "Fuzz Rust code with american-fuzzy-lop.")
+    (license license:asl2.0)))
+
 (define-public rust-afl-0.4
   (package
     (name "rust-afl")
@@ -156,9 +217,6 @@ (define-public rust-afl-0.4
        (("rust-cc" ,rust-cc-1.0)
         ("rust-clap" ,rust-clap-2)
         ("rust-rustc-version" ,rust-rustc-version-0.2)
-        ("rust-xdg" ,rust-xdg-2.2))
-       #:cargo-development-inputs
-       (("rust-rustc-version" ,rust-rustc-version-0.2)
         ("rust-xdg" ,rust-xdg-2.2))))
     (home-page "https://github.com/rust-fuzz/afl.rs")
     (synopsis
@@ -170,7 +228,7 @@ (define-public rust-afl-0.4
 (define-public rust-aho-corasick-0.7
   (package
     (name "rust-aho-corasick")
-    (version "0.7.8")
+    (version "0.7.10")
     (source
      (origin
        (method url-fetch)
@@ -179,10 +237,10 @@ (define-public rust-aho-corasick-0.7
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "048q5vr1qac4lf90z80lw8kcya6qmlxw857xhwxsssk832jdafkl"))))
+         "1nka9509afjgal6lpymn8w2lq11dmjwxs8yjcmzys966if5l05l7"))))
     (build-system cargo-build-system)
     (arguments
-     `(#:cargo-inputs (("rust-memchr" ,rust-memchr-2.2))
+     `(#:cargo-inputs (("rust-memchr" ,rust-memchr-2.3))
        #:cargo-development-inputs
        (("rust-doc-comment" ,rust-doc-comment-0.3))))
     (home-page "https://github.com/BurntSushi/aho-corasick")
@@ -450,6 +508,44 @@ (define-public rust-anyhow-1.0
 @code{std::error::Error}.")
     (license (list license:expat license:asl2.0))))
 
+(define-public rust-aom-sys-0.1
+  (package
+    (name "rust-aom-sys")
+    (version "0.1.3")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "aom-sys" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0ix3djcf84kk53h6fac73n7jc614745n7kbmikxwi3s73b6vzgsr"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(;#:skip-build? #t
+       #:cargo-inputs
+       (("rust-bindgen" ,rust-bindgen-0.51)
+        ("rust-metadeps" ,rust-metadeps-1.1))
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'set-environmental-variable
+           (lambda* (#:key inputs #:allow-other-keys)
+             (let ((clang (assoc-ref inputs "libclang")))
+               (setenv "LIBCLANG_PATH"
+                       (string-append clang "/lib")))
+             #t)))))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (inputs
+     `(("libaom" ,libaom)
+       ("libclang" ,clang)
+       ("llvm" ,llvm)))
+    (home-page "https://github.com/rust-av/aom-rs")
+    (synopsis "FFI bindings to aom")
+    (description "This package provides FFI bindings to aom.")
+    (license license:expat)))
+
 (define-public rust-approx-0.3
   (package
     (name "rust-approx")
@@ -492,6 +588,26 @@ (define-public rust-approx-0.1
          "153awzwywmb61xg857b80l63b1x6hifx2pha7lxf6fck9qxwraq8"))))
     (arguments '())))
 
+(define-public rust-arbitrary-0.2
+  (package
+    (name "rust-arbitrary")
+    (version "0.2.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "arbitrary" version))
+        (file-name
+          (string-append name "-" version ".tar.gz"))
+        (sha256
+          (base32
+            "1i3fhcdyjq4isn22xx2svmpfr5hwyzi0wavbm07fs8i2dv5pdkv4"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/nagisa/rust_arbitrary/")
+    (synopsis "Trait for generating structured data from unstructured data")
+    (description
+     "The trait for generating structured data from unstructured data.")
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-arc-swap-0.4
   (package
     (name "rust-arc-swap")
@@ -547,6 +663,32 @@ (define-public rust-arc-swap-0.3
         ("rust-proptest" ,rust-proptest-0.9)
         ("rust-version-sync" ,rust-version-sync-0.8))))))
 
+(define-public rust-arg-enum-proc-macro-0.3
+  (package
+    (name "rust-arg-enum-proc-macro")
+    (version "0.3.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "arg_enum_proc_macro" version))
+        (file-name
+          (string-append name "-" version ".tar.gz"))
+        (sha256
+          (base32
+            "021rr6j3n031ynfbm7kwb3j3bxvbsz40n0nqi78k47d3p92rihcv"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-proc-macro2" ,rust-proc-macro2-1.0)
+        ("rust-syn" ,rust-syn-1.0)
+        ("rust-quote" ,rust-quote-1.0))))
+    (home-page "https://github.com/lu-zero/arg_enum_proc_macro")
+    (synopsis "Procedural macro compatible with clap arg_enum")
+    (description
+     "This package provides a procedural macro compatible with clap's
+@code{arg_enum}.")
+    (license license:expat)))
+
 (define-public rust-argon2rs-0.2
   (package
     (name "rust-argon2rs")
@@ -638,7 +780,7 @@ (define-public rust-arrayvec-0.4
   (package
     (inherit rust-arrayvec-0.5)
     (name "rust-arrayvec")
-    (version "0.4.10")
+    (version "0.4.12")
     (source
      (origin
        (method url-fetch)
@@ -647,7 +789,7 @@ (define-public rust-arrayvec-0.4
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0wcch3ca9qvkixgdbd2afrv1xa27l83vpraf7frsh9l8pivgpiwj"))))
+         "1fdiv5m627gh6flp4mpmi1mh647imm9x423licsr11psz97d97yd"))))
     (arguments
      `(#:skip-build? #t
        #:cargo-inputs
@@ -658,10 +800,38 @@ (define-public rust-arrayvec-0.4
         ("rust-matches" ,rust-matches-0.1)
         ("rust-serde-test" ,rust-serde-test-1.0))))))
 
+(define-public rust-ascii-1.0
+  (package
+    (name "rust-ascii")
+    (version "1.0.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "ascii" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0281gc828q4j692gb66jfdr5k16gyszgqflylh0pp30rllv63xdv"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-serde" ,rust-serde-1.0)
+        ("rust-serde-test" ,rust-serde-test-1.0))))
+    (home-page "https://github.com/tomprogrammer/rust-ascii")
+    (synopsis "ASCII-only equivalents to `char`, `str` and `String`.")
+    (description
+     "A rust library that provides ASCII-only string and character types,
+equivalent to the @code{char}, @code{str} and @code{String} types in the
+standard library.")
+    (license (list license:asl2.0 license:expat))))
+
 (define-public rust-ascii-0.9
   (package
+    (inherit rust-ascii-1.0)
     (name "rust-ascii")
-    (version "0.9.1")
+    (version "0.9.3")
     (source
      (origin
        (method url-fetch)
@@ -670,20 +840,12 @@ (define-public rust-ascii-0.9
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0dck6rsjnxlczyjnncn8hf16bxj42m1vi6s2n32c1jg2ijd9dz55"))))
-    (build-system cargo-build-system)
+         "0km3zzkhrr22drf9p1zcblqirlxkdc7zra25acpi0h8qax5c1cga"))))
     (arguments
-     `(#:skip-build? #t
-       #:cargo-inputs
-       (("rust-quickcheck" ,rust-quickcheck-0.8)
+     `(#:cargo-inputs
+       (("rust-quickcheck" ,rust-quickcheck-0.6)
         ("rust-serde" ,rust-serde-1.0)
-        ("rust-serde-test" ,rust-serde-test-1.0))))
-    (home-page "https://github.com/tomprogrammer/rust-ascii")
-    (synopsis
-     "ASCII-only equivalents to char, str and String")
-    (description
-     "ASCII-only equivalents to @code{char}, @code{str} and @code{String}.")
-    (license (list license:expat license:asl2.0))))
+        ("rust-serde-test" ,rust-serde-test-1.0))))))
 
 (define-public rust-assert-matches-1.3
   (package
@@ -733,7 +895,7 @@ (define-public rust-aster-0.41
 (define-public rust-atty-0.2
   (package
     (name "rust-atty")
-    (version "0.2.13")
+    (version "0.2.14")
     (source
       (origin
         (method url-fetch)
@@ -741,12 +903,13 @@ (define-public rust-atty-0.2
         (file-name (string-append name "-" version ".crate"))
         (sha256
          (base32
-          "140sswp1bwqwc4zk80bxkbnfb3g936hgrb77g9g0k1zcld3wc0qq"))))
+          "1s7yslcs6a28c5vz7jwj63lkfgyx8mx99fdirlhi9lbhhzhrpcyr"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
        #:cargo-inputs
-       (("rust-libc" ,rust-libc-0.2)
+       (("rust-hermit-abi" ,rust-hermit-abi-0.1)
+        ("rust-libc" ,rust-libc-0.2)
         ("rust-winapi" ,rust-winapi-0.3))))
     (home-page "https://github.com/softprops/atty")
     (synopsis "Simple interface for querying atty")
@@ -827,7 +990,7 @@ (define-public rust-average-0.9
 (define-public rust-backtrace-0.3
   (package
     (name "rust-backtrace")
-    (version "0.3.32")
+    (version "0.3.46")
     (source
      (origin
        (method url-fetch)
@@ -836,18 +999,18 @@ (define-public rust-backtrace-0.3
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "1rgsaha3b6wxh564s4jqn5hl5pkmg214blyjjs1svafib190zd8q"))))
+         "17hh1vrhfd01qpjilrdpy7q0lf2j2qv36achpg37q92rff4r5rmi"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
        #:cargo-inputs
-       (("rust-addr2line" ,rust-addr2line-0.9)
+       (("rust-addr2line" ,rust-addr2line-0.11)
         ("rust-backtrace-sys" ,rust-backtrace-sys-0.1)
         ("rust-cfg-if" ,rust-cfg-if-0.1)
         ("rust-compiler-builtins" ,rust-compiler-builtins-0.1)
         ("rust-cpp-demangle" ,rust-cpp-demangle-0.2)
         ("rust-findshlibs" ,rust-findshlibs-0.5)
-        ("rust-goblin" ,rust-goblin-0.0)
+        ("rust-goblin" ,rust-goblin-0.2)
         ("rust-libc" ,rust-libc-0.2)
         ("rust-memmap" ,rust-memmap-0.7)
         ("rust-rustc-demangle" ,rust-rustc-demangle-0.1)
@@ -866,7 +1029,7 @@ (define-public rust-backtrace-0.3
 (define-public rust-backtrace-sys-0.1
   (package
     (name "rust-backtrace-sys")
-    (version "0.1.32")
+    (version "0.1.35")
     (source
       (origin
         (method url-fetch)
@@ -874,16 +1037,14 @@ (define-public rust-backtrace-sys-0.1
         (file-name (string-append name "-" version ".crate"))
         (sha256
          (base32
-          "14c406z8bdmms8a5l8cv79jfkz1mk10qk5p97izf4vai53qparax"))))
+          "066iviphi72mx9hd3njzsplk5v45jhi10mrccbbyij391ahsps3x"))))
     (build-system cargo-build-system)
     (arguments
-     `(#:skip-build? #t
-       #:cargo-inputs
+     `(#:cargo-inputs
        (("rust-libc" ,rust-libc-0.2)
         ("rust-compiler-builtins" ,rust-compiler-builtins-0.1)
-        ("rust-rustc-std-workspace-core" ,rust-rustc-std-workspace-core-1.0))
-       #:cargo-development-inputs
-       (("rust-cc" ,rust-cc-1.0))))
+        ("rust-rustc-std-workspace-core" ,rust-rustc-std-workspace-core-1.0)
+        ("rust-cc" ,rust-cc-1.0))))
     (home-page "https://github.com/rust-lang/backtrace-rs")
     (synopsis "Bindings to the libbacktrace gcc library")
     (description
@@ -983,8 +1144,64 @@ (define-public rust-bencher-0.1
     (license (list license:asl2.0
                    license:expat))))
 
+(define-public rust-better-panic-0.2
+  (package
+    (name "rust-better-panic")
+    (version "0.2.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "better-panic" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0xl48v6pd9ys7wp0ni62i6q73xpd1nhf92z09sjc9n3lrj0ac4ix"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-backtrace" ,rust-backtrace-0.3)
+        ("rust-console" ,rust-console-0.9)
+        ("rust-syntect" ,rust-syntect-3.3))))
+    (home-page "https://github.com/mitsuhiko/better-panic")
+    (synopsis "Pretty backtraces inspired by Python's tracebacks")
+    (description
+     "This package provides pretty panic backtraces inspired by Python's
+tracebacks.")
+    (license (list license:expat license:asl2.0))))
+
+(define-public rust-bincode-1.2
+  (package
+    (name "rust-bincode")
+    (version "1.2.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "bincode" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1gvxm3n67xv1874fwxmnlircdlphlk1hcw75ykrrnw9l2nky4lsp"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-serde" ,rust-serde-1.0)
+        ("rust-byteorder" ,rust-byteorder-1.3))
+       #:cargo-development-inputs
+       (("rust-serde-bytes" ,rust-serde-bytes-0.11)
+        ("rust-serde-derive" ,rust-serde-derive-1.0))))
+    (home-page "https://github.com/servo/bincode")
+    (synopsis
+     "Binary serialization/deserialization strategy")
+    (description
+     "This package provides a binary serialization/deserialization strategy
+that uses Serde for transforming structs into bytes and vice versa!")
+    (license license:expat)))
+
 (define-public rust-bincode-1.1
   (package
+    (inherit rust-bincode-1.2)
     (name "rust-bincode")
     (version "1.1.4")
     (source
@@ -996,7 +1213,6 @@ (define-public rust-bincode-1.1
        (sha256
         (base32
          "1xx6bp39irvsndk6prnmmq8m1l9p6q2qj21j6mfks2y81pjsa14z"))))
-    (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
        #:cargo-inputs
@@ -1005,58 +1221,170 @@ (define-public rust-bincode-1.1
         ("rust-serde" ,rust-serde-1.0))
        #:cargo-development-inputs
        (("rust-serde-bytes" ,rust-serde-bytes-0.11)
-        ("rust-serde-derive" ,rust-serde-derive-1.0))))
-    (home-page "https://github.com/servo/bincode")
-    (synopsis
-     "Binary serialization/deserialization strategy")
-    (description
-     "This package provides a binary serialization/deserialization strategy
-that uses Serde for transforming structs into bytes and vice versa!")
-    (license license:expat)))
+        ("rust-serde-derive" ,rust-serde-derive-1.0))))))
 
-(define-public rust-bindgen-0.50
+(define-public rust-bindgen-0.52
   (package
     (name "rust-bindgen")
-    (version "0.50.0")
+    (version "0.52.0")
     (source
-     (origin
-       (method url-fetch)
-       (uri (crate-uri "bindgen" version))
-       (file-name
-        (string-append name "-" version ".tar.gz"))
-       (sha256
-        (base32
-         "1k4n1d002vrfn1mlpww3ib7f275yn4rpxfwkqpr9bym27zg17ab5"))))
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "bindgen" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0mzy2gjiaggl602yn4a11xzrxfj18kl7pwqa5yv32njkxd257j7i"))))
     (build-system cargo-build-system)
     (arguments
      `(#:cargo-inputs
-       (("rust-bitflags" ,rust-bitflags-1)
-        ("rust-cexpr" ,rust-cexpr-0.3)
+       (("rust-shlex" ,rust-shlex-0.1)
         ("rust-cfg-if" ,rust-cfg-if-0.1)
+        ("rust-peeking-take-while"
+         ,rust-peeking-take-while-0.1)
         ("rust-clang-sys" ,rust-clang-sys-0.28)
-        ("rust-clap" ,rust-clap-2)
-        ("rust-env-logger" ,rust-env-logger-0.6)
-        ("rust-fxhash" ,rust-fxhash-0.2)
-        ("rust-lazy-static" ,rust-lazy-static-1)
+        ("rust-cexpr" ,rust-cexpr-0.3)
         ("rust-log" ,rust-log-0.4)
-        ("rust-peeking-take-while" ,rust-peeking-take-while-0.1)
-        ("rust-proc-macro2" ,rust-proc-macro2-0.4)
+        ("rust-env-logger" ,rust-env-logger-0.7)
+        ("rust-proc-macro2" ,rust-proc-macro2-1.0)
         ("rust-quote" ,rust-quote-1.0)
-        ("rust-regex" ,rust-regex-1.1)
-        ("rust-shlex" ,rust-shlex-0.1)
-        ("rust-which" ,rust-which-2.0))
+        ("rust-rustc-hash" ,rust-rustc-hash-1.1)
+        ("rust-bitflags" ,rust-bitflags-1)
+        ("rust-lazycell" ,rust-lazycell-1.2)
+        ("rust-regex" ,rust-regex-1.3)
+        ("rust-lazy-static" ,rust-lazy-static-1)
+        ("rust-clap" ,rust-clap-2)
+        ("rust-which" ,rust-which-3.1))
        #:cargo-development-inputs
        (("rust-clap" ,rust-clap-2)
         ("rust-diff" ,rust-diff-0.1)
-        ("rust-shlex" ,rust-shlex-0.1))))
-    (home-page
-     "https://rust-lang.github.io/rust-bindgen/")
-    (synopsis
-     "Automatically generates FFI bindings to C and C++ libraries")
-    (description
-     "Automatically generates Rust FFI bindings to C and C++
-libraries.")
-    (license license:bsd-3)))
+        ("rust-shlex" ,rust-shlex-0.1))
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'set-environmental-variable
+           (lambda* (#:key inputs #:allow-other-keys)
+             (let ((clang (assoc-ref inputs "libclang")))
+               (setenv "LIBCLANG_PATH"
+                       (string-append clang "/lib")))
+             #t)))))
+    (inputs
+     `(("libclang" ,clang)))
+    (home-page "https://rust-lang.github.io/rust-bindgen/")
+    (synopsis
+     "Automatically generates Rust FFI bindings to C and C++ libraries")
+    (description
+     "Automatically generates Rust FFI bindings to C and C++ libraries.")
+    (license license:bsd-3)))
+
+(define-public rust-bindgen-0.51
+  (package
+    (inherit rust-bindgen-0.52)
+    (name "rust-bindgen")
+    (version "0.51.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "bindgen" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0x9gndlnwmxsihxvsc3izyyss7g8b2djn0daafshj1gcy69i7mzb"))))
+    (arguments
+     `(#:cargo-inputs
+       (("rust-shlex" ,rust-shlex-0.1)
+        ("rust-cfg-if" ,rust-cfg-if-0.1)
+        ("rust-peeking-take-while"
+         ,rust-peeking-take-while-0.1)
+        ("rust-clang-sys" ,rust-clang-sys-0.28)
+        ("rust-cexpr" ,rust-cexpr-0.3)
+        ("rust-log" ,rust-log-0.4)
+        ("rust-env-logger" ,rust-env-logger-0.6)
+        ("rust-proc-macro2" ,rust-proc-macro2-1.0)
+        ("rust-quote" ,rust-quote-1.0)
+        ("rust-rustc-hash" ,rust-rustc-hash-1.1)
+        ("rust-bitflags" ,rust-bitflags-1)
+        ("rust-regex" ,rust-regex-1.3)
+        ("rust-lazy-static" ,rust-lazy-static-1)
+        ("rust-clap" ,rust-clap-2)
+        ("rust-which" ,rust-which-3.1))
+       #:cargo-development-inputs
+       (("rust-clap" ,rust-clap-2)
+        ("rust-diff" ,rust-diff-0.1)
+        ("rust-shlex" ,rust-shlex-0.1))))
+    (inputs `())))
+
+(define-public rust-bindgen-0.50
+  (package
+    (inherit rust-bindgen-0.51)
+    (name "rust-bindgen")
+    (version "0.50.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (crate-uri "bindgen" version))
+       (file-name
+        (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "1fp98x0k4cawil3rqxsfrb58pq3mb5mn37rp745zxfmjfigml3nb"))))
+    (arguments
+     `(#:cargo-inputs
+       (("rust-bitflags" ,rust-bitflags-1)
+        ("rust-cexpr" ,rust-cexpr-0.3)
+        ("rust-cfg-if" ,rust-cfg-if-0.1)
+        ("rust-clang-sys" ,rust-clang-sys-0.28)
+        ("rust-clap" ,rust-clap-2)
+        ("rust-env-logger" ,rust-env-logger-0.6)
+        ("rust-fxhash" ,rust-fxhash-0.2)
+        ("rust-lazy-static" ,rust-lazy-static-1)
+        ("rust-log" ,rust-log-0.4)
+        ("rust-peeking-take-while" ,rust-peeking-take-while-0.1)
+        ("rust-proc-macro2" ,rust-proc-macro2-0.4)
+        ("rust-quote" ,rust-quote-0.6)
+        ("rust-regex" ,rust-regex-1.1)
+        ("rust-shlex" ,rust-shlex-0.1)
+        ("rust-which" ,rust-which-2.0))
+       #:cargo-development-inputs
+       (("rust-clap" ,rust-clap-2)
+        ("rust-diff" ,rust-diff-0.1)
+        ("rust-shlex" ,rust-shlex-0.1))))))
+
+(define-public rust-bindgen-0.37
+  (package
+    (inherit rust-bindgen-0.50)
+    (name "rust-bindgen")
+    (version "0.37.4")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "bindgen" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "08f2cyzr8fc027mzj2lhmn5j3w318g2ql7yfw5ngxa3yhy1an98v"))))
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-cfg-if" ,rust-cfg-if-0.1)
+        ("rust-peeking-take-while"
+         ,rust-peeking-take-while-0.1)
+        ("rust-cexpr" ,rust-cexpr-0.2)
+        ("rust-clang-sys" ,rust-clang-sys-0.23)
+        ("rust-proc-macro2" ,rust-proc-macro2-0.3)  ; 0.3.5
+        ("rust-log" ,rust-log-0.4)
+        ("rust-env-logger" ,rust-env-logger-0.5)
+        ("rust-quote" ,rust-quote-0.5)
+        ("rust-which" ,rust-which-1.0)
+        ("rust-regex" ,rust-regex-1.3)
+        ("rust-lazy-static" ,rust-lazy-static-1)
+        ("rust-clap" ,rust-clap-2))
+       #:cargo-development-inputs
+       (("rust-clap" ,rust-clap-2)
+        ("rust-diff" ,rust-diff-0.1)
+        ("rust-shlex" ,rust-shlex-0.1))))))
 
 (define-public rust-bindgen-0.33
   (package
@@ -1193,6 +1521,29 @@ (define-public rust-bitflags-0.7
         (base32
          "0v8hh6wdkpk9my8z8442g4hqrqf05h0qj53dsay6mv18lqvqklda"))))))
 
+(define-public rust-bitstream-io-0.8
+  (package
+    (name "rust-bitstream-io")
+    (version "0.8.5")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "bitstream-io" version))
+        (file-name
+          (string-append name "-" version ".tar.gz"))
+        (sha256
+          (base32
+            "00a6wy54s1dmadm5xz8k2cbsd7ixvm48mlc45bk0fdy0pbra6jk1"))))
+    (build-system cargo-build-system)
+    (arguments `(#:skip-build? #t))
+    (home-page
+      "https://github.com/tuffy/bitstream-io")
+    (synopsis
+      "Library for reading/writing un-aligned values from/to streams in big-endian and little-endian formats.")
+    (description
+      "Library for reading/writing un-aligned values from/to streams in big-endian and little-endian formats.")
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-blake2-0.8
   (package
     (name "rust-blake2")
@@ -1428,7 +1779,7 @@ (define-public rust-bresenham-0.1
 (define-public rust-bstr-0.2
   (package
     (name "rust-bstr")
-    (version "0.2.1")
+    (version "0.2.12")
     (source
      (origin
        (method url-fetch)
@@ -1437,7 +1788,7 @@ (define-public rust-bstr-0.2
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0prq6yk3da0k5bg2czcgg1i4ynsq1l59xc89ycsv6v7p08p5gh3c"))))
+         "0hazfback6i2k3vhhwyj8h46id3y58zxqh22pz46hj9r1zayd298"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
@@ -1567,6 +1918,34 @@ (define-public rust-bytecount-0.5
 in a byte slice, fast.")
     (license (list license:asl2.0 license:expat))))
 
+(define-public rust-bytecount-0.4
+  (package
+    (name "rust-bytecount")
+    (version "0.4.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "bytecount" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "13qpy38z5wx0rzcdvr2h0ixbfgi1dbrif068il3hwn3k2mah88mr"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-packed-simd" ,rust-packed-simd-0.3))
+       #:cargo-development-inputs
+       (("rust-criterion" ,rust-criterion-0.2)
+        ("rust-quickcheck" ,rust-quickcheck-0.6)
+        ("rust-rand" ,rust-rand-0.4))))
+    (home-page "https://github.com/llogiq/bytecount")
+    (synopsis "Counting bytes really fast")
+    (description
+     "This package counts occurrences of a given byte, or the number of UTF-8
+code points, in a byte slice, fast.")
+    (license (list license:asl2.0 license:expat))))
+
 (define-public rust-byteorder-1.3
   (package
     (name "rust-byteorder")
@@ -1910,6 +2289,64 @@ (define-public rust-caps-0.3
 capabilities")
     (license (list license:expat license:asl2.0))))
 
+(define-public rust-cargo-metadata-0.9
+  (package
+    (name "rust-cargo-metadata")
+    (version "0.9.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "cargo_metadata" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "00pjms89lghvizh4d55lz80hvrih9r55xv9m5wd9vcsgc163gqs6"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:tests? #f
+       #:cargo-inputs
+       (("rust-semver" ,rust-semver-0.9)
+        ("rust-serde" ,rust-serde-1.0)
+        ("rust-serde-derive" ,rust-serde-derive-1.0)
+        ("rust-serde-json" ,rust-serde-json-1.0))
+       #:cargo-development-inputs
+       (("rust-clap" ,rust-clap-2)
+        ("rust-docopt" ,rust-docopt-1.1)
+        ("rust-structopt" ,rust-structopt-0.2))))
+    (home-page "https://github.com/oli-obk/cargo_metadata")
+    (synopsis "Structured access to the output of `cargo metadata`")
+    (description
+     "This package provides structured access to the output of @code{cargo
+metadata}.")
+    (license license:expat)))
+
+(define-public rust-cargo-metadata-0.6
+  (package
+    (inherit rust-cargo-metadata-0.9)
+    (name "rust-cargo-metadata")
+    (version "0.6.4")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "cargo_metadata" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1givpi2w7iwqqnl87x5yc15zcm5hs6yw490sb6abkfp1h39v9lg5"))))
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-error-chain" ,rust-error-chain-0.12)
+        ("rust-semver" ,rust-semver-0.9)
+        ("rust-serde" ,rust-serde-1.0)
+        ("rust-serde-derive" ,rust-serde-derive-1.0)
+        ("rust-serde-json" ,rust-serde-json-1.0))
+       #:cargo-development-inputs
+       (;("rust-docopt" ,rust-docopt-0.8)
+        ("rust-clap" ,rust-clap-2))))))
+
 (define-public rust-cargon-0.0
   (package
     (name "rust-cargon")
@@ -1936,7 +2373,7 @@ (define-public rust-cargon-0.0
 (define-public rust-cast-0.2
   (package
     (name "rust-cast")
-    (version "0.2.2")
+    (version "0.2.3")
     (source
      (origin
        (method url-fetch)
@@ -1945,12 +2382,14 @@ (define-public rust-cast-0.2
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "09yl2700crxa4n860b080msij25klvs1kfzazhp2aihchvr16q4j"))))
+         "1c5z7zryj0zwnhdgs6rw5dfvnlwc1vm19jzrlgx5055alnwk952b"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-rustc-version" ,rust-rustc-version-0.2))
        #:cargo-development-inputs
-       (("rust-quickcheck" ,rust-quickcheck-0.8))))
+       (("rust-quickcheck" ,rust-quickcheck-0.9))))
     (home-page "https://github.com/japaric/cast.rs")
     (synopsis
      "Ergonomic, checked cast functions for primitive types")
@@ -2012,7 +2451,7 @@ (define-public rust-cc-1.0
 (define-public rust-cexpr-0.3
   (package
     (name "rust-cexpr")
-    (version "0.3.5")
+    (version "0.3.6")
     (source
      (origin
        (method url-fetch)
@@ -2021,7 +2460,7 @@ (define-public rust-cexpr-0.3
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "1by64ini3f058pwad3immx5cc12wr0m0kwgaxa8apzym03mj9ym7"))))
+         "07fdfj4ff2974y33yixrb657riq9zl9b9h9lr0h7ridhhvxvbrgw"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
@@ -2197,7 +2636,7 @@ (define-public rust-cgmath-0.16
 (define-public rust-chrono-0.4
   (package
     (name "rust-chrono")
-    (version "0.4.7")
+    (version "0.4.11")
     (source
      (origin
        (method url-fetch)
@@ -2206,23 +2645,26 @@ (define-public rust-chrono-0.4
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "1glam3iqhshbamzgf0npn7hgghski92r31lm7gg8841hnxc1zn3p"))))
+         "1cmmxamkzzs36zncqjjr7qm7xkb6zyrkjslnlj3axdgqki84y2c0"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
        #:cargo-inputs
-       (("rust-libc" ,rust-libc-0.2)
-        ("rust-num-integer" ,rust-num-integer-0.1)
+       (("rust-num-integer" ,rust-num-integer-0.1)
         ("rust-num-traits" ,rust-num-traits-0.2)
+        ("rust-js-sys" ,rust-js-sys-0.3)
         ("rust-rustc-serialize" ,rust-rustc-serialize-0.3)
         ("rust-serde" ,rust-serde-1.0)
-        ("rust-time" ,rust-time-0.1))
+        ("rust-time" ,rust-time-0.1)
+        ("rust-wasm-bindgen" ,rust-wasm-bindgen-0.2))
        #:cargo-development-inputs
-       (("rust-bincode" ,rust-bincode-1.1)
+       (;("rust-bincode" ,rust-bincode-0.8)
+        ("rust-criterion" ,rust-criterion-0.2)
         ("rust-doc-comment" ,rust-doc-comment-0.3)
         ("rust-num-iter" ,rust-num-iter-0.1)
         ("rust-serde-derive" ,rust-serde-derive-1.0)
-        ("rust-serde-json" ,rust-serde-json-1.0))))
+        ("rust-serde-json" ,rust-serde-json-1.0)
+        ("rust-wasm-bindgen-test" ,rust-wasm-bindgen-test-0.2))))
     (home-page
      "https://github.com/chronotope/chrono")
     (synopsis "Date and time library for Rust")
@@ -2315,6 +2757,21 @@ (define-public rust-clang-sys-0.26
                        (string-append clang "/lib")))
              #t)))))))
 
+(define-public rust-clang-sys-0.23
+  (package
+    (inherit rust-clang-sys-0.26)
+    (name "rust-clang-sys")
+    (version "0.23.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "clang-sys" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1hjr333izzhs6bic84qwnyzy5xzmvasib8f3zkzj4ln3a97c1xyp"))))))
+
 (define-public rust-clang-sys-0.22
   (package
     (inherit rust-clang-sys-0.26)
@@ -2512,6 +2969,35 @@ (define-public rust-cloudabi-0.0
      "Low level interface to CloudABI.  Contains all syscalls and related types.")
     (license license:bsd-2)))
 
+(define-public rust-cloudflare-zlib-sys-0.2
+  (package
+    (name "rust-cloudflare-zlib-sys")
+    (version "0.2.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "cloudflare-zlib-sys" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "01lwfd15ijw4d8jsqp87yv4wpmzcp84qm0qqwy3yxmm0fjr5q6by"))))
+    ;; This crate bundles cloudflare's fork of zlib, so we don't unbundle it.
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-cc" ,rust-cc-1.0))))
+    (home-page "https://github.com/cloudflare/zlib")
+    (synopsis
+     "Cloudflare fork of zlib with massive performance improvements")
+    (description
+     "Cloudflare fork of zlib with massive performance improvements.")
+    (license
+      (list license:expat
+            license:asl2.0
+            license:zlib))))
+
 (define-public rust-cmake-0.1
   (package
     (name "rust-cmake")
@@ -2602,12 +3088,42 @@ (define-public rust-color-quant-1.0
      "Color quantization library to reduce n colors to 256 colors.")
     (license license:expat)))
 
+(define-public rust-colored-1.9
+  (package
+    (name "rust-colored")
+    (version "1.9.3")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "colored" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0nbc1czs512h1k696y7glv1kjrb2b914zpxraic6q5fgv80wizzl"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-atty" ,rust-atty-0.2)
+        ("rust-winapi" ,rust-winapi-0.3)
+        ("rust-lazy-static" ,rust-lazy-static-1))
+       #:cargo-development-inputs
+       (("rust-ansi-term" ,rust-ansi-term-0.12)
+        ;("rust-rspec" ,rust-rspec-1.0)
+        )))
+    (home-page "https://github.com/mackwic/colored")
+    (synopsis "Add colors in your terminal")
+    (description
+     "The most simple way to add colors in your terminal.")
+    (license license:mpl2.0)))
+
 ;; This package requires features which are unavailable
 ;; on the stable releases of Rust.
 (define-public rust-compiler-builtins-0.1
   (package
     (name "rust-compiler-builtins")
-    (version "0.1.23")
+    (version "0.1.26")
     (source
       (origin
         (method url-fetch)
@@ -2615,14 +3131,13 @@ (define-public rust-compiler-builtins-0.1
         (file-name (string-append name "-" version ".crate"))
         (sha256
          (base32
-          "0m8rfikg08av2plyp32drjfsv7i10nf2kwzajjjkvl13yhj9s5fn"))))
+          "1rhj6ccmfkh9gcxnxgjq4fg257yi4f9325nfzsphbmxwkrg06sq3"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
        #:cargo-inputs
-       (("rust-rustc-std-workspace-core" ,rust-rustc-std-workspace-core-1.0))
-       #:cargo-development-inputs
-       (("rust-cc" ,rust-cc-1.0))))
+       (("rust-rustc-std-workspace-core" ,rust-rustc-std-workspace-core-1.0)
+        ("rust-cc" ,rust-cc-1.0))))
     (home-page "https://github.com/rust-lang/compiler-builtins")
     (synopsis "Compiler intrinsics used by the Rust compiler")
     (description
@@ -2711,15 +3226,45 @@ (define-public rust-compiletest-rs-0.2
         ("rust-rustc-serialize" ,rust-rustc-serialize-0.3)
         ("rust-tempdir" ,rust-tempdir-0.3))))))
 
-(define-public rust-console-0.7
+(define-public rust-console-0.9
   (package
     (name "rust-console")
-    (version "0.7.7")
+    (version "0.9.2")
     (source
-     (origin
-       (method url-fetch)
-       (uri (crate-uri "console" version))
-       (file-name
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "console" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1h765951c9mywff534f0191slazykmif4290g2yarcwhd2cg7q25"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-unicode-width" ,rust-unicode-width-0.1)
+        ("rust-libc" ,rust-libc-0.2)
+        ("rust-termios" ,rust-termios-0.3)
+        ("rust-encode-unicode" ,rust-encode-unicode-0.3)
+        ("rust-winapi" ,rust-winapi-0.3)
+        ("rust-clicolors-control" ,rust-clicolors-control-1.0)
+        ("rust-regex" ,rust-regex-1.3)
+        ("rust-lazy-static" ,rust-lazy-static-1))))
+    (home-page "https://github.com/mitsuhiko/console")
+    (synopsis "Terminal and console abstraction for Rust")
+    (description
+     "This package provides a terminal and console abstraction for Rust")
+    (license license:expat)))
+
+(define-public rust-console-0.7
+  (package
+    (name "rust-console")
+    (version "0.7.7")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (crate-uri "console" version))
+       (file-name
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
@@ -3010,7 +3555,7 @@ (define-public rust-core-video-sys-0.1
 (define-public rust-cpp-demangle-0.2
   (package
     (name "rust-cpp-demangle")
-    (version "0.2.12")
+    (version "0.2.14")
     (source
      (origin
        (method url-fetch)
@@ -3019,17 +3564,17 @@ (define-public rust-cpp-demangle-0.2
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0a4hqsfc0sfdwy7pcr0rc1fjp2j47fxbkqfc2lfrbi4zlm5hq36k"))))
+         "1mm064x84868q06r4m4b7byf999nrkbhx7iyc4nchyssaxpsy5a1"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
        #:cargo-inputs
        (("rust-afl" ,rust-afl-0.4)
-        ("rust-cfg-if" ,rust-cfg-if-0.1))
+        ("rust-cfg-if" ,rust-cfg-if-0.1)
+        ("rust-glob" ,rust-glob-0.3))
        #:cargo-development-inputs
        (("rust-clap" ,rust-clap-2)
-        ("rust-diff" ,rust-diff-0.1)
-        ("rust-glob" ,rust-glob-0.3))))
+        ("rust-diff" ,rust-diff-0.1))))
     (home-page "https://github.com/gimli-rs/cpp_demangle")
     (synopsis "Demangle C++ symbols")
     (description
@@ -3101,7 +3646,7 @@ (define-public rust-crc32fast-1.2
 (define-public rust-criterion-0.3
   (package
     (name "rust-criterion")
-    (version "0.3.0")
+    (version "0.3.1")
     (source
      (origin
        (method url-fetch)
@@ -3110,7 +3655,7 @@ (define-public rust-criterion-0.3
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "1iig7r9c6bkn5qb6axxkblc1amif6k49lix35rhqs728cphh71wk"))))
+         "1lgpr82rlmg6rm4gr3c3pla2xgxnakbf8w9sabjsig8jkikmbiqz"))))
     (build-system cargo-build-system)
     (arguments
      `(#:cargo-inputs
@@ -3122,15 +3667,14 @@ (define-public rust-criterion-0.3
         ("rust-itertools" ,rust-itertools-0.8)
         ("rust-lazy-static" ,rust-lazy-static-1)
         ("rust-num-traits" ,rust-num-traits-0.2)
-        ("rust-rand-core" ,rust-rand-core-0.5)
-        ("rust-rand-os" ,rust-rand-os-0.2)
-        ("rust-rand-xoshiro" ,rust-rand-xoshiro-0.3)
-        ("rust-rayon" ,rust-rayon-1.1)
+        ("rust-oorandom" ,rust-oorandom-11.1)
+        ("rust-plotters" ,rust-plotters-0.2)
+        ("rust-rayon" ,rust-rayon-1.3)
         ("rust-serde" ,rust-serde-1.0)
         ("rust-serde-derive" ,rust-serde-derive-1.0)
         ("rust-serde-json" ,rust-serde-json-1.0)
         ("rust-tinytemplate" ,rust-tinytemplate-1.0)
-        ("rust-walkdir" ,rust-walkdir-2.2))
+        ("rust-walkdir" ,rust-walkdir-2.3))
        #:cargo-development-inputs
        (("rust-approx" ,rust-approx-0.3)
         ("rust-quickcheck" ,rust-quickcheck-0.9)
@@ -3478,7 +4022,7 @@ (define-public rust-crossbeam-queue-0.1
 (define-public rust-crossbeam-utils-0.7
   (package
     (name "rust-crossbeam-utils")
-    (version "0.7.0")
+    (version "0.7.2")
     (source
      (origin
        (method url-fetch)
@@ -3487,7 +4031,7 @@ (define-public rust-crossbeam-utils-0.7
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "1x1rn35q2v05qif14ijfg7800d3rf3ji2cg79awnacfw5jq6si6f"))))
+         "1a31wbrda1320gj2a6az1lin2d34xfc3xf88da4c17qy5lxcgiy3"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
@@ -3621,7 +4165,7 @@ (define-public rust-cssparser-macros-0.3
 (define-public rust-csv-1.1
   (package
     (name "rust-csv")
-    (version "1.1.0")
+    (version "1.1.3")
     (source
      (origin
        (method url-fetch)
@@ -3630,7 +4174,7 @@ (define-public rust-csv-1.1
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0qxvzq030hi915dszazv6a7f0apzzi7gn193ni0g2lzkawjxck55"))))
+         "0yd2z55m2pg4al4yng4nl2y7c9dw2v7yhg5ynihxyrmmd9zzxbq0"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
@@ -3672,7 +4216,7 @@ (define-public rust-csv-0.14
 (define-public rust-csv-core-0.1
   (package
     (name "rust-csv-core")
-    (version "0.1.6")
+    (version "0.1.10")
     (source
      (origin
        (method url-fetch)
@@ -3681,11 +4225,11 @@ (define-public rust-csv-core-0.1
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0k5zs0x0qmmn27pa5kcg86lg84s29491fw5sh3zswxswnavasp4v"))))
+         "145wcc3560v1kmysqqspvddppiysr2rifqzy4nnlh3r6kxanc91b"))))
     (build-system cargo-build-system)
     (arguments
      `(#:cargo-inputs
-       (("rust-memchr" ,rust-memchr-2.2))
+       (("rust-memchr" ,rust-memchr-2.3))
        #:cargo-development-inputs
        (("rust-arrayvec" ,rust-arrayvec-0.4))))
     (home-page "https://github.com/BurntSushi/rust-csv")
@@ -3695,6 +4239,34 @@ (define-public rust-csv-core-0.1
      "Bare bones CSV parsing with no_std support.")
     (license (list license:unlicense license:expat))))
 
+(define-public rust-ctor-0.1
+  (package
+    (name "rust-ctor")
+    (version "0.1.13")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "ctor" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1qgwkwyxishpp3wkbwq5i27zdxz539ii0sz129xj061ffnnfbia7"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-syn" ,rust-syn-1.0)
+        ("rust-quote" ,rust-quote-1.0))
+       ;#:cargo-development-inputs
+       ;(("rust-libc-print" ,rust-libc-print-0.1))
+       ))
+    (home-page "https://github.com/mmastrac/rust-ctor")
+    (synopsis "__attribute__((constructor)) for Rust")
+    (description
+     "This package provides an @code{__attribute__((constructor))} for Rust.")
+    (license (list license:asl2.0 license:expat))))
+
 (define-public rust-ctrlc-3.1
   (package
     (name "rust-ctrlc")
@@ -3862,6 +4434,43 @@ (define-public rust-datetime-0.4
 and arithmetic.")
     (license license:expat)))
 
+(define-public rust-dav1d-sys-0.3
+  (package
+    (name "rust-dav1d-sys")
+    (version "0.3.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "dav1d-sys" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1022czzp3s54r42x6rhr870w1fwzyp7b6qn0zirpz55zmqjpgnwa"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-pkg-config" ,rust-pkg-config-0.3)
+        ("rust-bindgen" ,rust-bindgen-0.52)
+        ("rust-metadeps" ,rust-metadeps-1.1))
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'set-environmental-variable
+           (lambda* (#:key inputs #:allow-other-keys)
+             (let ((clang (assoc-ref inputs "libclang")))
+               (setenv "LIBCLANG_PATH"
+                       (string-append clang "/lib")))
+             #t)))))
+    (inputs
+     `(("dav1d" ,dav1d)
+       ("pkg-config" ,pkg-config)
+       ("libclang" ,clang)
+       ("llvm" ,llvm)))
+    (home-page "https://github.com/rust-av/dav1d-rs")
+    (synopsis "FFI bindings to dav1d")
+    (description "FFI bindings to dav1d")
+    (license license:expat)))
+
 (define-public rust-decimal-2.0
   (package
     (name "rust-decimal")
@@ -4109,7 +4718,7 @@ (define-public rust-dirs-1.0
   (package
     (inherit rust-dirs-2.0)
     (name "rust-dirs")
-    (version "1.0.3")
+    (version "1.0.5")
     (source
       (origin
         (method url-fetch)
@@ -4117,11 +4726,12 @@ (define-public rust-dirs-1.0
         (file-name (string-append name "-" version ".crate"))
         (sha256
          (base32
-          "02vigc566z5i6n9wr2x8sch39qp4arn89xhhrh18fhpm3jfc0ygn"))))
+          "009rrhzj9pxyncmm2vhlj70npg0cgggv2hjbbkiwdl9vccq8kmrz"))))
     (arguments
      `(#:skip-build? #t
        #:cargo-inputs
        (("rust-libc" ,rust-libc-0.2)
+        ("rust-redox-users" ,rust-redox-users-0.3)
         ("rust-winapi" ,rust-winapi-0.3))))))
 
 (define-public rust-dirs-sys-0.3
@@ -4348,6 +4958,29 @@ (define-public rust-downcast-rs-1.1
 parameters, associated types, and type constraints.")
     (license (list license:expat license:asl2.0))))
 
+(define-public rust-draw-state-0.8
+  (package
+    (name "rust-draw-state")
+    (version "0.8.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "draw_state" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0lfng4fz9x7bwsmzv9r20ply10w0iid6vfcrhx292s6hw8vrbkrk"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-serde" ,rust-serde-1.0)
+        ("rust-bitflags" ,rust-bitflags-1))))
+    (home-page "https://github.com/gfx-rs/draw_state")
+    (synopsis "Graphics state blocks for gfx-rs")
+    (description "Graphics state blocks for gfx-rs.")
+    (license license:asl2.0)))
+
 (define-public rust-dtoa-0.4
   (package
     (name "rust-dtoa")
@@ -4494,7 +5127,7 @@ (define-public rust-edit-distance-2.1
 (define-public rust-either-1.5
   (package
     (name "rust-either")
-    (version "1.5.2")
+    (version "1.5.3")
     (source
      (origin
        (method url-fetch)
@@ -4503,7 +5136,7 @@ (define-public rust-either-1.5
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0yyggfd5yq9hyyp0bd5jj0fgz3rwws42d19ri0znxwwqs3hcy9sm"))))
+         "1qyz1b1acad6w0k5928jw5zaq900zhsk7p8dlcp4hh61w4f6n7xv"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
@@ -4545,7 +5178,7 @@ (define-public rust-embed-resource-1.3
 (define-public rust-encode-unicode-0.3
   (package
     (name "rust-encode-unicode")
-    (version "0.3.5")
+    (version "0.3.6")
     (source
      (origin
        (method url-fetch)
@@ -4554,12 +5187,12 @@ (define-public rust-encode-unicode-0.3
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "1g8a8pixkxz6r927f4sc4r15qyc0szxdxb1732v8q7h0di4wkclh"))))
+         "07w3vzrhxh9lpjgsg2y5bwzfar2aq35mdznvcp3zjl0ssj7d4mx3"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
        #:cargo-inputs
-       (("rust-ascii" ,rust-ascii-0.9)
+       (("rust-ascii" ,rust-ascii-1.0)
         ("rust-clippy" ,rust-clippy-0.0))
        #:cargo-development-inputs
        (("rust-lazy-static" ,rust-lazy-static-1))))
@@ -4946,7 +5579,7 @@ (define-public rust-envmnt-0.6
 (define-public rust-erased-serde-0.3
   (package
     (name "rust-erased-serde")
-    (version "0.3.9")
+    (version "0.3.11")
     (source
      (origin
        (method url-fetch)
@@ -4955,14 +5588,14 @@ (define-public rust-erased-serde-0.3
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0q7bnxs5zskfq5iillig55g7891dllcxh2p8y8k1p2j72syf9viv"))))
+         "1lgkpkk7nx6f24gmr3psyj8d2avc9701r9jyw1i4ssp10lbnv2yq"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
        #:cargo-inputs
        (("rust-serde" ,rust-serde-1.0))
        #:cargo-development-inputs
-       (("rust-serde-cbor" ,rust-serde-cbor-0.10)
+       (;("rust-serde-cbor" ,rust-serde-cbor-0.9)
         ("rust-serde-derive" ,rust-serde-derive-1.0)
         ("rust-serde-json" ,rust-serde-json-1.0))))
     (home-page "https://github.com/dtolnay/erased-serde")
@@ -4971,6 +5604,37 @@ (define-public rust-erased-serde-0.3
      "Type-erased Serialize and Serializer traits.")
     (license (list license:asl2.0 license:expat))))
 
+(define-public rust-err-derive-0.2
+  (package
+    (name "rust-err-derive")
+    (version "0.2.3")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "err-derive" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0v6wxrshfpg7mwaxzq8jwxbfiyn7zk5rlm4m8kkrwh7dpf8nrx42"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-synstructure" ,rust-synstructure-0.12)
+        ("rust-skeptic" ,rust-skeptic-0.13)
+        ("rust-proc-macro-error" ,rust-proc-macro-error-0.4)
+        ("rust-proc-macro2" ,rust-proc-macro2-1.0)
+        ("rust-syn" ,rust-syn-1.0)
+        ("rust-rustversion" ,rust-rustversion-1.0)
+        ("rust-quote" ,rust-quote-1.0))
+       #:cargo-development-inputs
+       (("rust-skeptic" ,rust-skeptic-0.13))))
+    (home-page "https://gitlab.com/torkleyy/err-derive")
+    (synopsis "Derive macro for `std::error::Error`")
+    (description
+     "Derive macro for @code{std::error::Error}.")
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-errno-0.2
   (package
     (name "rust-errno")
@@ -5025,7 +5689,7 @@ (define-public rust-errno-dragonfly-0.1
 (define-public rust-error-chain-0.12
   (package
     (name "rust-error-chain")
-    (version "0.12.1")
+    (version "0.12.2")
     (source
      (origin
        (method url-fetch)
@@ -5034,23 +5698,60 @@ (define-public rust-error-chain-0.12
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "1ndpw1ny2kxqpw6k1shq8k56z4vfpk4xz9zr8ay988k0rffrxd1s"))))
+         "1ka5y0fmymxzx3gz2yrd7rpz2i555m1iw4fpmcggpzcgr1n10wfk"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
        #:cargo-inputs
        (("rust-backtrace" ,rust-backtrace-0.3)
-        ("rust-version-check" ,rust-version-check-0.1))))
+        ("rust-version-check" ,rust-version-check-0.9))))
     (home-page "https://github.com/rust-lang-nursery/error-chain")
     (synopsis "Yet another error boilerplate library")
     (description
      "Yet another error boilerplate library.")
     (license (list license:asl2.0 license:expat))))
 
+(define-public rust-error-chain-0.11
+  (package
+    (inherit rust-error-chain-0.12)
+    (name "rust-error-chain")
+    (version "0.11.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "error-chain" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1wykkr0naizbkwxjwia1rch8xhwvgij9khqvjzs07mrmqifislgz"))))
+    (arguments
+     `(#:tests? #f      ; Not all test files included.
+       #:cargo-inputs
+       (("rust-backtrace" ,rust-backtrace-0.3))))))
+
+(define-public rust-error-chain-0.10
+  (package
+    (inherit rust-error-chain-0.11)
+    (name "rust-error-chain")
+    (version "0.10.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "error-chain" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1y1gyj9g5c3k1nzkvxrgry8v9k86kcc585mczrm3qz019s35shyr"))))
+    (arguments
+     `(#:cargo-inputs
+       (("rust-backtrace" ,rust-backtrace-0.3))))))
+
 (define-public rust-euclid-0.20
   (package
     (name "rust-euclid")
-    (version "0.20.7")
+    (version "0.20.10")
     (source
      (origin
        (method url-fetch)
@@ -5059,7 +5760,7 @@ (define-public rust-euclid-0.20
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0pa8kxblvc0s9gia9n0966w7169aswpg7knw2pmwrqa204r2v19z"))))
+         "0c3hbl0kvc53k6nws0v9d46hi0giza1j079sqx2bgl4wfw65nshc"))))
     (build-system cargo-build-system)
     (arguments
      `(#:cargo-inputs
@@ -5127,7 +5828,7 @@ (define-public rust-fake-simd-0.1
 (define-public rust-failure-0.1
   (package
     (name "rust-failure")
-    (version "0.1.5")
+    (version "0.1.7")
     (source
      (origin
        (method url-fetch)
@@ -5136,7 +5837,7 @@ (define-public rust-failure-0.1
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "1qppmgv4i5jj6vrss91qackqnl0a12h7lnby4l7j5fdy78yxhnvr"))))
+         "0js6i6mb42q1g6q3csfbmi6q40s64k96705xbim0d8zg44j9qlmq"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
@@ -5152,7 +5853,7 @@ (define-public rust-failure-0.1
 (define-public rust-failure-derive-0.1
   (package
     (name "rust-failure-derive")
-    (version "0.1.5")
+    (version "0.1.7")
     (source
      (origin
        (method url-fetch)
@@ -5161,15 +5862,15 @@ (define-public rust-failure-derive-0.1
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "1q97n7dp51j5hndzic9ng2fgn6f3z5ya1992w84l7vypby8n647a"))))
+         "0cfjz0c9szqpxn43b2r722p6m3swzxj7aj6xhqw23ml7h8y762h3"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
        #:cargo-inputs
-       (("rust-proc-macro2" ,rust-proc-macro2-0.4)
-        ("rust-quote" ,rust-quote-0.6)
-        ("rust-syn" ,rust-syn-0.15)
-        ("rust-synstructure" ,rust-synstructure-0.10))
+       (("rust-proc-macro2" ,rust-proc-macro2-1.0)
+        ("rust-quote" ,rust-quote-1.0)
+        ("rust-syn" ,rust-syn-1.0)
+        ("rust-synstructure" ,rust-synstructure-0.12))
        #:cargo-development-inputs
        (("rust-failure" ,rust-failure-0.1))))
     (home-page "https://rust-lang-nursery.github.io/failure/")
@@ -5190,7 +5891,6 @@ (define-public rust-fallible-iterator-0.2
          (base32
           "1xq759lsr8gqss7hva42azn3whgrbrs2sd9xpn92c5ickxm1fhs4"))))
     (build-system cargo-build-system)
-    (arguments '(#:skip-build? #t))
     (home-page "https://github.com/sfackler/rust-fallible-iterator")
     (synopsis "Fallible iterator traits")
     (description "If the @code{std} or @code{alloc} features are enabled, this
@@ -5200,6 +5900,38 @@ (define-public rust-fallible-iterator-0.2
     (license (list license:asl2.0
                    license:expat))))
 
+(define-public rust-fern-0.5
+  (package
+    (name "rust-fern")
+    (version "0.5.9")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "fern" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1anslk0hx9an4ypcaxqff080hgbcxm7ji7d4qf4f6qx1mkav16p6"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-libc" ,rust-libc-0.2)
+        ("rust-reopen" ,rust-reopen-0.3)
+        ("rust-log" ,rust-log-0.4)
+        ("rust-chrono" ,rust-chrono-0.4)
+        ("rust-colored" ,rust-colored-1.9)
+        ("rust-syslog" ,rust-syslog-3.3)
+        ("rust-syslog" ,rust-syslog-4.0))
+       #:cargo-development-inputs
+       (("rust-clap" ,rust-clap-2)
+        ("rust-tempdir" ,rust-tempdir-0.3))))
+    (home-page "https://github.com/daboross/fern")
+    (synopsis "Simple, efficient logging")
+    (description
+     "This package provides a simple, efficient logging system for Rust.")
+    (license license:expat)))
+
 (define-public rust-filetime-0.2
   (package
     (name "rust-filetime")
@@ -5334,7 +6066,7 @@ (define-public rust-flamer-0.3
 (define-public rust-flate2-1.0
   (package
     (name "rust-flate2")
-    (version "1.0.9")
+    (version "1.0.14")
     (source
      (origin
        (method url-fetch)
@@ -5343,22 +6075,25 @@ (define-public rust-flate2-1.0
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "1n639gc7sbmrkir6pif608xqpwcv60kigmp5cn9x7m8892nk82am"))))
+         "0hlb2zmn5ixrgr0i1qvrd3a7j4fpp002d0kddn2hm7hjj49z9zrc"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
        #:cargo-inputs
-       (("rust-crc32fast" ,rust-crc32fast-1.2)
+       (("rust-cfg-if" ,rust-cfg-if-0.1)
+        ("rust-cloudflare-zlib-sys"
+         ,rust-cloudflare-zlib-sys-0.2)
+        ("rust-crc32fast" ,rust-crc32fast-1.2)
         ("rust-futures" ,rust-futures-0.1)
         ("rust-libc" ,rust-libc-0.2)
         ("rust-libz-sys" ,rust-libz-sys-1.0)
         ("rust-miniz-sys" ,rust-miniz-sys-0.1)
-        ("rust-miniz-oxide-c-api" ,rust-miniz-oxide-c-api-0.2)
+        ("rust-miniz-oxide" ,rust-miniz-oxide-0.3)
         ("rust-tokio-io" ,rust-tokio-io-0.1))
        #:cargo-development-inputs
        (("rust-futures" ,rust-futures-0.1)
-        ("rust-quickcheck" ,rust-quickcheck-0.8)
-        ("rust-rand" ,rust-rand-0.4)
+        ("rust-quickcheck" ,rust-quickcheck-0.9)
+        ("rust-rand" ,rust-rand-0.7)
         ("rust-tokio-io" ,rust-tokio-io-0.1)
         ("rust-tokio-tcp" ,rust-tokio-tcp-0.1)
         ("rust-tokio-threadpool" ,rust-tokio-threadpool-0.1))))
@@ -5454,6 +6189,48 @@ (define-public rust-fnv-1.0
     (license (list license:asl2.0
                    license:expat))))
 
+(define-public rust-font-kit-0.4
+  (package
+    (name "rust-font-kit")
+    (version "0.4.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "font-kit" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1fmg1jmqdvsjxjbyz8chpx1mhp544mwq128ns1shhrha5a6zzdqp"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-lyon-path" ,rust-lyon-path-0.14)
+        ("rust-core-graphics" ,rust-core-graphics-0.17)
+        ("rust-float-ord" ,rust-float-ord-0.2)
+        ("rust-libc" ,rust-libc-0.2)
+        ("rust-euclid" ,rust-euclid-0.20)
+        ("rust-winapi" ,rust-winapi-0.3)
+        ("rust-servo-fontconfig"
+         ,rust-servo-fontconfig-0.4)
+        ("rust-freetype" ,rust-freetype-0.4)
+        ("rust-log" ,rust-log-0.4)
+        ("rust-core-foundation"
+         ,rust-core-foundation-0.6)
+        ("rust-memmap" ,rust-memmap-0.7)
+        ("rust-dwrote" ,rust-dwrote-0.9)
+        ("rust-dirs" ,rust-dirs-1.0)
+        ("rust-byteorder" ,rust-byteorder-1.3)
+        ("rust-lazy-static" ,rust-lazy-static-1)
+        ("rust-core-text" ,rust-core-text-13)
+        ("rust-walkdir" ,rust-walkdir-2.3))))
+    (home-page "https://github.com/servo/font-kit")
+    (synopsis "Cross-platform font loading library")
+    (description
+     "This package provides a cross-platform font loading library.")
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-foreign-types-0.5
   (package
     (name "rust-foreign-types")
@@ -5606,6 +6383,31 @@ (define-public rust-fragile-0.3
 values to other threads.")
     (license license:asl2.0)))
 
+(define-public rust-freetype-0.4
+  (package
+    (name "rust-freetype")
+    (version "0.4.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "freetype" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0a70x03n68997f08bi3n47q9wyi3pv5s9v4rjc79sihb84mnp4hi"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-libc" ,rust-libc-0.2)
+        ("rust-servo-freetype-sys" ,rust-servo-freetype-sys-4))))
+    (home-page "https://github.com/servo/rust-freetype")
+    (synopsis "Bindings for Freetype used by Servo")
+    (description
+     "Bindings for Freetype used by Servo.")
+    (license (list license:asl2.0 license:expat))))
+
 (define-public rust-freetype-rs-0.23
   (package
     (name "rust-freetype-rs")
@@ -5764,6 +6566,31 @@ (define-public rust-fsevent-sys-2
 macOS API for file changes notifications")
     (license license:expat)))
 
+(define-public rust-fst-0.4
+  (package
+    (name "rust-fst")
+    (version "0.4.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "fst" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0ybmdzkknhv1wx6ws86iyixfyzc04l4nm71b9va7953r1m3i6z1z"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-utf8-ranges" ,rust-utf8-ranges-1.0))))
+    (home-page "https://github.com/BurntSushi/fst")
+    (synopsis "Represent sets or maps of large numbers of strings.")
+    (description
+     "Use finite state transducers to compactly represent sets or maps of many
+strings (> 1 billion is possible).")
+    (license (list license:unlicense license:expat))))
+
 (define-public rust-fuchsia-cprng-0.1
   (package
     (name "rust-fuchsia-cprng")
@@ -6616,7 +7443,7 @@ (define-public rust-getopts-0.2
 (define-public rust-getrandom-0.1
   (package
     (name "rust-getrandom")
-    (version "0.1.6")
+    (version "0.1.14")
     (source
      (origin
        (method url-fetch)
@@ -6625,16 +7452,19 @@ (define-public rust-getrandom-0.1
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0macrjfkgsjn6ikr94agapp4fkxmr8w7y2g7qis4icc4a17cwp76"))))
+         "1sq30li71h19rhnhs1h6576ja68insajx8wvh1nn088r8pc8vg3s"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
        #:cargo-inputs
-       (("rust-lazy-static" ,rust-lazy-static-1)
+       (("rust-cfg-if" ,rust-cfg-if-0.1)
+        ("rust-compiler-builtins" ,rust-compiler-builtins-0.1)
+        ("rust-wasm-bindgen" ,rust-wasm-bindgen-0.2)
         ("rust-libc" ,rust-libc-0.2)
         ("rust-log" ,rust-log-0.4)
         ("rust-stdweb" ,rust-stdweb-0.4)
-        ("rust-wasm-bindgen" ,rust-wasm-bindgen-0.2))))
+        ("rust-wasi" ,rust-wasi-0.9)
+        ("rust-rustc-std-workspace-core" ,rust-rustc-std-workspace-core-1.0))))
     (home-page "https://github.com/rust-random/getrandom")
     (synopsis "Retrieve random data from system source")
     (description
@@ -6642,6 +7472,109 @@ (define-public rust-getrandom-0.1
 retrieving random data from system source.")
     (license (list license:expat license:asl2.0))))
 
+(define-public rust-gfx-0.18
+  (package
+    (name "rust-gfx")
+    (version "0.18.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "gfx" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0nqmxqi3x4ni0g78g77a6aldrv8cfvzhnpqhxyd2ap4aa3wldph1"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-log" ,rust-log-0.4)
+        ("rust-mint" ,rust-mint-0.5)
+        ("rust-draw-state" ,rust-draw-state-0.8)
+        ("rust-gfx-core" ,rust-gfx-core-0.9))))
+    (home-page "https://github.com/gfx-rs/gfx")
+    (synopsis "High-performance, bindless graphics API")
+    (description
+     "This package provides a high-performance, bindless graphics API.")
+    (license license:asl2.0)))
+
+(define-public rust-gfx-core-0.9
+  (package
+    (name "rust-gfx-core")
+    (version "0.9.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "gfx_core" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0haldr99n12d90vqgvl77n59hywlklhdff85j2aljaz1yapdvyvm"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-log" ,rust-log-0.4)
+        ("rust-mint" ,rust-mint-0.5)
+        ("rust-draw-state" ,rust-draw-state-0.8)
+        ("rust-serde" ,rust-serde-1.0)
+        ("rust-bitflags" ,rust-bitflags-1))))
+    (home-page "https://github.com/gfx-rs/gfx")
+    (synopsis "Core library of Gfx-rs")
+    (description "This package is a core library of Gfx-rs.")
+    (license license:asl2.0)))
+
+(define-public rust-gfx-device-gl-0.16
+  (package
+    (name "rust-gfx-device-gl")
+    (version "0.16.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "gfx_device_gl" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1g5yg19jvxdmviljyakhd6253bnb2qg7v8iscf48ihc0ldgki70h"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-log" ,rust-log-0.4)
+        ("rust-gfx-gl" ,rust-gfx-gl-0.6)
+        ("rust-gfx-core" ,rust-gfx-core-0.9))))
+    (home-page "https://github.com/gfx-rs/gfx")
+    (synopsis "OpenGL backend for gfx-rs")
+    (description "This package provides the openGL backend for gfx-rs.")
+    (license license:asl2.0)))
+
+(define-public rust-gfx-gl-0.6
+  (package
+    (name "rust-gfx-gl")
+    (version "0.6.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "gfx_gl" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0ppzj4bgjawdqz3fvnscqk8lnmgh95pwzh0v96vwy809cxj83lzj"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-gl-generator" ,rust-gl-generator-0.14))))
+    (home-page "https://github.com/gfx-rs/gfx_gl")
+    (synopsis "OpenGL bindings for gfx, based on gl-rs")
+    (description
+     "This package provides OpenGL bindings for gfx, based on gl-rs.")
+    (license license:asl2.0)))
+
 (define-public rust-gif-0.10
   (package
     (name "rust-gif")
@@ -6669,6 +7602,37 @@ (define-public rust-gif-0.10
     (description "This package provides a GIF decoder and encoder in Rust.")
     (license (list license:expat license:asl2.0))))
 
+(define-public rust-gimli-0.20
+  (package
+    (name "rust-gimli")
+    (version "0.20.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "gimli" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0cz6wg1niwfqf0mk28igsdnsm92cs57cai9jpzdmvw6hma863pc1"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-fallible-iterator"
+         ,rust-fallible-iterator-0.2)
+        ("rust-arrayvec" ,rust-arrayvec-0.5)
+        ("rust-stable-deref-trait"
+         ,rust-stable-deref-trait-1.1)
+        ("rust-smallvec" ,rust-smallvec-1)
+        ("rust-indexmap" ,rust-indexmap-1.3)
+        ("rust-byteorder" ,rust-byteorder-1.3))))
+    (home-page "https://github.com/gimli-rs/gimli")
+    (synopsis "Library for reading and writing the DWARF debugging format")
+    (description
+     "This package provides a library for reading and writing the DWARF debugging format.")
+    (license (list license:asl2.0 license:expat))))
+
 (define-public rust-gimli-0.18
   (package
     (name "rust-gimli")
@@ -6868,6 +7832,29 @@ (define-public rust-git2-0.9
         ("rust-thread-id" ,rust-thread-id-3.3)
         ("rust-time" ,rust-time-0.1))))))
 
+(define-public rust-gl-0.11
+  (package
+    (name "rust-gl")
+    (version "0.11.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "gl" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1wcqpyhck0xriffkmgmldy33lwk2044hb4l02d44vm4fbvicin6p"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-gl-generator" ,rust-gl-generator-0.10))))
+    (home-page "https://github.com/brendanzab/gl-rs/")
+    (synopsis "OpenGL bindings for rust")
+    (description "This package provides OpenGL bindings for rust.")
+    (license license:asl2.0)))
+
 (define-public rust-gl-generator-0.14
   (package
     (name "rust-gl-generator")
@@ -6923,6 +7910,33 @@ (define-public rust-gl-generator-0.11
        (base32
         "1gdchvay0k0g931b2ki33mkfixcw4radk5b8sqsm29rahxg3v8ir"))))))
 
+(define-public rust-gl-generator-0.10
+  (package
+    (name "rust-gl-generator")
+    (version "0.10.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "gl_generator" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0146yd4i9wbgfrhnkc04w7n7civbanznc0q87skp6v7p7hbszzx0"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-log" ,rust-log-0.4)
+        ("rust-xml-rs" ,rust-xml-rs-0.8)
+        ("rust-khronos-api" ,rust-khronos-api-3))))
+    (home-page "https://github.com/brendanzab/gl-rs/")
+    (synopsis
+     "Code generators for creating bindings to the Khronos OpenGL APIs")
+    (description
+     "Code generators for creating bindings to the Khronos OpenGL APIs.")
+    (license license:asl2.0)))
+
 (define-public rust-gleam-0.6
   (package
     (name "rust-gleam")
@@ -7365,6 +8379,53 @@ (define-public rust-gobject-sys-0.9
     (description "This package provides FFI bindings to libgobject-2.0.")
     (license license:expat)))
 
+(define-public rust-goblin-0.2
+  (package
+    (name "rust-goblin")
+    (version "0.2.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "goblin" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1j38fkqadbsjxawr3wnj9m0qaihcwp6pmfakmhsar881509y7mfx"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-scroll" ,rust-scroll-0.10)
+        ("rust-plain" ,rust-plain-0.2)
+        ("rust-log" ,rust-log-0.4))))
+    (home-page "https://github.com/m4b/goblin")
+    (synopsis "ELF, Mach-o, and PE binary parsing and loading crate")
+    (description "This package provides an ELF, Mach-o, and PE binary parsing
+and loading crate.")
+    (license license:expat)))
+
+(define-public rust-goblin-0.1
+  (package
+    (inherit rust-goblin-0.2)
+    (name "rust-goblin")
+    (version "0.1.3")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "goblin" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1nn0aa2jf207gbyccxnrzm7n217di025z5y1ybblp7nkk11j309h"))))
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-scroll" ,rust-scroll-0.10)
+        ("rust-plain" ,rust-plain-0.2)
+        ("rust-log" ,rust-log-0.4))))))
+
 (define-public rust-goblin-0.0
   (package
     (name "rust-goblin")
@@ -7845,7 +8906,7 @@ (define-public rust-heck-0.3
 (define-public rust-hermit-abi-0.1
   (package
     (name "rust-hermit-abi")
-    (version "0.1.6")
+    (version "0.1.10")
     (source
       (origin
         (method url-fetch)
@@ -7854,7 +8915,7 @@ (define-public rust-hermit-abi-0.1
          (string-append name "-" version ".tar.gz"))
         (sha256
          (base32
-         "0wippj5nkw9q5yyyaqpdrgdhag3l3nbrwja7149cwn7ii1nnbwpg"))))
+          "0blmmzik5cs79ivq70s9gal8ypgzj50wnl2hwsaam46gjjbz2p3j"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
@@ -8364,6 +9425,38 @@ (define-public rust-image-0.20
         ("rust-num-complex" ,rust-num-complex-0.2)
         ("rust-quickcheck" ,rust-quickcheck-0.6))))))
 
+(define-public rust-indexmap-1.3
+  (package
+    (name "rust-indexmap")
+    (version "1.3.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "indexmap" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "14i2gmq9pwaafvlxmsc12j6539hjgqk4j4jz40fz763vbcn08vq7"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-autocfg" ,rust-autocfg-1.0)
+        ("rust-serde" ,rust-serde-1.0)
+        ("rust-rayon" ,rust-rayon-1.3))))
+    (home-page "https://github.com/bluss/indexmap")
+    (synopsis "Hash table with consistent order and fast iteration.")
+    (description
+     "This package provides a hash table with consistent order and fast iteration.
+
+The indexmap is a hash table where the iteration order of the key-value
+pairs is independent of the hash values of the keys.  It has the usual
+hash table functionality, it preserves insertion order except after
+removals, and it allows lookup of its elements by either hash table key
+or numerical index.  A corresponding hash set type is also provided.")
+    (license (list license:asl2.0 license:expat))))
+
 (define-public rust-indexmap-1.0
   (package
     (name "rust-indexmap")
@@ -8546,6 +9639,53 @@ (define-public rust-instant-0.1
 that works on WASM too.")
     (license license:bsd-3)))
 
+(define-public rust-interpolate-name-0.2
+  (package
+    (name "rust-interpolate-name")
+    (version "0.2.3")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "interpolate_name" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "05vzsiqb69d1mbpaphcg4ifjsjs6g03b8pacskfcydqhh555zcxl"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-proc-macro2" ,rust-proc-macro2-1.0)
+        ("rust-syn" ,rust-syn-1.0)
+        ("rust-quote" ,rust-quote-1.0))))
+    (home-page "https://github.com/lu-zero/interpolate_name")
+    (synopsis "Simple procedural macro attribute for repetitive tests")
+    (description
+     "Simple procedural macro attribute for repetitive tests.")
+    (license license:expat)))
+
+(define-public rust-interpolation-0.2
+  (package
+    (name "rust-interpolation")
+    (version "0.2.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "interpolation" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "00icvvgc72zdgyrwwg2p0wad4hry4d2vd6l9iqpyjpmw5dykbdyk"))))
+    (build-system cargo-build-system)
+    (arguments `(#:skip-build? #t))
+    (home-page "https://github.com/pistondevelopers/interpolation")
+    (synopsis "Library for interpolation")
+    (description
+     "This package provides a library for interpolation.")
+    (license license:expat)))
+
 (define-public rust-intervaltree-0.2
   (package
     (name "rust-intervaltree")
@@ -8620,7 +9760,7 @@ (define-public rust-iso8601-0.1
 (define-public rust-itertools-0.8
   (package
     (name "rust-itertools")
-    (version "0.8.0")
+    (version "0.8.2")
     (source
      (origin
        (method url-fetch)
@@ -8629,7 +9769,7 @@ (define-public rust-itertools-0.8
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0n2k13b6w4x2x6np2lykh9bj3b3z4hwh2r4cn3z2dgnfq7cng12v"))))
+         "1154j48aw913v5jnyhpxialxhdn2sfpl4d7bwididyb1r05jsspm"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
@@ -8637,8 +9777,8 @@ (define-public rust-itertools-0.8
        (("rust-either" ,rust-either-1.5))
        #:cargo-development-inputs
        (("rust-permutohedron" ,rust-permutohedron-0.2)
-        ("rust-quickcheck" ,rust-quickcheck-0.8)
-        ("rust-rand" ,rust-rand-0.4))))
+        ("rust-quickcheck" ,rust-quickcheck-0.7)
+        ("rust-rand" ,rust-rand-0.6))))
     (home-page
      "https://github.com/rust-itertools/itertools")
     (synopsis
@@ -8700,7 +9840,7 @@ (define-public rust-itertools-num-0.1
 (define-public rust-itoa-0.4
   (package
     (name "rust-itoa")
-    (version "0.4.4")
+    (version "0.4.5")
     (source
       (origin
         (method url-fetch)
@@ -8708,7 +9848,7 @@ (define-public rust-itoa-0.4
         (file-name (string-append name "-" version ".crate"))
         (sha256
          (base32
-          "0zvg2d9qv3avhf3d8ggglh6fdyw8kkwqg3r4622ly5yhxnvnc4jh"))))
+          "13nxqrfnh83a7x5rw4wq2ilp8nxvwy74dxzysdg59dbxqk0agdxq"))))
     (build-system cargo-build-system)
     (home-page "https://github.com/dtolnay/itoa")
     (synopsis "Fast functions for printing integer primitives")
@@ -8746,6 +9886,29 @@ (define-public rust-itoa-0.1
         (base32
          "18g7p2hrb3dk84z3frfgmszfc9hjb4ps9vp99qlb1kmf9gm8hc5f"))))))
 
+(define-public rust-ivf-0.1
+  (package
+    (name "rust-ivf")
+    (version "0.1.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "ivf" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1wfjf3rilqavrhvwagzinvng9dg28wcjk3c6c6p5qmc1xy65qfh1"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-bitstream-io" ,rust-bitstream-io-0.8))))
+    (home-page "https://github.com/xiph/rav1e")
+    (synopsis "Simple ivf muxer")
+    (description "This package provides a simple ivf muxer.")
+    (license license:bsd-2)))
+
 (define-public rust-jemalloc-sys-0.3
   (package
     (name "rust-jemalloc-sys")
@@ -8919,7 +10082,7 @@ (define-public rust-jpeg-decoder-0.1
 (define-public rust-js-sys-0.3
   (package
     (name "rust-js-sys")
-    (version "0.3.35")
+    (version "0.3.37")
     (source
      (origin
        (method url-fetch)
@@ -8928,7 +10091,7 @@ (define-public rust-js-sys-0.3
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "1ybwazllkbif71i195dadgrsw64k6l04ggk5yimiy5c2cb1wg2bq"))))
+         "0mbhpbw3zjjl51m24qx3ilq4y8xipm5sfa5hsavaabqs6wsx89va"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
@@ -9181,7 +10344,7 @@ (define-public rust-lexical-core-0.4
 (define-public rust-libc-0.2
   (package
     (name "rust-libc")
-    (version "0.2.66")
+    (version "0.2.68")
     (source
      (origin
        (method url-fetch)
@@ -9189,7 +10352,7 @@ (define-public rust-libc-0.2
        (file-name (string-append name "-" version ".crate"))
        (sha256
         (base32
-         "0n0mwry21fxfwc063k33mvxk8xj7ia5ar8m42c9ymbam2ksb25fm"))))
+         "1w6z9krcqn7p200sb80dxx76iyvw3jdz949zxr1sgfr3a50c186y"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
@@ -9462,6 +10625,30 @@ (define-public rust-line-drawing-0.7
 graphics and video games.")
     (license license:expat)))
 
+(define-public rust-line-wrap-0.1
+  (package
+    (name "rust-line-wrap")
+    (version "0.1.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "line-wrap" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1ffa2whkyh9mwvdlpk6v8pjkg8p8mlzyjfymq5adll9a18sl80zk"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-safemem" ,rust-safemem-0.3))))
+    (home-page "https://bitbucket.org/marshallpierce/line-wrap-rs/src")
+    (synopsis "Efficiently insert line separators")
+    (description
+     "Efficiently insert line separators.")
+    (license license:asl2.0)))
+
 (define-public rust-linked-hash-map-0.5
   (package
     (name "rust-linked-hash-map")
@@ -9717,7 +10904,7 @@ (define-public rust-log-0.3
   (package
     (inherit rust-log-0.4)
     (name "rust-log")
-    (version "0.3.8")
+    (version "0.3.9")
     (source
       (origin
         (method url-fetch)
@@ -9725,7 +10912,10 @@ (define-public rust-log-0.3
         (file-name (string-append name "-" version ".tar.gz"))
         (sha256
          (base32
-          "0nsn28syc49vvjhxcfc8261rd1frhjc0r4bn9v3mqvps3ra7f3w8"))))))
+          "0jq23hhn5h35k7pa8r7wqnsywji6x3wn1q5q7lif5q536if8v7p1"))))
+    (arguments
+     `(#:cargo-inputs
+       (("rust-log" ,rust-log-0.4))))))
 
 (define-public rust-loom-0.1
   (package
@@ -9780,6 +10970,58 @@ (define-public rust-lscolors-0.6
      "Colorize paths using the LS_COLORS environment variable.")
     (license (list license:expat license:asl2.0))))
 
+(define-public rust-lyon-geom-0.14
+  (package
+    (name "rust-lyon-geom")
+    (version "0.14.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "lyon_geom" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "178z4cqqmyw0rsabbgx9phkjxjzcnq0604062lqjlq87k063216a"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-num-traits" ,rust-num-traits-0.2)
+        ("rust-euclid" ,rust-euclid-0.20)
+        ("rust-arrayvec" ,rust-arrayvec-0.4)
+        ("rust-serde" ,rust-serde-1.0))))
+    (home-page "https://github.com/nical/lyon")
+    (synopsis "2D graphics rendering on the GPU using tessellation")
+    (description
+     "This package provides 2D graphics rendering on the GPU using tessellation.")
+    (license (list license:expat license:asl2.0))))
+
+(define-public rust-lyon-path-0.14
+  (package
+    (name "rust-lyon-path")
+    (version "0.14.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "lyon_path" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0qk8x46w0sf6j04l6gvhgn9kr4ymcqkmkh67w8wqahm54jn5gjqb"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-lyon-geom" ,rust-lyon-geom-0.14)
+        ("rust-serde" ,rust-serde-1.0))))
+    (home-page "https://github.com/nical/lyon")
+    (synopsis "Types and utilities to store, build and iterate over 2D paths")
+    (description
+     "Types and utilities to store, build and iterate over 2D paths.")
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-lzma-sys-0.1
   (package
     (name "rust-lzma-sys")
@@ -10082,6 +11324,30 @@ (define-public rust-md5-0.3
         (base32
          "0j2s8aqdkhwhy7awga2bmv5n8qq8bgy8672iha9f3y871dm6vibr"))))))
 
+(define-public rust-memchr-2.3
+  (package
+    (name "rust-memchr")
+    (version "2.3.3")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "memchr" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0074pvsfl938ndl5js14ibc7i9q0k3zp390z843w8nlyv4bxha1p"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-libc" ,rust-libc-0.2))))
+    (home-page "https://github.com/BurntSushi/rust-memchr")
+    (synopsis "Safe interface to memchr")
+    (description "The @code{memchr} crate provides heavily optimized routines
+for searching bytes.")
+    (license (list license:unlicense license:expat))))
+
 (define-public rust-memchr-2.2
   (package
     (name "rust-memchr")
@@ -10252,6 +11518,31 @@ (define-public rust-memoffset-0.2
          "1cvm2z7dy138s302ii7wlzcxbka5a8yfl5pl5di7lbdnw9hw578g"))))
     (arguments `(#:skip-build? #t))))
 
+(define-public rust-metadeps-1.1
+  (package
+    (name "rust-metadeps")
+    (version "1.1.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "metadeps" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1hjla9ypycqw1snd2qf87cckcc0d5z5qvxpcijn5yrrs3f825cbk"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-error-chain" ,rust-error-chain-0.10)
+        ("rust-toml" ,rust-toml-0.2)
+        ("rust-pkg-config" ,rust-pkg-config-0.3))))
+    (home-page "https://github.com/joshtriplett/metadeps")
+    (synopsis "Run pkg-config from declarative dependencies in Cargo.toml")
+    (description "Run pkg-config from declarative dependencies in Cargo.toml.")
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-metal-0.14
   (package
     (name "rust-metal")
@@ -10311,14 +11602,15 @@ (define-public rust-mime-0.3
 (define-public rust-miniz-oxide-0.3
   (package
     (name "rust-miniz-oxide")
-    (version "0.3.3")
+    (version "0.3.6")
     (source
       (origin
         (method url-fetch)
         (uri (crate-uri "miniz_oxide" version))
         (file-name (string-append name "-" version ".crate"))
         (sha256
-         (base32 "1bmanbbcdmssfbgik3fs323g7vljc5wkjz7s61jsbbz2kg0nckrh"))))
+         (base32
+          "198n4hfpq0qcxf275l6fpzh7b9cl7ck2xs6pjgpds74bazv9yrxa"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
@@ -10664,6 +11956,29 @@ (define-public rust-modifier-0.1
       "Chaining APIs for both self -> Self and &mut self methods.")
     (license license:expat)))
 
+(define-public rust-nasm-rs-0.1
+  (package
+    (name "rust-nasm-rs")
+    (version "0.1.7")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "nasm-rs" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0r34hiy1pc0aksrfc02zsl0zyw33i9yi7kyx8l214l7nm0mzm97y"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-rayon" ,rust-rayon-1.3))))
+    (home-page "https://github.com/medek/nasm-rs")
+    (synopsis "Run NASM during your Cargo build")
+    (description "Run NASM during your Cargo build.")
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-nalgebra-0.18
   (package
     (name "rust-nalgebra")
@@ -11081,6 +12396,29 @@ (define-public rust-nom-1.2
       ;; This is an ancient version and all inputs are optional.
      `(#:skip-build? #t))))
 
+(define-public rust-noop-proc-macro-0.2
+  (package
+    (name "rust-noop-proc-macro")
+    (version "0.2.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "noop_proc_macro" version))
+        (file-name
+          (string-append name "-" version ".tar.gz"))
+        (sha256
+          (base32
+            "0in1l0rjxzs4fylb6zad484z1c58jxyzchhc12k0cjrvm0y6zwsz"))))
+    (build-system cargo-build-system)
+    (arguments `(#:skip-build? #t))
+    (home-page
+      "https://github.com/lu-zero/noop_proc_macro")
+    (synopsis
+      "No-op proc_macro, literally does nothing")
+    (description
+      "No-op proc_macro, literally does nothing")
+    (license license:expat)))
+
 (define-public rust-notify-4
   (package
     (name "rust-notify")
@@ -11318,6 +12656,31 @@ (define-public rust-num-cpus-1.10
        #:cargo-development-inputs
        (("rust-doc-comment" ,rust-doc-comment-0.3))))))
 
+(define-public rust-num-derive-0.3
+  (package
+    (name "rust-num-derive")
+    (version "0.3.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "num-derive" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0imprwv8cs01k46g56ajlvc97dp8kz51y2vn6cp9jkw1c6r1b2qc"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-proc-macro2" ,rust-proc-macro2-1.0)
+        ("rust-syn" ,rust-syn-1.0)
+        ("rust-quote" ,rust-quote-1.0))))
+    (home-page "https://github.com/rust-num/num-derive")
+    (synopsis "Numeric syntax extensions")
+    (description "This package provides numeric syntax extensions.")
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-num-derive-0.2
   (package
     (name "rust-num-derive")
@@ -11671,6 +13034,37 @@ (define-public rust-objc-test-utils-0.0
      "This package provides utilities for testing Objective-C interop.")
     (license license:expat)))
 
+(define-public rust-object-0.17
+  (package
+    (name "rust-object")
+    (version "0.17.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "object" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1bmgbg4k0725lchfy9j1wnpfmywh5qhs0k4k6j2g7c0acvys8i7a"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-goblin" ,rust-goblin-0.1)
+        ("rust-target-lexicon" ,rust-target-lexicon-0.10)
+        ("rust-scroll" ,rust-scroll-0.10)
+        ("rust-parity-wasm" ,rust-parity-wasm-0.41)
+        ("rust-uuid" ,rust-uuid-0.8)
+        ("rust-flate2" ,rust-flate2-1.0)
+        ("rust-crc32fast" ,rust-crc32fast-1.2)
+        ("rust-indexmap" ,rust-indexmap-1.3))))
+    (home-page "https://github.com/gimli-rs/object")
+    (synopsis "Unified interface for reading and writing object file formats")
+    (description "This package provides a unified interface for reading and
+writing object file formats.")
+    (license (list license:asl2.0 license:expat))))
+
 (define-public rust-object-0.12
   (package
     (name "rust-object")
@@ -11735,6 +13129,67 @@ (define-public rust-odds-0.3
 Things in odds may move to more appropriate crates if we find them.")
     (license (list license:asl2.0 license:expat))))
 
+(define-public rust-onig-5.0
+  (package
+    (name "rust-onig")
+    (version "5.0.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "onig" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0ivr0wq1zlyjhhkxpsnmpncg92sjx3rha8pnp3m1mzvgk7y27rz4"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-libc" ,rust-libc-0.2)
+        ("rust-bitflags" ,rust-bitflags-1)
+        ("rust-lazy-static" ,rust-lazy-static-1)
+        ("rust-onig-sys" ,rust-onig-sys-69.2))))
+    (home-page "http://github.com/iwillspeak/rust-onig")
+    (synopsis
+     "Rust bindings for the Oniguruma regular expression library")
+    (description
+     "Rust-Onig is a set of Rust bindings for the Oniguruma regular expression
+library.  Oniguruma is a modern regex library with support for multiple
+character encodings and regex syntaxes.")
+    (license license:expat)))
+
+(define-public rust-onig-sys-69.2
+  (package
+    (name "rust-onig-sys")
+    (version "69.2.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "onig_sys" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0kjijq29yx05xxg9snvqnfn53dl52hchb4sk3zhfr77mypxlx38a"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-pkg-config" ,rust-pkg-config-0.3)
+        ("rust-bindgen" ,rust-bindgen-0.50)
+        ("rust-cc" ,rust-cc-1.0))))
+    (home-page "http://github.com/iwillspeak/rust-onig")
+    (synopsis
+     "Rust bindings to the oniguruma library.")
+    (description
+      "The @code{onig_sys} crate contains raw rust bindings to the oniguruma
+library.  This crate exposes a set of unsafe functions which can then be used by
+other crates to create safe wrappers around Oniguruma.
+You probably don't want to link to this crate directly; instead check out the
+@code{onig} crate.")
+    (license license:expat)))
+
 (define-public rust-once-cell-1.2
   (package
     (name "rust-once-cell")
@@ -11763,6 +13218,27 @@ (define-public rust-once-cell-1.2
      "Single assignment cells and lazy values.")
     (license (list license:expat license:asl2.0))))
 
+(define-public rust-oorandom-11.1
+  (package
+    (name "rust-oorandom")
+    (version "11.1.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "oorandom" version))
+        (file-name
+          (string-append name "-" version ".tar.gz"))
+        (sha256
+          (base32
+            "01clxfnz1zwg4maynvbgj09wlkj5m3c8kjqfrp3sqp59qb4wgkpb"))))
+    (build-system cargo-build-system)
+    (arguments `(#:skip-build? #t))
+    (home-page "https://hg.sr.ht/~icefox/oorandom")
+    (synopsis "A tiny, robust PRNG implementation.")
+    (description
+      "This package provides a tiny, robust PRNG implementation.")
+    (license license:expat)))
+
 (define-public rust-opaque-debug-0.2
   (package
     (name "rust-opaque-debug")
@@ -12088,6 +13564,31 @@ (define-public rust-os-pipe-0.8
      "A cross-platform library for opening OS pipes.")
     (license license:expat)))
 
+(define-public rust-output-vt100-0.1
+  (package
+    (name "rust-output-vt100")
+    (version "0.1.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "output_vt100" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1ygqplpxz4gg3i8f3rkan2q69pqll7gv65l2mmd8r9dphnvwbkak"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-winapi" ,rust-winapi-0.3))))
+    (home-page "https://github.com/Phundrak/output-vt100-rs")
+    (synopsis
+     "Utility to activate escape codes in Windows' CMD and PowerShell")
+    (description
+     "Utility to activate escape codes in Windows' CMD and PowerShell.")
+    (license license:expat)))
+
 (define-public rust-osmesa-sys-0.1
   (package
     (name "rust-osmesa-sys")
@@ -12187,6 +13688,61 @@ (define-public rust-pad-0.1
       "This package provides a library for padding strings at runtime.")
     (license license:expat)))
 
+(define-public rust-palette-0.5
+  (package
+    (name "rust-palette")
+    (version "0.5.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "palette" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0nfc4ycdsx2qgf2wkcpxqxc0vmx7188jjjx3ppgs8qlf8qs06p50"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-num-traits" ,rust-num-traits-0.2)
+        ("rust-approx" ,rust-approx-0.3)
+        ("rust-palette-derive" ,rust-palette-derive-0.5)
+        ("rust-phf" ,rust-phf-0.8)
+        ("rust-phf-codegen" ,rust-phf-codegen-0.8)
+        ("rust-serde" ,rust-serde-1.0))))
+    (home-page "https://github.com/Ogeon/palette")
+    (synopsis "Linear color calculations and conversion")
+    (description
+     "This package makes linear color calculations and conversion accessible.")
+    (license (list license:expat license:asl2.0))))
+
+(define-public rust-palette-derive-0.5
+  (package
+    (name "rust-palette-derive")
+    (version "0.5.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "palette_derive" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1x5icddb877923rpl27bg4cjsf1x0d3layxmgwa3mpb01rh5yjqb"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-proc-macro2" ,rust-proc-macro2-1.0)
+        ("rust-syn" ,rust-syn-1.0)
+        ("rust-quote" ,rust-quote-1.0))))
+    (home-page "https://github.com/Ogeon/palette")
+    (synopsis "Automatically implement traits from the palette crate")
+    (description
+     "Automatically implement traits from the palette crate.")
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-pango-0.7
   (package
     (name "rust-pango")
@@ -12320,18 +13876,40 @@ (define-public rust-pangocairo-sys-0.10
     (description "This package provides FFI bindings to libgtk-3.")
     (license license:expat)))
 
-(define-public rust-parity-wasm-0.40
+(define-public rust-parity-wasm-0.41
   (package
     (name "rust-parity-wasm")
-    (version "0.40.3")
+    (version "0.41.0")
     (source
       (origin
         (method url-fetch)
         (uri (crate-uri "parity-wasm" version))
-        (file-name (string-append name "-" version ".crate"))
+        (file-name
+          (string-append name "-" version ".tar.gz"))
         (sha256
-         (base32
-          "03qycy21avz4970zc7aj8rj5h4wvi4qsrc90a6hpws1a56mglf8y"))))
+          (base32
+            "0rfqgjyxrxrfjq5r5n81mdklahl8g4az6yhyyvw25nh0mj6qgz6x"))))
+    (build-system cargo-build-system)
+    (arguments `(#:skip-build? #t))
+    (home-page
+      "https://github.com/paritytech/parity-wasm")
+    (synopsis "WebAssembly low-level format library")
+    (description
+      "WebAssembly low-level format library")
+    (license (list license:expat license:asl2.0))))
+
+(define-public rust-parity-wasm-0.40
+  (package
+    (name "rust-parity-wasm")
+    (version "0.40.3")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "parity-wasm" version))
+        (file-name (string-append name "-" version ".crate"))
+        (sha256
+         (base32
+          "03qycy21avz4970zc7aj8rj5h4wvi4qsrc90a6hpws1a56mglf8y"))))
     (build-system cargo-build-system)
     (arguments
      `(#:tests? #f
@@ -12573,7 +14151,7 @@ (define-public rust-partial-io-0.2
 (define-public rust-paste-0.1
   (package
     (name "rust-paste")
-    (version "0.1.7")
+    (version "0.1.10")
     (source
      (origin
        (method url-fetch)
@@ -12582,12 +14160,15 @@ (define-public rust-paste-0.1
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0in0dqar8s16w6gbwyzwvckm80ala02pq87innx1w6yp73kszqb3"))))
+         "0yk4zbi7128dcrklsbwfa63d39x0dv8f7pdbrylvdlcj0s9v2kxb"))))
     (build-system cargo-build-system)
     (arguments
      `(#:cargo-inputs
        (("rust-paste-impl" ,rust-paste-impl-0.1)
-        ("rust-proc-macro-hack" ,rust-proc-macro-hack-0.5))))
+        ("rust-proc-macro-hack" ,rust-proc-macro-hack-0.5))
+       #:cargo-development-inputs
+       (("rust-rustversion" ,rust-rustversion-1.0)
+        ("rust-trybuild" ,rust-trybuild-1.0))))
     (home-page "https://github.com/dtolnay/paste")
     (synopsis "Macros for all your token pasting needs")
     (description
@@ -12597,7 +14178,7 @@ (define-public rust-paste-0.1
 (define-public rust-paste-impl-0.1
   (package
     (name "rust-paste-impl")
-    (version "0.1.7")
+    (version "0.1.10")
     (source
      (origin
        (method url-fetch)
@@ -12606,7 +14187,7 @@ (define-public rust-paste-impl-0.1
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "1fwj11j5lhya5fjr4gfljxfm74ahlr09c8xbb8f22hzpyskw8kbd"))))
+         "12jsm83dnsqnrcabfacnwcxh3h4kykl622vi7glv2wg527hqc956"))))
     (build-system cargo-build-system)
     (arguments
      `(#:cargo-inputs
@@ -12895,6 +14476,32 @@ (define-public rust-petgraph-0.4
 algorithms.")
     (license (list license:expat license:asl2.0))))
 
+(define-public rust-phf-0.8
+  (package
+    (name "rust-phf")
+    (version "0.8.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "phf" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "04pyv8bzqvw69rd5dynd5nb85py1hf7wa4ixyhrvdz1l5qin3yrx"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-proc-macro-hack" ,rust-proc-macro-hack-0.5)
+        ("rust-phf-shared" ,rust-phf-shared-0.8)
+        ("rust-phf-macros" ,rust-phf-macros-0.8))))
+    (home-page "https://github.com/sfackler/rust-phf")
+    (synopsis "Runtime support for perfect hash function data structures")
+    (description "This package provides runtime support for perfect hash
+function data structures.")
+    (license license:expat)))
+
 (define-public rust-phf-0.7
   (package
     (name "rust-phf")
@@ -12920,6 +14527,30 @@ (define-public rust-phf-0.7
      "Runtime support for perfect hash function data structures.")
     (license license:expat)))
 
+(define-public rust-phf-codegen-0.8
+  (package
+    (name "rust-phf-codegen")
+    (version "0.8.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "phf_codegen" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "05d8w7aqqjb6039pfm6404gk5dlwrrf97kiy1n21212vb1hyxzyb"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-phf-generator" ,rust-phf-generator-0.8)
+        ("rust-phf-shared" ,rust-phf-shared-0.8))))
+    (home-page "https://github.com/sfackler/rust-phf")
+    (synopsis "Codegen library for PHF types")
+    (description "Codegen library for PHF types.")
+    (license license:expat)))
+
 (define-public rust-phf-codegen-0.7
   (package
     (name "rust-phf-codegen")
@@ -12944,6 +14575,31 @@ (define-public rust-phf-codegen-0.7
     (description "Codegen library for PHF types.")
     (license license:expat)))
 
+(define-public rust-phf-generator-0.8
+  (package
+    (name "rust-phf-generator")
+    (version "0.8.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "phf_generator" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "09i5338d1kixq6a60fcayz6awgxjlxcfw9ic5f02abbgr067ydhp"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-criterion" ,rust-criterion-0.3)
+        ("rust-rand" ,rust-rand-0.7)
+        ("rust-phf-shared" ,rust-phf-shared-0.8))))
+    (home-page "https://github.com/sfackler/rust-phf")
+    (synopsis "PHF generation logic")
+    (description "PHF generation logic.")
+    (license license:expat)))
+
 (define-public rust-phf-generator-0.7
   (package
     (name "rust-phf-generator")
@@ -12967,6 +14623,35 @@ (define-public rust-phf-generator-0.7
     (description "PHF generation logic")
     (license license:expat)))
 
+(define-public rust-phf-macros-0.8
+  (package
+    (name "rust-phf-macros")
+    (version "0.8.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "phf_macros" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "170qm6yqn6b9mjlwb2xmm3iad9d5nzwgfawfwy7zr7s2zwcdwvvz"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-proc-macro-hack" ,rust-proc-macro-hack-0.5)
+        ("rust-phf-generator" ,rust-phf-generator-0.8)
+        ("rust-phf-shared" ,rust-phf-shared-0.8)
+        ("rust-proc-macro2" ,rust-proc-macro2-1.0)
+        ("rust-syn" ,rust-syn-1.0)
+        ("rust-quote" ,rust-quote-1.0))))
+    (home-page "https://github.com/sfackler/rust-phf")
+    (synopsis "Macros to generate types in the phf crate")
+    (description
+     "This package contains macros to generate types in the phf crate.")
+    (license license:expat)))
+
 (define-public rust-phf-macros-0.7
   (package
     (name "rust-phf-macros")
@@ -12999,68 +14684,455 @@ (define-public rust-phf-macros-0.7
      "Macros to generate types in the phf crate.")
     (license license:expat)))
 
+(define-public rust-phf-shared-0.8
+  (package
+    (name "rust-phf-shared")
+    (version "0.8.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "phf_shared" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1xssnqrrcn0nr9ayqrnm8xm37ac4xvwcx8pax7jxss7yxawzh360"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-siphasher" ,rust-siphasher-0.3)
+        ("rust-unicase" ,rust-unicase-2.6))))
+    (home-page "https://github.com/sfackler/rust-phf")
+    (synopsis "Support code shared by PHF libraries")
+    (description
+     "This package provides support code shared by PHF libraries.")
+    (license license:expat)))
+
 (define-public rust-phf-shared-0.7
   (package
     (name "rust-phf-shared")
     (version "0.7.24")
     (source
-     (origin
-       (method url-fetch)
-       (uri (crate-uri "phf-shared" version))
-       (file-name
-        (string-append name "-" version ".tar.gz"))
-       (sha256
-        (base32
-         "18371fla0vsj7d6d5rlfb747xbr2in11ar9vgv5qna72bnhp2kr3"))))
+     (origin
+       (method url-fetch)
+       (uri (crate-uri "phf-shared" version))
+       (file-name
+        (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "18371fla0vsj7d6d5rlfb747xbr2in11ar9vgv5qna72bnhp2kr3"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-siphasher" ,rust-siphasher-0.2)
+        ("rust-unicase" ,rust-unicase-1))))
+    (home-page "https://github.com/sfackler/rust-phf")
+    (synopsis "Support code shared by PHF libraries")
+    (description
+     "Support code shared by PHF libraries.")
+    (license license:expat)))
+
+(define-public rust-pico-sys-0.0
+  (package
+    (name "rust-pico-sys")
+    (version "0.0.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "pico-sys" version))
+        (file-name (string-append name "-" version ".crate"))
+        (sha256
+         (base32
+          "1q5pg0ms6szz6b5h26h4k40zb76zbwwjgyigac4wly9qngdj4yl5"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/reem/rust-pico-sys")
+    (synopsis "Bindings to the PicoHTTPParser")
+    (description
+     "This package provides bindings to the PicoHTTPParser.")
+    (properties '((hidden? . #t)))
+    (license license:expat)))
+
+(define-public rust-pin-utils-0.1
+  (package
+    (name "rust-pin-utils")
+    (version "0.1.0-alpha.4")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "pin-utils" version))
+        (file-name (string-append name "-" version ".crate"))
+        (sha256
+         (base32
+          "11xmyx00n4m37d546by2rxb8ryxs12v55cc172i3yak1rqccd52q"))))
+    (build-system cargo-build-system)
+    (home-page "https://github.com/rust-lang-nursery/pin-utils")
+    (synopsis "Utilities for pinning")
+    (description "This crate provides utilities for pinning values on the stack.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public rust-piston-0.49
+  (package
+    (name "rust-piston")
+    (version "0.49.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "piston" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1y0rbw92mzagqmwk79wv9axq0m7aid0s0d5cppyzh33wrxhdl3xj"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-pistoncore-input" ,rust-pistoncore-input-0.28)
+        ("rust-pistoncore-window" ,rust-pistoncore-window-0.44)
+        ("rust-pistoncore-event-loop" ,rust-pistoncore-event-loop-0.49))))
+    (home-page "https://github.com/PistonDevelopers/piston")
+    (synopsis "Piston game engine core libraries")
+    (description
+     "The Piston game engine core libraries.")
+    (license license:expat)))
+
+(define-public rust-piston-float-1.0
+  (package
+    (name "rust-piston-float")
+    (version "1.0.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "piston-float" version))
+        (file-name
+          (string-append name "-" version ".tar.gz"))
+        (sha256
+          (base32
+            "0r35aasycms79hf2vf1ap40kkp8ywgl4hmfkf762dq8jwd3vw07r"))))
+    (build-system cargo-build-system)
+    (arguments `(#:skip-build? #t))
+    (home-page
+      "https://github.com/pistondevelopers/float")
+    (synopsis
+      "Traits for generic floats in game development")
+    (description
+      "Traits for generic floats in game development")
+    (license license:expat)))
+
+(define-public rust-piston-gfx-texture-0.40
+  (package
+    (name "rust-piston-gfx-texture")
+    (version "0.40.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "piston-gfx_texture" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1nr5awdgk3njfvfanszrv4gxz93f6skid1c8yijswccygripchqz"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-gfx" ,rust-gfx-0.18)
+        ("rust-image" ,rust-image-0.22)
+        ("rust-piston-texture" ,rust-piston-texture-0.8)
+        ("rust-gfx-core" ,rust-gfx-core-0.9))))
+    (home-page "https://github.com/pistondevelopers/gfx_texture")
+    (synopsis
+      "Gfx texture representation that works nicely with Piston libraries")
+    (description "This package provides a Gfx texture representation that works
+nicely with Piston libraries.")
+    (license license:expat)))
+
+(define-public rust-piston-graphics-api-version-0.2
+  (package
+    (name "rust-piston-graphics-api-version")
+    (version "0.2.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "piston-graphics_api_version" version))
+        (file-name
+          (string-append name "-" version ".tar.gz"))
+        (sha256
+          (base32
+            "1b5p6s45jqv057lpbxkiq3yrdjjhvcynmi2vjf8292rf0yh4hky5"))))
+    (build-system cargo-build-system)
+    (arguments `(#:skip-build? #t))
+    (home-page
+      "https://github.com/PistonDevelopers/graphics_api_version")
+    (synopsis
+      "A library for storing graphics API versions")
+    (description
+      "This package provides a library for storing graphics API versions")
+    (license license:expat)))
+
+(define-public rust-piston-shaders-graphics2d-0.3
+  (package
+    (name "rust-piston-shaders-graphics2d")
+    (version "0.3.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "piston-shaders_graphics2d" version))
+        (file-name
+          (string-append name "-" version ".tar.gz"))
+        (sha256
+          (base32
+            "1dhh9bv4q19gdnj9d1nqq0yrvzs6gcn0c5j1p1f3xzyzq7d1gg4p"))))
+    (build-system cargo-build-system)
+    (arguments `(#:skip-build? #t))
+    (home-page
+      "https://github.com/PistonDevelopers/shaders")
+    (synopsis "Shaders for 2D graphics in Rust")
+    (description "Shaders for 2D graphics in Rust")
+    (license license:expat)))
+
+(define-public rust-piston-texture-0.8
+  (package
+    (name "rust-piston-texture")
+    (version "0.8.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "piston-texture" version))
+        (file-name
+          (string-append name "-" version ".tar.gz"))
+        (sha256
+          (base32
+            "1pcv5my49b8xzqcb87wqh2ndgvr4s9ipys96s0h9j2plxrj3bjb2"))))
+    (build-system cargo-build-system)
+    (arguments `(#:skip-build? #t))
+    (home-page
+      "https://github.com/pistondevelopers/texture")
+    (synopsis "A generic library for textures")
+    (description
+      "This package provides a generic library for textures")
+    (license license:expat)))
+
+(define-public rust-piston-viewport-1.0
+  (package
+    (name "rust-piston-viewport")
+    (version "1.0.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "piston-viewport" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "16378hcy41b7x3zj2z4har0wq6fl4r62kf9p106jjl8hg2dv3aq1"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-piston-float" ,rust-piston-float-1.0))))
+    (home-page "https://github.com/PistonDevelopers/viewport")
+    (synopsis "Library for storing viewport information")
+    (description
+     "This package provides a library for storing viewport information.")
+    (license license:expat)))
+
+(define-public rust-piston-window-0.105
+  (package
+    (name "rust-piston-window")
+    (version "0.105.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "piston_window" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "05n2905gkp5ck25kbq95ia6pj1xz63dpp247jz3xcw1d41xpvi95"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-gfx-device-gl" ,rust-gfx-device-gl-0.16)
+        ("rust-gfx" ,rust-gfx-0.18)
+        ("rust-piston2d-graphics" ,rust-piston2d-graphics-0.35)
+        ("rust-piston" ,rust-piston-0.49)
+        ("rust-shader-version" ,rust-shader-version-0.6)
+        ("rust-pistoncore-glutin-window" ,rust-pistoncore-glutin-window-0.63)
+        ("rust-piston2d-gfx-graphics" ,rust-piston2d-gfx-graphics-0.66)
+        ("rust-piston-texture" ,rust-piston-texture-0.8))))
+    (home-page "https://github.com/pistondevelopers/piston_window")
+    (synopsis "Official Piston window wrapper for the Piston game engine")
+    (description
+     "The official Piston window wrapper for the Piston game engine.")
+    (license license:expat)))
+
+(define-public rust-piston2d-gfx-graphics-0.66
+  (package
+    (name "rust-piston2d-gfx-graphics")
+    (version "0.66.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "piston2d-gfx_graphics" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1pmlkf5rl6pr0c1lqm0059xwj9pwlws7gaq9w6r9d916di6fzki1"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-gfx" ,rust-gfx-0.18)
+        ("rust-piston-shaders-graphics2d" ,rust-piston-shaders-graphics2d-0.3)
+        ("rust-piston-gfx-texture" ,rust-piston-gfx-texture-0.40)
+        ("rust-shader-version" ,rust-shader-version-0.6)
+        ("rust-draw-state" ,rust-draw-state-0.8))))
+    (home-page "https://github.com/PistonDevelopers/gfx_graphics")
+    (synopsis "Gfx 2D back-end for the Piston game engine")
+    (description
+     "This package provides a Gfx 2D back-end for the Piston game engine.")
+    (license license:expat)))
+
+(define-public rust-piston2d-graphics-0.35
+  (package
+    (name "rust-piston2d-graphics")
+    (version "0.35.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "piston2d-graphics" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1dx2fanxc2pj76hc5l72x0fh4qg9gchjlr8rmbhdk6jpggcmq56g"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-interpolation" ,rust-interpolation-0.2)
+        ("rust-rusttype" ,rust-rusttype-0.7)
+        ("rust-piston-texture" ,rust-piston-texture-0.8)
+        ("rust-piston-viewport" ,rust-piston-viewport-1.0)
+        ("rust-read-color" ,rust-read-color-1.0)
+        ("rust-vecmath" ,rust-vecmath-1.0)
+        ("rust-fnv" ,rust-fnv-1.0))))
+    (home-page "https://github.com/pistondevelopers/graphics")
+    (synopsis "Library for 2D graphics that works with multiple back-ends")
+    (description "This package provides a library for 2D graphics that works
+with multiple back-ends.")
+    (license license:expat)))
+
+(define-public rust-pistoncore-event-loop-0.49
+  (package
+    (name "rust-pistoncore-event-loop")
+    (version "0.49.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "pistoncore-event_loop" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1h9ij9vx42xg39198yxdlpk842pli5jqm2kwswiv3bqqcji0fwsm"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-pistoncore-input" ,rust-pistoncore-input-0.28)
+        ("rust-pistoncore-window" ,rust-pistoncore-window-0.44))))
+    (home-page "https://github.com/PistonDevelopers/piston")
+    (synopsis "Piston event loop for games and interactive applications")
+    (description "This package provides a Piston event loop for games and
+interactive applications.")
+    (license license:expat)))
+
+(define-public rust-pistoncore-glutin-window-0.63
+  (package
+    (name "rust-pistoncore-glutin-window")
+    (version "0.63.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "pistoncore-glutin_window" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0dhbyxarv5i742d400bmqdqq3f8c25kcgcg0xavrc18dc913rixc"))))
     (build-system cargo-build-system)
     (arguments
-     `(#:cargo-inputs
-       (("rust-siphasher" ,rust-siphasher-0.2)
-        ("rust-unicase" ,rust-unicase-1))))
-    (home-page "https://github.com/sfackler/rust-phf")
-    (synopsis "Support code shared by PHF libraries")
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-gl" ,rust-gl-0.11)
+        ("rust-glutin" ,rust-glutin-0.21)
+        ("rust-pistoncore-input" ,rust-pistoncore-input-0.28)
+        ("rust-pistoncore-window" ,rust-pistoncore-window-0.44)
+        ("rust-shader-version" ,rust-shader-version-0.6))))
+    (home-page "https://github.com/pistondevelopers/glutin_window")
+    (synopsis "Piston window back-end using the Glutin library")
     (description
-     "Support code shared by PHF libraries.")
+     "This package provides a Piston window back-end using the Glutin library.")
     (license license:expat)))
 
-(define-public rust-pico-sys-0.0
+(define-public rust-pistoncore-input-0.28
   (package
-    (name "rust-pico-sys")
-    (version "0.0.1")
+    (name "rust-pistoncore-input")
+    (version "0.28.0")
     (source
       (origin
         (method url-fetch)
-        (uri (crate-uri "pico-sys" version))
-        (file-name (string-append name "-" version ".crate"))
+        (uri (crate-uri "pistoncore-input" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
         (sha256
          (base32
-          "1q5pg0ms6szz6b5h26h4k40zb76zbwwjgyigac4wly9qngdj4yl5"))))
+          "1rrcz9px098m3nx98gvrvzirfdp3vg03cblfkcrp4wnvswc0hwq5"))))
     (build-system cargo-build-system)
-    (home-page "https://github.com/reem/rust-pico-sys")
-    (synopsis "Bindings to the PicoHTTPParser")
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-piston-viewport" ,rust-piston-viewport-1.0)
+        ("rust-serde" ,rust-serde-1.0)
+        ("rust-serde-derive" ,rust-serde-derive-1.0)
+        ("rust-bitflags" ,rust-bitflags-1))))
+    (home-page "https://github.com/PistonDevelopers/piston")
+    (synopsis "Structure for user input")
     (description
-     "This package provides bindings to the PicoHTTPParser.")
-    (properties '((hidden? . #t)))
+     "This package provides a structure for user input.")
     (license license:expat)))
 
-(define-public rust-pin-utils-0.1
+(define-public rust-pistoncore-window-0.44
   (package
-    (name "rust-pin-utils")
-    (version "0.1.0-alpha.4")
+    (name "rust-pistoncore-window")
+    (version "0.44.0")
     (source
       (origin
         (method url-fetch)
-        (uri (crate-uri "pin-utils" version))
-        (file-name (string-append name "-" version ".crate"))
+        (uri (crate-uri "pistoncore-window" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
         (sha256
          (base32
-          "11xmyx00n4m37d546by2rxb8ryxs12v55cc172i3yak1rqccd52q"))))
+          "18qy3nnpb9jczvkiyzzznamck0pzgiyi6073jrkldnci6b3in10q"))))
     (build-system cargo-build-system)
-    (home-page "https://github.com/rust-lang-nursery/pin-utils")
-    (synopsis "Utilities for pinning")
-    (description "This crate provides utilities for pinning values on the stack.")
-    (license (list license:asl2.0
-                   license:expat))))
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-piston-graphics-api-version"
+         ,rust-piston-graphics-api-version-0.2)
+        ("rust-pistoncore-input" ,rust-pistoncore-input-0.28))))
+    (home-page "https://github.com/PistonDevelopers/piston")
+    (synopsis "Library for window abstraction")
+    (description
+     "This package provides a library for window abstraction.")
+    (license license:expat)))
 
 (define-public rust-pkg-config-0.3
   (package
@@ -13108,6 +15180,72 @@ (define-public rust-plain-0.2
     (license (list license:asl2.0
                    license:expat))))
 
+(define-public rust-plist-0.4
+  (package
+    (name "rust-plist")
+    (version "0.4.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "plist" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0zqnxc5i4y6mj119vr0lzpb5j67vffpx2phhgh711533bw3ryajz"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-line-wrap" ,rust-line-wrap-0.1)
+        ("rust-base64" ,rust-base64-0.10)
+        ("rust-xml-rs" ,rust-xml-rs-0.8)
+        ("rust-serde" ,rust-serde-1.0)
+        ("rust-humantime" ,rust-humantime-1.3)
+        ("rust-byteorder" ,rust-byteorder-1.3))))
+    (home-page "https://github.com/ebarnard/rust-plist/")
+    (synopsis "Rusty plist parser")
+    (description
+     "This package provides a rusty plist parser.  Supports Serde serialization.")
+    (license license:expat)))
+
+(define-public rust-plotters-0.2
+  (package
+    (name "rust-plotters")
+    (version "0.2.12")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "plotters" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1ssycy9an23vs9hq098c7kl1dvp5ych20d994lhsw9vx4kdbhfsf"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-gif" ,rust-gif-0.10)
+        ("rust-piston-window" ,rust-piston-window-0.105)
+        ("rust-num-traits" ,rust-num-traits-0.2)
+        ("rust-wasm-bindgen" ,rust-wasm-bindgen-0.2)
+        ("rust-image" ,rust-image-0.22)
+        ("rust-js-sys" ,rust-js-sys-0.3)
+        ("rust-web-sys" ,rust-web-sys-0.3)
+        ("rust-font-kit" ,rust-font-kit-0.4)
+        ("rust-chrono" ,rust-chrono-0.4)
+        ("rust-palette" ,rust-palette-0.5)
+        ("rust-cairo-rs" ,rust-cairo-rs-0.7)
+        ("rust-rusttype" ,rust-rusttype-0.8)
+        ("rust-lazy-static" ,rust-lazy-static-1))))
+    (home-page "https://github.com/38/plotters")
+    (synopsis "Rust drawing library focus on data plotting")
+    (description
+     "This package provides a Rust drawing library focus on data plotting for
+both WASM and native applications")
+    (license license:expat)))
+
 (define-public rust-plugin-0.2
   (package
     (name "rust-plugin")
@@ -13332,11 +15470,119 @@ (define-public rust-precomputed-hash-0.1
 dependency to expose a precomputed hash.")
     (license license:expat)))
 
-;; Cyclic dependencies with rust-demo-hack.
+(define-public rust-pretty-assertions-0.6
+  (package
+    (name "rust-pretty-assertions")
+    (version "0.6.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "pretty_assertions" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "09yl14gnmpygiqrdlsa64lcl4w6ydjl9m8jri6kgam0v9rjf309z"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-ctor" ,rust-ctor-0.1)
+        ("rust-output-vt100" ,rust-output-vt100-0.1)
+        ("rust-ansi-term" ,rust-ansi-term-0.11)
+        ("rust-difference" ,rust-difference-2.0))))
+    (home-page "https://github.com/colin-kiegel/rust-pretty-assertions")
+    (synopsis "Drop-in replacements for assert_eq! and assert_ne!")
+    (description
+     "Overwrite @code{assert_eq!} and @code{assert_ne!} with drop-in
+replacements, adding colorful diffs.")
+    (license (list license:expat license:asl2.0))))
+
+(define-public rust-pretty-env-logger-0.3
+  (package
+    (name "rust-pretty-env-logger")
+    (version "0.3.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "pretty_env_logger" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0x4hyjlnvvhyk9m74iypzybm22w3dl2k8img4b956239n5vf8zki"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-log" ,rust-log-0.4)
+        ("rust-chrono" ,rust-chrono-0.4)
+        ("rust-env-logger" ,rust-env-logger-0.6))))
+    (home-page "https://github.com/seanmonstar/pretty-env-logger")
+    (synopsis "Visually pretty env_logger")
+    (description "This package provides a visually pretty env_logger.")
+    (license (list license:expat license:asl2.0))))
+
+(define-public rust-proc-macro-error-0.4
+  (package
+    (name "rust-proc-macro-error")
+    (version "0.4.12")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "proc-macro-error" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1rvpaadwv7vmsp142qqh2axqrr9v78f1nvdsi9nhmfhy10kk1wqq"))))
+    (build-system cargo-build-system)
+    (arguments
+      `(#:skip-build? #t
+        #:cargo-inputs
+        (("rust-proc-macro-error-attr" ,rust-proc-macro-error-attr-0.4)
+         ("rust-version-check" ,rust-version-check-0.9)
+         ("rust-proc-macro2" ,rust-proc-macro2-1.0)
+         ("rust-syn" ,rust-syn-1.0)
+         ("rust-quote" ,rust-quote-1.0))))
+    (home-page "https://gitlab.com/CreepySkeleton/proc-macro-error")
+    (synopsis "Almost drop-in replacement to panics in proc-macros")
+    (description
+     "Almost drop-in replacement to panics in proc-macros.")
+    (license (list license:expat license:asl2.0))))
+
+(define-public rust-proc-macro-error-attr-0.4
+  (package
+    (name "rust-proc-macro-error-attr")
+    (version "0.4.12")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "proc-macro-error-attr" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1pk9mwcfnpf8favgc2cl4sqlmi818p96hg8pfb51wg5nzmvlnnwa"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-syn-mid" ,rust-syn-mid-0.5)
+        ("rust-version-check" ,rust-version-check-0.9)
+        ("rust-proc-macro2" ,rust-proc-macro2-1.0)
+        ("rust-syn" ,rust-syn-1.0)
+        ("rust-quote" ,rust-quote-1.0))))
+    (home-page "https://gitlab.com/CreepySkeleton/proc-macro-error")
+    (synopsis "Attribute macro for proc-macro-error crate")
+    (description
+     "Attribute macro for proc-macro-error crate.")
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-proc-macro-hack-0.5
   (package
     (name "rust-proc-macro-hack")
-    (version "0.5.11")
+    (version "0.5.15")
     (source
      (origin
        (method url-fetch)
@@ -13345,15 +15591,15 @@ (define-public rust-proc-macro-hack-0.5
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "1idz5vmnjjhvr51yvwyjb45mza18wa53fr05m1skqvbdyw15gm7c"))))
+         "0qqbfm1byabjkph56r2rlvv4cliz4960j6hav3ljazyjqvkryr8d"))))
     (build-system cargo-build-system)
     (arguments
-     `(#:cargo-inputs
-       (("rust-proc-macro2" ,rust-proc-macro2-1.0)
-        ("rust-quote" ,rust-quote-1.0)
-        ("rust-syn" ,rust-syn-1.0))
-       #:cargo-development-inputs
-       (("rust-demo-hack" ,rust-demo-hack-0.0)
+     `(#:cargo-development-inputs
+       (("rust-quote" ,rust-quote-1.0)
+        ("rust-rustversion" ,rust-rustversion-1.0)
+        ("rust-syn" ,rust-syn-1.0)
+        ("rust-trybuild" ,rust-trybuild-1.0)
+        ("rust-demo-hack" ,rust-demo-hack-0.0)
         ("rust-demo-hack-impl" ,rust-demo-hack-impl-0.0))))
     (home-page "https://github.com/dtolnay/proc-macro-hack")
     (synopsis
@@ -13429,7 +15675,7 @@ (define-public rust-proc-macro-nested-0.1
 (define-public rust-proc-macro2-1.0
   (package
     (name "rust-proc-macro2")
-    (version "1.0.8")
+    (version "1.0.10")
     (source
       (origin
         (method url-fetch)
@@ -13437,7 +15683,7 @@ (define-public rust-proc-macro2-1.0
         (file-name (string-append name "-" version ".crate"))
         (sha256
          (base32
-          "0j45p176fnw0d02dzcky9sxyr4fadiggq07skmblwspqdxy33jrs"))))
+          "1qxbnl8i3a5b2nxb8kdxbq6kj3pd1ckhm35wm7z3jd7n5wlns96z"))))
     (build-system cargo-build-system)
     (arguments
      `(#:cargo-inputs
@@ -13465,11 +15711,39 @@ (define-public rust-proc-macro2-0.4
          (base32
           "0nd71fl24sys066jrha6j7i34nfkjv44yzw8yww9742wmc8j0gfg"))))
     (arguments
-     `(#:cargo-inputs
+     `(#:tests? #f      ; doc tests fail
+       #:cargo-inputs
        (("rust-unicode-xid" ,rust-unicode-xid-0.1))
        #:cargo-development-inputs
        (("rust-quote" ,rust-quote-0.6))))))
 
+(define-public rust-proc-macro2-0.3
+  (package
+    (name "rust-proc-macro2")
+    (version "0.3.8")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "proc-macro2" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1ryaynnaj39l4zphcg5w8wszndd80vsrv89m5d2293gl6pry41hv"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-unicode-xid" ,rust-unicode-xid-0.1))))
+    (home-page "https://github.com/alexcrichton/proc-macro2")
+    (synopsis
+     "Substitute implementation of the compiler's `proc_macro` API")
+    (description
+     "This package provides a substitute implementation of the compiler's
+@code{proc_macro} API to decouple token-based libraries from the procedural
+macro use case.")
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-procedural-masquerade-0.1
   (package
     (name "rust-procedural-masquerade")
@@ -13617,6 +15891,31 @@ (define-public rust-pulldown-cmark-0.4
      "This package provides a pull parser for CommonMark.")
     (license license:expat)))
 
+(define-public rust-pulldown-cmark-0.2
+  (package
+    (name "rust-pulldown-cmark")
+    (version "0.2.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "pulldown-cmark" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "05gfnqa0wzix5m17jrmgj0yyr9sflqm0knn79ndppsnhcan2zxgf"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-getopts" ,rust-getopts-0.2)
+        ("rust-bitflags" ,rust-bitflags-1))))
+    (home-page "https://github.com/raphlinus/pulldown-cmark")
+    (synopsis "Pull parser for CommonMark")
+    (description
+     "This package provides a pull parser for CommonMark.")
+    (license license:expat)))
+
 (define-public rust-quantiles-0.7
   (package
     (name "rust-quantiles")
@@ -13916,7 +16215,7 @@ (define-public rust-quickcheck-macros-0.8
 (define-public rust-quote-1.0
   (package
     (name "rust-quote")
-    (version "1.0.2")
+    (version "1.0.3")
     (source
       (origin
         (method url-fetch)
@@ -13924,13 +16223,13 @@ (define-public rust-quote-1.0
         (file-name (string-append name "-" version ".crate"))
         (sha256
          (base32
-          "1zkc46ryacf2jdkc6krsy2z615xbk1x8kp1830rcxz3irj5qqfh5"))))
+          "0zwd6fp74xfg4jnnnwj4v84lkzif2giwj4ch1hka9g35ghc6rp1b"))))
     (build-system cargo-build-system)
     (arguments
      `(#:cargo-inputs
        (("rust-proc-macro2" ,rust-proc-macro2-1.0))
        #:cargo-development-inputs
-       (("rust-rustversion" ,rust-rustversion-0.1)
+       (("rust-rustversion" ,rust-rustversion-1.0)
         ("rust-trybuild" ,rust-trybuild-1.0))))
     (home-page "https://github.com/dtolnay/quote")
     (synopsis "Quasi-quoting macro quote!(...)")
@@ -13953,6 +16252,25 @@ (define-public rust-quote-0.6
     (arguments
      `(#:cargo-inputs (("rust-proc-macro2" ,rust-proc-macro2-0.4))))))
 
+(define-public rust-quote-0.5
+  (package
+    (inherit rust-quote-0.6)
+    (name "rust-quote")
+    (version "0.5.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "quote" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1s01fh0jl8qv4xggs85yahw0h507nzrxkjbf7vay3zw8d3kcyjcr"))))
+    (arguments
+      `(#:skip-build? #t
+        #:cargo-inputs
+        (("rust-proc-macro2" ,rust-proc-macro2-0.3))))))
+
 (define-public rust-quote-0.3
   (package
     (inherit rust-quote-0.6)
@@ -14107,7 +16425,7 @@ (define-public rust-rand-0.3
 (define-public rust-rand-chacha-0.2
   (package
     (name "rust-rand-chacha")
-    (version "0.2.1")
+    (version "0.2.2")
     (source
      (origin
        (method url-fetch)
@@ -14116,7 +16434,7 @@ (define-public rust-rand-chacha-0.2
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0lv8imzzl4h2glm6sjj8mkvasgi8jym23ya48dakyln7m06sk8h3"))))
+         "00il36fkdbsmpr99p9ksmmp6dn1md7rmnwmz0rr77jbrca2yvj7l"))))
     (build-system cargo-build-system)
     (arguments
      `(#:cargo-inputs
@@ -14800,16 +17118,39 @@ (define-public rust-rdrand-0.4
          (base32
           "1cjq0kwx1bk7jx3kzyciiish5gqsj7620dm43dc52sr8fzmm9037"))))
     (build-system cargo-build-system)
-    (arguments
-     `(#:skip-build? #t
-       #:cargo-inputs
-       (("rust-rand-core" ,rust-rand-core-0.3))))
-    (home-page "https://github.com/nagisa/rust_rdrand/")
-    (synopsis "Random number generator")
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-rand-core" ,rust-rand-core-0.3))))
+    (home-page "https://github.com/nagisa/rust_rdrand/")
+    (synopsis "Random number generator")
+    (description
+     "This package is an implementation of random number generator based on
+@code{rdrand} and @code{rdseed} instructions")
+    (license license:isc)))
+
+(define-public rust-read-color-1.0
+  (package
+    (name "rust-read-color")
+    (version "1.0.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "read_color" version))
+        (file-name
+          (string-append name "-" version ".tar.gz"))
+        (sha256
+          (base32
+            "1np0pk31ak7hni4hri3m75mbf8py1wdfjshmrj5krbd4p9c8hk4z"))))
+    (build-system cargo-build-system)
+    (arguments `(#:skip-build? #t))
+    (home-page
+      "https://github.com/pistondevelopers/read_color")
+    (synopsis
+      "A simple library for reading hex colors")
     (description
-     "This package is an implementation of random number generator based on
-@code{rdrand} and @code{rdseed} instructions")
-    (license license:isc)))
+      "This package provides a simple library for reading hex colors")
+    (license (list license:expat license:asl2.0))))
 
 (define-public rust-recycler-0.1
   (package
@@ -14880,7 +17221,7 @@ (define-public rust-redox-termios-0.1
 (define-public rust-redox-users-0.3
   (package
     (name "rust-redox-users")
-    (version "0.3.1")
+    (version "0.3.4")
     (source
      (origin
        (method url-fetch)
@@ -14889,15 +17230,14 @@ (define-public rust-redox-users-0.3
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0vdn688q9wg997b1x5abx2gf7406rn1lvd62ypcgh1gj7g5dpkjf"))))
+         "0cbl5w16l3bqm22i4vszclf6hzpljxicghmllw7j13az4s9k1ch9"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
        #:cargo-inputs
-       (("rust-failure" ,rust-failure-0.1)
-        ("rust-rand-os" ,rust-rand-os-0.1)
+       (("rust-getrandom" ,rust-getrandom-0.1)
         ("rust-redox-syscall" ,rust-redox-syscall-0.1)
-        ("rust-rust-argon2" ,rust-rust-argon2-0.5))))
+        ("rust-rust-argon2" ,rust-rust-argon2-0.7))))
     (home-page "https://gitlab.redox-os.org/redox-os/users")
     (synopsis "Access Redox users and groups")
     (description
@@ -15000,7 +17340,7 @@ (define-public rust-ref-cast-impl-0.2
 (define-public rust-regex-1.3
   (package
     (name "rust-regex")
-    (version "1.3.4")
+    (version "1.3.6")
     (source
      (origin
        (method url-fetch)
@@ -15009,12 +17349,12 @@ (define-public rust-regex-1.3
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "1a1mh9mgr8jipnxdaykla6xlw4a6kjn2bzkq3cifx8xy4ivzjb1j"))))
+         "1cx4lcgy7vdi2kij2n1dp2whl33d7974g1kxwiklhs192nclcsbz"))))
     (build-system cargo-build-system)
     (arguments
      `(#:cargo-inputs
        (("rust-aho-corasick" ,rust-aho-corasick-0.7)
-        ("rust-memchr" ,rust-memchr-2.2)
+        ("rust-memchr" ,rust-memchr-2.3)
         ("rust-regex-syntax" ,rust-regex-syntax-0.6)
         ("rust-thread-local" ,rust-thread-local-1.0))
        #:cargo-development-inputs
@@ -15115,7 +17455,7 @@ (define-public rust-regex-0.1
 (define-public rust-regex-automata-0.1
   (package
     (name "rust-regex-automata")
-    (version "0.1.7")
+    (version "0.1.9")
     (source
      (origin
        (method url-fetch)
@@ -15124,21 +17464,22 @@ (define-public rust-regex-automata-0.1
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "11hzn3rz02vdgvx3ykhrbzkvs5c5sm59fyi3xwljn9qc48br5l1y"))))
+         "1r3aqa9c0s9sfrmd2w0mli16ldjzbar0rzb1x7srfjkasrqys7df"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
        #:cargo-inputs
-       (("rust-byteorder" ,rust-byteorder-1.3)
-        ("rust-regex-syntax" ,rust-regex-syntax-0.6)
-        ("rust-utf8-ranges" ,rust-utf8-ranges-1.0))
+       (("rust-fst" ,rust-fst-0.4)
+        ("rust-byteorder" ,rust-byteorder-1.3)
+        ("rust-regex-syntax" ,rust-regex-syntax-0.6))
        #:cargo-development-inputs
-       (("rust-lazy-static" ,rust-lazy-static-1)
+       (("rust-bstr" ,rust-bstr-0.2)
+        ("rust-lazy-static" ,rust-lazy-static-1)
         ("rust-regex" ,rust-regex-1.1)
         ("rust-serde" ,rust-serde-1.0)
         ("rust-serde-bytes" ,rust-serde-bytes-0.11)
         ("rust-serde-derive" ,rust-serde-derive-1.0)
-        ("rust-toml" ,rust-toml-0.5))))
+        ("rust-toml" ,rust-toml-0.5)))) ; 0.4
     (home-page "https://github.com/BurntSushi/regex-automata")
     (synopsis
      "Automata construction and matching using regular expressions")
@@ -15149,7 +17490,7 @@ (define-public rust-regex-automata-0.1
 (define-public rust-regex-syntax-0.6
   (package
     (name "rust-regex-syntax")
-    (version "0.6.14")
+    (version "0.6.17")
     (source
       (origin
         (method url-fetch)
@@ -15157,7 +17498,7 @@ (define-public rust-regex-syntax-0.6
         (file-name (string-append name "-" version ".crate"))
         (sha256
          (base32
-          "01myl8xqpbnird23xnsb92sjmz1cmp69r6m7y3dwbpmsx4zzx3dj"))))
+          "1blmlgzcg7in3kcxqabpfzzrbnamr2i671flbrmlqhfps5bvvrbz"))))
     (build-system cargo-build-system)
     (home-page "https://github.com/rust-lang/regex")
     (synopsis "Regular expression parser")
@@ -15230,6 +17571,30 @@ (define-public rust-remove-dir-all-0.5
     (license (list license:asl2.0
                    license:expat))))
 
+(define-public rust-reopen-0.3
+  (package
+    (name "rust-reopen")
+    (version "0.3.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "reopen" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "12b3mfxkwb8akdfa701nzvqr6lsc6n84vrq088gmjy8lxlmr4an6"))))
+    (build-system cargo-build-system)
+    (arguments
+      `(#:skip-build? #t
+        #:cargo-inputs
+        (("rust-signal-hook" ,rust-signal-hook-0.1)
+         ("rust-libc" ,rust-libc-0.2))))
+    (home-page "https://github.com/vorner/reopen")
+    (synopsis "File reopening utility")
+    (description "File reopening utility.")
+    (license (list license:asl2.0 license:expat))))
+
 (define-public rust-resolv-conf-0.6
   (package
     (name "rust-resolv-conf")
@@ -15284,6 +17649,35 @@ (define-public rust-ron-0.4
     (license (list license:asl2.0
                    license:expat))))
 
+(define-public rust-rust-argon2-0.7
+  (package
+    (name "rust-rust-argon2")
+    (version "0.7.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "rust-argon2" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "05xh5wfxgzq3b6jys8r34f3hmqqfs8ylvf934n9z87wfv95szj1b"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-constant-time-eq" ,rust-constant-time-eq-0.1)
+        ("rust-base64" ,rust-base64-0.11)
+        ("rust-blake2b-simd" ,rust-blake2b-simd-0.5)
+        ("rust-crossbeam-utils" ,rust-crossbeam-utils-0.7))))
+    (home-page "https://github.com/sru-systems/rust-argon2")
+    (synopsis
+     "Rust implementation of the Argon2 password hashing function")
+    (description
+     "This package provides a Rust implementation of the Argon2 password
+hashing function.")
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-rust-argon2-0.5
   (package
     (name "rust-rust-argon2")
@@ -15312,6 +17706,112 @@ (define-public rust-rust-argon2-0.5
 password hashing function.")
     (license (list license:expat license:asl2.0))))
 
+(define-public rust-rust-hawktracer-0.7
+  (package
+    (name "rust-rust-hawktracer")
+    (version "0.7.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "rust_hawktracer" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1h9an3b73pmhhpzc2kk93nh93lplkvsffysj0rp6rxi7p4lhlj73"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-rust-hawktracer-normal-macro"
+         ,rust-rust-hawktracer-normal-macro-0.4)
+        ("rust-rust-hawktracer-proc-macro"
+         ,rust-rust-hawktracer-proc-macro-0.4))))
+    (home-page "https://github.com/AlexEne/rust_hawktracer")
+    (synopsis "Rust bindings for hawktracer profiling library")
+    (description
+     "Rust bindings for hawktracer profiling library.")
+    (license (list license:expat license:asl2.0))))
+
+(define-public rust-rust-hawktracer-proc-macro-0.4
+  (package
+    (name "rust-rust-hawktracer-proc-macro")
+    (version "0.4.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "rust_hawktracer_proc_macro" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1qfksscfv8rbbzv2zb0i9sbbqmig0dr0vrma3c1kzsfmpsynlqnb"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-rust-hawktracer-sys" ,rust-rust-hawktracer-sys-0.4))))
+    (home-page "https://github.com/AlexEne/rust_hawktracer_proc_macro")
+    (synopsis
+     "Helper crate for hawktracer profiling library")
+    (description
+     "This package is a helper crate for hawktracer profiling library.")
+    (license (list license:expat license:asl2.0))))
+
+(define-public rust-rust-hawktracer-normal-macro-0.4
+  (package
+    (name "rust-rust-hawktracer-normal-macro")
+    (version "0.4.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri
+               "rust_hawktracer_normal_macro"
+               version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1sfjmipdbb5s498c150czr6wihjlkwwgla2jyg3cs7cyjich0mwa"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-rust-hawktracer-sys" ,rust-rust-hawktracer-sys-0.4))))
+    (home-page "https://github.com/AlexEne/rust_hawktracer_normal_macro")
+    (synopsis "Helper crate for hawktracer profiling library")
+    (description
+     "This package provides a helper crate for hawktracer profiling library.")
+    (license (list license:expat license:asl2.0))))
+
+(define-public rust-rust-hawktracer-sys-0.4
+  (package
+    (name "rust-rust-hawktracer-sys")
+    (version "0.4.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "rust_hawktracer_sys" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "15acrj881y2g7cwsgf1nr22cixrknp8m4x08dkx1an6zf4q8bk37"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-cmake" ,rust-cmake-0.1)
+        ("rust-pkg-config" ,rust-pkg-config-0.3)
+        ("rust-bindgen" ,rust-bindgen-0.37)
+        ("rust-itertools" ,rust-itertools-0.8))))
+    (home-page "https://github.com/AlexEne/rust_hawktracer_sys")
+    (synopsis
+     "Sys crate for the rust_hawktracer library")
+    (description
+     "This package provides a sys crate for the rust_hawktracer library.")
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-rustc-demangle-0.1
   (package
     (name "rust-rustc-demangle")
@@ -15337,6 +17837,29 @@ (define-public rust-rustc-demangle-0.1
     (license (list license:asl2.0
                    license:expat))))
 
+(define-public rust-rustc-hash-1.1
+  (package
+    (name "rust-rustc-hash")
+    (version "1.1.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "rustc-hash" version))
+        (file-name
+          (string-append name "-" version ".tar.gz"))
+        (sha256
+          (base32
+            "1qkc5khrmv5pqi5l5ca9p5nl5hs742cagrndhbrlk3dhlrx3zm08"))))
+    (build-system cargo-build-system)
+    (arguments `(#:skip-build? #t))
+    (home-page
+      "https://github.com/rust-lang-nursery/rustc-hash")
+    (synopsis
+      "speed, non-cryptographic hash used in rustc")
+    (description
+      "speed, non-cryptographic hash used in rustc")
+    (license (list license:asl2.0 license:expat))))
+
 (define-public rust-rustc-hash-1.0
   (package
     (name "rust-rustc-hash")
@@ -15728,7 +18251,7 @@ (define-public rust-rusty-fork-0.2
 (define-public rust-ryu-1.0
   (package
     (name "rust-ryu")
-    (version "1.0.2")
+    (version "1.0.3")
     (source
       (origin
         (method url-fetch)
@@ -15736,14 +18259,15 @@ (define-public rust-ryu-1.0
         (file-name (string-append name "-" version ".crate"))
         (sha256
          (base32
-          "1j0h74f1xqf9hjkhanp8i20mqc1aw35kr1iq9i79q7713mn51a5z"))))
+          "0xlx9ybzncrb7d6r9533g8ydlg6mr252pfzl4g9cqaqkpvk24mjk"))))
     (build-system cargo-build-system)
     (arguments
      `(#:cargo-inputs
        (("rust-no-panic" ,rust-no-panic-0.1))
        #:cargo-development-inputs
        (("rust-num-cpus" ,rust-num-cpus-1.11)
-        ("rust-rand" ,rust-rand-0.5))))
+        ("rust-rand" ,rust-rand-0.7)
+        ("rust-rand-xorshift" ,rust-rand-xorshift-0.2))))
     (home-page "https://github.com/dtolnay/ryu")
     (synopsis "Fast floating point to string conversion")
     (description
@@ -15820,6 +18344,30 @@ (define-public rust-same-file-0.1
        #:cargo-development-inputs
        (("rust-rand" ,rust-rand-0.3))))))
 
+(define-public rust-scan-fmt-0.2
+  (package
+    (name "rust-scan-fmt")
+    (version "0.2.5")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "scan_fmt" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1gmaa07z8bkkdv5xhq2lrgml6ri7fqyyrjpiks3phmpmq3p8d0i4"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-regex" ,rust-regex-1.3))))
+    (home-page "https://github.com/wlentz/scan_fmt")
+    (synopsis "Simple scanf()-like input for Rust")
+    (description
+     "This package provides a simple scanf()-like input for Rust")
+    (license license:expat)))
+
 (define-public rust-schannel-0.1
   (package
     (name "rust-schannel")
@@ -15949,6 +18497,31 @@ (define-public rust-scopeguard-0.3
          (base32
           "09sy9wbqp409pkwmqni40qmwa99ldqpl48pp95m1xw8sc19qy9cl"))))))
 
+(define-public rust-scroll-0.10
+  (package
+    (name "rust-scroll")
+    (version "0.10.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "scroll" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1cbcns8538sqmfnmdbphqy0fd4j8z75z802pvmz3zlwmnln37cmb"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-scroll-derive" ,rust-scroll-derive-0.10))))
+    (home-page "https://github.com/m4b/scroll")
+    (synopsis "Endian-aware Read/Write traits for byte buffers")
+    (description
+     "This package provides a suite of powerful, extensible, generic,
+endian-aware Read/Write traits for byte buffers.")
+    (license license:expat)))
+
 (define-public rust-scroll-0.9
   (package
     (name "rust-scroll")
@@ -15978,6 +18551,33 @@ (define-public rust-scroll-0.9
 endian-aware Read/Write traits for byte buffers.")
     (license license:expat)))
 
+(define-public rust-scroll-derive-0.10
+  (package
+    (name "rust-scroll-derive")
+    (version "0.10.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "scroll_derive" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0a7f0xybi27p1njs4bqmxh9zyb2dqal4dbvgnhjjix4zkgm4wn7q"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-proc-macro2" ,rust-proc-macro2-1.0)
+        ("rust-syn" ,rust-syn-1.0)
+        ("rust-quote" ,rust-quote-1.0))))
+    (home-page "https://github.com/m4b/scroll")
+    (synopsis "Pread and Pwrite traits from the scroll crate")
+    (description
+     "This package provides a macros 1.1 derive implementation for Pread and
+Pwrite traits from the scroll crate.")
+    (license license:expat)))
+
 (define-public rust-scroll-derive-0.9
   (package
     (name "rust-scroll-derive")
@@ -16182,7 +18782,7 @@ (define-public rust-semver-parser-0.7
 (define-public rust-serde-1.0
   (package
     (name "rust-serde")
-    (version "1.0.104")
+    (version "1.0.105")
     (source
       (origin
         (method url-fetch)
@@ -16190,7 +18790,7 @@ (define-public rust-serde-1.0
         (file-name (string-append name "-" version ".crate"))
         (sha256
          (base32
-          "0ja4mgw4p42syjk7jkzwhj2yg6llfrfm7vn8rvy7v3c1bzr1aha1"))))
+          "1zrj157dxvmymp5ii60anap2qqks4pkr3fwsp71wi3sv4nzzn1z7"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
@@ -16425,7 +19025,7 @@ (define-public rust-serde-codegen-internals-0.14
 (define-public rust-serde-derive-1.0
   (package
     (name "rust-serde-derive")
-    (version "1.0.104")
+    (version "1.0.105")
     (source
       (origin
         (method url-fetch)
@@ -16433,7 +19033,7 @@ (define-public rust-serde-derive-1.0
         (file-name (string-append name "-" version ".crate"))
         (sha256
          (base32
-          "0r7gjlwfry44b4ylz524ynjp9v3qiwdj4c588lh94aas78q9x3qj"))))
+          "1y5gzwpy8yjv9pwh1js11vr18nfz4gg1g2kmyr6p58hvavy00pdc"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
@@ -16480,7 +19080,7 @@ (define-public rust-serde-derive-0.9
 (define-public rust-serde-json-1.0
   (package
     (name "rust-serde-json")
-    (version "1.0.44")
+    (version "1.0.50")
     (source
       (origin
         (method url-fetch)
@@ -16488,18 +19088,21 @@ (define-public rust-serde-json-1.0
         (file-name (string-append name "-" version ".crate"))
         (sha256
          (base32
-          "1mysl675nqhzzkbcrqy4x63cbbsrrx3gcc7k8ydx1gajrkh7bia8"))))
+          "0rs8rsk59kgkgsrw8hyyjrlhas9k1by2jwxxqcz3c2bq2qna39vq"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
        #:cargo-inputs
-       (("rust-indexmap" ,rust-indexmap-1.0)
+       (("rust-indexmap" ,rust-indexmap-1.3)
         ("rust-itoa" ,rust-itoa-0.4)
         ("rust-ryu" ,rust-ryu-1.0)
         ("rust-serde" ,rust-serde-1.0))
        #:cargo-development-inputs
-       (("rust-serde-bytes" ,rust-serde-bytes-0.11)
+       (;("rust-automod" ,rust-automod-0.1)
+        ("rust-rustversion" ,rust-rustversion-1.0)
+        ("rust-serde-bytes" ,rust-serde-bytes-0.11)
         ("rust-serde-derive" ,rust-serde-derive-1.0)
+        ;("rust-serde-stacker" ,rust-serde-stacker-0.1)
         ("rust-trybuild" ,rust-trybuild-1.0))))
     (home-page "https://github.com/serde-rs/json")
     (synopsis "JSON serialization file format")
@@ -16571,7 +19174,7 @@ (define-public rust-serde-macros-0.4
 (define-public rust-serde-test-1.0
   (package
     (name "rust-serde-test")
-    (version "1.0.101")
+    (version "1.0.105")
     (source
      (origin
        (method url-fetch)
@@ -16580,7 +19183,7 @@ (define-public rust-serde-test-1.0
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0070ycbh47yhxb5vxwa15vi2wpdkw3v1m14v4mjryz1568fqkbsa"))))
+         "1vnp0wld20z1wjr8qp2hxcy6yh2zhicg1mfb0qrzxgwq2a4n6raa"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
@@ -16876,6 +19479,32 @@ (define-public rust-sha1-asm-0.4
      "Assembly implementation of SHA-1 compression function.")
     (license license:expat)))
 
+(define-public rust-shader-version-0.6
+  (package
+    (name "rust-shader-version")
+    (version "0.6.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "shader_version" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1yk651xc9irl3pl0rlplypzyzy44d0j03ji0j7hjjdjknwzpi3j7"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-piston-graphics-api-version"
+         ,rust-piston-graphics-api-version-0.2))))
+    (home-page "https://github.com/pistondevelopers/shader_version")
+    (synopsis
+     "Helper library for detecting and picking compatible shaders")
+    (description "This package provides a helper library for detecting and
+picking compatible shaders.")
+    (license license:expat)))
+
 (define-public rust-shared-child-0.3
   (package
     (name "rust-shared-child")
@@ -17092,10 +19721,58 @@ (define-public rust-simd-0.1
     (arguments
      `(#:skip-build? #t
        #:cargo-inputs
-       (("rust-serde" ,rust-serde-0.4)
-        ("rust-serde-macros" ,rust-serde-macros-0.4))
-       #:cargo-development-inputs
-       (("rust-cfg-if" ,rust-cfg-if-0.1))))))
+       (("rust-serde" ,rust-serde-0.4)
+        ("rust-serde-macros" ,rust-serde-macros-0.4))
+       #:cargo-development-inputs
+       (("rust-cfg-if" ,rust-cfg-if-0.1))))))
+
+(define-public rust-simd-helpers-0.1
+  (package
+    (name "rust-simd-helpers")
+    (version "0.1.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "simd_helpers" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "19idqicn9k4vhd04ifh2ff41wvna79zphdf2c81rlmpc7f3hz2cm"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-quote" ,rust-quote-1.0))))
+    (home-page "https://github.com/lu-zero/simd_helpers")
+    (synopsis "Helpers to write more compact simd code")
+    (description
+     "This package provides helpers to write more compact simd code.")
+    (license license:expat)))
+
+(define-public rust-siphasher-0.3
+  (package
+    (name "rust-siphasher")
+    (version "0.3.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "siphasher" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "08xvk3yi4vawppm1f81s4zrkksf95psz8gczh36y808candgi24f"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-serde" ,rust-serde-1.0))))
+    (home-page "https://docs.rs/siphasher")
+    (synopsis "SipHash-2-4, SipHash-1-3 and 128-bit variants in pure Rust")
+    (description "This package provides SipHash-2-4, SipHash-1-3 and 128-bit
+variants in pure Rust.")
+    (license (list license:expat license:asl2.0))))
 
 (define-public rust-siphasher-0.2
   (package
@@ -17117,6 +19794,37 @@ (define-public rust-siphasher-0.2
      "SipHash functions from rust-core < 1.13.")
     (license (list license:asl2.0 license:expat))))
 
+(define-public rust-skeptic-0.13
+  (package
+    (name "rust-skeptic")
+    (version "0.13.4")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "skeptic" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0rai61hbs65nbvbhqlk1nap5hlav5qx3zmjjjzh9rhgxagc8xyyn"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-error-chain" ,rust-error-chain-0.12)
+        ("rust-pulldown-cmark" ,rust-pulldown-cmark-0.2)
+        ("rust-glob" ,rust-glob-0.2)
+        ("rust-tempdir" ,rust-tempdir-0.3)
+        ("rust-bytecount" ,rust-bytecount-0.4)
+        ("rust-cargo-metadata" ,rust-cargo-metadata-0.6)
+        ("rust-serde-json" ,rust-serde-json-1.0)
+        ("rust-walkdir" ,rust-walkdir-2.3))))
+    (home-page "https://github.com/budziq/rust-skeptic")
+    (synopsis "Test your Rust markdown documentation via Cargo")
+    (description
+     "Test your Rust markdown documentation via Cargo.")
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-slab-0.4
   (package
     (name "rust-slab")
@@ -17166,6 +19874,33 @@ (define-public rust-sleef-sys-0.1
      "Rust FFI bindings to the SLEEF Vectorized Math Library.")
     (license (list license:asl2.0 license:expat))))
 
+(define-public rust-slog-2.5
+  (package
+    (name "rust-slog")
+    (version "2.5.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "slog" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "16bv6zrdn1sm315vbnia02g31xvsmbjyz5gv3z0vrgxdli0cdj8w"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-erased-serde" ,rust-erased-serde-0.3))))
+    (home-page "https://github.com/slog-rs/slog")
+    (synopsis "Structured, extensible, composable logging for Rust")
+    (description
+     "This package provides structured, extensible, composable logging for Rust.")
+    (license
+      (list license:mpl2.0
+            license:expat
+            license:asl2.0))))
+
 (define-public rust-slog-2.4
   (package
     (name "rust-slog")
@@ -17936,6 +20671,32 @@ (define-public rust-strsim-0.5
         (base32
          "0z3zzvmilfldp4xw42qbkjf901dcnbk58igrzsvivydjzd24ry37"))))))
 
+(define-public rust-structopt-0.3
+  (package
+    (name "rust-structopt")
+    (version "0.3.12")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "structopt" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "178m7wxnjyy9a8a961z74nazjsg79rfv3gv9g3bykfrrjmqs5yn8"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-structopt-derive" ,rust-structopt-derive-0.4)
+        ("rust-lazy-static" ,rust-lazy-static-1)
+        ("rust-clap" ,rust-clap-2))))
+    (home-page "https://github.com/TeXitoi/structopt")
+    (synopsis "Parse command line argument by defining a struct")
+    (description
+     "Parse command line argument by defining a struct.")
+    (license (list license:asl2.0 license:expat))))
+
 (define-public rust-structopt-0.2
   (package
     (name "rust-structopt")
@@ -17960,6 +20721,34 @@ (define-public rust-structopt-0.2
      "Parse command line arguments by defining a struct.")
     (license (list license:asl2.0 license:expat))))
 
+(define-public rust-structopt-derive-0.4
+  (package
+    (name "rust-structopt-derive")
+    (version "0.4.5")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "structopt-derive" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0c04bbzc5bmr2ns6qy35yz55nn3xvlq4dpwxdynnljb9ikhvi21z"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-heck" ,rust-heck-0.3)
+        ("rust-proc-macro-error" ,rust-proc-macro-error-0.4)
+        ("rust-proc-macro2" ,rust-proc-macro2-1.0)
+        ("rust-syn" ,rust-syn-1.0)
+        ("rust-quote" ,rust-quote-1.0))))
+    (home-page "https://github.com/TeXitoi/structopt")
+    (synopsis "Parse command line argument by defining a struct, derive crate")
+    (description
+     "Parse command line argument by defining a struct, derive crate.")
+    (license (list license:asl2.0 license:expat))))
+
 (define-public rust-structopt-derive-0.2
   (package
     (name "rust-structopt-derive")
@@ -18008,10 +20797,61 @@ (define-public rust-subtle-1.0
 cryptographic implementations.")
     (license license:bsd-3)))
 
+(define-public rust-sval-0.4
+  (package
+    (name "rust-sval")
+    (version "0.4.7")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "sval" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1aljggx64481q4wp3wx9hxsfh2bs7d64nqsrwbb2zxcpmdnbn6yk"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-sval-derive" ,rust-sval-derive-0.4)
+        ("rust-smallvec" ,rust-smallvec-0.6)
+        ("rust-serde" ,rust-serde-1.0))))
+    (home-page "https://github.com/sval-rs/sval")
+    (synopsis "No-std, object-safe serialization framework")
+    (description
+     "This package provides a no-std, object-safe serialization framework.")
+    (license (list license:asl2.0 license:expat))))
+
+(define-public rust-sval-derive-0.4
+  (package
+    (name "rust-sval-derive")
+    (version "0.4.7")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "sval_derive" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "07s7jqsdczsg0wnydfnxyrsj8zyrjmiwl4is1dfgn8dfvyi8n2bj"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-proc-macro2" ,rust-proc-macro2-1.0)
+        ("rust-syn" ,rust-syn-1.0)
+        ("rust-quote" ,rust-quote-1.0))))
+    (home-page "https://github.com/sval-rs/sval")
+    (synopsis "Custom derive for sval")
+    (description "Custom derive for sval.")
+    (license (list license:asl2.0 license:expat))))
+
 (define-public rust-syn-1.0
   (package
     (name "rust-syn")
-    (version "1.0.5")
+    (version "1.0.17")
     (source
       (origin
         (method url-fetch)
@@ -18019,12 +20859,28 @@ (define-public rust-syn-1.0
         (file-name (string-append name "-" version ".crate"))
         (sha256
          (base32
-          "1gw03w7lzrlqmp2vislcybikgl5wkhrqi6sy70w93xss2abhx1b6"))))
+          "00xvf772ys4fj9fr8kplmsqb9if215dsipi3nv54aw9q7xkfpw0d"))))
     (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-unicode-xid" ,rust-unicode-xid-0.2)
+        ("rust-proc-macro2" ,rust-proc-macro2-1.0)
+        ("rust-quote" ,rust-quote-1.0))
+       #:cargo-development-inputs
+       (("rust-anyhow" ,rust-anyhow-1.0)
+        ("rust-flate2" ,rust-flate2-1.0)
+        ;("rust-insta" ,rust-insta-0.12)
+        ("rust-rayon" ,rust-rayon-1.3)
+        ("rust-ref-cast" ,rust-ref-cast-1.0)
+        ("rust-regex" ,rust-regex-1.3)
+        ;("rust-reqwest" ,rust-reqwest-0.10)
+        ("rust-tar" ,rust-tar-0.4)
+        ("rust-termcolor" ,rust-termcolor-1.0)
+        ("rust-walkdir" ,rust-walkdir-2.3))))
     (home-page "https://github.com/dtolnay/syn")
     (synopsis "Parser for Rust source code")
     (description "Parser for Rust source code")
-    (properties '((hidden? . #t)))
     (license (list license:expat license:asl2.0))))
 
 (define-public rust-syn-0.15
@@ -18088,6 +20944,33 @@ (define-public rust-syn-0.11
         ("rust-tempdir" ,rust-tempdir-0.3)
         ("rust-walkdir" ,rust-walkdir-1.0))))))
 
+(define-public rust-syn-mid-0.5
+  (package
+    (name "rust-syn-mid")
+    (version "0.5.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "syn-mid" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "12ikg5jfklixq0wsgfl7sdzjqlxgq50ygklxy4f972hjdjgm7qvv"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-proc-macro2" ,rust-proc-macro2-1.0)
+        ("rust-syn" ,rust-syn-1.0)
+        ("rust-quote" ,rust-quote-1.0))))
+    (home-page "https://github.com/taiki-e/syn-mid")
+    (synopsis
+     "Provide the features between \"full\" and \"derive\" of syn.")
+    (description
+     "This package provides the features between \"full\" and \"derive\" of syn.")
+    (license (list license:asl2.0 license:expat))))
+
 (define-public rust-synom-0.11
   (package
     (name "rust-synom")
@@ -18121,6 +21004,33 @@ (define-public rust-synom-0.11
      "Stripped-down Nom parser used by Syn.")
     (license (list license:expat license:asl2.0))))
 
+(define-public rust-synstructure-0.12
+  (package
+    (name "rust-synstructure")
+    (version "0.12.3")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "synstructure" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0igmc5fzpk6fg7kgff914j05lbpc6ai2wmji312v2h8vvjhnwrb7"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-unicode-xid" ,rust-unicode-xid-0.2)
+        ("rust-proc-macro2" ,rust-proc-macro2-1.0)
+        ("rust-syn" ,rust-syn-1.0)
+        ("rust-quote" ,rust-quote-1.0))))
+    (home-page "https://github.com/mystor/synstructure")
+    (synopsis "Helper methods and macros for custom derives")
+    (description
+     "This package provides helper methods and macros for custom derives.")
+    (license license:expat)))
+
 (define-public rust-synstructure-0.10
   (package
     (name "rust-synstructure")
@@ -18168,6 +21078,44 @@ (define-public rust-synstructure-test-traits-0.1
      "This package provides helper test traits for synstructure doctests.")
     (license license:expat)))
 
+(define-public rust-syntect-3.3
+  (package
+    (name "rust-syntect")
+    (version "3.3.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "syntect" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1f6qn1yy15b0hq9h6q1rikqnm3lh56ic6bq3ywsmdsjy8ni9splm"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-plist" ,rust-plist-0.4)
+        ("rust-yaml-rust" ,rust-yaml-rust-0.4)
+        ("rust-regex-syntax" ,rust-regex-syntax-0.6)
+        ("rust-serde" ,rust-serde-1.0)
+        ("rust-serde-derive" ,rust-serde-derive-1.0)
+        ("rust-flate2" ,rust-flate2-1.0)
+        ("rust-serde-json" ,rust-serde-json-1.0)
+        ("rust-fnv" ,rust-fnv-1.0)
+        ("rust-bitflags" ,rust-bitflags-1)
+        ("rust-lazycell" ,rust-lazycell-1.2)
+        ("rust-bincode" ,rust-bincode-1.2)
+        ("rust-lazy-static" ,rust-lazy-static-1)
+        ("rust-walkdir" ,rust-walkdir-2.3)
+        ("rust-onig" ,rust-onig-5.0))))
+    (home-page "https://github.com/trishume/syntect")
+    (synopsis "Library for syntax highlighting and code intelligence")
+    (description
+     "This package provides a library for syntax highlighting and code
+intelligence using Sublime Text's grammars.")
+    (license license:expat)))
+
 (define-public rust-syntex-0.58
  (package
    (name "rust-syntex")
@@ -18288,37 +21236,89 @@ (define-public rust-sysctl-0.4
     (arguments
      `(#:skip-build? #t
        #:cargo-inputs
-       (("rust-bitflags" ,rust-bitflags-1)
-        ("rust-byteorder" ,rust-byteorder-1.3)
-        ("rust-failure" ,rust-failure-0.1)
+       (("rust-bitflags" ,rust-bitflags-1)
+        ("rust-byteorder" ,rust-byteorder-1.3)
+        ("rust-failure" ,rust-failure-0.1)
+        ("rust-libc" ,rust-libc-0.2)
+        ("rust-walkdir" ,rust-walkdir-2.2))))
+    (home-page "https://github.com/johalun/sysctl-rs")
+    (synopsis "Simplified interface to libc::sysctl")
+    (description
+     "Simplified interface to libc::sysctl.")
+    (license license:expat)))
+
+(define-public rust-sysctl-0.1
+  (package
+    (inherit rust-sysctl-0.4)
+    (name "rust-sysctl")
+    (version "0.1.4")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "sysctl" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "10wxlk4nkzlxp4fg435jmdmfwl4hy0y4w2rcsgs634lvbp8pgksb"))))
+    (arguments
+     `(#:skip-build? #t ; Unsupported on Linux.
+       #:cargo-inputs
+       (("rust-byteorder" ,rust-byteorder-1.3)
+        ("rust-errno" ,rust-errno-0.2)
+        ("rust-libc" ,rust-libc-0.2))))))
+
+(define-public rust-syslog-4.0
+  (package
+    (name "rust-syslog")
+    (version "4.0.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "syslog" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "09ykcbvwx8icvf303mqyz76ji8j6fgyyx97zpr23s788ni112r50"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-time" ,rust-time-0.1)
+        ("rust-error-chain" ,rust-error-chain-0.11)
         ("rust-libc" ,rust-libc-0.2)
-        ("rust-walkdir" ,rust-walkdir-2.2))))
-    (home-page "https://github.com/johalun/sysctl-rs")
-    (synopsis "Simplified interface to libc::sysctl")
-    (description
-     "Simplified interface to libc::sysctl.")
+        ("rust-log" ,rust-log-0.4))))
+    (home-page "https://github.com/Geal/rust-syslog")
+    (synopsis "Send log messages to syslog")
+    (description "Send log messages to syslog.")
     (license license:expat)))
 
-(define-public rust-sysctl-0.1
+(define-public rust-syslog-3.3
   (package
-    (inherit rust-sysctl-0.4)
-    (name "rust-sysctl")
-    (version "0.1.4")
+    (name "rust-syslog")
+    (version "3.3.0")
     (source
       (origin
         (method url-fetch)
-        (uri (crate-uri "sysctl" version))
+        (uri (crate-uri "syslog" version))
         (file-name
          (string-append name "-" version ".tar.gz"))
         (sha256
          (base32
-          "10wxlk4nkzlxp4fg435jmdmfwl4hy0y4w2rcsgs634lvbp8pgksb"))))
+          "0hpdnk2zm6xawpz6fv6qbn0ncfm5p0wm5c6gq7yhaz2gvsnb1jdv"))))
+    (build-system cargo-build-system)
     (arguments
-     `(#:skip-build? #t ; Unsupported on Linux.
+     `(#:skip-build? #t
        #:cargo-inputs
-       (("rust-byteorder" ,rust-byteorder-1.3)
-        ("rust-errno" ,rust-errno-0.2)
-        ("rust-libc" ,rust-libc-0.2))))))
+       (("rust-time" ,rust-time-0.1)
+        ("rust-libc" ,rust-libc-0.2)
+        ("rust-log" ,rust-log-0.3)
+        ("rust-unix-socket" ,rust-unix-socket-0.5))))
+    (home-page "https://github.com/Geal/rust-syslog")
+    (synopsis "Send log messages to syslog")
+    (description "Send log messages to syslog.")
+    (license license:expat)))
 
 (define-public rust-takeable-option-0.4
   (package
@@ -18399,6 +21399,29 @@ (define-public rust-target-build-utils-0.3
 @code{build.rs} scripts.")
     (license (list license:isc license:asl2.0))))
 
+(define-public rust-target-lexicon-0.10
+  (package
+    (name "rust-target-lexicon")
+    (version "0.10.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "target-lexicon" version))
+        (file-name
+          (string-append name "-" version ".tar.gz"))
+        (sha256
+          (base32
+            "17diw9c3d1vb5rmwwk2ghsyhfs0gj5jm78hrwxxhmd67vhw743mb"))))
+    (build-system cargo-build-system)
+    (arguments `(#:skip-build? #t))
+    (home-page
+      "https://github.com/CraneStation/target-lexicon")
+    (synopsis
+      "Targeting utilities for compilers and related tools")
+    (description
+      "Targeting utilities for compilers and related tools")
+    (license license:asl2.0)))
+
 (define-public rust-tempdir-0.3
   (package
     (name "rust-tempdir")
@@ -19083,7 +22106,7 @@ (define-public rust-time-0.1
 (define-public rust-tinytemplate-1.0
   (package
     (name "rust-tinytemplate")
-    (version "1.0.2")
+    (version "1.0.3")
     (source
      (origin
        (method url-fetch)
@@ -19092,7 +22115,7 @@ (define-public rust-tinytemplate-1.0
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "084w41m75i95sdid1wwlnav80jsl1ggyryl4nawxvb6amigvfx25"))))
+         "06ipxjwl1w6synvql8b50qxbqv0w04agvmmfqcdynr9ygmkcd8sp"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
@@ -19100,7 +22123,7 @@ (define-public rust-tinytemplate-1.0
        (("rust-serde" ,rust-serde-1.0)
         ("rust-serde-json" ,rust-serde-json-1.0))
        #:cargo-development-inputs
-       (("rust-criterion" ,rust-criterion-0.2)
+       (("rust-criterion" ,rust-criterion-0.3)
         ("rust-serde-derive" ,rust-serde-derive-1.0))))
     (home-page "https://github.com/bheisler/TinyTemplate")
     (synopsis "Simple, lightweight template engine")
@@ -19328,7 +22351,7 @@ (define-public rust-tokio-fs-0.1
 (define-public rust-tokio-io-0.1
   (package
     (name "rust-tokio-io")
-    (version "0.1.12")
+    (version "0.1.13")
     (source
      (origin
        (method url-fetch)
@@ -19337,7 +22360,7 @@ (define-public rust-tokio-io-0.1
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "09jrz1hh4h1vj45qy09y7m7m8jsy1hl6g32clnky25mdim3dp42h"))))
+         "0x06zyzinans1pn90g6i150lgixijdf1cg8y2gipjd09ms58dz2p"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
@@ -19768,6 +22791,34 @@ (define-public rust-toml-0.5
     (license (list license:asl2.0
                    license:expat))))
 
+(define-public rust-toml-0.2
+  (package
+    (name "rust-toml")
+    (version "0.2.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "toml" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1d1cz43bxrx4fd6j2p6myckf81f72bp47akg36y3flxjkhj60svk"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-rustc-serialize" ,rust-rustc-serialize-0.3)
+        ("rust-serde" ,rust-serde-0.8))))
+    (home-page "https://github.com/alexcrichton/toml-rs")
+    (synopsis "Rust encoder and decoder of TOML-formatted files and streams")
+    (description
+     "This package provides a native Rust encoder and decoder of TOML-formatted
+files and streams.  Provides implementations of the standard
+Serialize/Deserialize traits for TOML data to facilitate deserializing and
+serializing Rust str")
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-tracing-core-0.1
   (package
     (name "rust-tracing-core")
@@ -20053,6 +23104,30 @@ (define-public rust-unchecked-index-0.2
      "Unchecked indexing wrapper using regular index syntax.")
     (license (list license:asl2.0 license:expat))))
 
+(define-public rust-unicase-2.6
+  (package
+    (name "rust-unicase")
+    (version "2.6.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "unicase" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1xmlbink4ycgxrkjspp0mf7pghcx4m7vxq7fpfm04ikr2zk7pwsh"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-version-check" ,rust-version-check-0.9))))
+    (home-page "https://github.com/seanmonstar/unicase")
+    (synopsis "Case-insensitive wrapper around strings")
+    (description
+     "This package provides a case-insensitive wrapper around strings.")
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-unicase-2.4
   (package
     (name "rust-unicase")
@@ -20283,6 +23358,30 @@ (define-public rust-unindent-0.1
     (license (list license:asl2.0
                    license:expat))))
 
+(define-public rust-unix-socket-0.5
+  (package
+    (name "rust-unix-socket")
+    (version "0.5.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "unix_socket" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0r0mxf3mmqvimnx4mpks1f6c4haj6jcxc0k9bs7w61f42w2718ka"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-cfg-if" ,rust-cfg-if-0.1)
+        ("rust-libc" ,rust-libc-0.2))))
+    (home-page "https://github.com/rust-lang-nursery/unix-socket")
+    (synopsis "Unix domain socket bindings")
+    (description "This package provides unix domain socket bindings.")
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-unreachable-1.0
   (package
     (name "rust-unreachable")
@@ -20508,7 +23607,7 @@ (define-public rust-utf-8-0.7
 (define-public rust-utf8-ranges-1.0
   (package
     (name "rust-utf8-ranges")
-    (version "1.0.3")
+    (version "1.0.4")
     (source
      (origin
        (method url-fetch)
@@ -20517,7 +23616,7 @@ (define-public rust-utf8-ranges-1.0
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "1ppzjsxmv1p1xfid8wwn07ciikk84k30frl28bwsny6za1vall4x"))))
+         "1fpc32znar5v02nwsw7icl41jzzzzhy0si6ngqjylzrbxxpi3bml"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
@@ -20568,6 +23667,35 @@ (define-public rust-utf8parse-0.1
     (description "This package provides a table-driven UTF-8 parser.")
     (license (list license:asl2.0 license:expat))))
 
+(define-public rust-uuid-0.8
+  (package
+    (name "rust-uuid")
+    (version "0.8.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "uuid" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "049w16qwk3d3b9cmpgvd7fvcnwgs75l8rlsagh06w7ga9dm2zplz"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-winapi" ,rust-winapi-0.3)
+        ("rust-sha1" ,rust-sha1-0.6)
+        ("rust-md5" ,rust-md5-0.6)
+        ("rust-rand" ,rust-rand-0.7)
+        ("rust-serde" ,rust-serde-1.0)
+        ("rust-slog" ,rust-slog-2.5))))
+    (home-page "https://github.com/uuid-rs/uuid")
+    (synopsis "Library to generate and parse UUIDs")
+    (description
+     "This package provides a library to generate and parse UUIDs.")
+    (license (list license:asl2.0 license:expat))))
+
 (define-public rust-uuid-0.7
   (package
     (name "rust-uuid")
@@ -20674,6 +23802,57 @@ (define-public rust-vec-map-0.8
     (license (list license:asl2.0
                    license:expat))))
 
+(define-public rust-vecmath-1.0
+  (package
+    (name "rust-vecmath")
+    (version "1.0.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "vecmath" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0shmj76rj7rqv377vy365xwr5rx23kxqgkqxxrymdjjvv3hf2slm"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-piston-float" ,rust-piston-float-1.0))))
+    (home-page "https://github.com/pistondevelopers/vecmath")
+    (synopsis "Library for vector math designed for reexporting")
+    (description
+     "This package provides a simple and type agnostic library for vector math
+designed for reexporting.")
+    (license license:expat)))
+
+(define-public rust-vergen-3.1
+  (package
+    (name "rust-vergen")
+    (version "3.1.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "vergen" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1jrr0wihm9si98qz8ghjfnalfvmfv8rqvkgj2npqa7yzjs4hvrac"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-chrono" ,rust-chrono-0.4)
+        ("rust-chrono" ,rust-chrono-0.4)
+        ("rust-bitflags" ,rust-bitflags-1))))
+    (home-page "http://github.com/rustyhorde/vergen")
+    (synopsis "Generate version related functions")
+    (description
+     "Generate version related functions.")
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-version-check-0.9
   (package
     (name "rust-version-check")
@@ -20860,6 +24039,31 @@ (define-public rust-wait-timeout-0.2
 specified across Unix and Windows platforms.")
     (license (list license:expat license:asl2.0))))
 
+(define-public rust-walkdir-2.3
+  (package
+    (name "rust-walkdir")
+    (version "2.3.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "walkdir" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0z9g39f49cycdm9vzjf8hnfh3f1csxgd65kmlphj8r2vffy84wbp"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-winapi-util" ,rust-winapi-util-0.1)
+        ("rust-winapi" ,rust-winapi-0.3)
+        ("rust-same-file" ,rust-same-file-1.0))))
+    (home-page "https://github.com/BurntSushi/walkdir")
+    (synopsis "Recursively walk a directory")
+    (description "Recursively walk a directory.")
+    (license (list license:unlicense license:expat))))
+
 (define-public rust-walkdir-2.2
   (package
     (name "rust-walkdir")
@@ -20911,6 +24115,33 @@ (define-public rust-walkdir-1.0
         ("rust-rand" ,rust-rand-0.3)
         ("rust-rustc-serialize" ,rust-rustc-serialize-0.3))))))
 
+(define-public rust-wasi-0.9
+  (package
+    (name "rust-wasi")
+    (version "0.9.0+wasi-snapshot-preview1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "wasi" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "06g5v3vrdapfzvfq662cij7v8a1flwr2my45nnncdv2galrdzkfc"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-compiler-builtins" ,rust-compiler-builtins-0.1)
+        ("rust-rustc-std-workspace-alloc" ,rust-rustc-std-workspace-alloc-1.0)
+        ("rust-rustc-std-workspace-core" ,rust-rustc-std-workspace-core-1.0))))
+    (home-page "https://github.com/bytecodealliance/wasi")
+    (synopsis "Experimental WASI API bindings for Rust")
+    (description
+     "This package provides an experimental WASI API bindings for Rust.")
+    (license (list license:asl2.0
+                   license:expat))))
+
 (define-public rust-wasi-0.5
   (package
     (name "rust-wasi")
@@ -20934,7 +24165,7 @@ (define-public rust-wasi-0.5
 (define-public rust-wasm-bindgen-0.2
   (package
     (name "rust-wasm-bindgen")
-    (version "0.2.58")
+    (version "0.2.60")
     (source
      (origin
        (method url-fetch)
@@ -20943,7 +24174,7 @@ (define-public rust-wasm-bindgen-0.2
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0v31s91andxcj73w63g3fkbw3ld6cfsaa4135qcjna22vypyj1aj"))))
+         "0zx42zryw03w3maz8p65gr5bhhybr2sdzgcck5p3gy47abh7ri9c"))))
     (build-system cargo-build-system)
     (arguments
      `(#:cargo-inputs
@@ -20969,7 +24200,7 @@ (define-public rust-wasm-bindgen-0.2
 (define-public rust-wasm-bindgen-backend-0.2
   (package
     (name "rust-wasm-bindgen-backend")
-    (version "0.2.58")
+    (version "0.2.60")
     (source
      (origin
        (method url-fetch)
@@ -20978,7 +24209,7 @@ (define-public rust-wasm-bindgen-backend-0.2
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0icskn0qlj30np6x6nbyl1i9dndckx0pczaq69dm42r92rcbkk8i"))))
+         "1k9p8a7ng6nqan0m9555wj936lm2s1qz0fnafclwlv61yrxx6ryr"))))
     (build-system cargo-build-system)
     (arguments
      `(#:cargo-inputs
@@ -21056,7 +24287,7 @@ (define-public rust-wasm-bindgen-futures-0.3
 (define-public rust-wasm-bindgen-macro-0.2
   (package
     (name "rust-wasm-bindgen-macro")
-    (version "0.2.58")
+    (version "0.2.60")
     (source
      (origin
        (method url-fetch)
@@ -21065,7 +24296,7 @@ (define-public rust-wasm-bindgen-macro-0.2
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "1hwxw0nhi2n4izhjn2fvnrrn59xqjxs3ybkgzdv1b4p65ivr8h2p"))))
+         "1973xr0vr2aj85fkp3smk61z5ki7c4fhxlicfjxq3a0y7sv53lcb"))))
     (build-system cargo-build-system)
     (arguments
      `(#:tests? #f      ; 'Async blocks are unstable'
@@ -21087,7 +24318,7 @@ (define-public rust-wasm-bindgen-macro-0.2
 (define-public rust-wasm-bindgen-macro-support-0.2
   (package
     (name "rust-wasm-bindgen-macro-support")
-    (version "0.2.58")
+    (version "0.2.60")
     (source
      (origin
        (method url-fetch)
@@ -21096,7 +24327,7 @@ (define-public rust-wasm-bindgen-macro-support-0.2
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0s3n7v741i4wkzib41m126li40qlhqyirnxpigkypsi59wsk2l78"))))
+         "0ca9bb9hnyzcmjww83x8asb76drf55ijhqv8yrl7igpixqv5p2nn"))))
     (build-system cargo-build-system)
     (arguments
      `(#:cargo-inputs
@@ -21115,7 +24346,7 @@ (define-public rust-wasm-bindgen-macro-support-0.2
 (define-public rust-wasm-bindgen-shared-0.2
   (package
     (name "rust-wasm-bindgen-shared")
-    (version "0.2.58")
+    (version "0.2.60")
     (source
       (origin
         (method url-fetch)
@@ -21123,9 +24354,8 @@ (define-public rust-wasm-bindgen-shared-0.2
         (file-name (string-append name "-" version ".crate"))
         (sha256
          (base32
-          "00cnbabf4k9bahb217vkilmjwqwzpwp112vlvgfw1x19r4gydrzm"))))
+          "0ffn4152w8n629f29lwjgj3adiyixvdbff3mld49gisssbknzxys"))))
     (build-system cargo-build-system)
-    ;(arguments '(#:skip-build? #t))
     (home-page "https://rustwasm.github.io/wasm-bindgen/")
     (synopsis "Shared support between wasm-bindgen and wasm-bindgen cli")
     (description "This package provides shared support between
@@ -21617,7 +24847,7 @@ (define-public rust-wayland-sys-0.21
 (define-public rust-web-sys-0.3
   (package
     (name "rust-web-sys")
-    (version "0.3.35")
+    (version "0.3.37")
     (source
      (origin
        (method url-fetch)
@@ -21626,16 +24856,12 @@ (define-public rust-web-sys-0.3
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0fzmxcyahy3ghl8lkjkchj9krmnr56shvbqgr7db3hm8dappryda"))))
+         "1jy4q5jawzg3dxzhfwa0g3fsz7h4j0ra6y232ikc6mlcimj52vrd"))))
     (build-system cargo-build-system)
     (arguments
      `(#:cargo-inputs
        (("rust-js-sys" ,rust-js-sys-0.3)
-        ("rust-wasm-bindgen" ,rust-wasm-bindgen-0.2)
-        ("rust-anyhow" ,rust-anyhow-1.0)
-        ("rust-env-logger" ,rust-env-logger-0.7)
-        ("rust-sourcefile" ,rust-sourcefile-0.1)
-        ("rust-wasm-bindgen-webidl" ,rust-wasm-bindgen-webidl-0.2))
+        ("rust-wasm-bindgen" ,rust-wasm-bindgen-0.2))
        #:cargo-development-inputs
        (("rust-wasm-bindgen-futures" ,rust-wasm-bindgen-futures-0.4)
         ("rust-wasm-bindgen-test" ,rust-wasm-bindgen-test-0.3))))
@@ -21668,6 +24894,32 @@ (define-public rust-weedle-0.10
      "This package provides a WebIDL Parser.")
     (license license:expat)))
 
+(define-public rust-which-3.1
+  (package
+    (name "rust-which")
+    (version "3.1.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "which" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "094pw9pi48szshn9ln69z2kg7syq1jp80h5ps1qncbsaw4d0f4fh"))))
+    (build-system cargo-build-system)
+    (arguments
+      `(#:skip-build? #t
+        #:cargo-inputs
+        (("rust-failure" ,rust-failure-0.1)
+         ("rust-libc" ,rust-libc-0.2))))
+    (home-page "https://github.com/harryfei/which-rs.git")
+    (synopsis "Rust equivalent of Unix command \"which\"")
+    (description
+     "This package provides a Rust equivalent of Unix command \"which\".  Locate
+installed executable in cross platforms.")
+    (license license:expat)))
+
 (define-public rust-which-2.0
   (package
     (name "rust-which")
@@ -21826,7 +25078,7 @@ (define-public rust-winapi-i686-pc-windows-gnu-0.4
 (define-public rust-winapi-util-0.1
   (package
     (name "rust-winapi-util")
-    (version "0.1.2")
+    (version "0.1.4")
     (source
       (origin
         (method url-fetch)
@@ -21834,7 +25086,7 @@ (define-public rust-winapi-util-0.1
         (file-name (string-append name "-" version ".crate"))
         (sha256
          (base32
-          "1j839dc6y8vszvrsb7yk0qvs0w6asnahxzbyans37vnsw6vbls3i"))))
+          "0vj3984cxwnf1ys3fdz6bpl7p0kdsgykpzbhmcmwi759cd8mqlgs"))))
     (build-system cargo-build-system)
     (arguments
      `(#:cargo-inputs (("rust-winapi" ,rust-winapi-0.3))))
@@ -22246,7 +25498,7 @@ (define-public rust-xdg-2.2
 (define-public rust-xml-rs-0.8
   (package
     (name "rust-xml-rs")
-    (version "0.8.0")
+    (version "0.8.1")
     (source
      (origin
        (method url-fetch)
@@ -22255,14 +25507,37 @@ (define-public rust-xml-rs-0.8
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "1db4v716rbpgjiasaim2s17rmvsfcq1qzwg6nji6mdf5k34i46sl"))))
+         "0c905wsmk995xypxljpxzq6vv660r1pzgyrpsfiz13kw3hf0dzcs"))))
     (build-system cargo-build-system)
-    (arguments `(#:skip-build? #t))
+    (arguments
+     `(#:cargo-development-inputs
+       (("rust-doc-comment" ,rust-doc-comment-0.3)
+        ("rust-lazy-static" ,rust-lazy-static-1))))
     (home-page "https://github.com/netvl/xml-rs")
     (synopsis "XML library in pure Rust")
     (description "An XML library in pure Rust.")
     (license license:expat)))
 
+(define-public rust-y4m-0.5
+  (package
+    (name "rust-y4m")
+    (version "0.5.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "y4m" version))
+        (file-name
+          (string-append name "-" version ".tar.gz"))
+        (sha256
+          (base32
+            "06g8c53qk4cla3xczywx5qlklvzsw54x77vm727mhizlsp5n93ar"))))
+    (build-system cargo-build-system)
+    (arguments `(#:skip-build? #t))
+    (home-page "https://github.com/image-rs/y4m")
+    (synopsis "YUV4MPEG2 (.y4m) Encoder/Decoder.")
+    (description "YUV4MPEG2 (.y4m) Encoder/Decoder.")
+    (license license:expat)))
+
 (define-public rust-yaml-rust-0.4
   (package
     (name "rust-yaml-rust")
diff --git a/gnu/packages/rust-apps.scm b/gnu/packages/rust-apps.scm
index af51c0fcfc..5d0521a216 100644
--- a/gnu/packages/rust-apps.scm
+++ b/gnu/packages/rust-apps.scm
@@ -3,6 +3,7 @@
 ;;; Copyright © 2019, 2020 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
 ;;; Copyright © 2020 Michael Rohleder <mike@rohleder.de>
+;;; Copyright © 2020 Leo Famulari <leo@famulari.name>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -290,7 +291,7 @@ (define-public rust-cbindgen
         ("serde" ,rust-serde-1.0)
         ("serde-json" ,rust-serde-json-1.0)
         ("syn" ,rust-syn-1.0)
-        ("tempfile" ,rust-tempfile-3.0)
+        ("tempfile" ,rust-tempfile-3.1)
         ("toml" ,rust-toml-0.5))))
     (home-page "https://github.com/eqrion/cbindgen/")
     (synopsis "Tool for generating C bindings to Rust code")
@@ -298,6 +299,21 @@ (define-public rust-cbindgen
      "This package provides a tool for generating C/C++ bindings to Rust code.")
     (license license:mpl2.0)))
 
+(define-public rust-cbindgen-0.12
+  (package
+    (inherit rust-cbindgen)
+    (name "rust-cbindgen")
+    (version "0.12.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "cbindgen" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "13jzbmjz1bmmfr0i80hw6ar484mgabx3hbpb2ynhk0ddqi0yr58m"))))))
+
 (define-public tokei
   (package
     (name "tokei")
@@ -358,3 +374,36 @@ (define-public tokei
 show number of files, total lines within those files and code, comments, and
 blanks grouped by language.")
     (license (list license:expat license:asl2.0))))
+
+(define-public rust-cargo-c
+  (package
+    (name "rust-cargo-c")
+    (version "0.5.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "cargo-c" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1is72jm0r73pqx2g3h1n6lvrcirwd91mmajsmb3jjg4jnayfkp0w"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-cbindgen" ,rust-cbindgen-0.12)
+        ("rust-pretty-env-logger" ,rust-pretty-env-logger-0.3)
+        ("rust-structopt" ,rust-structopt-0.3)
+        ("rust-log" ,rust-log-0.4)
+        ("rust-toml" ,rust-toml-0.5)
+        ("rust-cargo-metadata" ,rust-cargo-metadata-0.9)
+        ("rust-serde" ,rust-serde-1.0)
+        ("rust-serde-derive" ,rust-serde-derive-1.0)
+        ("rust-regex" ,rust-regex-1.3))))
+    (home-page "https://github.com/lu-zero/cargo-c")
+    (synopsis "Build and install C-compatible libraries")
+    (description
+     "This package produces and installs a correct pkg-config file, a static
+library and a dynamic library, and a C header to be used by any C (and
+C-compatible) software.")
+    (license license:expat)))
diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm
index 84b051832a..ce5261c788 100644
--- a/gnu/packages/video.scm
+++ b/gnu/packages/video.scm
@@ -66,6 +66,7 @@ (define-module (gnu packages video)
   #:use-module (guix download)
   #:use-module (guix git-download)
   #:use-module (guix svn-download)
+  #:use-module (guix build-system cargo)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system copy)
   #:use-module (guix build-system gnu)
@@ -90,6 +91,7 @@ (define-module (gnu packages video)
   #:use-module (gnu packages cmake)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages cpp)
+  #:use-module (gnu packages crates-io)
   #:use-module (gnu packages curl)
   #:use-module (gnu packages dejagnu)
   #:use-module (gnu packages dns)
@@ -140,6 +142,7 @@ (define-module (gnu packages video)
   #:use-module (gnu packages qt)
   #:use-module (gnu packages rdesktop)
   #:use-module (gnu packages ruby)
+  #:use-module (gnu packages rust-apps)
   #:use-module (gnu packages samba)
   #:use-module (gnu packages sdl)
   #:use-module (gnu packages serialization)
@@ -3949,3 +3952,87 @@ (define-public w-scan
 @end itemize\n")
     (home-page "https://www.gen2vdr.de/wirbel/w_scan/index2.html")
     (license license:gpl2+)))
+
+(define-public rav1e
+  (package
+    (name "rav1e")
+    (version "0.3.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "rav1e" version))
+        (file-name
+         (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1bsmj8kqzs5pf8dl98rsl6a67cljj1gkj3b5hmd8hn8wdy4ya173"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-simd-helpers" ,rust-simd-helpers-0.1)
+        ("rust-ivf" ,rust-ivf-0.1)
+        ("rust-cfg-if" ,rust-cfg-if-0.1)
+        ("rust-paste" ,rust-paste-0.1)
+        ("rust-signal-hook" ,rust-signal-hook-0.1)
+        ("rust-aom-sys" ,rust-aom-sys-0.1)
+        ("rust-nasm-rs" ,rust-nasm-rs-0.1)
+        ("rust-arbitrary" ,rust-arbitrary-0.2)
+        ("rust-better-panic" ,rust-better-panic-0.2)
+        ("rust-noop-proc-macro"
+         ,rust-noop-proc-macro-0.2)
+        ("rust-num-traits" ,rust-num-traits-0.2)
+        ("rust-rand-chacha" ,rust-rand-chacha-0.2)
+        ("rust-err-derive" ,rust-err-derive-0.2)
+        ("rust-interpolate-name"
+         ,rust-interpolate-name-0.2)
+        ("rust-rustc-version" ,rust-rustc-version-0.2)
+        ("rust-scan-fmt" ,rust-scan-fmt-0.2)
+        ("rust-libc" ,rust-libc-0.2)
+        ("rust-image" ,rust-image-0.22)
+        ("rust-arg-enum-proc-macro"
+         ,rust-arg-enum-proc-macro-0.3)
+        ("rust-num-derive" ,rust-num-derive-0.3)
+        ("rust-dav1d-sys" ,rust-dav1d-sys-0.3)
+        ("rust-backtrace" ,rust-backtrace-0.3)
+        ("rust-log" ,rust-log-0.4)
+        ("rust-y4m" ,rust-y4m-0.5)
+        ("rust-arrayvec" ,rust-arrayvec-0.5)
+        ("rust-toml" ,rust-toml-0.5)
+        ("rust-fern" ,rust-fern-0.5)
+        ("rust-rust-hawktracer"
+         ,rust-rust-hawktracer-0.7)
+        ("rust-rand" ,rust-rand-0.7)
+        ("rust-itertools" ,rust-itertools-0.8)
+        ("rust-bitstream-io" ,rust-bitstream-io-0.8)
+        ("rust-console" ,rust-console-0.9)
+        ("rust-serde" ,rust-serde-1.0)
+        ("rust-cc" ,rust-cc-1.0)
+        ("rust-rayon" ,rust-rayon-1.3)
+        ("rust-byteorder" ,rust-byteorder-1.3)
+        ("rust-clap" ,rust-clap-2)
+        ("rust-vergen" ,rust-vergen-3.1))
+       #:cargo-development-inputs
+       (("rust-rand-chacha" ,rust-rand-chacha-0.2)
+        ("rust-interpolate-name"
+         ,rust-interpolate-name-0.2)
+        ("rust-criterion" ,rust-criterion-0.3)
+        ("rust-pretty-assertions"
+         ,rust-pretty-assertions-0.6)
+        ("rust-rand" ,rust-rand-0.7)
+        ("rust-semver" ,rust-semver-0.9))
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'build
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out")))
+               (invoke "cargo" "cinstall" "--release"
+                       (string-append "--prefix=" out))))))))
+    (native-inputs
+     `(("cargo-c" ,rust-cargo-c)))
+    (inputs
+     `(("nasm" ,nasm)))
+    (home-page "https://github.com/xiph/rav1e/")
+    (synopsis "The fastest and safest AV1 encoder")
+    (description
+     "The fastest and safest AV1 encoder.")
+    (license license:bsd-2)))
-- 
cgit v1.2.3


From 910bf1f7a11b669b9c307fb5af8c1fb0be01d537 Mon Sep 17 00:00:00 2001
From: Lars-Dominik Braun <lars@6xq.net>
Date: Sun, 26 Apr 2020 17:54:54 +0200
Subject: gnu: Add tarsplitter.

* gnu/packages/compression.scm (tarsplitter): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
---
 gnu/packages/compression.scm | 36 ++++++++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm
index 33801d201d..8b93cc93dc 100644
--- a/gnu/packages/compression.scm
+++ b/gnu/packages/compression.scm
@@ -27,6 +27,7 @@
 ;;; Copyright © 2019 Jan (janneke) Nieuwenhuizen <janneke@gnu.org>
 ;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
 ;;; Copyright © 2020 Arun Isaac <arunisaac@systemreboot.net>
+;;; Copyright © 2020 Lars-Dominik Braun <lars@6xq.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -52,6 +53,7 @@ (define-module (gnu packages compression)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system glib-or-gtk)
   #:use-module (guix build-system gnu)
+  #:use-module (guix build-system go)
   #:use-module (guix build-system python)
   #:use-module (guix build-system trivial)
   #:use-module (gnu packages)
@@ -2131,3 +2133,37 @@ (define-public xarchiver
 RAR, RPM, DEB, tar, and ZIP.  It cannot perform functions for archives, whose
 archiver is not installed.")
     (license license:gpl2+)))
+
+(define-public tarsplitter
+  (package
+    (name "tarsplitter")
+    (version "2.2.0")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/AQUAOSOTech/tarsplitter.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "17qkg95r97kcrs17b0mcqswx99280ni47j5yx8xa7nl3bdhm6325"))))
+    (build-system go-build-system)
+    (arguments
+     `(#:import-path "github.com/AQUAOSOTech/tarsplitter"
+       #:install-source? #f
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'install 'install-documentation
+           (lambda* (#:key import-path outputs #:allow-other-keys)
+             (let* ((source (string-append "src/" import-path))
+                    (out (assoc-ref outputs "out"))
+                    (doc (string-append out "/share/doc/" ,name "-" ,version)))
+               (with-directory-excursion source
+                 (install-file "README.md" doc))
+               #t))))))
+    (home-page "https://github.com/AQUAOSOTech/tarsplitter")
+    (synopsis "Multithreaded tar utility")
+    (description
+     "Archive huge numbers of files, or spilt massive tar archives into smaller
+chunks.")
+    (license license:expat)))
-- 
cgit v1.2.3


From f47623843116c4a83240bb646edfcd9c0e1d8187 Mon Sep 17 00:00:00 2001
From: Christopher Baines <mail@cbaines.net>
Date: Tue, 7 Apr 2020 22:21:58 +0100
Subject: gnu: guile3.0-chickadee: Rename to guile3.0-chickadee.

This avoids having to packages, both called guile-chickadee.

* gnu/packages/game-development.scm (guile3.0-chickadee)[name]: Change from
guile-chickadee to guile3.0-chickadee.
---
 gnu/packages/game-development.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm
index 2a66f4a40c..d4b2fdcab2 100644
--- a/gnu/packages/game-development.scm
+++ b/gnu/packages/game-development.scm
@@ -1777,7 +1777,7 @@ (define-public guile-chickadee
 (define-public guile3.0-chickadee
   (package
     (inherit guile-chickadee)
-    (name "guile-chickadee")
+    (name "guile3.0-chickadee")
     (version "0.4.0")
     (source (origin
               (method url-fetch)
-- 
cgit v1.2.3


From ec20858a6a9453af1d9bcf3b6efe564f352af2a7 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Sun, 26 Apr 2020 21:02:00 +0200
Subject: gnu: Add r-pasilla.

* gnu/packages/bioconductor.scm (r-pasilla): New variable.
---
 gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 68d8e5b574..2d7663715a 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -811,6 +811,32 @@ (define-public r-do-db
 Disease Ontology.")
     (license license:artistic2.0)))
 
+(define-public r-pasilla
+  (package
+    (name "r-pasilla")
+    (version "1.14.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "http://bioconductor.org/packages/release/data/experiment"
+                    "/src/contrib/pasilla_" version ".tar.gz"))
+              (sha256
+               (base32
+                "0h124i2fb2lbj2k48zzf1n7ldqa471bs26fbd9vw50299aqx28x0"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocstyle" ,r-biocstyle)
+       ("r-dexseq" ,r-dexseq)
+       ("r-knitr" ,r-knitr)
+       ("r-rmarkdown" ,r-rmarkdown)))
+    (home-page "https://www.bioconductor.org/packages/pasilla/")
+    (synopsis "Data package with per-exon and per-gene read counts")
+    (description "This package provides per-exon and per-gene read counts
+computed for selected genes from RNA-seq data that were presented in the
+article 'Conservation of an RNA regulatory map between Drosophila and mammals'
+by Brooks et al., Genome Research 2011.")
+    (license license:lgpl2.1+)))
+
 (define-public r-pfam-db
   (package
     (name "r-pfam-db")
-- 
cgit v1.2.3


From 3699bcf54ac51c99c2807afd60d1eeebc00329ec Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Sun, 26 Apr 2020 21:07:45 +0200
Subject: gnu: Add r-motifdb.

* gnu/packages/bioconductor.scm (r-motifdb): New variable.
---
 gnu/packages/bioconductor.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 2d7663715a..9ecf42e783 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3998,6 +3998,30 @@ (define-public r-motiv
 distributions, modules and filter motifs.")
     (license license:gpl2)))
 
+(define-public r-motifdb
+  (package
+   (name "r-motifdb")
+   (version "1.28.0")
+   (source (origin
+            (method url-fetch)
+            (uri (bioconductor-uri "MotifDb" version))
+            (sha256
+             (base32 "0m5apkjlvdq9yhjdyds3hivfnkbm6f059hy2bkjhalrlhd2si2jc"))))
+   (properties `((upstream-name . "MotifDb")))
+   (build-system r-build-system)
+   (propagated-inputs
+    `(("r-biocgenerics" ,r-biocgenerics)
+      ("r-biostrings" ,r-biostrings)
+      ("r-iranges" ,r-iranges)
+      ("r-rtracklayer" ,r-rtracklayer)
+      ("r-s4vectors" ,r-s4vectors)
+      ("r-splitstackshape" ,r-splitstackshape)))
+   (home-page "https://www.bioconductor.org/packages/MotifDb/")
+   (synopsis "Annotated collection of protein-DNA binding sequence motifs")
+   (description "This package provides more than 2000 annotated position
+frequency matrices from nine public sources, for multiple organisms.")
+   (license license:artistic2.0)))
+
 (define-public r-motifstack
   (package
     (name "r-motifstack")
-- 
cgit v1.2.3


From 886125d791bd1e0ca9d28f7adbb74ffb6f662a33 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Sun, 26 Apr 2020 21:24:03 +0200
Subject: gnu: Add r-motifbreakr.

* gnu/packages/bioconductor.scm (r-motifbreakr): New variable.
---
 gnu/packages/bioconductor.scm | 48 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 48 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 9ecf42e783..a27845581f 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4022,6 +4022,54 @@ (define-public r-motifdb
 frequency matrices from nine public sources, for multiple organisms.")
    (license license:artistic2.0)))
 
+(define-public r-motifbreakr
+  (package
+   (name "r-motifbreakr")
+   (version "2.0.0")
+   (source (origin
+            (method url-fetch)
+            (uri (bioconductor-uri "motifbreakR" version))
+            (sha256
+             (base32 "190z8gj393qdpq5wz7gph96k0l8c1j9wd0p0llscysvk5kr1hf9n"))))
+   (properties `((upstream-name . "motifbreakR")))
+   (build-system r-build-system)
+   (propagated-inputs
+    `(("r-grimport" ,r-grimport)
+      ("r-stringr" ,r-stringr)
+      ("r-biocgenerics" ,r-biocgenerics)
+      ("r-s4vectors" ,r-s4vectors)
+      ("r-iranges" ,r-iranges)
+      ("r-genomeinfodb" ,r-genomeinfodb)
+      ("r-genomicranges" ,r-genomicranges)
+      ("r-biostrings" ,r-biostrings)
+      ("r-bsgenome" ,r-bsgenome)
+      ("r-rtracklayer" ,r-rtracklayer)
+      ("r-variantannotation" ,r-variantannotation)
+      ("r-biocparallel" ,r-biocparallel)
+      ("r-motifstack" ,r-motifstack)
+      ("r-gviz" ,r-gviz)
+      ("r-matrixstats" ,r-matrixstats)
+      ("r-tfmpvalue" ,r-tfmpvalue)
+      ("r-motifdb" ,r-motifdb)))
+   (home-page "https://www.bioconductor.org/packages/motifbreakR/")
+   (synopsis "Predicting disruptiveness of single nucleotide polymorphisms")
+   (description "This package allows biologists to judge in the first place
+whether the sequence surrounding the polymorphism is a good match, and in
+the second place how much information is gained or lost in one allele of
+the polymorphism relative to another.  This package gives a choice of
+algorithms for interrogation of genomes with motifs from public sources:
+@enumerate
+@item a weighted-sum probability matrix;
+@item log-probabilities;
+@item weighted by relative entropy.
+@end enumerate
+
+This package can predict effects for novel or previously described variants in
+public databases, making it suitable for tasks beyond the scope of its original
+design.  Lastly, it can be used to interrogate any genome curated within
+Bioconductor.")
+   (license license:gpl2+)))
+
 (define-public r-motifstack
   (package
     (name "r-motifstack")
-- 
cgit v1.2.3


From b58a22e5b7468906b1e223309e110109808f40ea Mon Sep 17 00:00:00 2001
From: Maxim Cournoyer <maxim.cournoyer@gmail.com>
Date: Sun, 26 Apr 2020 03:36:57 -0400
Subject: gnu: Add hackneyed-x11-cursors.

* gnu/packages/xorg.scm (hackneyed-x11-cursors): New variable.
---
 gnu/packages/xorg.scm | 62 +++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 62 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm
index 80158b1cab..95479f18da 100644
--- a/gnu/packages/xorg.scm
+++ b/gnu/packages/xorg.scm
@@ -22,6 +22,7 @@
 ;;; Copyright © 2019 Yoshinori Arai <kumagusu08@gmail.com>
 ;;; Copyright © 2020 Leo Prikler <leo.prikler@student.tugraz.at>
 ;;; Copyright © 2020 Florian Pelz <pelzflorian@pelzflorian.de>
+;;; Copyright © 2020 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -63,7 +64,9 @@ (define-module (gnu packages xorg)
   #:use-module (gnu packages gnupg)
   #:use-module (gnu packages gperf)
   #:use-module (gnu packages gtk)
+  #:use-module (gnu packages inkscape)
   #:use-module (gnu packages image)
+  #:use-module (gnu packages imagemagick)
   #:use-module (gnu packages libbsd)
   #:use-module (gnu packages libedit)
   #:use-module (gnu packages linux)
@@ -2218,6 +2221,65 @@ (define-public xcursor-themes
     (license license:x11)))
 
 
+(define-public hackneyed-x11-cursors
+  ;; The current release 0.8 suffers from non-deterministic build problems.
+  (let ((revision "1")
+        (commit "9423cef2e2e5ff6b1d65d61f7108c97bc7f5fdfb"))
+    (package
+      (name "hackneyed-x11-cursors")
+      (version (git-version "0.8.1" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://gitlab.com/Enthymeme/hackneyed-x11-cursors.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32
+           "0f637i76sdwz3nm1g1iynamq6j0i6k3c70fpl0fmd0dlynm8ga96"))))
+      (build-system gnu-build-system)
+      (arguments
+       `(#:tests? #f                    ;no test suite
+         #:make-flags (list (string-append "PREFIX=" %output))
+         #:phases
+         (modify-phases %standard-phases
+           (delete 'configure)
+           (add-before 'build 'set-inkscape-environment-variable
+             (lambda* (#:key inputs #:allow-other-keys)
+               (let ((inkscape (string-append (assoc-ref inputs "inkscape")
+                                              "/bin/inkscape")))
+                 (setenv "INKSCAPE" inkscape)
+                 #t)))
+           (add-before 'build 'placate-inkscape-warnings
+             (lambda _
+               (setenv "HOME" (getcwd))
+               #t))
+           (add-after 'build 'generate-black-cursors
+             (lambda* (#:key make-flags parallel-build #:allow-other-keys)
+               (let ((build (assoc-ref %standard-phases 'build))
+                     (make-flags/extended
+                      `(,@make-flags
+                        "THEME_NAME=Hackneyed-Dark"
+                        "COMMON_SOURCE=theme/common-dark.svg"
+                        "RSVG_SOURCE=theme/right-handed-dark.svg"
+                        "LSVG_SOURCE=theme/left-handed-dark.svg")))
+                 (build #:make-flags make-flags/extended
+                        #:parallel-build parallel-build))))
+           (add-after 'install 'install-black-cursors
+             (lambda* (#:key make-flags #:allow-other-keys)
+               (apply invoke `("make" "install" ,@make-flags
+                               "THEME_NAME=Hackneyed-Dark")))))))
+      (native-inputs `(("imagemagick" ,imagemagick)
+                       ("inkscape" ,inkscape)
+                       ("xcursorgen" ,xcursorgen)))
+      (home-page "https://gitlab.com/Enthymeme/hackneyed-x11-cursors")
+      (synopsis "Classic cursor theme for X11")
+      (description "Hackneyed is a scalable cursor theme mildly resembling old
+Windows 3.x cursors.  The cursors are available in white and black colors.  A
+left-handed version of the cursors is also included.")
+      (license license:x11))))
+
 (define-public xcursorgen
   (package
     (name "xcursorgen")
-- 
cgit v1.2.3


From 63daca1e927136d184f41ebdd9b01923d1ee3bff Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Sun, 26 Apr 2020 21:33:42 +0200
Subject: gnu: Add r-snplocs-hsapiens-dbsnp144-grch37.

* gnu/packages/bioconductor.scm (r-snplocs-hsapiens-dbsnp144-grch37): New
  variable.
---
 gnu/packages/bioconductor.scm | 38 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 38 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index a27845581f..b5fa77655c 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6466,6 +6466,44 @@ (define-public r-seqbias
 genome sequence.")
     (license license:lgpl3)))
 
+(define-public r-snplocs-hsapiens-dbsnp144-grch37
+  (package
+    (name "r-snplocs-hsapiens-dbsnp144-grch37")
+    (version "0.99.20")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "SNPlocs.Hsapiens.dbSNP144.GRCh37"
+                                     version 'annotation))
+              (sha256
+               (base32
+                "1z8kx43ki1jvj7ms7pcybakcdimfwr6zpjvspkjmma97bdz093iz"))))
+    (build-system r-build-system)
+    ;; As this package provides little more than a very large data file it
+    ;; doesn't make sense to build substitutes.
+    (arguments `(#:substitutable? #f))
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-iranges" ,r-iranges)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-bsgenome" ,r-bsgenome)
+       ("r-biostrings" ,r-biostrings)))
+    (home-page
+     "https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37/")
+    (synopsis "SNP locations for Homo sapiens (dbSNP Build 144)")
+    (description "This package provides SNP locations and alleles for Homo
+sapiens extracted from NCBI dbSNP Build 144.  The source data files used for
+this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped
+to reference genome GRCh37.p13.  Note that the GRCh37.p13 genome is a
+patched version of GRCh37.  However the patch doesn't alter chromosomes 1-22,
+X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for
+the mitochondrion chromosome.  Therefore, the SNPs in this package can be
+injected in @code{BSgenome.Hsapiens.UCSC.hg19} and they will land at the
+correct position but this injection will exclude chrM (i.e. nothing will be
+injected in that sequence).")
+    (license license:artistic2.0)))
+
 (define-public r-reqon
   (package
     (name "r-reqon")
-- 
cgit v1.2.3


From 1408e2abeb6e521c6929fb79b37b7d880dc78975 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Sun, 26 Apr 2020 21:47:19 +0200
Subject: gnu: r-snplocs-hsapiens-dbsnp144-grch37: Fix description.

* gnu/packages/bioconductor.scm: Use two spaces after ending a sentence.
---
 gnu/packages/bioconductor.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index b5fa77655c..0fc0d7b839 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6497,7 +6497,7 @@ (define-public r-snplocs-hsapiens-dbsnp144-grch37
 this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped
 to reference genome GRCh37.p13.  Note that the GRCh37.p13 genome is a
 patched version of GRCh37.  However the patch doesn't alter chromosomes 1-22,
-X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for
+X, Y, MT.  GRCh37 itself is the same as the hg19 genome from UCSC *except* for
 the mitochondrion chromosome.  Therefore, the SNPs in this package can be
 injected in @code{BSgenome.Hsapiens.UCSC.hg19} and they will land at the
 correct position but this injection will exclude chrM (i.e. nothing will be
-- 
cgit v1.2.3


From 3b177a6c33baa0d78ebd5407119511807d59a590 Mon Sep 17 00:00:00 2001
From: Brice Waegeneire <brice@waegenei.re>
Date: Sun, 26 Apr 2020 22:51:02 +0200
Subject: gnu: Add loadable module to wireguard-linux-compat.

* gnu/packages/vpn.scm (wireguard-linux-compat)[build-system]: Replace
'gnu-build-system' by 'linux-module-build-system'.
[outputs]: Add 'kernel-patch'.
[arguments]: Adjust the build system. Add phases 'change-directory' and
'reset-cwd'. Rename phases 'build' to 'build-patch' and 'install' to
'install-patch'.
[description]: Mention the loadable module.

Signed-off-by: Leo Famulari <leo@famulari.name>
---
 gnu/packages/vpn.scm | 31 ++++++++++++++++++++++---------
 1 file changed, 22 insertions(+), 9 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/vpn.scm b/gnu/packages/vpn.scm
index 739522959c..a9e20049c6 100644
--- a/gnu/packages/vpn.scm
+++ b/gnu/packages/vpn.scm
@@ -11,6 +11,7 @@
 ;;; Copyright © 2019, 2020 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2019 Rutger Helling <rhelling@mykolab.com>
 ;;; Copyright © 2019 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2020 Brice Waegeneire <brice@waegenei.re>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -34,6 +35,7 @@ (define-module (gnu packages vpn)
   #:use-module (guix git-download)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
+  #:use-module (guix build-system linux-module)
   #:use-module (guix build-system python)
   #:use-module (gnu packages)
   #:use-module (gnu packages admin)
@@ -465,19 +467,24 @@ (define-public wireguard-linux-compat
               (sha256
                (base32
                 "0ymprz3h4b92wlcqm5k5vmcgap8pjv202bgkdx0axmp12n1lmyvx"))))
-    (build-system gnu-build-system)
+    (build-system linux-module-build-system)
+    (outputs '("out"
+               "kernel-patch"))
     (arguments
      `(#:tests? #f ; No test suite
-       #:modules ((guix build gnu-build-system)
+       #:modules ((guix build linux-module-build-system)
                   (guix build utils)
                   (ice-9 popen)
                   (ice-9 textual-ports))
        #:phases
        (modify-phases %standard-phases
-         (delete 'configure) ; No ./configure script
-         (replace 'build
+         (add-before 'build 'change-directory
+           (lambda _
+             (chdir "./src")
+             #t))
+         (add-after 'build 'build-patch
            (lambda* (#:key outputs #:allow-other-keys)
-             (let* ((patch-builder "./kernel-tree-scripts/create-patch.sh")
+             (let* ((patch-builder "../kernel-tree-scripts/create-patch.sh")
                     (port (open-input-pipe patch-builder))
                     (str (get-string-all port)))
                (close-pipe port)
@@ -485,15 +492,21 @@ (define-public wireguard-linux-compat
                  (lambda (port)
                    (format port "~a" str))))
                #t))
-         (replace 'install
+         (add-after 'install 'install-patch
            (lambda* (#:key outputs #:allow-other-keys)
              (install-file "wireguard.patch"
-                           (assoc-ref %outputs "out"))
+                           (assoc-ref %outputs "kernel-patch"))
+             #t))
+         ;; So that 'install-license-files' works...
+         (add-before 'install-license-files 'reset-cwd
+           (lambda _
+             (chdir "..")
              #t)))))
     (home-page "https://git.zx2c4.com/wireguard-linux-compat/")
     (synopsis "WireGuard kernel module for Linux 3.10 through 5.5")
-    (description "This is an out-of-tree Linux kernel patch adding WireGuard to
-kernel versions 3.10 through 5.5.  WireGuard was added to Linux 5.6.")
+    (description "This package contains an out-of-tree kernel patch and
+a loadable module adding WireGuard to Linux kernel versions 3.10 through 5.5.
+WireGuard was added to Linux 5.6.")
     (license license:gpl2)))
 
 (define-public wireguard-tools
-- 
cgit v1.2.3


From 8472c26c254c0381018a3903feb55f31b1ea96f1 Mon Sep 17 00:00:00 2001
From: Maxim Cournoyer <maxim.cournoyer@gmail.com>
Date: Sun, 26 Apr 2020 23:01:03 -0400
Subject: gnu: liblinphone: Remove hicolor-icon-theme and murrine inputs.

Icon themes and theme engines are best left for the users to select and
install themselves.

* gnu/packages/linphone.scm (liblinphone)[inputs]: Remove hicolor-icon-theme.
[propagated-inputs]: Remove murrine.
---
 gnu/packages/linphone.scm | 3 ---
 1 file changed, 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/linphone.scm b/gnu/packages/linphone.scm
index 8962f2001e..e8aeabe419 100644
--- a/gnu/packages/linphone.scm
+++ b/gnu/packages/linphone.scm
@@ -459,7 +459,6 @@ (define-public liblinphone
        ("belcard" ,belcard)
        ("bellesip" ,belle-sip)
        ("bzrtp", bzrtp)
-       ("hicolor-icon-theme" ,hicolor-icon-theme) ; Hard-coded for GTK UI
        ("glib" ,glib)
        ("gtk2" ,gtk+-2)
        ("mediastreamer2" ,mediastreamer2)
@@ -469,8 +468,6 @@ (define-public liblinphone
        ("six" ,python-six)
        ("sqlite" ,sqlite)
        ("udev" ,eudev)))
-    (propagated-inputs
-     `(("murrine" ,murrine)))           ; Required for GTK UI
     (synopsis "Belledonne Communications Softphone Library")
     (description "Liblinphone is a high-level SIP library integrating
 all calling and instant messaging features into an unified
-- 
cgit v1.2.3


From 1ae43257347db6e93c6aac37fa622969f245294c Mon Sep 17 00:00:00 2001
From: Maxim Cournoyer <maxim.cournoyer@gmail.com>
Date: Sun, 26 Apr 2020 23:10:21 -0400
Subject: gnu: liblinphone: Fix the input type of some dependencies.

Libraries being linked to such as libxml2, libiconv and zlib should appear as
'inputs' rather than 'native-inputs'.

* gnu/packages/linphone.scm (liblinphone)[native-inputs]: Move libiconv,
libxml2 and zlib to...
[inputs]: ...here.  Move eudev, python-pystache and python-six to
native-inputs.
---
 gnu/packages/linphone.scm | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/linphone.scm b/gnu/packages/linphone.scm
index e8aeabe419..09d5a1121e 100644
--- a/gnu/packages/linphone.scm
+++ b/gnu/packages/linphone.scm
@@ -447,27 +447,28 @@ (define-public liblinphone
                 ""))
              #t)))))
     (native-inputs
-     `(("dot" ,graphviz)
+     `(("gettext" ,gettext-minimal)
+       ("udev" ,eudev)                  ;for libudev.h
+       ;; For generating the C++ wrappers.
+       ("dot" ,graphviz)
        ("doxygen" ,doxygen)
-       ("gettext" ,gettext-minimal)
-       ("iconv" ,libiconv)
        ("python" ,python)
-       ("xml2" ,libxml2)
-       ("zlib" ,zlib)))
+       ("pystache" ,python-pystache)
+       ("six" ,python-six)))
     (inputs
      `(("bctoolbox" ,bctoolbox)
        ("belcard" ,belcard)
        ("bellesip" ,belle-sip)
        ("bzrtp", bzrtp)
+       ("iconv" ,libiconv)
        ("glib" ,glib)
        ("gtk2" ,gtk+-2)
        ("mediastreamer2" ,mediastreamer2)
        ("notify" ,libnotify)
        ("ortp" ,ortp)
-       ("pystache" ,python-pystache)
-       ("six" ,python-six)
        ("sqlite" ,sqlite)
-       ("udev" ,eudev)))
+       ("xml2" ,libxml2)
+       ("zlib" ,zlib)))
     (synopsis "Belledonne Communications Softphone Library")
     (description "Liblinphone is a high-level SIP library integrating
 all calling and instant messaging features into an unified
-- 
cgit v1.2.3


From 9c63165d9ee33a7a7e9017d7a36f658b5c2c415c Mon Sep 17 00:00:00 2001
From: Maxim Cournoyer <maxim.cournoyer@gmail.com>
Date: Mon, 27 Apr 2020 00:50:48 -0400
Subject: gnu: liblinphone: Move documentation and tester to separate outputs.

* gnu/packages/linphone.scm (liblinphone)[outputs]: Add a "doc" and "tester"
outputs.
[phases]: Add a separate-outputs phase.  Move the
glib-or-gtk-compile-schemas and glib-or-gtk-wrap phases after it.
---
 gnu/packages/linphone.scm | 32 +++++++++++++++++++++++++++-----
 1 file changed, 27 insertions(+), 5 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/linphone.scm b/gnu/packages/linphone.scm
index 09d5a1121e..e7d3cf7aaf 100644
--- a/gnu/packages/linphone.scm
+++ b/gnu/packages/linphone.scm
@@ -416,6 +416,7 @@ (define-public liblinphone
                        "/linphone-" version ".tar.gz"))
        (sha256
         (base32 "0phhkx55xdyg28d4wn8l8q4yvsmdgzmjiw584d4s190sq1azm91x"))))
+    (outputs '("out" "doc" "tester"))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f                      ; No test target
@@ -436,16 +437,37 @@ (define-public liblinphone
                   (guix build utils))
        #:phases
        (modify-phases %standard-phases
-         (add-after 'install 'glib-or-gtk-compile-schemas
-           (assoc-ref glib-or-gtk:%standard-phases 'glib-or-gtk-compile-schemas))
-         (add-after 'install 'glib-or-gtk-wrap
-           (assoc-ref glib-or-gtk:%standard-phases 'glib-or-gtk-wrap))
          (add-after 'unpack 'patch
            (lambda _
              (substitute* "gtk/main.c"
                (("#include \"liblinphone_gitversion.h\"")
                 ""))
-             #t)))))
+             #t))
+         (add-after 'install 'separate-outputs
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (doc (assoc-ref outputs "doc"))
+                    (tester (assoc-ref outputs "tester"))
+                    (tester-name (string-append ,name "_tester")))
+               ;; Copy the tester executable.
+               (mkdir-p (string-append tester "/bin"))
+               (rename-file (string-append out "/bin/" tester-name)
+                            (string-append tester "/bin/" tester-name))
+               ;; Copy the tester data files.
+               (mkdir-p (string-append tester "/share/"))
+               (rename-file (string-append out "/share/" tester-name)
+                            (string-append tester "/share/" tester-name))
+               ;; Copy the HTML and XML documentation.
+               (copy-recursively
+                (string-append out "/share/doc/linphone-" ,version)
+                (string-append doc "/share/doc/" ,name "-" ,version))
+               (delete-file-recursively
+                (string-append out "/share/doc/linphone-" ,version))
+               #t)))
+         (add-after 'separate-outputs 'glib-or-gtk-compile-schemas
+           (assoc-ref glib-or-gtk:%standard-phases 'glib-or-gtk-compile-schemas))
+         (add-after 'glib-or-gtk-compile-schemas 'glib-or-gtk-wrap
+           (assoc-ref glib-or-gtk:%standard-phases 'glib-or-gtk-wrap)))))
     (native-inputs
      `(("gettext" ,gettext-minimal)
        ("udev" ,eudev)                  ;for libudev.h
-- 
cgit v1.2.3


From 8521d93854db773806824416be0fef6675ed3719 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Mon, 27 Apr 2020 10:11:21 +0200
Subject: gnu: Add r-reordercluster.

* gnu/packages/cran.scm (r-reordercluster): New variable.
---
 gnu/packages/cran.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index b918a4aa49..94ed889609 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -449,6 +449,27 @@ (define-public r-reprex
 such as copy/paste from an R session.")
     (license license:expat)))
 
+(define-public r-reordercluster
+  (package
+   (name "r-reordercluster")
+   (version "1.0")
+   (source (origin
+            (method url-fetch)
+            (uri (cran-uri "ReorderCluster" version))
+            (sha256
+             (base32
+              "0ss750frzvj0bm1w7zblmcsjpszhnbffwlkaw31sm003lbx9hy58"))))
+   (build-system r-build-system)
+   (propagated-inputs
+    `(("r-gplots" ,r-gplots)
+      ("r-rcpp" ,r-rcpp)))
+   (home-page "https://cran.r-project.org/web/packages/ReorderCluster")
+   (synopsis "Reordering the dendrogram according to the class labels")
+   (description "This package provides tools for performing the leaf reordering
+for the dendrogram that preserves the hierarchical clustering result and at the
+same time tries to group instances from the same class together.")
+   (license license:gpl3+)))
+
 (define-public r-callr
   (package
     (name "r-callr")
-- 
cgit v1.2.3


From df6c7f04878f9881d805517f77a8dc493edd8a8f Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Mon, 27 Apr 2020 10:18:48 +0200
Subject: gnu: Add r-ecp.

* gnu/packages/cran.scm (r-ecp): New variable.
---
 gnu/packages/cran.scm | 26 +++++++++++++++++++++++++-
 1 file changed, 25 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 94ed889609..246a76a6e2 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2,7 +2,7 @@
 ;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2016, 2017 Ben Woodcroft <donttrustben@gmail.com>
-;;; Copyright © 2016, 2017, 2018 Roel Janssen <roel@gnu.org>
+;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org>
 ;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2017 Raoul Bonnal <ilpuccio.febo@gmail.com>
 ;;; Copyright © 2018 Vijayalakshmi Vedantham <vijimay12@gmail.com>
@@ -177,6 +177,30 @@ (define-public r-pheatmap
 control over dimensions and appearance.")
     (license license:gpl2+)))
 
+(define-public r-ecp
+  (package
+    (name "r-ecp")
+    (version "3.1.2")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "ecp" version))
+              (sha256
+               (base32
+                "11f9p869xr0zg779i46gmflxlq4xclk9wxbab0nj2fan26pn4sfy"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-rcpp" ,r-rcpp)))
+    (home-page "https://cran.r-project.org/web/packages/ecp/")
+    (synopsis "Multiple change-point analysis of multivariate data")
+    (description
+     "This package implements various procedures for finding multiple
+change-points.  Two methods make use of dynamic programming and pruning, with
+no distributional assumptions other than the existence of certain absolute
+moments in one method.  Hierarchical and exact search methods are included.
+All methods return the set of estimated change-points as well as other summary
+information.")
+    (license license:gpl2+)))
+
 (define-public r-ellipsis
   (package
     (name "r-ellipsis")
-- 
cgit v1.2.3


From e8d435f7a2919e8f05fc3822d1a43f50c6c5cc8a Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Mon, 27 Apr 2020 10:24:20 +0200
Subject: gnu: Add r-ideoviz.

* gnu/packages/bioconductor.scm (r-ideoviz): New variable.
---
 gnu/packages/bioconductor.scm | 26 +++++++++++++++++++++++++-
 1 file changed, 25 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 0fc0d7b839..9540de3b72 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
-;;; Copyright © 2016, 2017, 2018 Roel Janssen <roel@gnu.org>
+;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org>
 ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2019 Simon Tournier <zimon.toutoune@gmail.com>
 ;;;
@@ -718,6 +718,30 @@ (define-public r-illuminahumanmethylationepicmanifest
      "This is a manifest package for Illumina's EPIC methylation arrays.")
     (license license:artistic2.0)))
 
+(define-public r-ideoviz
+  (package
+    (name "r-ideoviz")
+    (version "1.22.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "IdeoViz" version))
+              (sha256
+               (base32
+                "0rsz6dawrx5qdrypxs2hgihmx3kbpdg1y73h876yxccgdlabvzil"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-iranges" ,r-iranges)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-rcolorbrewer" ,r-rcolorbrewer)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-genomeinfodb" ,r-genomeinfodb)))
+    (home-page "https://bioconductor.org/packages/IdeoViz/")
+    (synopsis "Plots data along a chromosomal ideogram")
+    (description "This package provides functions to plot data associated with
+arbitrary genomic intervals along chromosomal ideogram.")
+    (license license:gpl2)))
+
 ;; This is a CRAN package, but it depends on r-bsgenome-hsapiens-ucsc-hg19
 ;; from Bioconductor.
 (define-public r-deconstructsigs
-- 
cgit v1.2.3


From e658838c62062482f2cdcbc2f94aaae9130c1257 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Mon, 27 Apr 2020 10:28:50 +0200
Subject: gnu: Add r-bezier.

* gnu/packages/cran.scm (r-bezier): New variable.
---
 gnu/packages/cran.scm | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 246a76a6e2..529424480a 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -83,6 +83,25 @@ (define-module (gnu packages cran)
   #:use-module (gnu packages web)
   #:use-module (gnu packages xorg))
 
+(define-public r-bezier
+  (package
+    (name "r-bezier")
+    (version "1.1.2")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "bezier" version))
+              (sha256
+               (base32
+                "1vw5128v8h973xwa1fdm9cw2jvrldj87nd55lddlp3qsz3ag4br6"))))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/web/packages/bezier/")
+    (synopsis "Bezier curve and spline toolkit")
+    (description
+     "This package is a toolkit for working with Bezier curves and splines.
+The package provides functions for point generation, arc length estimation,
+degree elevation and curve fitting.")
+    (license license:gpl2+)))
+
 (define-public r-clipr
   (package
     (name "r-clipr")
-- 
cgit v1.2.3


From cb1ab0352b1f70dd1a5c56c7bd12de82c0b7fde5 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Mon, 27 Apr 2020 10:37:42 +0200
Subject: gnu: Add r-karyoploter.

* gnu/packages/bioconductor.scm (r-karyoploter): New variable.
---
 gnu/packages/bioconductor.scm | 35 +++++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 9540de3b72..d74d1cf706 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2583,6 +2583,41 @@ (define-public r-ebseq
 gene and isoform level using RNA-seq data")
     (license license:artistic2.0)))
 
+(define-public r-karyoploter
+  (package
+    (name "r-karyoploter")
+    (version "1.12.4")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "karyoploteR" version))
+              (sha256
+               (base32
+                "03jmfgmw35hrgn3pc5lq6pblzhfx9fp4l6dx50rp303lr7kjxp9v"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-regioner" ,r-regioner)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-iranges" ,r-iranges)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-memoise" ,r-memoise)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-biovizbase" ,r-biovizbase)
+       ("r-digest" ,r-digest)
+       ("r-bezier" ,r-bezier)
+       ("r-bamsignals" ,r-bamsignals)
+       ("r-annotationdbi" ,r-annotationdbi)
+       ("r-variantannotation" ,r-variantannotation)))
+    (home-page "https://bioconductor.org/packages/karyoploteR/")
+    (synopsis "Plot customizable linear genomes displaying arbitrary data")
+    (description "This package creates karyotype plots of arbitrary genomes and
+offers a complete set of functions to plot arbitrary data on them.  It mimicks
+many R base graphics functions coupling them with a coordinate change function
+automatically mapping the chromosome and data coordinates into the plot
+coordinates.")
+    (license license:artistic2.0)))
+
 (define-public r-lpsymphony
   (package
     (name "r-lpsymphony")
-- 
cgit v1.2.3


From 8ce240fdbf05539b0d13f981b0520be5d84e0e61 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Mon, 27 Apr 2020 10:43:51 +0200
Subject: gnu: Add r-bsgenome-hsapiens-ucsc-hg38.

* gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-ucsc-hg38): New variable.
---
 gnu/packages/bioconductor.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index d74d1cf706..66ff6114c3 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -493,6 +493,30 @@ (define-public r-bsgenome-hsapiens-ucsc-hg19
 by UCSC (hg19, February 2009) and stored in Biostrings objects.")
     (license license:artistic2.0)))
 
+(define-public r-bsgenome-hsapiens-ucsc-hg38
+  (package
+    (name "r-bsgenome-hsapiens-ucsc-hg38")
+    (version "1.4.1")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg38"
+                                     version 'annotation))
+              (sha256
+               (base32
+                "1ql08pvi4vv0ynvg4qs9kysw1c7s3crkgin6zxvgzqk6fray9mvi"))))
+    (properties
+     `((upstream-name . "BSgenome.Hsapiens.UCSC.hg38")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-bsgenome" ,r-bsgenome)))
+    (home-page
+     "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38/")
+    (synopsis "Full genome sequences for Homo sapiens")
+    (description
+     "This package provides full genome sequences for Homo sapiens (Human)
+as provided by UCSC (hg38, Dec. 2013) and stored in Biostrings objects.")
+    (license license:artistic2.0)))
+
 (define-public r-ensdb-hsapiens-v75
   (package
     (name "r-ensdb-hsapiens-v75")
-- 
cgit v1.2.3


From 320dd1195e6ff3bc10001e37e97c161650091ebe Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 26 Apr 2020 10:26:32 +0200
Subject: gnu: Add texlive-inconsolata.

* gnu/packages/tex.scm (texlive-inconsolata): New variable.
---
 gnu/packages/tex.scm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm
index d5bcff0371..10270271c9 100644
--- a/gnu/packages/tex.scm
+++ b/gnu/packages/tex.scm
@@ -4902,6 +4902,32 @@ (define-public texlive-ae
 via the CM-super, Latin Modern and (in a restricted way) CM-LGC font sets.")
     (license license:lppl1.3+)))
 
+(define-public texlive-inconsolata
+  (package
+    (inherit (simple-texlive-package
+              "texlive-inconsolata"
+              (list "/doc/fonts/inconsolata/"
+                    "/fonts/enc/dvips/inconsolata/"
+                    "/fonts/map/dvips/inconsolata/"
+                    "/fonts/opentype/public/inconsolata/"
+                    "/fonts/tfm/public/inconsolata/"
+                    "/fonts/type1/public/inconsolata/"
+                    "/tex/latex/inconsolata/")
+              (base32
+               "1a77w26m4c4j0202s1qkikz7ha6cxlv8zxhzi9s3l0x1l2pl7cr2")
+              #:trivial? #t))
+    (home-page "https://www.ctan.org/pkg/inconsolata")
+    (synopsis "Monospaced font with support files for use with TeX")
+    (description
+     "Inconsolata is a monospaced font designed by Raph Levien.  This package
+contains the font (in both Adobe Type 1 and OpenType formats) in regular and
+bold weights, with additional glyphs and options to control slashed zero,
+upright quotes and a shapelier lower-case L, plus metric files for use with
+TeX, and LaTeX font definition and other relevant files.")
+    (license (list license:lppl1.3+
+                   license:silofl1.1
+                   license:asl2.0))))
+
 (define-public texlive-times
   (package
     (inherit (simple-texlive-package
-- 
cgit v1.2.3


From c170a15996caeca35d1077452f15eaba1a9db1de Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 26 Apr 2020 21:00:24 +0200
Subject: gnu: emacs-org-reveal: Fix syntax error in description.

* gnu/packages/emacs-xyz.scm (emacs-org-reveal)[description]: Fix Texinfo
syntax error.
---
 gnu/packages/emacs-xyz.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm
index 17aea794c4..a0275cbe18 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -14314,7 +14314,7 @@ (define-public emacs-org-reveal
       (build-system emacs-build-system)
       (home-page "https://github.com/yjwen/org-reveal")
       (synopsis "Org and Reveal.js powered HTML presentation tool")
-      (description "Org-Reveal is a command@{org-mode} extension that allows
+      (description "Org-Reveal is a @command{org-mode} extension that allows
 to create beautiful presentations (slides) with 3D effects from simple but
 powerful Org contents.")
       (license license:gpl3+))))
-- 
cgit v1.2.3


From d4f86c8b6634d0814ceb51cce4d05da1e16bf408 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 10:40:00 +0200
Subject: gnu: Add peek.

* gnu/packages/video.scm (peek): New variable.
---
 gnu/packages/video.scm | 37 ++++++++++++++++++++++++++++++++++++-
 1 file changed, 36 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm
index ce5261c788..1ae678da85 100644
--- a/gnu/packages/video.scm
+++ b/gnu/packages/video.scm
@@ -5,7 +5,7 @@
 ;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
 ;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2015 Andy Patterson <ajpatter@uwaterloo.ca>
-;;; Copyright © 2015, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2015, 2016, 2017, 2018, 2019 Alex Vong <alexvong1995@gmail.com>
 ;;; Copyright © 2016, 2017 Alex Griffin <a@ajgrf.com>
 ;;; Copyright © 2016 Kei Kebreau <kkebreau@posteo.net>
@@ -4036,3 +4036,38 @@ (define-public rav1e
     (description
      "The fastest and safest AV1 encoder.")
     (license license:bsd-2)))
+
+(define-public peek
+  (package
+    (name "peek")
+    (version "1.5.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/phw/peek.git")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1xwlfizga6hvjqq127py8vabaphsny928ar7mwqj9cyqfl6fx41x"))))
+    (build-system meson-build-system)
+    (arguments '(#:glib-or-gtk? #t))
+    (inputs
+     `(("gtk+" ,gtk+)))
+    (native-inputs
+     `(("desktop-file-utils" ,desktop-file-utils) ; for update-desktop-database
+       ("gettext" ,gettext-minimal)
+       ("glib:bin" ,glib "bin")         ; for glib-compile-resources
+       ("gtk+-bin" ,gtk+ "bin")         ; For gtk-update-icon-cache
+       ("pkg-config" ,pkg-config)
+       ("vala" ,vala)))
+    (home-page "https://github.com/phw/peek")
+    (synopsis "Simple animated GIF screen recorder")
+    (description
+     "Peek makes it easy to create short screencasts of a screen area.  It was
+built for the specific use case of recording screen areas, e.g. for easily
+showing UI features of your own apps or for showing a bug in bug reports.
+With Peek, you simply place the Peek window over the area you want to record
+and press \"Record\".  Peek is optimized for generating animated GIFs, but you
+can also directly record to WebM or MP4 if you prefer.")
+    (license license:gpl3+)))
-- 
cgit v1.2.3


From 0c0ef9c5a6e54206eb9ca51f242cd95e07406f26 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Mon, 27 Apr 2020 10:56:07 +0200
Subject: gnu: Add r-coverageview.

* gnu/packages/bioconductor.scm (r-coverageview): New variable.
---
 gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 66ff6114c3..83ac5dcf7c 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1069,6 +1069,33 @@ (define-public r-affydata
 package @code{affy}.")
     (license license:gpl2+)))
 
+(define-public r-coverageview
+  (package
+    (name "r-coverageview")
+    (version "1.24.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "CoverageView" version))
+              (sha256
+               (base32
+                "0s47svs7xnr9jkylq0dxidqrigihdddiprcl0951vjr4w7kmb5nf"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-s4vectors" ,r-s4vectors)
+       ("r-iranges" ,r-iranges)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-genomicalignments" ,r-genomicalignments)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-rsamtools" ,r-rsamtools)))
+    (home-page "https://bioconductor.org/packages/CoverageView/")
+    (synopsis "Coverage visualization package for R")
+    (description "This package provides a framework for the visualization of
+genome coverage profiles.  It can be used for ChIP-seq experiments, but it can
+be also used for genome-wide nucleosome positioning experiments or other
+experiment types where it is important to have a framework in order to inspect
+how the coverage distributed across the genome.")
+    (license license:artistic2.0)))
+
 (define-public r-curatedtcgadata
   (package
     (name "r-curatedtcgadata")
-- 
cgit v1.2.3


From 415176e89df200c0e8d4cee348bc67b739112bbb Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Mon, 27 Apr 2020 11:05:49 +0200
Subject: gnu: Add r-ggpmisc.

* gnu/packages/cran.scm (r-ggpmisc): New variable.
---
 gnu/packages/cran.scm | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 529424480a..86f33100f1 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -121,6 +121,36 @@ (define-public r-clipr
 the system clipboards.")
     (license license:gpl3)))
 
+(define-public r-ggpmisc
+  (package
+    (name "r-ggpmisc")
+    (version "0.3.4")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "ggpmisc" version))
+              (sha256
+               (base32
+                "0xc1yp0kphipq23ri4ij93garx1x2nrf4i0lhs6m10pp9yz7fbmj"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-broom" ,r-broom)
+       ("r-dplyr" ,r-dplyr)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-gridextra" ,r-gridextra)
+       ("r-lubridate" ,r-lubridate)
+       ("r-mass" ,r-mass)
+       ("r-plyr" ,r-plyr)
+       ("r-polynom" ,r-polynom)
+       ("r-splus2r" ,r-splus2r)
+       ("r-tibble" ,r-tibble)
+       ("r-xts" ,r-xts)
+       ("r-zoo" ,r-zoo)))
+    (home-page "https://www.r4photobiology.info/")
+    (synopsis "Miscellaneous Extensions to @code{ggplot2}")
+    (description "This package provides extensions to @code{ggplot2},
+respecting the grammar of its graphics paradigm.")
+    (license license:gpl2+)))
+
 (define-public r-oenb
   (package
     (name "r-oenb")
-- 
cgit v1.2.3


From 91370829f4b7d043673e283466d1795143e91684 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Mon, 27 Apr 2020 11:15:38 +0200
Subject: gnu: Add r-inum.

* gnu/packages/cran.scm (r-inum): New variable.
---
 gnu/packages/cran.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 86f33100f1..74e5fa2b1e 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2494,6 +2494,27 @@ (define-public r-inline
     ;; Any version of the LGPL.
     (license license:lgpl3+)))
 
+(define-public r-inum
+  (package
+    (name "r-inum")
+    (version "1.0-1")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "inum" version))
+              (sha256
+               (base32
+                "16d09391l65w557dkzhhx1aqn1ljamcmjj3yh42pwq037k0r8brw"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-libcoin" ,r-libcoin)))
+    (home-page "https://cran.r-project.org/web/packages/inum/")
+    (synopsis "Interval and enum-type representation of vectors")
+    (description
+     "This package provides an enum-type representation of vectors and
+representation of intervals, including a method of coercing variables
+in data frames.")
+    (license license:gpl2)))
+
 (define-public r-bdsmatrix
   (package
     (name "r-bdsmatrix")
-- 
cgit v1.2.3


From 06fc1a51427f5af0e337e16602cb4920865d54fb Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Mon, 27 Apr 2020 11:46:08 +0200
Subject: gnu: Add r-cummerbund.

* gnu/packages/bioconductor.scm (r-cummerbund): New variable.
---
 gnu/packages/bioconductor.scm | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 83ac5dcf7c..b4be8aee15 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1096,6 +1096,36 @@ (define-public r-coverageview
 how the coverage distributed across the genome.")
     (license license:artistic2.0)))
 
+(define-public r-cummerbund
+  (package
+   (name "r-cummerbund")
+   (version "2.28.0")
+   (source (origin
+             (method url-fetch)
+             (uri (bioconductor-uri "cummeRbund" version))
+             (sha256
+              (base32
+               "1fjc3bcclm4gsvw4nq6cv3a1kbrldvrxbkyfb9306708si1n4dwk"))))
+   (build-system r-build-system)
+   (propagated-inputs
+    `(("r-biobase" ,r-biobase)
+      ("r-biocgenerics" ,r-biocgenerics)
+      ("r-fastcluster", r-fastcluster)
+      ("r-ggplot2" ,r-ggplot2)
+      ("r-gviz" ,r-gviz)
+      ("r-plyr" ,r-plyr)
+      ("r-reshape2" ,r-reshape2)
+      ("r-rsqlite" ,r-rsqlite)
+      ("r-rtracklayer" ,r-rtracklayer)
+      ("r-s4vectors" ,r-s4vectors)))
+   (home-page "https://bioconductor.org/packages/cummeRbund/")
+   (synopsis "Analyze Cufflinks high-throughput sequencing data")
+   (description "This package allows for persistent storage, access,
+exploration, and manipulation of Cufflinks high-throughput sequencing
+data.  In addition, provides numerous plotting functions for commonly
+used visualizations.")
+   (license license:artistic2.0)))
+
 (define-public r-curatedtcgadata
   (package
     (name "r-curatedtcgadata")
-- 
cgit v1.2.3


From 4c24186ae0798cd3263c1647d5f9aab0719b3d15 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Mon, 27 Apr 2020 13:09:02 +0200
Subject: gnu: Add python-bitarray.

* gnu/packages/python-xyz.scm (python-bitarray): New variable.
---
 gnu/packages/python-xyz.scm | 26 +++++++++++++++++++++++++-
 1 file changed, 25 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 9460a59e31..31cafd47d1 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -39,7 +39,7 @@
 ;;; Copyright © 2017 Ben Sturmfels <ben@sturm.com.au>
 ;;; Copyright © 2017, 2018, 2019 Mathieu Othacehe <m.othacehe@gmail.com>
 ;;; Copyright © 2017 José Miguel Sánchez García <jmi2k@openmailbox.org>
-;;; Copyright © 2017 Roel Janssen <roel@gnu.org>
+;;; Copyright © 2017, 2020 Roel Janssen <roel@gnu.org>
 ;;; Copyright © 2017, 2018, 2019 Kei Kebreau <kkebreau@posteo.net>
 ;;; Copyright © 2017 Rutger Helling <rhelling@mykolab.com>
 ;;; Copyright © 2017 Muriithi Frederick Muriuki <fredmanglis@gmail.com>
@@ -640,6 +640,30 @@ (define-public python2-backport-ssl-match-hostname
 and verifies that it matches the intended target hostname.")
     (license license:psfl)))
 
+(define-public python-bitarray
+  (package
+    (name "python-bitarray")
+    (version "1.2.1")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "bitarray" version))
+              (sha256
+               (base32
+                "1kxrlxfj9nrx512sfwifwl9z4v6ky3qschl0zmk3s3dvc3s7bmif"))))
+    (build-system python-build-system)
+    (home-page "https://github.com/ilanschnell/bitarray")
+    (synopsis "Efficient arrays of booleans")
+    (description "This package provides an object type which efficiently
+represents an array of booleans.  Bitarrays are sequence types and behave very
+much like usual lists.  Eight bits are represented by one byte in a contiguous
+block of memory.  The user can select between two representations:
+little-endian and big-endian.  All of the functionality is implemented in C.
+Methods for accessing the machine representation are provided.  This can be
+useful when bit level access to binary files is required, such as portable
+bitmap image files.  Also, when dealing with compressed data which uses
+variable bit length encoding, you may find this module useful.")
+    (license license:psfl)))
+
 (define-public python-boolean.py
   (package
     (name "python-boolean.py")
-- 
cgit v1.2.3


From c43edf6f3012436aef8196a406bb407beda3e533 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Mon, 27 Apr 2020 13:39:25 +0200
Subject: gnu: Add python-deeptoolsintervals.

* gnu/packages/bioinformatics.scm (python-deeptoolsintervals): New variable.
---
 gnu/packages/bioinformatics.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 6c5b49e37e..cd401d97f3 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2334,6 +2334,27 @@ (define-public python-dnaio
 files.  The code was previously part of the cutadapt tool.")
     (license license:expat)))
 
+(define-public python-deeptoolsintervals
+  (package
+    (name "python-deeptoolsintervals")
+    (version "0.1.9")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "deeptoolsintervals" version))
+              (sha256
+               (base32
+                "1xnl80nblysj6dylj4683wgrfa425rkx4dp5k65hvwdns9pw753x"))))
+    (build-system python-build-system)
+    (inputs
+     `(("zlib" ,zlib)))
+    (home-page "https://github.com/deeptools/deeptools_intervals")
+    (synopsis "Create GTF-based interval trees with associated meta-data")
+    (description
+     "This package provides a Python module creating/accessing GTF-based
+interval trees with associated meta-data.  It is primarily used by the
+@code{deeptools} package.")
+    (license license:expat)))
+
 (define-public cutadapt
   (package
     (name "cutadapt")
-- 
cgit v1.2.3


From ccf70a80a12be86ed609ce7d37d3ae32f75edc39 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Mon, 27 Apr 2020 13:40:00 +0200
Subject: gnu: Add python-deeptools.

* gnu/packages/bioinformatics.scm (python-deeptools): New variable.
---
 gnu/packages/bioinformatics.scm | 37 ++++++++++++++++++++++++++++++++++++-
 1 file changed, 36 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index cd401d97f3..8ef2880472 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3,7 +3,7 @@
 ;;; Copyright © 2015, 2016, 2017, 2018 Ben Woodcroft <donttrustben@gmail.com>
 ;;; Copyright © 2015, 2016 Pjotr Prins <pjotr.guix@thebird.nl>
 ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
-;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
+;;; Copyright © 2016, 2020 Roel Janssen <roel@gnu.org>
 ;;; Copyright © 2016, 2017, 2018, 2019, 2020 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016, 2020 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2016, 2018 Raoul Bonnal <ilpuccio.febo@gmail.com>
@@ -2355,6 +2355,41 @@ (define-public python-deeptoolsintervals
 @code{deeptools} package.")
     (license license:expat)))
 
+(define-public python-deeptools
+  (package
+    (name "python-deeptools")
+    (version "3.4.3")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "deepTools" version))
+              (sha256
+               (base32
+                "1azgjniss5ff6a90nicdjkxyjwqmi3gzfn09gra42hwlz19hipxb"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-matplotlib" ,python-matplotlib)
+       ("python-numpy" ,python-numpy)
+       ("python-numpydoc" ,python-numpydoc)
+       ("python-py2bit" ,python-py2bit)
+       ("python-pybigwig" ,python-pybigwig)
+       ("python-pysam" ,python-pysam)
+       ("python-scipy" ,python-scipy)
+       ("python-deeptoolsintervals" ,python-deeptoolsintervals)
+       ("python-plotly" ,python-plotly)))
+    (home-page "https://pypi.org/project/deepTools/")
+    (synopsis "Useful tools for exploring deep sequencing data")
+    (description "This package addresses the challenge of handling large amounts
+of data that are now routinely generated from DNA sequencing centers.
+@code{deepTools} contains useful modules to process the mapped reads data for
+multiple quality checks, creating normalized coverage files in standard bedGraph
+and bigWig file formats, that allow comparison between different files.  Finally,
+using such normalized and standardized files, deepTools can create many
+publication-ready visualizations to identify enrichments and for functional
+annotations of the genome.")
+    ;; The file deeptools/cm.py is licensed under the BSD license.  The
+    ;; remainder of the code is licensed under the MIT license.
+    (license (list license:bsd-3 license:expat))))
+
 (define-public cutadapt
   (package
     (name "cutadapt")
-- 
cgit v1.2.3


From 639ae3f20bea5ccd7f4a4df7a828569639220e79 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Mon, 27 Apr 2020 13:54:43 +0200
Subject: gnu: Add python-scikit-rebate.

* gnu/packages/machine-learning.scm (python-scikit-rebate): New variable.
---
 gnu/packages/machine-learning.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 9a88b53415..223d03e979 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -867,6 +867,35 @@ (define-public python2-scikit-learn
                  (base32
                   "08zbzi8yx5wdlxfx9jap61vg1malc9ajf576w7a0liv6jvvrxlpj")))))))
 
+(define-public python-scikit-rebate
+  (package
+    (name "python-scikit-rebate")
+    (version "0.6")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "skrebate" version))
+              (sha256
+               (base32
+                "1h7qs9gjxpzqabzhb8rmpv3jpmi5iq41kqdibg48299h94iikiw7"))))
+    (build-system python-build-system)
+    ;; Pandas is only needed to run the tests.
+    (native-inputs
+     `(("python-pandas" ,python-pandas)))
+    (propagated-inputs
+     `(("python-numpy" ,python-numpy)
+       ("python-scipy" ,python-scipy)
+       ("python-scikit-learn" ,python-scikit-learn)
+       ("python-joblib" ,python-joblib)))
+    (home-page "https://epistasislab.github.io/scikit-rebate/")
+    (synopsis "Relief-based feature selection algorithms for Python")
+    (description "Scikit-rebate is a scikit-learn-compatible Python
+implementation of ReBATE, a suite of Relief-based feature selection algorithms
+for Machine Learning.  These algorithms excel at identifying features that are
+predictive of the outcome in supervised learning problems, and are especially
+good at identifying feature interactions that are normally overlooked by
+standard feature selection algorithms.")
+    (license license:expat)))
+
 (define-public python-autograd
   (let* ((commit "442205dfefe407beffb33550846434baa90c4de7")
          (revision "0")
-- 
cgit v1.2.3


From f38ba7b65dca8a4116ba8983357588f8a73a543f Mon Sep 17 00:00:00 2001
From: Guillaume Le Vaillant <glv@posteo.net>
Date: Mon, 27 Apr 2020 16:54:34 +0200
Subject: gnu: fldigi: Update to 4.1.12.

* gnu/packages/radio.scm (fldigi): Update to 4.1.12.
---
 gnu/packages/radio.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm
index fff68cf657..b748aa4183 100644
--- a/gnu/packages/radio.scm
+++ b/gnu/packages/radio.scm
@@ -537,14 +537,14 @@ (define-public gqrx
 (define-public fldigi
   (package
     (name "fldigi")
-    (version "4.1.11")
+    (version "4.1.12")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "http://www.w1hkj.com/files/fldigi/fldigi-"
                            version ".tar.gz"))
        (sha256
-        (base32 "1y62xn1pim38ibaf2mbl8b7aq20jdaac6lgggb9r402w9bj5b196"))))
+        (base32 "1yjjv2ss84xfiaidypp476mhrbpnw4zf7mb5cdqwhdh604x0svr1"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)))
-- 
cgit v1.2.3


From 138896e1ea4d0ba420d04bff067692fecf93a613 Mon Sep 17 00:00:00 2001
From: "Boris A. Dekshteyn" <boris.dekshteyn@gmail.com>
Date: Tue, 28 Apr 2020 02:36:38 +1200
Subject: gnu: herbstluftwm: Update to 0.8.1
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

 * gnu/packages/wm.scm: herbstluftwm: Update to 0.8.1

Signed-off-by: Jakub Kądziołka <kuba@kadziolka.net>
---
 gnu/packages/wm.scm | 34 ++++++++++++++++------------------
 1 file changed, 16 insertions(+), 18 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/wm.scm b/gnu/packages/wm.scm
index a2c992d2c6..e173e5443a 100644
--- a/gnu/packages/wm.scm
+++ b/gnu/packages/wm.scm
@@ -33,6 +33,7 @@
 ;;; Copyright © 2019, 2020 Alexandru-Sergiu Marton <brown121407@member.fsf.org>
 ;;; Copyright © 2020 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;; Copyright © 2020 Brice Waegeneire <brice@waegenei.re>
+;;; Copyright © 2020 Boris A. Dekshteyn <harlequin78@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -149,7 +150,7 @@ (define-public bspwm
 (define-public herbstluftwm
   (package
     (name "herbstluftwm")
-    (version "0.7.2")
+    (version "0.8.1")
     (source
      (origin
        (method url-fetch)
@@ -157,9 +158,9 @@ (define-public herbstluftwm
                            version ".tar.gz"))
        (sha256
         (base32
-         "1kc18aj9j3nfz6fj4qxg9s3gg4jvn6kzi3ii24hfm0vqdpy17xnz"))
+         "0c1lf82z6a56g8asin91cmqhzk3anw0xwc44b31bpjixadmns57y"))
        (file-name (string-append "herbstluftwm-" version ".tar.gz"))))
-    (build-system gnu-build-system)
+    (build-system cmake-build-system)
     (inputs
      `(("dzen"        ,dzen)
        ("dmenu"       ,dmenu)
@@ -169,13 +170,20 @@ (define-public herbstluftwm
        ("xsetroot"    ,xsetroot)
        ("libx11"      ,libx11)
        ("libxext"     ,libxext)
-       ("libxinerama" ,libxinerama)))
+       ("libxinerama" ,libxinerama)
+       ("libxrandr"   ,libxrandr)))
     (native-inputs
-     `(("pkg-config" ,pkg-config)))
+     `(("asciidoc"   ,asciidoc)
+       ("pkg-config" ,pkg-config)))
     (arguments
-     '(#:phases
+     '(#:tests? #f
+       #:configure-flags
+       (let ((out (assoc-ref %outputs "out")))
+         (list "-DCC=gcc"
+               (string-append "-DCMAKE_INSTALL_SYSCONF_PREFIX=" out "/etc")
+               (string-append "-DBASHCOMPLETIONDIR=" out "/etc/bash_completion.d")))
+       #:phases
        (modify-phases %standard-phases
-         (delete 'configure)            ; no configure script
          (add-after 'install 'install-xsession
            (lambda* (#:key outputs #:allow-other-keys)
              (let* ((out (assoc-ref outputs "out"))
@@ -190,17 +198,7 @@ (define-public herbstluftwm
                      Comment=Manual tiling window manager~@
                      Exec=~a/bin/herbstluftwm~@
                      Type=XSession~%" out)))
-               #t))))
-       #:tests? #f
-       #:make-flags
-       (let ((out (assoc-ref %outputs "out")))
-         (list "CC=gcc"
-               (string-append "PREFIX=''")
-               (string-append "DESTDIR=" out)
-               (string-append "FISHCOMPLETIONDIR="
-                              "/share/fish/vendor_completions.d")
-               (string-append "BASHCOMPLETIONDIR=" out
-                              "/etc/bash_completion.d")))))
+               #t))))))
     (synopsis "Tiling window manager for X11")
     (description "herbstluftwm is a manual tiling window manager for X11 using
 Xlib and GLib.  Its main features are:
-- 
cgit v1.2.3


From c53886a55a40e106740209cf587fef4e52226aae Mon Sep 17 00:00:00 2001
From: Raghav Gururajan <raghavgururajan@disroot.org>
Date: Mon, 27 Apr 2020 09:32:43 -0400
Subject: gnu: ktsuss: Use setuid "su" and "sudo" commands.

This has ktsudo actually gain root access.

* gnu/packages/admin.scm (ktsuss)[arguments]: Instead of <sudo>/bin/{su,sudo}
file names, use the setuid' verrsions.
---
 gnu/packages/admin.scm | 14 ++++++--------
 1 file changed, 6 insertions(+), 8 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm
index 236eebe53c..cb3de79713 100644
--- a/gnu/packages/admin.scm
+++ b/gnu/packages/admin.scm
@@ -150,24 +150,22 @@ (define-public ktsuss
        (list "--enable-sudo=yes")
        #:phases
        (modify-phases %standard-phases
-         (add-after 'unpack 'patch-sudo-path
-           (lambda* (#:key inputs #:allow-other-keys)
+         (add-after 'unpack 'patch-file-names
+           (lambda _
              (substitute* "configure.ac"
+               (("supath=`which su 2>/dev/null`")
+                "supath=/run/setuid-programs/su")
                (("sudopath=`which sudo 2>/dev/null`")
-                (string-append "sudopath="
-                               (string-append (assoc-ref inputs "sudo")
-                                              "/bin/sudo"))))
+                "sudopath=/run/setuid-programs/sudo"))
              #t)))))
     (native-inputs
      `(("autoconf" ,autoconf)
-       ("autogen" ,autogen)
        ("automake" ,automake)
        ("libtool" ,libtool)
        ("pkg-config" ,pkg-config)))
     (inputs
      `(("glib" ,glib)
-       ("gtk+" ,gtk+-2)
-       ("sudo" ,sudo)))
+       ("gtk+" ,gtk+-2)))
     (synopsis "Graphical front end for @command{su}")
     (description
      "Ktsuss stands for ``Keep the @command{su} simple, stupid''.
-- 
cgit v1.2.3


From 58a361fef40f86d28938c7a964ca38032ff7f5a0 Mon Sep 17 00:00:00 2001
From: Alex McGrath <amk@amk.ie>
Date: Thu, 16 Apr 2020 21:55:28 +0100
Subject: gnu: Add wf-recorder.

* gnu/packages/video.scm (wf-recorder): New variable.

Signed-off-by: Mathieu Othacehe <m.othacehe@gmail.com>
---
 gnu/packages/video.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm
index 1ae678da85..e3d145a840 100644
--- a/gnu/packages/video.scm
+++ b/gnu/packages/video.scm
@@ -40,6 +40,7 @@
 ;;; Copyright © 2020 Brice Waegeneire <brice@waegenei.re>
 ;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
 ;;; Copyright © 2020 Guillaume Le Vaillant <glv@posteo.net>
+;;; Copyright © 2020 Alex McGrath <amk@amk.ie>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -4071,3 +4072,33 @@ (define-public peek
 and press \"Record\".  Peek is optimized for generating animated GIFs, but you
 can also directly record to WebM or MP4 if you prefer.")
     (license license:gpl3+)))
+
+(define-public wf-recorder
+  (package
+    (name "wf-recorder")
+    (version "0.2.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/ammen99/wf-recorder.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1cw6kpcbl33wh95pvy32xrsrm6kkk1awccr3phyh885xjs3b3iim"))))
+    (build-system meson-build-system)
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (inputs
+     `(("ffmpeg" ,ffmpeg)
+       ("pulseaudio" ,pulseaudio)
+       ("wayland" ,wayland)
+       ("wayland-protocols" ,wayland-protocols)
+       ("libx264" ,libx264)))
+    (home-page "https://github.com/ammen99/wf-recorder")
+    (synopsis "Screen recorder for wlroots-based compositors")
+    (description
+     "@code{wf-recorder} is a utility program for screen recording of
+wlroots-based compositors.  More specifically, those that support
+@code{wlr-screencopy-v1} and @code{xdg-output}.")
+    (license license:expat)))
-- 
cgit v1.2.3


From bb6d9e26334c93b84553eb273d1540d08fd15852 Mon Sep 17 00:00:00 2001
From: Vincent Legoll <vincent.legoll@gmail.com>
Date: Sun, 26 Apr 2020 23:10:10 +0200
Subject: gnu: tarsplitter: Fix typo in description (spilt/split).

* gnu/packages/compression.scm (tarsplitter)[description]: Fix typo.
---
 gnu/packages/compression.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm
index 8b93cc93dc..18512ee1bc 100644
--- a/gnu/packages/compression.scm
+++ b/gnu/packages/compression.scm
@@ -2164,6 +2164,6 @@ (define-public tarsplitter
     (home-page "https://github.com/AQUAOSOTech/tarsplitter")
     (synopsis "Multithreaded tar utility")
     (description
-     "Archive huge numbers of files, or spilt massive tar archives into smaller
+     "Archive huge numbers of files, or split massive tar archives into smaller
 chunks.")
     (license license:expat)))
-- 
cgit v1.2.3


From 693d0fffc81ab7ebcc05622f88cc41a25c2d3c7a Mon Sep 17 00:00:00 2001
From: Oleg Pykhalov <go.wigust@gmail.com>
Date: Mon, 27 Apr 2020 22:21:11 +0300
Subject: gnu: Add sbcl-stumpwm-swm-gaps.

* gnu/packages/wm.scm (sbcl-stumpwm-swm-gaps): New variable.
---
 gnu/packages/wm.scm | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/wm.scm b/gnu/packages/wm.scm
index e173e5443a..4d1b6b3fd4 100644
--- a/gnu/packages/wm.scm
+++ b/gnu/packages/wm.scm
@@ -1760,6 +1760,36 @@ (define-public sbcl-stumpwm-globalwindows
 windows in the current X session.")
       (license (list license:gpl2+ license:gpl3+ license:bsd-2)))))
 
+(define-public sbcl-stumpwm-swm-gaps
+  (let ((commit "dd5b037923ec7d3cc27c55806bcec5a1b8cf4e91")
+        (revision "1"))
+    (package
+      (name "sbcl-swm-gaps")
+      (version (git-version "0.0.1" revision commit)) ;no upstream release
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/stumpwm/stumpwm-contrib.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "0ahxdj9f884afpzxczx6mx7l4nwg4kw6afqaq7lwhf7lxcwylldn"))))
+      (inputs
+       `(("stumpwm" ,stumpwm "lib")))
+      (build-system asdf-build-system/sbcl)
+      (arguments
+       '(#:phases
+         (modify-phases %standard-phases
+           (add-after 'unpack 'chdir
+             (lambda _
+               (chdir "util/swm-gaps"))))))
+      (home-page "https://github.com/stumpwm/stumpwm-contrib")
+      (synopsis "Gaps between windows for StumpWM")
+      (description "This package provides a StumpWM module which adds gaps
+between windows.")
+      (license (list license:gpl2+ license:gpl3+ license:bsd-2)))))
+
 (define-public lemonbar
   (let ((commit "35183ab81d2128dbb7b6d8e119cc57846bcefdb4")
         (revision "1"))
-- 
cgit v1.2.3


From 78799a6fdc5a00b3a0e62c0e99c3340298d36eff Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Mon, 27 Apr 2020 21:34:10 +0200
Subject: gnu: Update minimap2 to 2.17.

* gnu/packages/bioinformatics.scm (minimap2): Update to 2.17.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 8ef2880472..7b24d8bb64 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13207,7 +13207,7 @@ (define-public sjcount
 (define-public minimap2
   (package
     (name "minimap2")
-    (version "2.10")
+    (version "2.17")
     (source
      (origin
        (method url-fetch)
@@ -13216,7 +13216,7 @@ (define-public minimap2
                            "minimap2-" version ".tar.bz2"))
        (sha256
         (base32
-         "080w9066irkbhbyr4nmf19pzkdd2s4v31hpzlajgq2y0drr6zcsj"))))
+         "0hi7i9pzxhvjj44khzzzj1lrn5gb5837arr4wgln7k1k5n4ci2mn"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f                      ; there are none
-- 
cgit v1.2.3


From 89909327d017198969436237acc7c93823ff8147 Mon Sep 17 00:00:00 2001
From: Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
Date: Tue, 28 Apr 2020 00:15:34 +0200
Subject: gnu: stellarium: Update to 0.20.1.

* gnu/packages/astronomy.scm (stellarium): Update to 0.20.1.
---
 gnu/packages/astronomy.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 2c976354f1..28c010ad6a 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -157,7 +157,7 @@ (define-public gnuastro
 (define-public stellarium
   (package
     (name "stellarium")
-    (version "0.19.3")
+    (version "0.20.1")
     (source
      (origin
        (method url-fetch)
@@ -165,7 +165,7 @@ (define-public stellarium
                            "/releases/download/v" version
                            "/stellarium-" version ".tar.gz"))
        (sha256
-        (base32 "0p92rgclag0nkic9gk3p9vclb8xx9hv4zlgyij6cyh43s7c1avhp"))))
+        (base32 "034jkrdaaamvbrkfwi3qcl6h8hwfnw2nvf7a82faj55rskcpnkhm"))))
     (build-system cmake-build-system)
     (inputs
      `(("qtbase" ,qtbase)
-- 
cgit v1.2.3


From c1dc7858d7e460b17f13354cb75d3c9599b775f3 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 14:37:07 +0200
Subject: gnu: r-with-tests, r-minimal: Update to 4.0.0.

* gnu/packages/statistics.scm (r-with-tests, r-minimal): Update to 4.0.0.
(r-with-tests)[arguments]: Add phase "set-locales".
[native-inputs]: Add texlive-ae, texlive-inconsolata, and
texlive-latex-xkeyval to texlive-union.
[inputs]: Replace pcre with pcre2.
---
 gnu/packages/statistics.scm | 18 +++++++++++++-----
 1 file changed, 13 insertions(+), 5 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index b8e516f49c..f1cd024274 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -183,7 +183,7 @@ (define-public libxls
 (define r-with-tests
   (package
     (name "r-with-tests")
-    (version "3.6.3")
+    (version "4.0.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://cran/src/base/R-"
@@ -191,7 +191,7 @@ (define r-with-tests
                                   version ".tar.gz"))
               (sha256
                (base32
-                "13xaxwfbzj0bd6rn2n27z0n04lb93mcyq991w4vdbbg8v282jc49"))))
+                "0h1995smlyiyhx7gpg9paxsfqrcn6g9bbp5h9r47i6an3clv1gh6"))))
     (build-system gnu-build-system)
     (arguments
      `(#:disallowed-references (,tzdata-for-tests)
@@ -269,6 +269,11 @@ (define r-with-tests
                  (("my \\$date = strftime \"%B %Y\", localtime" line)
                   (string-append line " 1"))))
              #t))
+         (add-before 'build 'set-locales
+           (lambda _
+             (setlocale LC_ALL "C")
+             (setenv "LC_ALL" "C")
+             #t))
          (add-before 'configure 'set-default-pager
           ;; Set default pager to "cat", because otherwise it is "false",
           ;; making "help()" print nothing at all.
@@ -322,7 +327,9 @@ (define r-with-tests
        ("perl" ,perl)
        ("pkg-config" ,pkg-config)
        ("texinfo" ,texinfo) ; for building HTML manuals
-       ("texlive" ,(texlive-union (list texlive-fonts-ec
+       ("texlive" ,(texlive-union (list texlive-ae
+                                        texlive-inconsolata
+                                        texlive-fonts-ec
                                         texlive-amsfonts
                                         texlive-latex-base
                                         texlive-latex-fancyvrb
@@ -331,7 +338,8 @@ (define r-with-tests
                                         texlive-latex-oberdiek
                                         texlive-latex-tools
                                         texlive-latex-upquote
-                                        texlive-latex-url)))
+                                        texlive-latex-url
+                                        texlive-latex-xkeyval)))
        ("tzdata" ,tzdata-for-tests)
        ("xz" ,xz)))
     (inputs
@@ -347,7 +355,7 @@ (define r-with-tests
        ("libpng" ,libpng)
        ("libtiff" ,libtiff)
        ("libxt" ,libxt)
-       ("pcre" ,pcre)
+       ("pcre2" ,pcre2)
        ("readline" ,readline)
        ;; This avoids a reference to the ungraftable static bash.  R uses the
        ;; detected shell for the "system" procedure.
-- 
cgit v1.2.3


From 288ab9039be11d167f0bc7c502c244a4d6982735 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 14:38:56 +0200
Subject: gnu: r-foreign: Update to 0.8-78.

* gnu/packages/statistics.scm (r-foreign): Update to 0.8-78.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index f1cd024274..9c2f717195 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -512,14 +512,14 @@ (define-public r-codetools
 (define-public r-foreign
   (package
     (name "r-foreign")
-    (version "0.8-76")
+    (version "0.8-78")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "foreign" version))
        (sha256
         (base32
-         "1z6x2x1z12wnv0z4p74d91r5wfaq30sdz4ynwx0lncz1q45mhbh5"))))
+         "01anirfbfa3ip5pyqv72cg4x7p0jsppmbvxrllw7bm28fl1hgiyq"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/foreign")
     (synopsis "Read data stored by other statistics software")
-- 
cgit v1.2.3


From 666d97964ae3c96f416845a83155cadd35bdedb4 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 14:39:02 +0200
Subject: gnu: r-tibble: Update to 3.0.1.

* gnu/packages/statistics.scm (r-tibble): Update to 3.0.1.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 9c2f717195..083fbca7a7 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -1632,14 +1632,14 @@ (define-public r-rlang
 (define-public r-tibble
   (package
     (name "r-tibble")
-    (version "3.0.0")
+    (version "3.0.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tibble" version))
        (sha256
         (base32
-         "0s84h8ls5qwixbs1n5safr3xqmg3p0llzdrd9sp4vs2572mwzqzi"))))
+         "17m7xvn423snq9dmr0bhx42j5rbc53w1viizxx4bvq37nz7m4i8m"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-cli" ,r-cli)
-- 
cgit v1.2.3


From 568d1d7bfc4d47764bc6c63c036a6ba4f412d81f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 14:39:14 +0200
Subject: gnu: r-dbplyr: Update to 1.4.3.

* gnu/packages/statistics.scm (r-dbplyr): Update to 1.4.3.
[propagated-inputs]: Add r-lifecycle.
[native-inputs]: Add r-knitr.
---
 gnu/packages/statistics.scm | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 083fbca7a7..bba86279ad 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -1702,25 +1702,28 @@ (define-public r-dplyr
 (define-public r-dbplyr
   (package
     (name "r-dbplyr")
-    (version "1.4.2")
+    (version "1.4.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "dbplyr" version))
        (sha256
         (base32
-         "1q2dflr88s5a1amzfld3087q422vf70052qn84zyd8895kdg10xp"))))
+         "1si8sahr1kwq1xgjzi9klkahad07pyrsngy75y1f74f64907pb39"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-assertthat" ,r-assertthat)
        ("r-dbi" ,r-dbi)
        ("r-dplyr" ,r-dplyr)
        ("r-glue" ,r-glue)
+       ("r-lifecycle" ,r-lifecycle)
        ("r-purrr" ,r-purrr)
        ("r-r6" ,r-r6)
        ("r-rlang" ,r-rlang)
        ("r-tibble" ,r-tibble)
        ("r-tidyselect" ,r-tidyselect)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://github.com/tidyverse/dbplyr")
     (synopsis "Dplyr back end for databases")
     (description
-- 
cgit v1.2.3


From 7ef5f77b910fe44a36cb8057f8800d33d8672f32 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 14:39:41 +0200
Subject: gnu: r-xml2: Update to 1.3.2.

* gnu/packages/statistics.scm (r-xml2): Update to 1.3.2.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index bba86279ad..8d17bbe74a 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -2000,14 +2000,14 @@ (define-public r-ade4
 (define-public r-xml2
   (package
     (name "r-xml2")
-    (version "1.3.1")
+    (version "1.3.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "xml2" version))
        (sha256
         (base32
-         "0r7rxp922785dcryghbb3wxqgdav7mafwnmxjqfx8zaj3v1q2j3z"))))
+         "1kx400v62xkd5xal7rzz7jcarz94ac8g1sh4i2dqr78qwgkzj8nz"))))
     (build-system r-build-system)
     (inputs
      `(("libxml2" ,libxml2)
-- 
cgit v1.2.3


From 67aced632384e608cf6edbd29eea216d17cf8bfc Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 14:40:41 +0200
Subject: gnu: r-withr: Update to 2.2.0.

* gnu/packages/statistics.scm (r-withr): Update to 2.2.0.
[native-inputs]: Add r-knitr.
---
 gnu/packages/statistics.scm | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 8d17bbe74a..e27c8a6110 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -2457,14 +2457,16 @@ (define-public r-devtools
 (define-public r-withr
   (package
     (name "r-withr")
-    (version "2.1.2")
+    (version "2.2.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "withr" version))
               (sha256
                (base32
-                "11j6zykklxnvp4xqsr6a2xib665i38m3khdspp887nwagmvnydj1"))))
+                "10mmfffjbnb2zq5x0kqhhb4z6va4micc6pjzvlfji34gyhffa8ac"))))
     (build-system r-build-system)
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://github.com/jimhester/withr")
     (synopsis "Run code with temporarily modified global state")
     (description
-- 
cgit v1.2.3


From 0e3003930e0e302e641db7060893c06ad36f30c9 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 14:40:58 +0200
Subject: gnu: r-plotrix: Update to 3.7-8.

* gnu/packages/statistics.scm (r-plotrix): Update to 3.7-8.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index e27c8a6110..2c2179bff5 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -2527,13 +2527,13 @@ (define-public r-readr
 (define-public r-plotrix
   (package
     (name "r-plotrix")
-    (version "3.7-7")
+    (version "3.7-8")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "plotrix" version))
               (sha256
                (base32
-                "1x92mmyfry127zzr6cmcj6kjsc4zhxrrdlr0jcxn3bb0hpdfps54"))))
+                "104llmr6dvlcnfpmd8zbdlv63k79djc4qqgadjavj4v4cmz1zkcc"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/plotrix")
     (synopsis "Various plotting functions")
-- 
cgit v1.2.3


From d29cd83bd8f4bc76ab92cfe5503a5ab3276778cd Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 14:41:04 +0200
Subject: gnu: r-purrr: Update to 0.3.4.

* gnu/packages/statistics.scm (r-purrr): Update to 0.3.4.
[native-inputs]: Add r-knitr.
---
 gnu/packages/statistics.scm | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 2c2179bff5..6bf952734c 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -3756,18 +3756,20 @@ (define-public r-hexbin
 (define-public r-purrr
   (package
     (name "r-purrr")
-    (version "0.3.3")
+    (version "0.3.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "purrr" version))
        (sha256
         (base32
-         "17lyys7dxjrwsfkq7a7hw65iy3qn3pp1sn70srdy64jf8adahc8g"))))
+         "1cj091rsjdj2xz16qhynyw72gh5cyhznifcfbrbygndfr4xwksr3"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-magrittr" ,r-magrittr)
        ("r-rlang" ,r-rlang)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://github.com/hadley/purrr")
     (synopsis "Functional programming tools")
     (description
-- 
cgit v1.2.3


From befa394f454901c51a735acf495d701464823a38 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 16:22:21 +0200
Subject: gnu: Add r-ingredients.

* gnu/packages/cran.scm (r-ingredients): New variable.
---
 gnu/packages/cran.scm | 40 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 74e5fa2b1e..b8549ec3e3 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -15357,6 +15357,46 @@ (define-public r-dqrng
     ;; whole is distributed under the terms of the AGPL 3.
     (license license:agpl3)))
 
+(define-public r-ingredients
+  (package
+    (name "r-ingredients")
+    (version "1.2.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ingredients" version))
+       (sha256
+        (base32
+         "1q196y9xzn4wk44fa1bvh0hcbizgm93rwir82nyk31k5pgixk967"))))
+    (properties `((upstream-name . "ingredients")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-ggplot2" ,r-ggplot2)
+       ("r-gridextra" ,r-gridextra)
+       ("r-scales" ,r-scales)))
+    (native-inputs `(("r-knitr" ,r-knitr)))
+    (home-page "https://ModelOriented.github.io/ingredients/")
+    (synopsis "Effects and importances of model ingredients")
+    (description
+     "This is a collection of tools for assessment of feature importance and
+feature effects.  Key functions are:
+
+@itemize
+@item @code{feature_importance()} for assessment of global level feature
+  importance,
+@item @code{ceteris_paribus()} for calculation of the what-if plots,
+@item @code{partial_dependence()} for partial dependence plots,
+@item @code{conditional_dependence()} for conditional dependence plots,
+@item @code{accumulated_dependence()} for accumulated local effects plots,
+@item @code{aggregate_profiles()} and @code{cluster_profiles()} for
+  aggregation of ceteris paribus profiles,
+@item generic @code{print()} and @code{plot()} for better usability of
+  selected explainers,
+@item generic @code{plotD3()} for interactive, D3 based explanations, and
+@item generic @code{describe()} for explanations in natural language.
+@end itemize\n")
+    (license license:gpl3)))
+
 (define-public r-dalex
   (package
     (name "r-dalex")
-- 
cgit v1.2.3


From 50f298a54f4db6a34406ca475909b800c24fee69 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 16:22:32 +0200
Subject: gnu: Add r-ibreakdown.

* gnu/packages/cran.scm (r-ibreakdown): New variable.
---
 gnu/packages/cran.scm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index b8549ec3e3..f5e69fb1bc 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -15397,6 +15397,32 @@ (define-public r-ingredients
 @end itemize\n")
     (license license:gpl3)))
 
+(define-public r-ibreakdown
+  (package
+    (name "r-ibreakdown")
+    (version "1.2.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "iBreakDown" version))
+       (sha256
+        (base32
+         "0y4zjpyn8j76jrs5phjzs5lfq3lqjspmrwcksqv9wq0rbdgh14vk"))))
+    (properties `((upstream-name . "iBreakDown")))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
+    (native-inputs `(("r-knitr" ,r-knitr)))
+    (home-page "https://ModelOriented.github.io/iBreakDown/")
+    (synopsis "Model agnostic instance level variable attributions")
+    (description
+     "This package provides a model agnostic tool for decomposition of
+predictions from black boxes.  It supports additive attributions and
+attributions with interactions.  The Break Down Table shows contributions of
+every variable to a final prediction.  The Break Down Plot presents variable
+contributions in a concise graphical way.  This package works for
+classification and regression models.")
+    (license license:gpl3)))
+
 (define-public r-dalex
   (package
     (name "r-dalex")
-- 
cgit v1.2.3


From 92f5ed2fd79b2ff7147e91d0581b8cae8af2ed67 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 17:26:21 +0200
Subject: gnu: r-shinyfiles: Update to 0.8.0.

* gnu/packages/cran.scm (r-shinyfiles): Update to 0.8.0.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index f5e69fb1bc..819e55509d 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -1121,13 +1121,13 @@ (define-public r-shinydashboard
 (define-public r-shinyfiles
   (package
     (name "r-shinyfiles")
-    (version "0.7.5")
+    (version "0.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "shinyFiles" version))
        (sha256
-        (base32 "1143m941hma9hc77c3xcw26c0ygfhn9ii2sbp9wrydxv4gc7mr8a"))))
+        (base32 "0gwyx37f2r86cldsyknws9pafpj8g5mg3mchlyl9ymgnk5f4b88w"))))
     (properties `((upstream-name . "shinyFiles")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From d911e22af3f14ab1abc241c51687f6a1f102605a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 17:26:32 +0200
Subject: gnu: r-powerlaw: Update to 0.70.6.

* gnu/packages/cran.scm (r-powerlaw): Update to 0.70.6.
[propagated-inputs]: Remove r-vgam; add r-pracma.
[native-inputs]: Add r-knitr.
---
 gnu/packages/cran.scm | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 819e55509d..a23af8eb3e 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2004,17 +2004,19 @@ (define-public r-circlize
 (define-public r-powerlaw
   (package
     (name "r-powerlaw")
-    (version "0.70.4")
+    (version "0.70.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "poweRlaw" version))
        (sha256
-        (base32 "19zah9mx93az5lh9vicn3c8q1xb12g0w46dh5p901fbyimc32vwk"))))
+        (base32 "14d1myxllvm1grnfiszzzxaiqpb2jpmsi19wq70r8r2wki293h7g"))))
     (properties `((upstream-name . "poweRlaw")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-vgam" ,r-vgam)))
+     `(("r-pracma" ,r-pracma)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://github.com/csgillespie/poweRlaw")
     (synopsis "Tools for the analysis of heavy tailed distributions")
     (description
-- 
cgit v1.2.3


From 4c0cf66cfcca77001bc98109a13819d9f425b415 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 17:27:01 +0200
Subject: gnu: r-ff: Update to 2.2-14.2.

* gnu/packages/cran.scm (r-ff): Update to 2.2-14.2.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index a23af8eb3e..f242f1cff7 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2125,14 +2125,14 @@ (define-public r-fastmatch
 (define-public r-ff
   (package
     (name "r-ff")
-    (version "2.2-14")
+    (version "2.2-14.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ff" version))
        (sha256
         (base32
-         "1w724q4jpzbvzpilb2ifviaxkjgk9lzwxz9gksnvicbmfa20fqqw"))))
+         "1r1pbrf5s4rdm3msxxr8fy1f2xjihqciclsnvxf59qzz6g1nmh7q"))))
     (build-system r-build-system)
     (propagated-inputs `(("r-bit" ,r-bit)))
     (home-page "http://ff.r-forge.r-project.org/")
-- 
cgit v1.2.3


From 92d81a5e5b80a8c8522571804dc05c661b5eec63 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 17:27:07 +0200
Subject: gnu: r-distillery: Update to 1.0-7.

* gnu/packages/cran.scm (r-distillery): Update to 1.0-7.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index f242f1cff7..98512ef65d 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2389,14 +2389,14 @@ (define-public r-lmoments
 (define-public r-distillery
   (package
     (name "r-distillery")
-    (version "1.0-6")
+    (version "1.0-7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "distillery" version))
        (sha256
         (base32
-         "1mi3ig9jq0kd7yrwc5m37lmrw04p1b4lirnbsxi10z3n5yay4429"))))
+         "0w72vb3p51m0hwms9icwgy1xg3dplmpjrxibl2s92lpdrv737249"))))
     (build-system r-build-system)
     (home-page "https://ral.ucar.edu/staff/ericg/")
     (synopsis "Functions for confidence intervals and object information")
-- 
cgit v1.2.3


From 839c39b178d84e1d2d75d3a5a051edde5003063d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 17:27:15 +0200
Subject: gnu: r-broom: Update to 0.5.6.

* gnu/packages/cran.scm (r-broom): Update to 0.5.6.
[native-inputs]: Add r-knitr.
---
 gnu/packages/cran.scm | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 98512ef65d..ba4460c865 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -3222,14 +3222,14 @@ (define-public r-generics
 (define-public r-broom
   (package
     (name "r-broom")
-    (version "0.5.5")
+    (version "0.5.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "broom" version))
        (sha256
         (base32
-         "0n7zd64263kfavdi28rl2bxrsa00c3m4vjhhjdrfwvvmrcxj39fx"))))
+         "0da3jsb02xckrk6alznicn6l5lnyvdhc64qklyarnd77miqgc1hb"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-backports" ,r-backports)
@@ -3241,6 +3241,8 @@ (define-public r-broom
        ("r-stringr" ,r-stringr)
        ("r-tibble" ,r-tibble)
        ("r-tidyr" ,r-tidyr)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://github.com/tidyverse/broom")
     (synopsis "Convert statistical analysis objects into tidy data frames")
     (description
-- 
cgit v1.2.3


From e965442b381ff3408d5085c44c308be008945098 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 17:27:31 +0200
Subject: gnu: r-tsp: Update to 1.1-10.

* gnu/packages/cran.scm (r-tsp): Update to 1.1-10.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index ba4460c865..cda16a7c3a 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -4045,14 +4045,14 @@ (define-public r-processx
 (define-public r-tsp
   (package
     (name "r-tsp")
-    (version "1.1-9")
+    (version "1.1-10")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "TSP" version))
        (sha256
         (base32
-         "183m6crb0dv17llj86059n3hbgsahbhfcqlx0ijdzkssg11i1cy7"))))
+         "0z1v6m0vqjzxc4az3zyjaayygx0jr3mdmc56jjd421iqh0b9z5s4"))))
     (properties `((upstream-name . "TSP")))
     (build-system r-build-system)
     (propagated-inputs `(("r-foreach" ,r-foreach)))
-- 
cgit v1.2.3


From f1f77bb64e5b1b11c3e17434e7d37b1b0061a134 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 17:27:42 +0200
Subject: gnu: r-tinytex: Update to 0.22.

* gnu/packages/cran.scm (r-tinytex): Update to 0.22.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index cda16a7c3a..e31a222035 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -4314,14 +4314,14 @@ (define-public r-uuid
 (define-public r-tinytex
   (package
     (name "r-tinytex")
-    (version "0.21")
+    (version "0.22")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tinytex" version))
        (sha256
         (base32
-         "088zzc2v0izbcs45p19v547pi78vkr08ibpvvi1g9bkbya4x3mq9"))))
+         "0s9f62v3ps5f8903ar6kxlf1z3b4v78vlw1nb05bq55dgj8brg3b"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-xfun" ,r-xfun)))
-- 
cgit v1.2.3


From 35f84a7f2761dd4547c9fe6f12908963c7bf9579 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 17:27:50 +0200
Subject: gnu: r-insight: Update to 0.8.3.

* gnu/packages/cran.scm (r-insight): Update to 0.8.3.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index e31a222035..acf9e71cf5 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -6575,14 +6575,14 @@ (define-public r-prediction
 (define-public r-insight
   (package
     (name "r-insight")
-    (version "0.8.2")
+    (version "0.8.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "insight" version))
        (sha256
         (base32
-         "0fjf7dwpv1a7qfbzixppg348z1ksq19kdjm08vcb2am7w0k3plcj"))))
+         "0lm5a4r368mq1pwmxjk2xnz25lb9j4v7mdkl1bahk2alklxgb8yj"))))
     (build-system r-build-system)
     (native-inputs
      `(("r-knitr" ,r-knitr)))
-- 
cgit v1.2.3


From 09bb872aff9351ad3953fb5345bb9df5912bd54d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 17:27:54 +0200
Subject: gnu: r-raster: Update to 3.1-5.

* gnu/packages/cran.scm (r-raster): Update to 3.1-5.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index acf9e71cf5..84ec8727a3 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -7432,14 +7432,14 @@ (define-public r-mosaicdata
 (define-public r-raster
   (package
     (name "r-raster")
-    (version "3.0-12")
+    (version "3.1-5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "raster" version))
        (sha256
         (base32
-         "0rrbsigkqxsdic8fly6nrsc79zsliwvr1x2b4xqpl9d34vr50dvg"))))
+         "010sq00ijpmwac280ip9rryw0pxk0al8g675v2lc9rdrbgaj4rnv"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-rcpp" ,r-rcpp)
-- 
cgit v1.2.3


From 27588b365f05635d1e57f8193211eeb0715d2e14 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 17:28:03 +0200
Subject: gnu: r-emmeans: Update to 1.4.6.

* gnu/packages/cran.scm (r-emmeans): Update to 1.4.6.
[native-inputs]: Add r-knitr.
---
 gnu/packages/cran.scm | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 84ec8727a3..1520f72ffa 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -8443,14 +8443,14 @@ (define-public r-multcomp
 (define-public r-emmeans
   (package
     (name "r-emmeans")
-    (version "1.4.5")
+    (version "1.4.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "emmeans" version))
        (sha256
         (base32
-         "10fmvmd6q4zjr6b18hhc85mwrzv778qzj6lwl9kbs2fsfvsgw7mm"))))
+         "0mxk7ghlv4r6sna4897q1la2xgyn1dw3r9srhm9x4h5l4701avfa"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-estimability" ,r-estimability)
@@ -8458,6 +8458,8 @@ (define-public r-emmeans
        ("r-numderiv" ,r-numderiv)
        ("r-plyr" ,r-plyr)
        ("r-xtable" ,r-xtable)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://github.com/rvlenth/emmeans")
     (synopsis "Estimated marginal means, aka least-squares means")
     (description
-- 
cgit v1.2.3


From 09410f17d2eb0a5a151e0417b4206ad9c844f0eb Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 17:28:18 +0200
Subject: gnu: r-bayestestr: Update to 0.6.0.

* gnu/packages/cran.scm (r-bayestestr): Update to 0.6.0.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 1520f72ffa..9a2d455e4c 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -8678,14 +8678,14 @@ (define-public r-glmmtmb
 (define-public r-bayestestr
   (package
     (name "r-bayestestr")
-    (version "0.5.3")
+    (version "0.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "bayestestR" version))
        (sha256
         (base32
-         "1q24qh5p6bz4nbf4546kckh7d518x5pm1yhhbc8fwcnbca4kgqjz"))))
+         "0s7wdmk8avgaqk2b7fcf4bsh13isrkl1q4y7z2y8jhdagxxxnzd1"))))
     (properties `((upstream-name . "bayestestR")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From e2a50e5ec4859824557c6e63606541af8b4cf0d8 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 17:28:26 +0200
Subject: gnu: r-ggeffects: Update to 0.14.3.

* gnu/packages/cran.scm (r-ggeffects): Update to 0.14.3.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 9a2d455e4c..0b417e9c01 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -8732,14 +8732,14 @@ (define-public r-performance
 (define-public r-ggeffects
   (package
     (name "r-ggeffects")
-    (version "0.14.2")
+    (version "0.14.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ggeffects" version))
        (sha256
         (base32
-         "1y3yfb07jrr6vkc8hk6rp52l70dj7042jvqgjzllslzy7hx2jhyw"))))
+         "06p80bgjhjknzlb4vs4n41i9n9vv5agncakl9f92zkaahgyzd6sd"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-insight" ,r-insight)
-- 
cgit v1.2.3


From 71c0a61cac534992e27f87af610c1bdc1f264b67 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 17:28:33 +0200
Subject: gnu: r-rgl: Update to 0.100.54.

* gnu/packages/cran.scm (r-rgl): Update to 0.100.54.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 0b417e9c01..02a57850f9 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -9516,14 +9516,14 @@ (define-public r-biocmanager
 (define-public r-rgl
   (package
     (name "r-rgl")
-    (version "0.100.50")
+    (version "0.100.54")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rgl" version))
        (sha256
         (base32
-         "165p932ml7dpjkm41zc47p5cdxar69il0m5yvg0avi8q01vr17ay"))))
+         "1mgs2d8igmcdzzymfwbqdrypmaidd4pra5n5gnhsn9pm6pqzidqp"))))
     (build-system r-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)))
-- 
cgit v1.2.3


From d62d838bf9e0bcd4850c6e2f2513e5cd74c87c5e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 17:28:40 +0200
Subject: gnu: r-protviz: Update to 0.6.4.

* gnu/packages/cran.scm (r-protviz): Update to 0.6.4.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 02a57850f9..4a7cc14fae 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -11599,14 +11599,14 @@ (define-public r-rbamtools
 (define-public r-protviz
   (package
     (name "r-protviz")
-    (version "0.6.3")
+    (version "0.6.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "protViz" version))
        (sha256
         (base32
-         "1ldciqh3f43xr9663yyhd9r6qwrg4c4vmkprlcancbnd460wakg7"))))
+         "1qq9bf4485x8cviry9fmhnv4hw9aw657w134003myzcv42c4pml6"))))
     (properties `((upstream-name . "protViz")))
     (build-system r-build-system)
     (propagated-inputs `(("r-rcpp" ,r-rcpp)))
-- 
cgit v1.2.3


From fbcbf8d5862ad003376bf039b35f023e04adbe21 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 17:28:50 +0200
Subject: gnu: r-future: Update to 1.17.0.

* gnu/packages/cran.scm (r-future): Update to 1.17.0.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 4a7cc14fae..6dac025b90 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -11857,14 +11857,14 @@ (define-public r-globals
 (define-public r-future
   (package
     (name "r-future")
-    (version "1.16.0")
+    (version "1.17.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "future" version))
        (sha256
         (base32
-         "1xaqh0b2knf5bp23mc0kriq0iqhqna31q3b7d960piqjhzrb03dm"))))
+         "0d4y7gwcgqx2z0y6h5bh4lrz0m7b0inii5cjcq0kk8za762bi8rg"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-digest" ,r-digest)
-- 
cgit v1.2.3


From c6eb1fe616a4eb8c487b994d3d1aec2f930e78ff Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 17:28:55 +0200
Subject: gnu: r-etm: Update to 1.1.

* gnu/packages/cran.scm (r-etm): Update to 1.1.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 6dac025b90..5f1089e36f 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -11649,14 +11649,14 @@ (define-public r-cmprsk
 (define-public r-etm
   (package
     (name "r-etm")
-    (version "1.0.5.1")
+    (version "1.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "etm" version))
        (sha256
         (base32
-         "0m41pm277sd50pharigcqzr1a2g92wnmdf6fcab6fx16ia2fzrm7"))))
+         "02yvh473l5qajaymhsxwb235a9r7q3nsig9a9mrfca68xih8yvgd"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-data-table" ,r-data-table)
-- 
cgit v1.2.3


From 5123ec7858528c323898c99895e891af244a4f67 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 17:29:00 +0200
Subject: gnu: r-future-apply: Update to 1.5.0.

* gnu/packages/cran.scm (r-future-apply): Update to 1.5.0.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 5f1089e36f..8ff6bcbe2d 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -11889,14 +11889,14 @@ (define-public r-future
 (define-public r-future-apply
   (package
     (name "r-future-apply")
-    (version "1.4.0")
+    (version "1.5.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "future.apply" version))
        (sha256
         (base32
-         "1kgq6dv96hdy35kysqkn606nj7s9dp4ibgpm6n46gqhc5n75lzkk"))))
+         "095a681ngbwbp7v53ladwya7ar8fgwnlgr3r1yklf3vdxwd54xll"))))
     (properties `((upstream-name . "future.apply")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From bf4e440c194ddff9ea8dcc0a9a9713bd65d4ad6c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 17:29:05 +0200
Subject: gnu: r-sf: Update to 0.9-2.

* gnu/packages/cran.scm (r-sf): Update to 0.9-2.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 8ff6bcbe2d..ac979a3a4a 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -13355,14 +13355,14 @@ (define-public r-deldir
 (define-public r-sf
   (package
     (name "r-sf")
-    (version "0.9-1")
+    (version "0.9-2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "sf" version))
        (sha256
         (base32
-         "1qghrskqwwlwxmmvkv7knhlr1a32ngyimycasy5gfazgviljsfn4"))))
+         "01xplgy5nlwy3ajfch4h1ssa1xhm7q0jzscpz04dmvgqfzwhhdfh"))))
     (build-system r-build-system)
     (inputs
      `(("gdal" ,gdal)
-- 
cgit v1.2.3


From 838ec254a0aada2c95906d8ea29ab9ee5390032f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 17:29:09 +0200
Subject: gnu: r-optparse: Update to 1.6.6.

* gnu/packages/cran.scm (r-optparse): Update to 1.6.6.
[native-inputs]: Add r-knitr.
---
 gnu/packages/cran.scm | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index ac979a3a4a..75adaa24ff 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -13851,17 +13851,19 @@ (define-public r-bookdown
 (define-public r-optparse
   (package
     (name "r-optparse")
-    (version "1.6.4")
+    (version "1.6.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "optparse" version))
        (sha256
         (base32
-         "0wyrc42ja3ab5szx46zmz8lm7vzfqxkjca0m0sms8g9hqbmmay6d"))))
+         "1l301dy3gc8pn7j00awcjh41wmc1ks9kswak255kbsa6f54rsxsi"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-getopt" ,r-getopt)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://github.com/trevorld/optparse")
     (synopsis "Command line option parser")
     (description
-- 
cgit v1.2.3


From 1816cb262c6cdb7c3b443b90311b0695594d38a2 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 17:29:23 +0200
Subject: gnu: r-rex: Update to 1.2.0.

* gnu/packages/cran.scm (r-rex): Update to 1.2.0.
[propagated-inputs]: Remove r-magrittr.
[native-inputs]: Add r-knitr.
---
 gnu/packages/cran.scm | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 75adaa24ff..13a7cb56b5 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -15023,18 +15023,19 @@ (define-public r-downloader
 (define-public r-rex
   (package
     (name "r-rex")
-    (version "1.1.2")
+    (version "1.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rex" version))
        (sha256
         (base32
-         "0alsadgjgass3wr8y5d247j12qqzg454sc84vpskclrkmz778g5x"))))
+         "0m7bq8db3m5dhf01rw7xc7xy1ciq3m7dfgsl80p8cy4h8vqr3d06"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-lazyeval" ,r-lazyeval)
-       ("r-magrittr" ,r-magrittr)))
+     `(("r-lazyeval" ,r-lazyeval)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://github.com/kevinushey/rex")
     (synopsis "Friendly regular expressions")
     (description
-- 
cgit v1.2.3


From 8165bf6d902c2e4b0a89f96f2f3f29ab3d24f6bb Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 17:29:48 +0200
Subject: gnu: r-dalex: Update to 1.2.0.

* gnu/packages/cran.scm (r-dalex): Update to 1.2.0.
[propagated-inputs]: Add r-ibreakdown and r-ingredients.
---
 gnu/packages/cran.scm | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 13a7cb56b5..87a4cc0517 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -15435,17 +15435,20 @@ (define-public r-ibreakdown
 (define-public r-dalex
   (package
     (name "r-dalex")
-    (version "1.0.1")
+    (version "1.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "DALEX" version))
        (sha256
         (base32
-         "1jbyn57vn6d281a5y15h5d8ljin8cdb9lr7lbgggc950blyfv4g0"))))
+         "0mfcci54622gnk8al9fl2jhs9i2vfly7lam04y5rdacbyiam49j6"))))
     (properties `((upstream-name . "DALEX")))
     (build-system r-build-system)
-    (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
+    (propagated-inputs
+     `(("r-ggplot2" ,r-ggplot2)
+       ("r-ibreakdown" ,r-ibreakdown)
+       ("r-ingredients" ,r-ingredients)))
     (home-page "https://pbiecek.github.io/DALEX/")
     (synopsis "Descriptive machine learning explanations")
     (description
-- 
cgit v1.2.3


From 5ffe706b84c2bb870410a3841a29e68a2b5d4683 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 17:30:10 +0200
Subject: gnu: r-systemfonts: Update to 0.2.0.

* gnu/packages/cran.scm (r-systemfonts): Update to 0.2.0.
[inputs]: Remove freetype.
[native-inputs]: Add r-knitr.
---
 gnu/packages/cran.scm | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 87a4cc0517..5058079249 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -16026,22 +16026,22 @@ (define-public r-covr
 (define-public r-systemfonts
   (package
     (name "r-systemfonts")
-    (version "0.1.1")
+    (version "0.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "systemfonts" version))
        (sha256
         (base32
-         "0m0ljid683xcam2f14x7k2zv1yx4npac38a3gfv11vhxfbnpgp0z"))))
+         "1aba07djvxqdmnsdbwvzcsbm2fddnhrssa54xyrlviiwsv2c1qsd"))))
     (properties `((upstream-name . "systemfonts")))
     (build-system r-build-system)
     (inputs
      `(("fontconfig" ,fontconfig)
-       ("freetype" ,freetype)
        ("zlib" ,zlib)))
     (native-inputs
-     `(("pkg-config" ,pkg-config)))
+     `(("pkg-config" ,pkg-config)
+       ("r-knitr" ,r-knitr)))
     (home-page "https://github.com/r-lib/systemfonts")
     (synopsis "System native font finding")
     (description
-- 
cgit v1.2.3


From 169f9fe13a4afd7ea4d51d26ce676e6eeb51f160 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 17:30:40 +0200
Subject: gnu: Add r-qgam.

* gnu/packages/cran.scm (r-qgam): New variable.
---
 gnu/packages/cran.scm | 33 +++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 5058079249..3b20ced31a 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -16949,6 +16949,39 @@ (define-public r-abstractr
 included.")
     (license license:gpl3)))
 
+(define-public r-qgam
+  (package
+    (name "r-qgam")
+    (version "1.3.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "qgam" version))
+       (sha256
+        (base32
+         "0lks2cj0p7irp1i01756v1l7i26d7alax1fbkc20qd6wpz840fi7"))))
+    (properties `((upstream-name . "qgam")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-doparallel" ,r-doparallel)
+       ("r-mgcv" ,r-mgcv)
+       ("r-plyr" ,r-plyr)
+       ("r-shiny" ,r-shiny)))
+    (native-inputs `(("r-knitr" ,r-knitr)))
+    (home-page "https://cran.r-project.org/web/packages/qgam/")
+    (synopsis "Smooth additive quantile regression models")
+    (description
+     "This package provides smooth additive quantile regression models, fitted
+using the methods of Fasiolo et al. (2017).  Differently from @code{quantreg},
+the smoothing parameters are estimated automatically by marginal loss
+minimization, while the regression coefficients are estimated using either
+PIRLS or Newton algorithm.  The learning rate is determined so that the
+Bayesian credible intervals of the estimated effects have approximately the
+correct coverage.  The main function is @code{qgam()} which is similar to
+@code{gam()} in the @code{mgcv} package, but fits non-parametric quantile
+regression models.")
+    (license license:gpl2+)))
+
 (define-public r-abtest
   (package
     (name "r-abtest")
-- 
cgit v1.2.3


From e1fe5e9bed78de5a64af326b562940092c2a49ea Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 17:30:46 +0200
Subject: gnu: r-abtest: Update to 0.2.1.

* gnu/packages/cran.scm (r-abtest): Update to 0.2.1.
[propagated-inputs]: Add r-qgam; remove r-vgam.
---
 gnu/packages/cran.scm | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 3b20ced31a..51825645a4 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -16985,25 +16985,25 @@ (define-public r-qgam
 (define-public r-abtest
   (package
     (name "r-abtest")
-    (version "0.2.0")
+    (version "0.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "abtest" version))
        (sha256
         (base32
-         "1ky3cf827kj24bhcpk00v5zl5jdkii1gca0x81ay1cjkzfispgws"))))
+         "1zfd13d7dplawk24dbdr1ka8cbdp5w6sxb0zlm7k4dhvn6ksi8h0"))))
     (properties `((upstream-name . "abtest")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-matrix" ,r-matrix)
        ("r-mvtnorm" ,r-mvtnorm)
        ("r-plotrix" ,r-plotrix)
+       ("r-qgam" ,r-qgam)
        ("r-rcolorbrewer" ,r-rcolorbrewer)
        ("r-rcpp" ,r-rcpp)
        ("r-sn" ,r-sn)
-       ("r-truncnorm" ,r-truncnorm)
-       ("r-vgam" ,r-vgam)))
+       ("r-truncnorm" ,r-truncnorm)))
     (home-page "https://cran.r-project.org/web/packages/abtest/")
     (synopsis "Bayesian A/B testing")
     (description
-- 
cgit v1.2.3


From 2c439cae92dc21192f8a33ca632d26d84af3844e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 17:31:09 +0200
Subject: gnu: r-fda: Update to 5.1.4.

* gnu/packages/cran.scm (r-fda): Update to 5.1.4.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 51825645a4..7ba591c607 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -18333,14 +18333,14 @@ (define-public r-actfrag
 (define-public r-fda
   (package
     (name "r-fda")
-    (version "2.4.8.1")
+    (version "5.1.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "fda" version))
        (sha256
         (base32
-         "0g50kj1dx7zarjv0lgwyzd2c7bv6di7nkndmywday5vjywgl8m7a"))))
+         "0js4ggl3aiwsqk6npwz72yhcznkb63smddds24ngf6a0p8yp5p2x"))))
     (properties `((upstream-name . "fda")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 1d9e71ed299ef048bbf4fe4ead43c8dae8e92885 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 17:31:17 +0200
Subject: gnu: r-stopwords: Update to 2.0.

* gnu/packages/cran.scm (r-stopwords): Update to 2.0.
[propagated-inputs]: Add r-desc and r-usethis.
---
 gnu/packages/cran.scm | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 7ba591c607..aaf3cd6618 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19739,17 +19739,20 @@ (define-public r-isocodes
 (define-public r-stopwords
   (package
     (name "r-stopwords")
-    (version "1.0")
+    (version "2.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "stopwords" version))
        (sha256
         (base32
-         "1nmi0bpd0c238g5b8ch1v034m5ng9llhs519cgxdrj3sh9fplwlv"))))
+         "155g00ansyqfpp1mzd2q6mn0k214xinf78nww2368h24kz761jjw"))))
     (properties `((upstream-name . "stopwords")))
     (build-system r-build-system)
-    (propagated-inputs `(("r-isocodes" ,r-isocodes)))
+    (propagated-inputs
+     `(("r-desc" ,r-desc)
+       ("r-isocodes" ,r-isocodes)
+       ("r-usethis" ,r-usethis)))
     (home-page "https://github.com/quanteda/stopwords")
     (synopsis "Multilingual stopword lists")
     (description
-- 
cgit v1.2.3


From ed720abc2605248590222f9a6e07501af3895cd0 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 17:31:35 +0200
Subject: gnu: r-topicmodels: Update to 0.2-11.

* gnu/packages/cran.scm (r-topicmodels): Update to 0.2-11.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index aaf3cd6618..baf1e0c18a 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -19856,14 +19856,14 @@ (define-public r-quanteda
 (define-public r-topicmodels
   (package
     (name "r-topicmodels")
-    (version "0.2-9")
+    (version "0.2-11")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "topicmodels" version))
        (sha256
         (base32
-         "1757r5x8bsl4dk106xg6481mvdkdz9vwg87n7rpbvdkavsvhyxs0"))))
+         "0jmp6wva99y0w40cfw7b0faylndhjam097x36ilc4vmyczcv89lw"))))
     (properties `((upstream-name . "topicmodels")))
     (build-system r-build-system)
     (native-inputs
-- 
cgit v1.2.3


From cda0683295210544e095aaa3828b679b74bb80ae Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 17:31:42 +0200
Subject: gnu: r-seurat: Update to 3.1.5.

* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.1.5.
[propagated-inputs]: Remove r-metap.
---
 gnu/packages/bioinformatics.scm | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 7b24d8bb64..bceea38087 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9716,13 +9716,13 @@ (define-public r-msnid
 (define-public r-seurat
   (package
     (name "r-seurat")
-    (version "3.1.4")
+    (version "3.1.5")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "Seurat" version))
               (sha256
                (base32
-                "0lhjbjhv1hnx5i3gkx41k68i8ykay3f24708h30wx9xywww9lsvi"))))
+                "1lbq2pqhb6ih6iqawlnzdh05zff71pwbw1cpfv2sld3pd7kz0zkm"))))
     (properties `((upstream-name . "Seurat")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9744,7 +9744,6 @@ (define-public r-seurat
        ("r-lmtest" ,r-lmtest)
        ("r-mass" ,r-mass)
        ("r-matrix" ,r-matrix)
-       ("r-metap" ,r-metap)
        ("r-patchwork" ,r-patchwork)
        ("r-pbapply" ,r-pbapply)
        ("r-plotly" ,r-plotly)
-- 
cgit v1.2.3


From 9c726c485a576d89ace6f789cfb778ecc6d76b49 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 27 Apr 2020 17:31:56 +0200
Subject: gnu: r-hdf5array: Update to 1.14.4.

* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.14.4.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index bceea38087..48b4ade7d8 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10689,14 +10689,14 @@ (define-public r-hitc
 (define-public r-hdf5array
   (package
     (name "r-hdf5array")
-    (version "1.14.3")
+    (version "1.14.4")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "HDF5Array" version))
        (sha256
         (base32
-         "1z153a7nxmlml72pl1saasj2il9g5ahpynkpv3mkhhsvl5kbwbh6"))))
+         "0ib0grhd9zbrn0dkrm4aa7qj7h0y6z1dvyx1ab3w6vczw7xghsfb"))))
     (properties `((upstream-name . "HDF5Array")))
     (build-system r-build-system)
     (inputs
-- 
cgit v1.2.3


From 0877b74f6e5ee30ce36caea57e3f165e1cd4a731 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 28 Apr 2020 00:24:38 +0200
Subject: gnu: kaldi: Update to 0-2.d4791c0.

* gnu/packages/machine-learning.scm (kaldi): Update to 0-2.d4791c0.
---
 gnu/packages/machine-learning.scm | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 223d03e979..1072930bfa 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2015, 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016, 2020 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016, 2017, 2020 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
@@ -1056,8 +1056,8 @@ (define-public python2-fastlmm
 
 ;; There have been no proper releases yet.
 (define-public kaldi
-  (let ((commit "2f95609f0bb085bd3a1dc5eb0a39f3edea59e606")
-        (revision "1"))
+  (let ((commit "d4791c0f3fc1a09c042dac365e120899ee2ad21e")
+        (revision "2"))
     (package
       (name "kaldi")
       (version (git-version "0" revision commit))
@@ -1069,7 +1069,7 @@ (define-public kaldi
                 (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "082qh3pfi7hvncylp4xsmkfahbd7gb0whdfa4rwrx7fxk9rdh3kz"))))
+                  "07k80my6f19mhrkwbzhjsnpf9871wmrwkl0ym468i830w67qyjrz"))))
       (build-system gnu-build-system)
       (arguments
        `(#:test-target "test"
-- 
cgit v1.2.3


From b3cf5f8601dd3e35295f0bc2f5193a12fb51ede6 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 28 Apr 2020 08:42:39 +0200
Subject: gnu: gst-kaldi-nnet2-online: Update to 0-2.cb227ef.

* gnu/packages/machine-learning.scm (gst-kaldi-nnet2-online): Update to
0-2.cb227ef.
---
 gnu/packages/machine-learning.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 1072930bfa..0f960ada95 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -1167,8 +1167,8 @@ (define-public kaldi
       (license license:asl2.0))))
 
 (define-public gst-kaldi-nnet2-online
-  (let ((commit "617e43e73c7cc45eb9119028c02bd4178f738c4a")
-        (revision "1"))
+  (let ((commit "cb227ef43b66a9835c14eb0ad39e08ee03c210ad")
+        (revision "2"))
     (package
       (name "gst-kaldi-nnet2-online")
       (version (git-version "0" revision commit))
@@ -1180,7 +1180,7 @@ (define-public gst-kaldi-nnet2-online
                 (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "0xh3w67b69818s6ib02ara4lw7wamjdmh4jznvkpzrs4skbs9jx9"))))
+                  "1i6ffwiavxx07ri0lxix6s8q0r31x7i4xxvhys5jxkixf5q34w8g"))))
       (build-system gnu-build-system)
       (arguments
        `(#:tests? #f                    ; there are none
-- 
cgit v1.2.3


From d9e9a2617664ae830c77e8a64aa733400a57c566 Mon Sep 17 00:00:00 2001
From: Konrad Hinsen <konrad.hinsen@fastmail.net>
Date: Fri, 24 Apr 2020 14:36:20 +0200
Subject: gnu: python-scikit-learn: Make python-joblib a propagated input.

* gnu/packages/machine-learning.scm (python-scikit-learn)
[native-inputs]: Move 'python-joblib' to ...
[propagated-inputs]: ... here.

Signed-off-by: Mathieu Othacehe <m.othacehe@gmail.com>
---
 gnu/packages/machine-learning.scm | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 0f960ada95..f979a64d55 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -13,6 +13,7 @@
 ;;; Copyright © 2019 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;; Copyright © 2019 Guillaume Le Vaillant <glv@posteo.net>
 ;;; Copyright © 2019 Brett Gilio <brettg@gnu.org>
+;;; Copyright © 2020 Konrad Hinsen <konrad.hinsen@fastmail.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -835,13 +836,13 @@ (define-public python-scikit-learn
     (inputs
      `(("openblas" ,openblas)))
     (native-inputs
-     `(("python-joblib" ,python-joblib)
-       ("python-pytest" ,python-pytest)
+     `(("python-pytest" ,python-pytest)
        ("python-pandas" ,python-pandas) ;for tests
        ("python-cython" ,python-cython)))
     (propagated-inputs
      `(("python-numpy" ,python-numpy)
-       ("python-scipy" ,python-scipy)))
+       ("python-scipy" ,python-scipy)
+       ("python-joblib" ,python-joblib)))
     (home-page "https://scikit-learn.org/")
     (synopsis "Machine Learning in Python")
     (description
-- 
cgit v1.2.3


From 0ae85052889d47c4ede88bb34c4b00b3e557e1d9 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Tue, 28 Apr 2020 10:11:22 +0200
Subject: gnu: hpcguix-web: Use guile3.0-guix.

* gnu/packages/web.scm (hpcguix-web): Update to latest revision and use
  guile3.0 inputs.
---
 gnu/packages/web.scm | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index 16e2832a62..f5189dc7f9 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -7153,8 +7153,8 @@ (define-public nghttp2-1.40
                "0wwhwv7cvi1vxpdjwvg0kpa4jzhszclpnwrwfcw728zz53a47z09"))))))
 
 (define-public hpcguix-web
-  (let ((commit "f39c90b35e99e4122b0866ec4337020d61c81508")
-        (revision "4"))
+  (let ((commit "9de63562b06b4aef3a3afe5ecb18d3c91e57ee74")
+        (revision "5"))
     (package
       (name "hpcguix-web")
       (version (git-version "0.0.1" revision commit))
@@ -7166,7 +7166,7 @@ (define-public hpcguix-web
                 (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "0idzzlwnaymk6hm5q9nh146h5m6vd8acp32vlmzp6qq08mimfkq7"))))
+                  "0wjgj2s7v2cyz6dx24c111rxs99i84sfvxl4ch8brnh02j2606jz"))))
       (build-system gnu-build-system)
       (arguments
        `(#:modules ((guix build gnu-build-system)
@@ -7222,11 +7222,11 @@ (define-public hpcguix-web
          ("uglify-js" ,uglify-js)
          ("pkg-config" ,pkg-config)))
       (inputs
-       `(("guix" ,guix)))
+       `(("guix" ,guile3.0-guix)))
       (propagated-inputs
-       `(("guile" ,guile-2.2)
-         ("guile-commonmark" ,guile-commonmark)
-         ("guile-json" ,guile-json-3)))
+       `(("guile" ,guile-next)
+         ("guile-commonmark" ,guile3.0-commonmark)
+         ("guile-json" ,guile3.0-json)))
       (home-page "https://github.com/UMCUGenetics/hpcguix-web")
       (synopsis "Web interface for cluster deployments of Guix")
       (description "Hpcguix-web provides a web interface to the list of packages
-- 
cgit v1.2.3


From 79c4fb4f366cff3ad75982b4a09c6bd82e604674 Mon Sep 17 00:00:00 2001
From: Christopher Howard <christopher@librehacker.com>
Date: Tue, 28 Apr 2020 10:06:34 +0200
Subject: gnu: Add hackrf.

* gnu/packages/radio.scm (hackrf): New variable.

Co-authored-by: Guillaume Le Vaillant <glv@posteo.net>
---
 gnu/packages/radio.scm | 69 +++++++++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 68 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm
index b748aa4183..24ee67017a 100644
--- a/gnu/packages/radio.scm
+++ b/gnu/packages/radio.scm
@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2017, 2018, 2019 Arun Isaac <arunisaac@systemreboot.net>
-;;; Copyright © 2019 Christopher Howard <christopher@librehacker.com>
+;;; Copyright © 2019, 2020 Christopher Howard <christopher@librehacker.com>
 ;;; Copyright © 2019, 2020 Evan Straw <evan.straw99@gmail.com>
 ;;; Copyright © 2020 Guillaume Le Vaillant <glv@posteo.net>
 ;;; Copyright © 2020 Danny Milosavljevic <dannym@scratchpost.org>
@@ -654,6 +654,73 @@ (define-public flwrap
     (home-page "http://www.w1hkj.com/")
     (license license:gpl3+)))
 
+(define-public hackrf
+  ;; Using a git commit because there have been many many commits
+  ;; since the relase two years ago, but no sign of a promised
+  ;; release for many months now.
+  (let ((commit "43e6f99fe8543094d18ff3a6550ed2066c398862")
+        (revision "0"))
+    (package
+     (name "hackrf")
+     (version (git-version "2018.01.1" revision commit))
+     (source
+      (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/mossmann/hackrf.git")
+             (commit commit)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0avnv693xi0zsnrvkbfn0ln1r3s1iyj0bz7sc3gxay909av0pvbc"))))
+     (build-system cmake-build-system)
+     (arguments
+      '(#:configure-flags
+        (list "-DUDEV_RULES_GROUP=dialout"
+              (string-append "-DUDEV_RULES_PATH="
+                             (assoc-ref %outputs "out")
+                             "/lib/udev/rules.d"))
+        #:phases
+        (modify-phases %standard-phases
+          (add-before 'configure 'enter-source-directory
+            (lambda _
+              (chdir "host")
+              #t))
+          (add-after 'install 'delete-static-library
+            (lambda* (#:key outputs #:allow-other-keys)
+              (delete-file (string-append (assoc-ref outputs "out")
+                                          "/lib/libhackrf.a"))
+              #t))
+          (add-before 'install-license-files 'leave-source-directory
+            (lambda _
+              (chdir "..")
+              #t)))
+        #:tests? #f)) ; no test suite
+     (native-inputs
+      `(("pkg-config" ,pkg-config)))
+     (inputs
+      `(("fftw" ,fftw)
+        ("fftwf" ,fftwf)
+        ("libusb" ,libusb)))
+     (home-page "https://greatscottgadgets.com/hackrf/")
+     (synopsis "User-space library and utilities for HackRF SDR")
+     (description
+      "Command line utilities and a C library for controlling the HackRF
+Software Defined Radio (SDR) over USB.  Installing this package installs
+the userspace hackrf utilities and C library.  To install the hackrf
+udev rules, you must add this package as a system service via
+modify-services.  E.g.:
+
+@lisp
+(services
+ (modify-services
+  %desktop-services
+  (udev-service-type config =>
+   (udev-configuration (inherit config)
+    (rules (cons hackrf
+            (udev-configuration-rules config)))))))
+@end lisp")
+     (license license:gpl2))))
+
 (define-public hamlib
   (package
     (name "hamlib")
-- 
cgit v1.2.3


From 62d45e463c3b1ecad90004c47356cba342dd23d8 Mon Sep 17 00:00:00 2001
From: Guillaume Le Vaillant <glv@posteo.net>
Date: Tue, 28 Apr 2020 10:10:16 +0200
Subject: gnu: gnuradio-osmosdr: Add hackrf support.

* gnu/packages/radio.scm (gnuradio-osmosdr)[inputs]: Add hackrf.
---
 gnu/packages/radio.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm
index 24ee67017a..4e11dda40a 100644
--- a/gnu/packages/radio.scm
+++ b/gnu/packages/radio.scm
@@ -399,8 +399,8 @@ (define-public gnuradio-osmosdr
        ("fftwf" ,fftwf)
        ("gmp" ,gmp)
        ("gnuradio" ,gnuradio)
+       ("hackrf" ,hackrf)
        ("log4cpp" ,log4cpp)
-       ;; TODO: Add more drivers.
        ("rtl-sdr" ,rtl-sdr)
        ("volk" ,volk)))
     (synopsis "GNU Radio block for interfacing with various radio hardware")
-- 
cgit v1.2.3


From ef3cc2d8833b0ec46b26c32413245ef8a8086e66 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Tue, 28 Apr 2020 10:37:10 +0200
Subject: gnu: Add emacs-trashed.

* gnu/packages/emacs-xyz.scm (emacs-trashed): New variable.
---
 gnu/packages/emacs-xyz.scm | 25 ++++++++++++++++++++++++-
 1 file changed, 24 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm
index a0275cbe18..0ae3f72fb7 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -34,7 +34,7 @@
 ;;; Copyright © 2017, 2018, 2019 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;; Copyright © 2018 Sohom Bhattacharjee <soham.bhattacharjee15@gmail.com>
 ;;; Copyright © 2018, 2019 Mathieu Lirzin <mthl@gnu.org>
-;;; Copyright © 2018, 2019 Pierre Neidhardt <mail@ambrevar.xyz>
+;;; Copyright © 2018, 2019, 2020 Pierre Neidhardt <mail@ambrevar.xyz>
 ;;; Copyright © 2018, 2019 Tim Gesthuizen <tim.gesthuizen@yahoo.de>
 ;;; Copyright © 2018, 2019 Jack Hill <jackhill@jackhill.us>
 ;;; Copyright © 2018 Pierre-Antoine Rouby <pierre-antoine.rouby@inria.fr>
@@ -22585,3 +22585,26 @@ (define-public emacs-uml-mode
 comments or emails.")
       (license license:gpl3+))))
 
+(define-public emacs-trashed
+  (package
+    (name "emacs-trashed")
+    (version "1.9.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/shingo256/trashed/")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "13grdi12iwlw4fiphdfmvclfpbr6ajlgfbfyi7v41z8k3rxz4ypz"))))
+    (build-system emacs-build-system)
+    (home-page "https://github.com/shingo256/trashed/")
+    (synopsis "View and edit system trash can in Emacs")
+    (description "Open, view, browse, restore or permanently delete trashed
+files or directories in trash can with Dired-like look and feel.  The trash
+can has to be compliant with freedesktop.org. In Emacs, you can trash files by
+deleting them with @code{(setq delete-by-moving-to-trash t)}.  This package
+provides a simple but convenient user interface to manage those trashed
+files.")
+    (license license:gpl3+)))
-- 
cgit v1.2.3


From eac71f54fe561aadc02067d114c8f32ff3f359cb Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Tue, 28 Apr 2020 10:42:44 +0200
Subject: gnu: sbcl-cl-cffi-gtk-gobject: Link source to parent to reduce
 closure size.

* gnu/packages/lisp-xyz.scm (sbcl-cl-cffi-gtk-gobject)[arguments]: Replace source
  folder with link to the same folder in the sbcl-cl-cffi-gtk-glib dependency.
---
 gnu/packages/lisp-xyz.scm | 15 ++++++++++++++-
 1 file changed, 14 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm
index cc9bda8ac6..b8efaf985f 100644
--- a/gnu/packages/lisp-xyz.scm
+++ b/gnu/packages/lisp-xyz.scm
@@ -2916,7 +2916,20 @@ (define-public sbcl-cl-cffi-gtk-gobject
            (lambda* (#:key inputs #:allow-other-keys)
              (substitute* "gobject/gobject.init.lisp"
                (("libgobject" all) (string-append
-                                    (assoc-ref inputs "glib") "/lib/" all))))))))))
+                                    (assoc-ref inputs "glib") "/lib/" all)))))
+         (add-after 'install 'link-source
+           ;; Since source is particularly heavy (16MiB+), let's reuse it
+           ;; across the different components of cl-ffi-gtk.
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((glib-source (string-append (assoc-ref inputs "cl-cffi-gtk-glib")
+                                               "/share/common-lisp/sbcl-source/"
+                                               "cl-cffi-gtk-glib"))
+                   (out-source (string-append (assoc-ref outputs "out")
+                                              "/share/common-lisp/sbcl-source/"
+                                              "cl-cffi-gtk-gobject")))
+               (delete-file-recursively out-source)
+               (symlink glib-source out-source)
+               #t))))))))
 
 (define-public sbcl-cl-cffi-gtk-gio
   (package
-- 
cgit v1.2.3


From 6a7f36686499086086b23cb7238c91c899de7f67 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Tue, 28 Apr 2020 10:44:47 +0200
Subject: gnu: sbcl-cl-cffi-gtk-gio: Link source to parent to reduce closure
 size.

* gnu/packages/lisp-xyz.scm (sbcl-cl-cffi-gtk-gio)[arguments]: Replace source
  folder with link to the same folder in the sbcl-cl-cffi-gtk-glib dependency.
---
 gnu/packages/lisp-xyz.scm | 15 ++++++++++++++-
 1 file changed, 14 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm
index b8efaf985f..fbb502cc73 100644
--- a/gnu/packages/lisp-xyz.scm
+++ b/gnu/packages/lisp-xyz.scm
@@ -2949,7 +2949,20 @@ (define-public sbcl-cl-cffi-gtk-gio
              (substitute* "gio/gio.init.lisp"
                (("libgio" all)
                 (string-append
-                 (assoc-ref inputs "glib") "/lib/" all))))))))))
+                 (assoc-ref inputs "glib") "/lib/" all)))))
+         (add-after 'install 'link-source
+           ;; Since source is particularly heavy (16MiB+), let's reuse it
+           ;; across the different components of cl-ffi-gtk.
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((glib-source (string-append (assoc-ref inputs "cl-cffi-gtk-glib")
+                                               "/share/common-lisp/sbcl-source/"
+                                               "cl-cffi-gtk-glib"))
+                   (out-source (string-append (assoc-ref outputs "out")
+                                              "/share/common-lisp/sbcl-source/"
+                                              "cl-cffi-gtk-gio")))
+               (delete-file-recursively out-source)
+               (symlink glib-source out-source)
+               #t))))))))
 
 (define-public sbcl-cl-cffi-gtk-cairo
   (package
-- 
cgit v1.2.3


From 8f46a9d67f54ffbe04d4201bdfcc8b460f640805 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Tue, 28 Apr 2020 10:45:05 +0200
Subject: gnu: sbcl-cl-cffi-gtk-cairo: Link source to parent to reduce closure
 size.

* gnu/packages/lisp-xyz.scm (sbcl-cl-cffi-gtk-cairo)[arguments]: Replace source
  folder with link to the same folder in the sbcl-cl-cffi-gtk-glib dependency.
---
 gnu/packages/lisp-xyz.scm | 15 ++++++++++++++-
 1 file changed, 14 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm
index fbb502cc73..e938bd6aa2 100644
--- a/gnu/packages/lisp-xyz.scm
+++ b/gnu/packages/lisp-xyz.scm
@@ -2981,7 +2981,20 @@ (define-public sbcl-cl-cffi-gtk-cairo
              (substitute* "cairo/cairo.init.lisp"
                (("libcairo" all)
                 (string-append
-                 (assoc-ref inputs "cairo") "/lib/" all))))))))))
+                 (assoc-ref inputs "cairo") "/lib/" all)))))
+         (add-after 'install 'link-source
+           ;; Since source is particularly heavy (16MiB+), let's reuse it
+           ;; across the different components of cl-ffi-gtk.
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((glib-source (string-append (assoc-ref inputs "cl-cffi-gtk-glib")
+                                               "/share/common-lisp/sbcl-source/"
+                                               "cl-cffi-gtk-glib"))
+                   (out-source (string-append (assoc-ref outputs "out")
+                                              "/share/common-lisp/sbcl-source/"
+                                              "cl-cffi-gtk-cairo")))
+               (delete-file-recursively out-source)
+               (symlink glib-source out-source)
+               #t))))))))
 
 (define-public sbcl-cl-cffi-gtk-pango
   (package
-- 
cgit v1.2.3


From d27f033f97ab7a71e0a3af004d3e11bea9374676 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Tue, 28 Apr 2020 10:45:18 +0200
Subject: gnu: sbcl-cl-cffi-gtk-pango: Link source to parent to reduce closure
 size.

* gnu/packages/lisp-xyz.scm (sbcl-cl-cffi-gtk-pango)[arguments]: Replace source
  folder with link to the same folder in the sbcl-cl-cffi-gtk-glib dependency.
---
 gnu/packages/lisp-xyz.scm | 15 ++++++++++++++-
 1 file changed, 14 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm
index e938bd6aa2..b2b5e006a6 100644
--- a/gnu/packages/lisp-xyz.scm
+++ b/gnu/packages/lisp-xyz.scm
@@ -3015,7 +3015,20 @@ (define-public sbcl-cl-cffi-gtk-pango
              (substitute* "pango/pango.init.lisp"
                (("libpango" all)
                 (string-append
-                 (assoc-ref inputs "pango") "/lib/" all))))))))))
+                 (assoc-ref inputs "pango") "/lib/" all)))))
+         (add-after 'install 'link-source
+           ;; Since source is particularly heavy (16MiB+), let's reuse it
+           ;; across the different components of cl-ffi-gtk.
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((glib-source (string-append (assoc-ref inputs "cl-cffi-gtk-glib")
+                                               "/share/common-lisp/sbcl-source/"
+                                               "cl-cffi-gtk-glib"))
+                   (out-source (string-append (assoc-ref outputs "out")
+                                              "/share/common-lisp/sbcl-source/"
+                                              "cl-cffi-gtk-pango")))
+               (delete-file-recursively out-source)
+               (symlink glib-source out-source)
+               #t))))))))
 
 (define-public sbcl-cl-cffi-gtk-gdk-pixbuf
   (package
-- 
cgit v1.2.3


From 2666a3361ec76fefe10257da3c6eb0f854ed24db Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Tue, 28 Apr 2020 10:45:32 +0200
Subject: gnu: sbcl-cl-cffi-gtk-gdk-pixbuf: Link source to parent to reduce
 closure size.

* gnu/packages/lisp-xyz.scm (sbcl-cl-cffi-gtk-gdk-pixbuf)[arguments]: Replace source
  folder with link to the same folder in the sbcl-cl-cffi-gtk-glib dependency.
---
 gnu/packages/lisp-xyz.scm | 16 +++++++++++++++-
 1 file changed, 15 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm
index b2b5e006a6..fa86769872 100644
--- a/gnu/packages/lisp-xyz.scm
+++ b/gnu/packages/lisp-xyz.scm
@@ -3037,6 +3037,7 @@ (define-public sbcl-cl-cffi-gtk-gdk-pixbuf
     (inputs
      `(("gdk-pixbuf" ,gdk-pixbuf)
        ("cl-cffi-gtk-gobject" ,sbcl-cl-cffi-gtk-gobject)
+       ("cl-cffi-gtk-glib" ,sbcl-cl-cffi-gtk-glib)
        ,@(package-inputs sbcl-cl-cffi-gtk-boot0)))
     (arguments
      `(#:asd-file "gdk-pixbuf/cl-cffi-gtk-gdk-pixbuf.asd"
@@ -3047,7 +3048,20 @@ (define-public sbcl-cl-cffi-gtk-gdk-pixbuf
              (substitute* "gdk-pixbuf/gdk-pixbuf.init.lisp"
                (("libgdk_pixbuf" all)
                 (string-append
-                 (assoc-ref inputs "gdk-pixbuf") "/lib/" all))))))))))
+                 (assoc-ref inputs "gdk-pixbuf") "/lib/" all)))))
+         (add-after 'install 'link-source
+           ;; Since source is particularly heavy (16MiB+), let's reuse it
+           ;; across the different components of cl-ffi-gtk.
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((glib-source (string-append (assoc-ref inputs "cl-cffi-gtk-glib")
+                                               "/share/common-lisp/sbcl-source/"
+                                               "cl-cffi-gtk-glib"))
+                   (out-source (string-append (assoc-ref outputs "out")
+                                              "/share/common-lisp/sbcl-source/"
+                                              "cl-cffi-gtk-gdk-pixbuf")))
+               (delete-file-recursively out-source)
+               (symlink glib-source out-source)
+               #t))))))))
 
 (define-public sbcl-cl-cffi-gtk-gdk
   (package
-- 
cgit v1.2.3


From 80d8c00c84191206e3c1edfb7d6a9d47a15ec1bf Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Tue, 28 Apr 2020 10:45:47 +0200
Subject: gnu: sbcl-cl-cffi-gtk-gdk: Link source to parent to reduce closure
 size.

* gnu/packages/lisp-xyz.scm (sbcl-cl-cffi-gtk-gdk)[arguments]: Replace source
  folder with link to the same folder in the sbcl-cl-cffi-gtk-glib dependency.
---
 gnu/packages/lisp-xyz.scm | 16 +++++++++++++++-
 1 file changed, 15 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm
index fa86769872..7f78a09ece 100644
--- a/gnu/packages/lisp-xyz.scm
+++ b/gnu/packages/lisp-xyz.scm
@@ -3069,6 +3069,7 @@ (define-public sbcl-cl-cffi-gtk-gdk
     (name "sbcl-cl-cffi-gtk-gdk")
     (inputs
      `(("gtk" ,gtk+)
+       ("cl-cffi-gtk-glib" ,sbcl-cl-cffi-gtk-glib)
        ("cl-cffi-gtk-gobject" ,sbcl-cl-cffi-gtk-gobject)
        ("cl-cffi-gtk-gio" ,sbcl-cl-cffi-gtk-gio)
        ("cl-cffi-gtk-gdk-pixbuf" ,sbcl-cl-cffi-gtk-gdk-pixbuf)
@@ -3088,7 +3089,20 @@ (define-public sbcl-cl-cffi-gtk-gdk
              (substitute* "gdk/gdk.package.lisp"
                (("libgtk" all)
                 (string-append
-                 (assoc-ref inputs "gtk") "/lib/" all))))))))))
+                 (assoc-ref inputs "gtk") "/lib/" all)))))
+         (add-after 'install 'link-source
+           ;; Since source is particularly heavy (16MiB+), let's reuse it
+           ;; across the different components of cl-ffi-gtk.
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((glib-source (string-append (assoc-ref inputs "cl-cffi-gtk-glib")
+                                               "/share/common-lisp/sbcl-source/"
+                                               "cl-cffi-gtk-glib"))
+                   (out-source (string-append (assoc-ref outputs "out")
+                                              "/share/common-lisp/sbcl-source/"
+                                              "cl-cffi-gtk-gdk")))
+               (delete-file-recursively out-source)
+               (symlink glib-source out-source)
+               #t))))))))
 
 (define-public sbcl-cl-cffi-gtk
   (package
-- 
cgit v1.2.3


From 143eaa82d6d7048705b42597465473bcf309204b Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Tue, 28 Apr 2020 10:46:05 +0200
Subject: gnu: sbcl-cl-cffi-gtk: Link source to parent to reduce closure size.

* gnu/packages/lisp-xyz.scm (sbcl-cl-cffi-gtk)[arguments]: Replace source
  folder with link to the same folder in the sbcl-cl-cffi-gtk-glib dependency.
---
 gnu/packages/lisp-xyz.scm | 17 ++++++++++++++++-
 1 file changed, 16 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm
index 7f78a09ece..5cf8a86940 100644
--- a/gnu/packages/lisp-xyz.scm
+++ b/gnu/packages/lisp-xyz.scm
@@ -3121,7 +3121,22 @@ (define-public sbcl-cl-cffi-gtk
        #:test-asd-file "test/cl-cffi-gtk-test.asd"
        ;; TODO: Tests fail with memory fault.
        ;; See https://github.com/Ferada/cl-cffi-gtk/issues/24.
-       #:tests? #f))))
+       #:tests? #f
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'install 'link-source
+           ;; Since source is particularly heavy (16MiB+), let's reuse it
+           ;; across the different components of cl-ffi-gtk.
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((glib-source (string-append (assoc-ref inputs "cl-cffi-gtk-glib")
+                                               "/share/common-lisp/sbcl-source/"
+                                               "cl-cffi-gtk-glib"))
+                   (out-source (string-append (assoc-ref outputs "out")
+                                              "/share/common-lisp/sbcl-source/"
+                                              "cl-cffi-gtk")))
+               (delete-file-recursively out-source)
+               (symlink glib-source out-source)
+               #t))))))))
 
 (define-public cl-cffi-gtk
   (sbcl-package->cl-source-package sbcl-cl-cffi-gtk))
-- 
cgit v1.2.3


From 8ac4be51defa0e6d578307645cf9e35e0b321848 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Tue, 28 Apr 2020 11:46:45 +0200
Subject: gnu: ecl: Update to 20.4.24.

* gnu/packages/lisp.scm (ecl): Update to 20.4.24.
[native-inputs]: Add texinfo to make the manual.
[license]: Set to lgpl2.1+.
---
 gnu/packages/lisp.scm | 26 ++++++++++++++++----------
 1 file changed, 16 insertions(+), 10 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index 27d38cd471..e57ce31dc7 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -222,7 +222,7 @@ (define-public gcl
 (define-public ecl
   (package
     (name "ecl")
-    (version "16.1.3")
+    (version "20.4.24")
     (source
      (origin
        (method url-fetch)
@@ -230,17 +230,22 @@ (define-public ecl
              "https://common-lisp.net/project/ecl/static/files/release/"
              name "-" version ".tgz"))
        (sha256
-        (base32 "0m0j24w5d5a9dwwqyrg0d35c0nys16ijb4r0nyk87yp82v38b9bn"))))
+        (base32 "01qgdmr54wkj854f69qdm9sybrvd6gd21dpx4askdaaqybnkh237"))))
     (build-system gnu-build-system)
     ;; src/configure uses 'which' to confirm the existence of 'gzip'.
-    (native-inputs `(("cl-asdf" ,cl-asdf)
-                     ("which" ,which)))
-    (inputs `(("gmp" ,gmp)
-              ("libatomic-ops" ,libatomic-ops)
-              ("libgc" ,libgc)
-              ("libffi" ,libffi)))
+    (native-inputs
+     `(("cl-asdf" ,cl-asdf)
+       ("which" ,which)
+       ("texinfo" ,texinfo)))
+    (inputs
+     `(("gmp" ,gmp)
+       ("libatomic-ops" ,libatomic-ops)
+       ("libgc" ,libgc)
+       ("libffi" ,libffi)))
     (arguments
      `(#:configure-flags '("--without-rt")
+       ;; FIXME: As of version 20.4.24, we pass 17995 tests and fail 7.
+       ;; 2-3 tests may be due to FHS assumptions.
        #:tests? #t
        #:parallel-tests? #f
        #:phases
@@ -301,9 +306,10 @@ (define-public ecl
 C/C++ compiler, being able to build standalone executables and libraries, and
 supporting ASDF, Sockets, Gray streams, MOP, and other useful components.")
     ;; Note that the file "Copyright" points to some files and directories
-    ;; which aren't under the lgpl2.0+ and instead contain many different,
+    ;; which aren't under the lgpl2.1+ and instead contain many different,
     ;; non-copyleft licenses.
-    (license license:lgpl2.0+)))
+    ;; See https://common-lisp.net/project/ecl/posts/ECL-license.html.
+    (license license:lgpl2.1+)))
 
 (define-public clisp
   (package
-- 
cgit v1.2.3


From 83812f34d7a01bb404d8dda17bd4c72bf30b8371 Mon Sep 17 00:00:00 2001
From: "Boris A. Dekshteyn" <boris.dekshteyn@gmail.com>
Date: Tue, 28 Apr 2020 14:09:19 +1200
Subject: gnu: Add kbdd-0.7.1
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/xdisorg.scm (kbdd): New variable.

Signed-off-by: Jakub Kądziołka <kuba@kadziolka.net>
---
 gnu/packages/xdisorg.scm | 38 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 38 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm
index bc2c9c4622..df61a95cbb 100644
--- a/gnu/packages/xdisorg.scm
+++ b/gnu/packages/xdisorg.scm
@@ -35,6 +35,7 @@
 ;;; Copyright © 2020 Brice Waegeneire <brice@waegenei.re>
 ;;; Copyright © 2020 Damien Cassou <damien@cassou.me>
 ;;; Copyright © 2020 John Soo <jsoo1@asu.edu>
+;;; Copyright © 2020 Boris A. Dekshteyn <boris.dekshteyn@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -2286,3 +2287,40 @@ (define-public clipmenu
 depending on the value of @code{CM_LAUNCHER}) to let the user select a clip.
 After selection, the clip is put onto the PRIMARY and CLIPBOARD X selections.")
       (license license:public-domain))))
+
+(define-public kbdd
+  (package
+    (name "kbdd")
+    (version "0.7.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/qnikst/kbdd.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "0qkq75grbd4wkx4nlvswgavpijk9ad0pzqyj89a0ayjsbsn36pqy"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("glib" ,glib "bin")
+       ("pkg-config" ,pkg-config)))
+    (inputs
+     `(("dbus-glib", dbus-glib)
+       ("glib" ,glib)
+       ("libx11" ,libx11)))
+    (home-page "https://github.com/qnikst/kbdd")
+    (synopsis "Per-window keyboard layout switching daemon for X")
+    (description "@command{kbdd} is a simple keyboard layout switching
+program, which is designed to run in an X11 session and remember
+keyboard layouts on a per-window basis.  That can be very handy for a
+user of a non-US keyboard who does not want to jump through layouts back
+and forth while typing in terminals (mostly in a latin alphabet) and
+some kind of chat (in native language).
+
+@command{kbdd} also supports D-Bus signals, which makes it possible to
+create layout indicator widgets.")
+    (license license:bsd-2)))
-- 
cgit v1.2.3


From 9a2fcb6325eb652971de4936911267d1fc5bb549 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 28 Apr 2020 11:22:47 +0200
Subject: gnu: Add c-blosc.

* gnu/packages/compression.scm (c-blosc): New variable.
---
 gnu/packages/compression.scm | 29 ++++++++++++++++++++++++++++-
 1 file changed, 28 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm
index 18512ee1bc..85f802a069 100644
--- a/gnu/packages/compression.scm
+++ b/gnu/packages/compression.scm
@@ -4,7 +4,7 @@
 ;;; Copyright © 2014, 2015, 2018 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
 ;;; Copyright © 2015, 2016 Eric Bavier <bavier@member.fsf.org>
-;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2016, 2017, 2018, 2020 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2015, 2017, 2018 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2015 Jeff Mickey <j@codemac.net>
 ;;; Copyright © 2015, 2016, 2017, 2018, 2019 Efraim Flashner <efraim@flashner.co.il>
@@ -2167,3 +2167,30 @@ (define-public tarsplitter
      "Archive huge numbers of files, or split massive tar archives into smaller
 chunks.")
     (license license:expat)))
+
+(define-public c-blosc
+  (package
+    (name "c-blosc")
+    (version "1.18.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/Blosc/c-blosc.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1ywq8j70149859vvs19wgjq89d6xsvvmvm2n1dmkzpchxgrvnw70"))))
+    (build-system cmake-build-system)
+    (home-page "https://blosc.org")
+    (synopsis "Blocking, shuffling and lossless compression library")
+    (description
+     "Blosc is a high performance compressor optimized for binary data. It has
+been designed to transmit data to the processor cache faster than the
+traditional, non-compressed, direct memory fetch approach via a
+@code{memcpy()} system call.  Blosc is meant not only to reduce the size of
+large datasets on-disk or in-memory, but also to accelerate memory-bound
+computations.")
+    ;; Blosc itself is released under BSD-3 but it incorporates code under
+    ;; other non-copyleft licenses.
+    (license license:bsd-3)))
-- 
cgit v1.2.3


From 0b2c88382830e281912cc04867f45e15c2f9657f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 28 Apr 2020 12:20:18 +0200
Subject: gnu: Add hdf5-blosc.

* gnu/packages/maths.scm (hdf5-blosc): New variable.
---
 gnu/packages/maths.scm | 41 ++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 40 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 73ee161e81..d7ce900682 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -5,7 +5,7 @@
 ;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019, 2020 Eric Bavier <bavier@posteo.net>
 ;;; Copyright © 2014 Federico Beffa <beffa@fbengineering.ch>
 ;;; Copyright © 2014 Mathieu Lirzin <mathieu.lirzin@openmailbox.org>
-;;; Copyright © 2015, 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
 ;;; Copyright © 2015, 2018 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2015, 2016, 2017, 2018, 2019 Efraim Flashner <efraim@flashner.co.il>
@@ -1298,6 +1298,45 @@ (define-public hdf5-parallel-openmpi
                #t))))))
     (synopsis "Management suite for data with parallel IO support")))
 
+(define-public hdf5-blosc
+  (package
+    (name "hdf5-blosc")
+    (version "1.0.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/Blosc/hdf5-blosc.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1nj2bm1v6ymm3fmyvhbn6ih5fgdiapavlfghh1pvbmhw71cysyqs"))))
+    (build-system cmake-build-system)
+    (arguments
+     `(#:configure-flags
+       (list (string-append "-DBLOSC_INSTALL_DIR="
+                            (assoc-ref %build-inputs "c-blosc"))
+             (string-append "-DPLUGIN_INSTALL_PATH="
+                            (assoc-ref %outputs "out")
+                            "/hdf5/lib/plugin"))
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'do-not-build-blosc
+           (lambda _
+             (substitute* "CMakeLists.txt"
+               (("set\\(BLOSC_INSTALL_DIR.*") "")
+               (("ExternalProject_Add\\(project_blosc") "message("))
+             #t)))))
+    (inputs
+     `(("c-blosc" ,c-blosc)
+       ("hdf5" ,hdf5-1.10)))
+    (home-page "https://github.com/Blosc/hdf5-blosc")
+    (synopsis "Filter for HDF5 using the Blosc compressor")
+    (description "This is a filter for HDF5 that uses the Blosc compressor; by
+installing this filter, you can read and write HDF5 files with
+Blosc-compressed datasets.")
+    (license license:expat)))
+
 (define-public h5check
   (package
     (name "h5check")
-- 
cgit v1.2.3


From 545e12f40dcd8cfc779e8802dadead7a7cdc8364 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 28 Apr 2020 12:23:13 +0200
Subject: gnu: Add variant-tools.

* gnu/packages/bioinformatics.scm (variant-tools): New variable.
---
 gnu/packages/bioinformatics.scm | 40 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 48b4ade7d8..f90a0bf90c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9158,6 +9158,46 @@ (define-public multiqc
 common bioinformatics tools.")
     (license license:gpl3+)))
 
+(define-public variant-tools
+  (package
+    (name "variant-tools")
+    (version "3.1.2")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/vatlab/varianttools.git")
+             ;; There is no tag corresponding to version 3.1.2
+             (commit "813ae4a90d25b69abc8a40f4f70441fe09015249")))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "12ibdmksj7icyqhks4xyvd61bygk4pjmxn618kp6vgk1af01y34g"))))
+    (build-system python-build-system)
+    (inputs
+     `(("boost" ,boost)
+       ("c-blosc" ,c-blosc)
+       ("gsl" ,gsl)
+       ("hdf5" ,hdf5)
+       ("hdf5-blosc" ,hdf5-blosc)
+       ("python-cython" ,python-cython)
+       ("zlib" ,zlib)))
+    (propagated-inputs
+     `(("python-numpy" ,python-numpy)
+       ("python-pycurl" ,python-pycurl)
+       ("python-pyzmq" ,python-pyzmq)
+       ("python-scipy" ,python-scipy)
+       ("python-tables" ,python-tables)))
+    (home-page "https://vatlab.github.io/vat-docs/")
+    (synopsis "Analyze genetic variants from Next-Gen sequencing studies")
+    (description
+     "Variant tools is a tool for the manipulation, annotation,
+selection, simulation, and analysis of variants in the context of next-gen
+sequencing analysis.  Unlike some other tools used for next-gen sequencing
+analysis, variant tools is project based and provides a whole set of tools to
+manipulate and analyze genetic variants.")
+    (license license:gpl3+)))
+
 (define-public r-chipseq
   (package
     (name "r-chipseq")
-- 
cgit v1.2.3


From 085948fbfc8aef4370d8df8784bbd239c333fa99 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Tue, 28 Apr 2020 14:38:38 +0200
Subject: gnu: ungoogled-chromium: Update to 81.0.4044.129-0.c2a89fb [security
 fixes].

This fixes CVE-2020-6462 and CVE-2020-6461.

* gnu/packages/chromium.scm (%chromium-version): Set to 81.0.4044.129.
(%ungoogled-revision): Set to c2a89fb6b5b559c826796c811741fa8ed3e11de8.
(%chromium-origin, %ungoogled-origin): Update hashes.
---
 gnu/packages/chromium.scm | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/chromium.scm b/gnu/packages/chromium.scm
index 45d68d2526..131943710a 100644
--- a/gnu/packages/chromium.scm
+++ b/gnu/packages/chromium.scm
@@ -248,8 +248,8 @@ (define* (computed-origin-method gexp-promise hash-algo hash
                       #:system system
                       #:guile-for-build guile)))
 
-(define %chromium-version "81.0.4044.122")
-(define %ungoogled-revision "31d6e60c96481599b42072b4489e4468280198e3")
+(define %chromium-version "81.0.4044.129")
+(define %ungoogled-revision "c2a89fb6b5b559c826796c811741fa8ed3e11de8")
 (define %debian-revision "debian/81.0.4044.92-1")
 (define package-revision "0")
 (define %package-version (string-append %chromium-version "-"
@@ -264,7 +264,7 @@ (define %chromium-origin
                         %chromium-version ".tar.xz"))
     (sha256
      (base32
-      "0ahqh3vmzbpai4xwn7qybgw9phc8ssjdvfc7384mxqk9swqgv7qg"))))
+      "1ls663s1f74p912x42qp3zcvm17kmjiv1ij6yy1c14gdhcpmjx7z"))))
 
 (define %ungoogled-origin
   (origin
@@ -275,7 +275,7 @@ (define %ungoogled-origin
                               (string-take %ungoogled-revision 7)))
     (sha256
      (base32
-      "1pj2vmzb2fagvypjsjn2kqf5n5k8vnhbisyb0snr6wqvpv09x0vv"))))
+      "0bbr4a2gkgm3ykdgpj8x58sd3dwam6qkifhzfs2997681g7b2v2q"))))
 
 (define %debian-origin
   (origin
-- 
cgit v1.2.3


From b3d04190f4ebbba9a7879ad72443ea6bf216ba76 Mon Sep 17 00:00:00 2001
From: Joseph LaFreniere <joseph@lafreniere.xyz>
Date: Sun, 26 Apr 2020 11:24:32 -0500
Subject: gnu: Add emacs-toml-mode.

* gnu/packages/emacs-xyz.scm (emacs-toml-mode): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
---
 gnu/packages/emacs-xyz.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm
index 0ae3f72fb7..b2da56f34d 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -2584,6 +2584,30 @@ (define-public emacs-sx
 Stack Overflow, Super User, and other StackExchange sites.")
       (license license:gpl3+))))
 
+(define-public emacs-toml-mode
+  (let ((version "0.1.3")
+        (revision "0")
+        (commit "f6c61817b00f9c4a3cab1bae9c309e0fc45cdd06"))
+    (package
+      (name "emacs-toml-mode")
+      (version (git-version version revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/dryman/toml-mode.el.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "05b4ksay85c8y5ncax0qsvnmplwsfiw24z16a58gkarjz938hb57"))))
+      (build-system emacs-build-system)
+      (home-page "https://github.com/dryman/toml-mode.el")
+      (synopsis "Emacs major mode for editing TOML files")
+      (description
+       "This package provides a major mode for editing files in @acronym{TOML,
+Tom's Obvious, Minimal Language} data format.")
+      (license license:gpl3+))))
+
 (define-public emacs-f
   (package
     (name "emacs-f")
-- 
cgit v1.2.3


From f15d324afa3b6525f606cc0b82eef6609e8fab9e Mon Sep 17 00:00:00 2001
From: Joseph LaFreniere <joseph@lafreniere.xyz>
Date: Sun, 26 Apr 2020 16:10:20 -0500
Subject: gnu: emacs-sx: Update to 20191229.

* gnu/packages/emacs-xyz.scm (emacs-sx): Update to 20191229.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
---
 gnu/packages/emacs-xyz.scm | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm
index b2da56f34d..1cd7dbca04 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -2558,9 +2558,9 @@ (define-public emacs-symon
     (license license:gpl2+)))
 
 (define-public emacs-sx
-  (let ((version "20180212")
-        (revision "1")
-        (commit "833435fbf90d1c9e927d165b155f3b1ef39271de"))
+  (let ((version "20191229")
+        (revision "0")
+        (commit "e9d1093c97507a6d7b4f4710ef65200dae725e5f"))
     (package
       (name "emacs-sx")
       (version (git-version version revision commit))
@@ -2572,8 +2572,7 @@ (define-public emacs-sx
                (commit commit)))
          (file-name (git-file-name name version))
          (sha256
-          (base32
-           "1369xaxq1vy3d9yh862ddnhddikdpg2d0wv1ly00pnvdp9v4cqgd"))))
+          (base32 "0m90ddwm8j0y6d1ppqhd2gil1107k202blw6mzm5bdambn4nfqkf"))))
       (build-system emacs-build-system)
       (propagated-inputs
        `(("emacs-markdown-mode" ,emacs-markdown-mode)))
-- 
cgit v1.2.3


From 9615c8511fe4ec4dbd98c80bc1f4549924f85099 Mon Sep 17 00:00:00 2001
From: John Soo <jsoo1@asu.edu>
Date: Mon, 27 Apr 2020 16:27:04 -0700
Subject: gnu: emacs-evil-org: Update to 1.0.2.

* gnu/packages/emacs-xyz.scm (emacs-evil-org): Update to 1.0.2.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
---
 gnu/packages/emacs-xyz.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm
index 1cd7dbca04..96be0aa195 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -15881,10 +15881,10 @@ (define-public emacs-evil-mc
       (license license:expat))))
 
 (define-public emacs-evil-org
-  (let ((commit "b6d652a9163d3430a9e0933a554bdbee5244bbf6"))
+  (let ((commit "9d4be14118bf27094a30dbff349b815f098aacbf"))
     (package
       (name "emacs-evil-org")
-      (version (git-version "0.1.1" "1" commit))
+      (version (git-version "1.0.2" "1" commit))
       (source
        (origin
          (method git-fetch)
@@ -15894,7 +15894,7 @@ (define-public emacs-evil-org
          (file-name (git-file-name name version))
          (sha256
           (base32
-           "176hrw7y7nczffbyhsa167b8rvfacsmcafm2gpkrdjqlrikbmrhl"))))
+           "1fxxfkinb0gq4p5b686r7z4jrkv98zfgh5z889zkjacncv8ibswn"))))
       (build-system emacs-build-system)
       (propagated-inputs `(("emacs-evil" ,emacs-evil)))
       (home-page
-- 
cgit v1.2.3


From 3b33e0e4baba4d121cad88fd116a1048789e5f64 Mon Sep 17 00:00:00 2001
From: Nicolas Goaziou <mail@nicolasgoaziou.fr>
Date: Tue, 28 Apr 2020 18:18:44 +0200
Subject: gnu: kakoune: Update to 2020.01.16.

* gnu/packages/text-editors.scm (kakoune): Update to 2020.01.16.
---
 gnu/packages/text-editors.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/text-editors.scm b/gnu/packages/text-editors.scm
index 36571e7846..f2f675d148 100644
--- a/gnu/packages/text-editors.scm
+++ b/gnu/packages/text-editors.scm
@@ -123,7 +123,7 @@ (define-public vis
 (define-public kakoune
   (package
     (name "kakoune")
-    (version "2019.12.10")
+    (version "2020.01.16")
     (source
      (origin
        (method url-fetch)
@@ -131,7 +131,7 @@ (define-public kakoune
                            "releases/download/v" version "/"
                            "kakoune-" version ".tar.bz2"))
        (sha256
-        (base32 "1y1gzax2dl7flh676k0rl1vacv10j7p5krkmb67b0afbrql8vbb6"))))
+        (base32 "1bhd990gywdwdhxc5dn83wwj418c5cw1ndqycf7k0a02kxlg3550"))))
     (build-system gnu-build-system)
     (arguments
      `(#:make-flags
-- 
cgit v1.2.3


From ae0f26b8f4e0221f1e6f1a5ebf6d5054da506761 Mon Sep 17 00:00:00 2001
From: Alexandros Theodotou <alex@zrythm.org>
Date: Tue, 28 Apr 2020 15:30:04 +0100
Subject: gnu: lv2: Update to 1.18.0.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/audio.scm (lv2): Update to 1.18.0.

Signed-off-by: Jakub Kądziołka <kuba@kadziolka.net>
---
 gnu/packages/audio.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index bf16e09f61..e2e276723b 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -1979,14 +1979,14 @@ (define-public lilv
 (define-public lv2
   (package
     (name "lv2")
-    (version "1.16.0")
+    (version "1.18.0")
     (source (origin
              (method url-fetch)
              (uri (string-append "http://lv2plug.in/spec/lv2-"
                                  version ".tar.bz2"))
              (sha256
               (base32
-               "1ppippbpdpv13ibs06b0bixnazwfhiw0d0ja6hx42jnkgdyp5hyy"))))
+               "0gs7401xz23q9vajqr31aa2db8dvssgyh5zrvr4ipa6wig7yb8wh"))))
     (build-system waf-build-system)
     (arguments
      `(#:tests? #f  ; no check target
-- 
cgit v1.2.3


From b2c1d4a27301b71d1273786b7aa869e5112d1e3a Mon Sep 17 00:00:00 2001
From: Christopher Lemmer Webber <cwebber@dustycloud.org>
Date: Thu, 2 Apr 2020 15:03:27 -0400
Subject: gnu: Add emacs-magit-annex.

* gnu/packages/emacs-xyz.scm (emacs-magit-annex): New variable.
---
 gnu/packages/emacs-xyz.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm
index 96be0aa195..3bf9ffa655 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -475,6 +475,31 @@ (define-public emacs-magit-popup
 process, passing on the arguments as command line arguments.")
     (license license:gpl3+)))
 
+(define-public emacs-magit-annex
+  (let ((commit "ef5dce6267e9118a5eca82a22bcad0b67826c23a")
+        (revision "1"))
+    (package
+      (name "emacs-magit-annex")
+      (version (git-version "1.7.1" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/magit/magit-annex.git")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "0vzkydgl889cq173zjl89g2vrddb9abc4a8gljiz3b4a7n5b1nrd"))))
+      (build-system emacs-build-system)
+      (propagated-inputs
+       `(("magit" ,emacs-magit)
+         ("transient" ,emacs-transient)))
+      (home-page "https://github.com/magit/magit-annex/")
+      (synopsis "Git-annex support for Magit")
+      (description
+       "Magit-annex adds a few git-annex operations to the Magit interface.")
+      (license license:gpl3+))))
+
 (define-public emacs-minions
   (package
     (name "emacs-minions")
-- 
cgit v1.2.3


From abbca232ca92678a46ab1fbf5f2f376bf6a4a7e2 Mon Sep 17 00:00:00 2001
From: Diego Nicola Barbato <dnbarbato@posteo.de>
Date: Sun, 29 Dec 2019 00:41:48 +0100
Subject: gnu: Add emacs-wide-int.

* gnu/packages/emacs.scm (emacs-wide-int): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
---
 gnu/packages/emacs.scm | 11 +++++++++++
 1 file changed, 11 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index 3d0368be4e..ab7cc20d10 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -401,6 +401,17 @@ (define-public emacs-no-x-toolkit
            ((#:configure-flags cf)
             `(cons "--with-x-toolkit=no" ,cf)))))))
 
+(define-public emacs-wide-int
+  (package
+    (inherit emacs)
+    (name "emacs-wide-int")
+    (synopsis "The extensible, customizable, self-documenting text
+editor (with wide ints)" )
+    (arguments
+     (substitute-keyword-arguments (package-arguments emacs)
+       ((#:configure-flags flags)
+        `(cons "--with-wide-int" ,flags))))))
+
 (define-public guile-emacs
   (let ((commit "41120e0f595b16387eebfbf731fff70481de1b4b")
         (revision "0"))
-- 
cgit v1.2.3


From a663b7040c3c7ed12d4f673c4ac090ad8d9b8e20 Mon Sep 17 00:00:00 2001
From: Diego Nicola Barbato <dnbarbato@posteo.de>
Date: Sun, 29 Dec 2019 01:03:38 +0100
Subject: gnu: emacs-telega: Build with emacs-wide-int on 32-bit systems.

Fixes <https://bugs.gnu.org/39406>.
Reported by <lmedeiros@riseup.net>.

* gnu/packages/emacs-xyz.scm (emacs-telega)[native-inputs]: Replace emacs with
emacs-wide-int on 32-bit systems.  This is needed because Telega requires
64-bit wide ints.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
---
 gnu/packages/emacs-xyz.scm | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm
index 3bf9ffa655..5d2aaa4061 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -21467,7 +21467,12 @@ (define-public emacs-telega
       (native-inputs
        `(("tdlib" ,tdlib)
          ("libtgvoip" ,libtgvoip) ; VoIP support.
-         ("emacs" ,emacs)
+         ;; Use Emacs with wide ints on 32-bit architectures.
+         ("emacs" ,(match (%current-system)
+                     ((or "i686-linux" "armhf-linux")
+                      emacs-wide-int)
+                     (_
+                      emacs)))
          ("python" ,python)))
       (synopsis "GNU Emacs client for the Telegram messenger")
       (description
-- 
cgit v1.2.3


From 19e1f12ce420104451c16ab5412cb65cd8fe68cd Mon Sep 17 00:00:00 2001
From: Diego Nicola Barbato <dnbarbato@posteo.de>
Date: Fri, 7 Feb 2020 17:59:31 +0100
Subject: gnu: emacs-telega: Test Emacs environment on startup.

Print a more helpful error message when someone attempts to run Telega on an
incompatible Emacs (e.g a 32-bit Emacs without wide ints).

* gnu/packages/patches/emacs-telega-test-env.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/emacs-xyz.scm (emacs-telega)[source]: Use it.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
---
 gnu/local.mk                                     |  1 +
 gnu/packages/emacs-xyz.scm                       |  1 +
 gnu/packages/patches/emacs-telega-test-env.patch | 14 ++++++++++++++
 3 files changed, 16 insertions(+)
 create mode 100644 gnu/packages/patches/emacs-telega-test-env.patch

(limited to 'gnu/packages')

diff --git a/gnu/local.mk b/gnu/local.mk
index 9f212434a9..9b082a6f2a 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -864,6 +864,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/emacs-magit-log-format-author-margin.patch	\
   %D%/packages/patches/emacs-scheme-complete-scheme-r5rs-info.patch	\
   %D%/packages/patches/emacs-source-date-epoch.patch		\
+  %D%/packages/patches/emacs-telega-test-env.patch		\
   %D%/packages/patches/emacs-undohist-ignored.patch	\
   %D%/packages/patches/emacs-wordnut-require-adaptive-wrap.patch	\
   %D%/packages/patches/emacs-zones-called-interactively.patch	\
diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm
index 5d2aaa4061..2c61c4189d 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -21376,6 +21376,7 @@ (define-public emacs-telega
          (sha256
           (base32
            "0mv6i80958d9crzspzik5xh5g8326115bvg2frgv0dp9p6rm86m3"))
+         (patches (search-patches "emacs-telega-test-env.patch"))
          (file-name (git-file-name name version))))
       (build-system gnu-build-system)
       (arguments
diff --git a/gnu/packages/patches/emacs-telega-test-env.patch b/gnu/packages/patches/emacs-telega-test-env.patch
new file mode 100644
index 0000000000..75fe2e12fc
--- /dev/null
+++ b/gnu/packages/patches/emacs-telega-test-env.patch
@@ -0,0 +1,14 @@
+Test Emacs environment on startup.
+
+Patch by Diego N. Barbato
+
+--- a/telega.el	2020-02-07 17:07:18.549970090 +0100
++++ b/telega.el	2020-02-07 17:10:08.383499765 +0100
+@@ -82,6 +82,7 @@
+   "Start telegramming.
+ If prefix ARG is given, then will not pop to telega root buffer."
+   (interactive "P")
++  (telega-test-env t)
+   (telega--create-hier)
+ 
+   (unless (telega-server-live-p)
-- 
cgit v1.2.3


From a84b7a4af53553c5816c9534e33ea52802e89b1d Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Tue, 28 Apr 2020 14:48:58 +0200
Subject: gnu: sbcl-parenscript: Update to 2.7.1.

* gnu/packages/lisp-xyz.scm (sbcl-parenscript): Update to 2.7.1.
---
 gnu/packages/lisp-xyz.scm | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm
index 5cf8a86940..c2029d940e 100644
--- a/gnu/packages/lisp-xyz.scm
+++ b/gnu/packages/lisp-xyz.scm
@@ -2670,10 +2670,11 @@ (define-public cl-sqlite
   (sbcl-package->cl-source-package sbcl-cl-sqlite))
 
 (define-public sbcl-parenscript
-  (let ((commit "061d8e286c81c3f45c84fb2b11ee7d83f590a8f8"))
+  ;; Source archives are overwritten on every release, we use the Git repo instead.
+  (let ((commit "7a1ac46353cecd144fc91915ba9f122aafcf4766"))
     (package
       (name "sbcl-parenscript")
-      (version (git-version "2.6" "1" commit))
+      (version (git-version "2.7.1" "1" commit))
       (source
        (origin
          (method git-fetch)
@@ -2683,7 +2684,7 @@ (define-public sbcl-parenscript
          (file-name (git-file-name "parenscript" version))
          (sha256
           (base32
-           "1kbhgsjbikc73m5cwdp4d4fdafyqcr1b7b630qjrziql0nh6mi3k"))))
+           "0c22lqarrpbq82dg1sb3y6mp6w2faczp34ymzhnmff88yfq1xzsf"))))
       (build-system asdf-build-system/sbcl)
       (inputs
        `(("cl-ppcre" ,sbcl-cl-ppcre)
-- 
cgit v1.2.3


From 27112236ce411cefdd5b5a66bdf73b688adf24f4 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Tue, 28 Apr 2020 21:07:23 +0200
Subject: gnu: sbcl: Update to 2.0.4.

* gnu/packages/lisp.scm (sbcl): Update to 2.0.4.
---
 gnu/packages/lisp.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index e57ce31dc7..219bc4dcf9 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -371,14 +371,14 @@ (define-public clisp
 (define-public sbcl
   (package
     (name "sbcl")
-    (version "2.0.3")
+    (version "2.0.4")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "mirror://sourceforge/sbcl/sbcl/" version "/sbcl-"
                            version "-source.tar.bz2"))
        (sha256
-        (base32 "001gckyw8hl842nk7nwf5kcspzkc1g8dycpwylzh5chl6893ym5m"))))
+        (base32 "1lc2i4qq1kfdybmxnj2zq2hn3hfx0vvlqim4gvlgvs3bfr0lcaqj"))))
     (build-system gnu-build-system)
     (outputs '("out" "doc"))
     (native-inputs
@@ -397,7 +397,7 @@ (define-public sbcl
      ;;
      ;; CCL is not bootstrappable so it won't do.  CLISP 2.49 seems to work.
      ;; ECL too.  ECL builds SBCL about 20% slower than CLISP.  As of
-     ;; 2019-09-05, ECL was last updated in 2016 while CLISP was last updated
+     ;; 2019-09-05, ECL was last updated in 2020 while CLISP was last updated
      ;; in 2010.
      ;;
      ;; For now we stick to CLISP for all systems.  We keep the `match' here to
-- 
cgit v1.2.3


From cd8c419722780765b075a7217b861e7608c0bac2 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 28 Apr 2020 21:07:14 +0300
Subject: gnu: valgrind: Update source uri.

* gnu/packages/valgrind.scm (valgrind)[source]: Remove valgrind host,
add sourceware host.
[home-page]: Use https.
---
 gnu/packages/valgrind.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/valgrind.scm b/gnu/packages/valgrind.scm
index da912dc465..dd080bb327 100644
--- a/gnu/packages/valgrind.scm
+++ b/gnu/packages/valgrind.scm
@@ -2,7 +2,7 @@
 ;;; Copyright © 2013, 2014 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
-;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2020 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -35,7 +35,7 @@ (define-public valgrind
     (version "3.15.0")
     (source (origin
               (method url-fetch)
-              (uri (list (string-append "http://www.valgrind.org/downloads"
+              (uri (list (string-append "https://sourceware.org/pub/valgrind"
                                         "/valgrind-" version ".tar.bz2")
                          (string-append "ftp://sourceware.org/pub/valgrind"
                                         "/valgrind-" version ".tar.bz2")))
@@ -71,7 +71,7 @@ (define-public valgrind
      `(("gdb" ,gdb)))
     (native-inputs
      `(("perl" ,perl)))
-    (home-page "http://www.valgrind.org/")
+    (home-page "https://www.valgrind.org/")
     (synopsis "Debugging and profiling tool suite")
     (description
      "Valgrind is an instrumentation framework for building dynamic analysis
-- 
cgit v1.2.3


From 0b25812872904d61024791778dae36636c52ded6 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 28 Apr 2020 22:52:20 +0300
Subject: gnu: openldap: Fix CVE-2020-12243.

* gnu/packages/openldap.scm (openldap)[replacement]: New field.
(openldap/fixed): New variable.
* gnu/packages/patches/openldap-CVE-2020-12243.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
---
 gnu/local.mk                                       |   3 +-
 gnu/packages/openldap.scm                          |   9 ++
 gnu/packages/patches/openldap-CVE-2020-12243.patch | 125 +++++++++++++++++++++
 3 files changed, 136 insertions(+), 1 deletion(-)
 create mode 100644 gnu/packages/patches/openldap-CVE-2020-12243.patch

(limited to 'gnu/packages')

diff --git a/gnu/local.mk b/gnu/local.mk
index 9b082a6f2a..67bf04547c 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -10,7 +10,7 @@
 # Copyright © 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
 # Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
 # Copyright © 2016, 2017, 2018, 2019 Alex Vong <alexvong1995@gmail.com>
-# Copyright © 2016, 2017, 2018, 2019 Efraim Flashner <efraim@flashner.co.il>
+# Copyright © 2016, 2017, 2018, 2019, 2020 Efraim Flashner <efraim@flashner.co.il>
 # Copyright © 2016, 2017, 2018, 2019 Jan (janneke) Nieuwenhuizen <janneke@gnu.org>
 # Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
 # Copyright © 2017, 2018 Clément Lassieur <clement@lassieur.org>
@@ -1276,6 +1276,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/opencv-rgbd-aarch64-test-fix.patch	\
   %D%/packages/patches/openfoam-4.1-cleanup.patch			\
   %D%/packages/patches/openjdk-10-idlj-reproducibility.patch	\
+  %D%/packages/patches/openldap-CVE-2020-12243.patch		\
   %D%/packages/patches/openmpi-mtl-priorities.patch		\
   %D%/packages/patches/openocd-nrf52.patch			\
   %D%/packages/patches/openssl-runpath.patch			\
diff --git a/gnu/packages/openldap.scm b/gnu/packages/openldap.scm
index de8239b7fe..aa51520654 100644
--- a/gnu/packages/openldap.scm
+++ b/gnu/packages/openldap.scm
@@ -5,6 +5,7 @@
 ;;; Copyright © 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2020 Lars-Dominik Braun <ldb@leibniz-psychology.org>
+;;; Copyright © 2020 Efraim Flashner <efraim@flashner.co.il>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -57,6 +58,7 @@ (define-module (gnu packages openldap)
 
 (define-public openldap
   (package
+   (replacement openldap/fixed)
    (name "openldap")
    (version "2.4.47")
    (source (origin
@@ -110,6 +112,13 @@ (define-public openldap
    (license openldap2.8)
    (home-page "https://www.openldap.org/")))
 
+(define openldap/fixed
+  (package
+    (inherit openldap)
+    (source
+      (origin (inherit (package-source openldap))
+              (patches (search-patches "openldap-CVE-2020-12243.patch"))))))
+
 (define-public nss-pam-ldapd
   (package
     (name "nss-pam-ldapd")
diff --git a/gnu/packages/patches/openldap-CVE-2020-12243.patch b/gnu/packages/patches/openldap-CVE-2020-12243.patch
new file mode 100644
index 0000000000..6321998198
--- /dev/null
+++ b/gnu/packages/patches/openldap-CVE-2020-12243.patch
@@ -0,0 +1,125 @@
+From 98464c11df8247d6a11b52e294ba5dd4f0380440 Mon Sep 17 00:00:00 2001
+From: Howard Chu <hyc@openldap.org>
+Date: Thu, 16 Apr 2020 01:08:19 +0100
+Subject: [PATCH] ITS#9202 limit depth of nested filters
+
+Using a hardcoded limit for now; no reasonable apps
+should ever run into it.
+---
+ servers/slapd/filter.c | 41 ++++++++++++++++++++++++++++++++---------
+ 1 file changed, 32 insertions(+), 9 deletions(-)
+
+diff --git a/servers/slapd/filter.c b/servers/slapd/filter.c
+index 3252cf2a7..ed57bbd7b 100644
+--- a/servers/slapd/filter.c
++++ b/servers/slapd/filter.c
+@@ -37,11 +37,16 @@
+ const Filter *slap_filter_objectClass_pres;
+ const struct berval *slap_filterstr_objectClass_pres;
+ 
++#ifndef SLAPD_MAX_FILTER_DEPTH
++#define SLAPD_MAX_FILTER_DEPTH	5000
++#endif
++
+ static int	get_filter_list(
+ 	Operation *op,
+ 	BerElement *ber,
+ 	Filter **f,
+-	const char **text );
++	const char **text,
++	int depth );
+ 
+ static int	get_ssa(
+ 	Operation *op,
+@@ -80,12 +85,13 @@ filter_destroy( void )
+ 	return;
+ }
+ 
+-int
+-get_filter(
++static int
++get_filter0(
+ 	Operation *op,
+ 	BerElement *ber,
+ 	Filter **filt,
+-	const char **text )
++	const char **text,
++	int depth )
+ {
+ 	ber_tag_t	tag;
+ 	ber_len_t	len;
+@@ -126,6 +132,11 @@ get_filter(
+ 	 *
+ 	 */
+ 
++	if( depth > SLAPD_MAX_FILTER_DEPTH ) {
++		*text = "filter nested too deeply";
++		return SLAPD_DISCONNECT;
++	}
++
+ 	tag = ber_peek_tag( ber, &len );
+ 
+ 	if( tag == LBER_ERROR ) {
+@@ -221,7 +232,7 @@ get_filter(
+ 
+ 	case LDAP_FILTER_AND:
+ 		Debug( LDAP_DEBUG_FILTER, "AND\n", 0, 0, 0 );
+-		err = get_filter_list( op, ber, &f.f_and, text );
++		err = get_filter_list( op, ber, &f.f_and, text, depth+1 );
+ 		if ( err != LDAP_SUCCESS ) {
+ 			break;
+ 		}
+@@ -234,7 +245,7 @@ get_filter(
+ 
+ 	case LDAP_FILTER_OR:
+ 		Debug( LDAP_DEBUG_FILTER, "OR\n", 0, 0, 0 );
+-		err = get_filter_list( op, ber, &f.f_or, text );
++		err = get_filter_list( op, ber, &f.f_or, text, depth+1 );
+ 		if ( err != LDAP_SUCCESS ) {
+ 			break;
+ 		}
+@@ -248,7 +259,7 @@ get_filter(
+ 	case LDAP_FILTER_NOT:
+ 		Debug( LDAP_DEBUG_FILTER, "NOT\n", 0, 0, 0 );
+ 		(void) ber_skip_tag( ber, &len );
+-		err = get_filter( op, ber, &f.f_not, text );
++		err = get_filter0( op, ber, &f.f_not, text, depth+1 );
+ 		if ( err != LDAP_SUCCESS ) {
+ 			break;
+ 		}
+@@ -311,10 +322,22 @@ get_filter(
+ 	return( err );
+ }
+ 
++int
++get_filter(
++	Operation *op,
++	BerElement *ber,
++	Filter **filt,
++	const char **text )
++{
++	return get_filter0( op, ber, filt, text, 0 );
++}
++
++
+ static int
+ get_filter_list( Operation *op, BerElement *ber,
+ 	Filter **f,
+-	const char **text )
++	const char **text,
++	int depth )
+ {
+ 	Filter		**new;
+ 	int		err;
+@@ -328,7 +351,7 @@ get_filter_list( Operation *op, BerElement *ber,
+ 		tag != LBER_DEFAULT;
+ 		tag = ber_next_element( ber, &len, last ) )
+ 	{
+-		err = get_filter( op, ber, new, text );
++		err = get_filter0( op, ber, new, text, depth );
+ 		if ( err != LDAP_SUCCESS )
+ 			return( err );
+ 		new = &(*new)->f_next;
+-- 
+2.26.2
+
-- 
cgit v1.2.3


From ce0f1b1eefbb6d7d6339c0919cc051f9f5cf9b8d Mon Sep 17 00:00:00 2001
From: Ludovic Courtès <ludo@gnu.org>
Date: Tue, 28 Apr 2020 22:31:32 +0200
Subject: gnu: guix: Update to 619f918.

* gnu/packages/package-management.scm (guix): Update to 619f918.
---
 gnu/packages/package-management.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm
index 011e442066..44fcb514b7 100644
--- a/gnu/packages/package-management.scm
+++ b/gnu/packages/package-management.scm
@@ -110,8 +110,8 @@ (define-public guix
   ;; Note: the 'update-guix-package.scm' script expects this definition to
   ;; start precisely like this.
   (let ((version "1.1.0")
-        (commit "7dd05396ef4539165f955d9ab57225091f801ce9")
-        (revision 1))
+        (commit "619f9181a363576894a433206008b139255062dd")
+        (revision 2))
     (package
       (name "guix")
 
@@ -127,7 +127,7 @@ (define-public guix
                       (commit commit)))
                 (sha256
                  (base32
-                  "110fz4qay4iywpynw1cbv6if8ac0pxp21zhzwvnp2jn1f6vbwf64"))
+                  "1lk0h9zgry7m78nv70gxwb57pw1d5yzay477gxsc43v1aa7zg8sp"))
                 (file-name (string-append "guix-" version "-checkout"))))
       (build-system gnu-build-system)
       (arguments
-- 
cgit v1.2.3


From 1797fe132177f8c6738e51130492868f4107f472 Mon Sep 17 00:00:00 2001
From: Ludovic Courtès <ludo@gnu.org>
Date: Tue, 28 Apr 2020 22:32:06 +0200
Subject: gnu: guile-json: Update to 3.5.0.

* gnu/packages/guile.scm (guile-json-3): Update to 3.5.0.
---
 gnu/packages/guile.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm
index c643f9d286..56dda89899 100644
--- a/gnu/packages/guile.scm
+++ b/gnu/packages/guile.scm
@@ -488,14 +488,14 @@ (define-public guile-json-3
   (package
     (inherit guile-json-1)
     (name "guile-json")
-    (version "3.2.0")
+    (version "3.5.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://savannah/guile-json/guile-json-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "14m6b6g2maw0mkvfm4x63rqb54vgbpn1gcqs715ijw4bikfzlqfz"))))))
+                "0nj0684qgh6ppkbdyxqfyjwsv2qbyairxpi8fzrhsi3xnc7jn4im"))))))
 
 (define-public guile3.0-json
   (package-for-guile-3.0 guile-json-3))
-- 
cgit v1.2.3


From f93eebbf9ca8477404827f44daf3121b11120e99 Mon Sep 17 00:00:00 2001
From: Guillaume Le Vaillant <glv@posteo.net>
Date: Wed, 29 Apr 2020 01:11:53 +0200
Subject: gnu: Add xnec2c.

* gnu/packages/radio.scm (xnec2c): New variable.
---
 gnu/packages/radio.scm | 49 +++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 49 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm
index 4e11dda40a..b439e5feff 100644
--- a/gnu/packages/radio.scm
+++ b/gnu/packages/radio.scm
@@ -829,3 +829,52 @@ (define-public wsjtx
 weak-signal conditions.")
     (home-page "https://www.physics.princeton.edu/pulsar/k1jt/wsjtx.html")
     (license license:gpl3)))
+
+(define-public xnec2c
+  (package
+    (name "xnec2c")
+    (version "4.1.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "http://www.5b4az.org/pkg/nec2/xnec2c/xnec2c-"
+                           version ".tar.bz2"))
+       (sha256
+        (base32 "1myvlkfybb2ha8l0h96ca3iz206zzy9z5iizm0sbab2zzp78n1r9"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (inputs
+     `(("gtk+" ,gtk+)))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-makefile
+           (lambda* (#:key outputs #:allow-other-keys)
+             (substitute* '("Makefile.am" "Makefile.in")
+               ;; The DESTDIR variable does not get replaced the prefix
+               ;; in the final Makefile, so let's do here.
+               (("\\$\\(DESTDIR\\)/usr")
+                (assoc-ref outputs "out")))
+             #t))
+         (add-after 'fix-makefile 'fix-paths
+           (lambda* (#:key outputs #:allow-other-keys)
+             ;; Increase the max length of the path to the glade file,
+             ;; so that the '/gnu/store/...' path can fit in.
+             (substitute* '("src/shared.c" "src/shared.h")
+               (("char xnec2c_glade\\[64\\];")
+                "char xnec2c_glade[256];"))
+             ;; Fix hard coded references to '/usr/...'.
+             (substitute* '("src/geom_edit.c" "src/main.c")
+               (("\"/usr")
+                (string-append "\"" (assoc-ref outputs "out"))))
+             #t)))))
+    (synopsis "Antenna modeling software")
+    (description
+     "Xnec2c is a GTK3-based graphical version of nec2c, a translation to the
+C language of NEC2, the FORTRAN Numerical Electromagnetics Code commonly used
+for antenna simulation and analysis.  It can be used to define the geometry of
+an antenna, and then plot the radiation pattern or frequency-related data like
+gain and standing wave ratio.")
+    (home-page "http://www.5b4az.org/")
+    (license license:gpl3+)))
-- 
cgit v1.2.3


From cf480830e22e7725b8607b5b895e49f74d4e1525 Mon Sep 17 00:00:00 2001
From: Guillaume Le Vaillant <glv@posteo.net>
Date: Wed, 29 Apr 2020 10:15:57 +0200
Subject: gnu: gnuradio: Fix search paths for third-party blocks.

* gnu/packages/radio.scm (gnuradio)[native-search-paths]: Add definition of
  the GRC_BLOCKS_PATH variable.
---
 gnu/packages/radio.scm | 4 ++++
 1 file changed, 4 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm
index b439e5feff..935880780f 100644
--- a/gnu/packages/radio.scm
+++ b/gnu/packages/radio.scm
@@ -363,6 +363,10 @@ (define-public gnuradio
                (wrap-program (string-append out "/bin/gnuradio-companion")
                  `("GI_TYPELIB_PATH" ":" prefix ,(filter identity paths))))
              #t)))))
+    (native-search-paths
+     (list (search-path-specification
+            (variable "GRC_BLOCKS_PATH")
+            (files '("/share/gnuradio/grc/blocks")))))
     (synopsis "Toolkit for software-defined radios")
     (description
      "GNU Radio is a development toolkit that provides signal processing blocks
-- 
cgit v1.2.3


From add3e168bb25e0af8a6225f5c93a311aae0268b2 Mon Sep 17 00:00:00 2001
From: Paul Garlick <pgarlick@tourbillion-technology.com>
Date: Fri, 24 Apr 2020 13:07:07 +0100
Subject: gnu: ikiwiki: Fetch sources from git repository.

* gnu/packages/web.scm (ikiwiki)[source]: Use GIT-FETCH and
GIT-FILE-NAME.
[source](snippet): New field.
[arguments]<#:phases>[set-modification-times]: New phase.
---
 gnu/packages/web.scm | 25 ++++++++++++++++++++-----
 1 file changed, 20 insertions(+), 5 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index f5189dc7f9..bfd8486dff 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -4813,13 +4813,20 @@ (define-public ikiwiki
     (version "3.20190228")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "http://snapshot.debian.org/archive/debian/"
-                           "20190301T035241Z/pool/main/i/ikiwiki/ikiwiki_"
-                           version ".orig.tar.xz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "git://git.ikiwiki.info/")
+             (commit version)))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "17pyblaqhkb61lxl63bzndiffism8k859p54k3k4sghclq6lsynh"))))
+         "1c0i48jp2vpiwn2pacr6jbjdj26v7s9vzzs7j7gc16bx37dfgbbi"))
+       (snippet
+        '(begin
+           ;; The POT file requires write permission during the build
+           ;; phase.
+           (chmod "po/ikiwiki.pot" #o644)
+           #t))))
     (build-system perl-build-system)
     (arguments
      `(#:phases
@@ -4838,6 +4845,14 @@ (define-public ikiwiki
              (substitute* "Makefile.PL"
                (("SYSCONFDIR\\?=") "SYSCONFDIR?=$(PREFIX)"))
              #t))
+         (add-before 'build 'set-modification-times
+           ;; The wiki '--refresh' steps, which are executed during
+           ;; the check phase, require recent timestamps on files in
+           ;; the 'doc' and 'underlays' directories.
+           (lambda _
+             (invoke "find"  "doc" "underlays" "-type" "f" "-exec"
+                     "touch" "{}" "+")
+             #t))
          (add-after 'install 'wrap-programs
            (lambda* (#:key outputs #:allow-other-keys)
              (let* ((out  (assoc-ref outputs "out"))
-- 
cgit v1.2.3


From 732ffac3bc8131ce0b3baceccafac6b1fa63fee8 Mon Sep 17 00:00:00 2001
From: Paul Garlick <pgarlick@tourbillion-technology.com>
Date: Fri, 24 Apr 2020 20:46:15 +0100
Subject: gnu: ikiwiki: Build perl inputs for target architecture.

* gnu/packages/web.scm (ikiwiki)[native-inputs]: Move perl dependencies ...
[inputs]: ...to here.
---
 gnu/packages/web.scm | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index bfd8486dff..37f2076bd1 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -4865,10 +4865,6 @@ (define-public ikiwiki
                #t))))))
     (native-inputs
      `(("which" ,which)
-       ("perl-html-tagset" ,perl-html-tagset)
-       ("perl-timedate" ,perl-timedate)
-       ("perl-xml-sax" ,perl-xml-sax)
-       ("perl-xml-simple" ,perl-xml-simple)
        ("gettext" ,gettext-minimal)
        ("subversion" ,subversion)
        ("git" ,git)
@@ -4883,11 +4879,15 @@ (define-public ikiwiki
        ("perl-db-file" ,perl-db-file)
        ("perl-html-parser" ,perl-html-parser)
        ("perl-html-scrubber" ,perl-html-scrubber)
+       ("perl-html-tagset" ,perl-html-tagset)
        ("perl-html-template" ,perl-html-template)
        ("perl-image-magick" ,perl-image-magick)
        ("perl-json" ,perl-json)
        ("perl-text-markdown-discount" ,perl-text-markdown-discount)
+       ("perl-timedate" ,perl-timedate)
        ("perl-uri" ,perl-uri)
+       ("perl-xml-sax" ,perl-xml-sax)
+       ("perl-xml-simple" ,perl-xml-simple)
        ("perl-yaml-libyaml" ,perl-yaml-libyaml)))
     (home-page "https://ikiwiki.info/")
     (synopsis "Wiki compiler, capable of generating HTML")
-- 
cgit v1.2.3


From b7392ecbbaa52eb54d9cefdccaa2af38d6b6fa62 Mon Sep 17 00:00:00 2001
From: Paul Garlick <pgarlick@tourbillion-technology.com>
Date: Mon, 27 Apr 2020 11:07:23 +0100
Subject: gnu: ikiwiki: Propagate some inputs.

* gnu/packages/web.scm (ikiwiki)[inputs]: Move perl-html-parser,
perl-html-scrubber, perl-html-template, perl-json,
perl-text-markdown-discount, perl-uri and perl-yaml-libyaml to...
[propagated-inputs]: ...here.  New field.
---
 gnu/packages/web.scm | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index 37f2076bd1..21acfcea24 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -4877,17 +4877,18 @@ (define-public ikiwiki
        ("perl-cgi-session" ,perl-cgi-session)
        ("perl-cgi-simple" ,perl-cgi-simple)
        ("perl-db-file" ,perl-db-file)
-       ("perl-html-parser" ,perl-html-parser)
-       ("perl-html-scrubber" ,perl-html-scrubber)
        ("perl-html-tagset" ,perl-html-tagset)
-       ("perl-html-template" ,perl-html-template)
        ("perl-image-magick" ,perl-image-magick)
+       ("perl-timedate" ,perl-timedate)
+       ("perl-xml-sax" ,perl-xml-sax)
+       ("perl-xml-simple" ,perl-xml-simple)))
+    (propagated-inputs
+     `(("perl-html-parser" ,perl-html-parser)
+       ("perl-html-scrubber" ,perl-html-scrubber)
+       ("perl-html-template" ,perl-html-template)
        ("perl-json" ,perl-json)
        ("perl-text-markdown-discount" ,perl-text-markdown-discount)
-       ("perl-timedate" ,perl-timedate)
        ("perl-uri" ,perl-uri)
-       ("perl-xml-sax" ,perl-xml-sax)
-       ("perl-xml-simple" ,perl-xml-simple)
        ("perl-yaml-libyaml" ,perl-yaml-libyaml)))
     (home-page "https://ikiwiki.info/")
     (synopsis "Wiki compiler, capable of generating HTML")
-- 
cgit v1.2.3


From cf47084a884c8cc76f81a0a396b84d56f8d01904 Mon Sep 17 00:00:00 2001
From: Paul Garlick <pgarlick@tourbillion-technology.com>
Date: Tue, 28 Apr 2020 16:13:55 +0100
Subject: gnu: ikiwiki: Add missing inputs.

* gnu/packages/web.scm (ikiwiki)[inputs]: Add perl-authen-passphrase,
perl-file-mimeinfo, perl-mail-sendmail and perl-xml-twig.
---
 gnu/packages/web.scm | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index 21acfcea24..15410f945b 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -4873,15 +4873,19 @@ (define-public ikiwiki
        ("mercurial" ,mercurial)))
     (inputs
      `(("python" ,python-wrapper)
+       ("perl-authen-passphrase" ,perl-authen-passphrase)
        ("perl-cgi-formbuilder" ,perl-cgi-formbuilder)
        ("perl-cgi-session" ,perl-cgi-session)
        ("perl-cgi-simple" ,perl-cgi-simple)
        ("perl-db-file" ,perl-db-file)
+       ("perl-file-mimeinfo" ,perl-file-mimeinfo)
        ("perl-html-tagset" ,perl-html-tagset)
        ("perl-image-magick" ,perl-image-magick)
+       ("perl-mail-sendmail" ,perl-mail-sendmail)
        ("perl-timedate" ,perl-timedate)
        ("perl-xml-sax" ,perl-xml-sax)
-       ("perl-xml-simple" ,perl-xml-simple)))
+       ("perl-xml-simple" ,perl-xml-simple)
+       ("perl-xml-twig" ,perl-xml-twig)))
     (propagated-inputs
      `(("perl-html-parser" ,perl-html-parser)
        ("perl-html-scrubber" ,perl-html-scrubber)
-- 
cgit v1.2.3


From 2933cdf88e2b978da7d3ea995931946a6581a8e7 Mon Sep 17 00:00:00 2001
From: Paul Garlick <pgarlick@tourbillion-technology.com>
Date: Tue, 28 Apr 2020 17:52:21 +0100
Subject: gnu: ikiwiki: Translate documentation.

* gnu/packages/web.scm (ikiwiki)[inputs]: Add po4a.
[arguments]<#:phases>[patch-Makefile]: Rename to...
[arguments]<#:phases>[patch-Makefiles]: ...this.  Add build environment
paths to the PERL5LIB environment variable that is used by the 'po2wiki'
script.
---
 gnu/packages/web.scm | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index 15410f945b..6bb8257c8d 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -4840,10 +4840,13 @@ (define-public ikiwiki
                  "        addenv(\"PERL5LIB\", \""
                  (getenv "PERL5LIB")
                  "\");")))))
-         (add-after 'patch-source-shebangs 'patch-Makefile
+         (add-after 'patch-source-shebangs 'patch-Makefiles
            (lambda _
              (substitute* "Makefile.PL"
-               (("SYSCONFDIR\\?=") "SYSCONFDIR?=$(PREFIX)"))
+                          (("SYSCONFDIR\\?=") "SYSCONFDIR?=$(PREFIX)"))
+             (with-directory-excursion "po"
+               (substitute* "Makefile"
+                            (("PERL5LIB=") "PERL5LIB=${PERL5LIB}:")))
              #t))
          (add-before 'build 'set-modification-times
            ;; The wiki '--refresh' steps, which are executed during
@@ -4885,7 +4888,8 @@ (define-public ikiwiki
        ("perl-timedate" ,perl-timedate)
        ("perl-xml-sax" ,perl-xml-sax)
        ("perl-xml-simple" ,perl-xml-simple)
-       ("perl-xml-twig" ,perl-xml-twig)))
+       ("perl-xml-twig" ,perl-xml-twig)
+       ("po4a" ,po4a)))
     (propagated-inputs
      `(("perl-html-parser" ,perl-html-parser)
        ("perl-html-scrubber" ,perl-html-scrubber)
-- 
cgit v1.2.3


From da6539d17b6fe8c73ea06c2cad5327e1a91af6d3 Mon Sep 17 00:00:00 2001
From: Paul Garlick <pgarlick@tourbillion-technology.com>
Date: Tue, 28 Apr 2020 21:32:56 +0100
Subject: gnu: ikiwiki: Update to 3.20200202.3.

* gnu/packages/web.scm (ikiwiki): Update to 3.20200202.3.
---
 gnu/packages/web.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index 6bb8257c8d..092ff30148 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -4810,7 +4810,7 @@ (define-public hubbub
 (define-public ikiwiki
   (package
     (name "ikiwiki")
-    (version "3.20190228")
+    (version "3.20200202.3")
     (source
      (origin
        (method git-fetch)
@@ -4820,7 +4820,7 @@ (define-public ikiwiki
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "1c0i48jp2vpiwn2pacr6jbjdj26v7s9vzzs7j7gc16bx37dfgbbi"))
+         "0fphyqzlk9y8v9s89ypsmrnbhyymzrpc2w0liy0n4knc7kk2pabq"))
        (snippet
         '(begin
            ;; The POT file requires write permission during the build
-- 
cgit v1.2.3


From 4f0f46e4af0e342d84c5ad448258702029601e4b Mon Sep 17 00:00:00 2001
From: Alexandros Theodotou <alex@zrythm.org>
Date: Tue, 28 Apr 2020 15:55:13 +0100
Subject: gnu: zrythm: Update to 0.8.333.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/music.scm (zrythm): Update to 0.8.333.
[inputs]: Add new dependencies graphviz and gtksourceview.

Signed-off-by: Jakub Kądziołka <kuba@kadziolka.net>
---
 gnu/packages/music.scm | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index 34d4adb33c..589f158afe 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -99,6 +99,7 @@ (define-module (gnu packages music)
   #:use-module (gnu packages gnome)
   #:use-module (gnu packages gpodder)
   #:use-module (gnu packages graphics)
+  #:use-module (gnu packages graphviz)
   #:use-module (gnu packages gstreamer)
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages guile)
@@ -5158,7 +5159,7 @@ (define-public helm
 (define-public zrythm
   (package
     (name "zrythm")
-    (version "0.8.200")
+    (version "0.8.333")
     (source
       (origin
         (method url-fetch)
@@ -5166,7 +5167,7 @@ (define-public zrythm
                             version ".tar.xz"))
         (sha256
           (base32
-            "13ivxbrd44qnhyh46dcr94dvqxg8cn4bbd8xm77ljw0p9b4ks4zs"))))
+            "0x2kxr5zz058jpy6k6ymj0fi2gqfcgrlv4qkwz9443hjy5345iwb"))))
    (build-system meson-build-system)
    (arguments
     `(#:glib-or-gtk? #t
@@ -5190,7 +5191,9 @@ (define-public zrythm
       ("fftwf" ,fftwf)
       ("gettext" ,gettext-minimal)
       ("glibc" ,glibc)
+      ("graphviz" ,graphviz)
       ("gtk+" ,gtk+)
+      ("gtksourceview" ,gtksourceview)
       ("guile" ,guile-2.2)
       ("libcyaml" ,libcyaml)
       ("libsamplerate" ,libsamplerate)
-- 
cgit v1.2.3


From 8fe681b9ffc5c5b0056e3174fade2f9e0b58fb97 Mon Sep 17 00:00:00 2001
From: Brice Waegeneire <brice@waegenei.re>
Date: Tue, 28 Apr 2020 11:53:23 +0200
Subject: gnu: Add edid-decode.

* gnu/packages/hardware.scm (edid-decode): New variable.

Signed-off-by: Mathieu Othacehe <m.othacehe@gmail.com>
---
 gnu/packages/hardware.scm | 37 +++++++++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/hardware.scm b/gnu/packages/hardware.scm
index 7ee657a75a..114332455e 100644
--- a/gnu/packages/hardware.scm
+++ b/gnu/packages/hardware.scm
@@ -79,6 +79,43 @@ (define-public ddcutil
     (license (list license:bsd-3        ; FindDDCUtil.cmake
                    license:gpl2+))))    ; everything else
 
+(define-public edid-decode
+  (let ((commit "74b64180d67bb009d8d9ea1b6f18ad41aaa16396") ; 2020-04-22
+        (revision "1"))
+    (package
+      (name "edid-decode")
+      (version (git-version "0.0.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (file-name (git-file-name name version))
+         (uri (git-reference
+               (url "git://linuxtv.org/edid-decode.git")
+               (commit commit)))
+         (sha256
+          (base32 "0nirp5bza08zj5d8bjgcm0p869hdg3qg3mwa7999pjdrzmn7s2ah"))))
+      (build-system gnu-build-system)
+      (arguments
+       `(#:tests? #f                     ; No test suite
+         #:make-flags
+         (list (string-append "DESTDIR=" (assoc-ref %outputs "out"))
+               "bindir=/bin" "mandir=/share/man")
+         #:phases
+         (modify-phases %standard-phases
+           (add-after 'unpack 'fix-cross-compilation
+             (lambda* (#:key native-inputs target #:allow-other-keys)
+               (when target
+                 (substitute* "Makefile"
+                   (("\\$\\(CXX\\)")
+                    (string-append target "-g++"))))
+               #t))
+           (delete 'configure))))
+      (home-page "https://git.linuxtv.org/edid-decode.git/")
+      (synopsis "Decode @dfn{EDID} data in human-readable format")
+      (description "edid-decode decodes @dfn{EDID} monitor description data in
+human-readable format and checks if it conforms to the standards.")
+      (license license:expat))))
+
 ;; Distinct from memtest86, which is obsolete.
 (define-public memtest86+
   (package
-- 
cgit v1.2.3


From 1228c2abcfd5b426385211e3b27379f27d655b17 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 28 Apr 2020 13:34:22 +0200
Subject: gnu: kaldi-gstreamer-server: Update to 0-2.f68cab4.

* gnu/packages/machine-learning.scm (kaldi-gstreamer-server): Update to
0-2.f68cab4.
[inputs]: Replace python-2 with python-wrapper, python2-pygobject with
python-pygobject, python2-pyyaml with python-pyyaml, and python2-tornado with
python-tornado; remove python2-ws4py-for-kaldi-gstreamer-server and
python2-futures.
---
 gnu/packages/machine-learning.scm | 21 ++++++++++++---------
 1 file changed, 12 insertions(+), 9 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index f979a64d55..425961ee14 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -1239,8 +1239,9 @@ (define-public gst-kaldi-nnet2-online
       (license license:asl2.0))))
 
 (define-public kaldi-gstreamer-server
-  (let ((commit "1735ba49c5dc0ebfc184e45105fc600cd9f1f508")
-        (revision "1"))
+  ;; This is the tip of the py3 branch
+  (let ((commit "f68cab490be7eb0da2af1475fbc16655f50a60cb")
+        (revision "2"))
     (package
       (name "kaldi-gstreamer-server")
       (version (git-version "0" revision commit))
@@ -1252,7 +1253,7 @@ (define-public kaldi-gstreamer-server
                 (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "0j701m7lbwmzqxsfanj882v7881hrbmpqybbczbxqpcbg8q34w0k"))))
+                  "17lh1368vkg8ngrcbn2phvigzlmalrqg6djx2gg61qq1a0nj87dm"))))
       (build-system gnu-build-system)
       (arguments
        `(#:tests? #f ; there are no tests that can be run automatically
@@ -1268,6 +1269,10 @@ (define-public kaldi-gstreamer-server
                ;; are reproducible.
                (setenv "PYTHONHASHSEED" "0")
                (with-directory-excursion "kaldigstserver"
+                 ;; This is a Python 2 file
+                 (delete-file "decoder_test.py")
+                 (delete-file "test-buffer.py")
+
                  (for-each (lambda (file)
                              (apply invoke
                                     `("python"
@@ -1318,12 +1323,10 @@ (define-public kaldi-gstreamer-server
                  #t))))))
       (inputs
        `(("gst-kaldi-nnet2-online" ,gst-kaldi-nnet2-online)
-         ("python2" ,python-2)
-         ("python2-futures" ,python2-futures)
-         ("python2-pygobject" ,python2-pygobject)
-         ("python2-pyyaml" ,python2-pyyaml)
-         ("python2-tornado" ,python2-tornado)
-         ("python2-ws4py" ,python2-ws4py-for-kaldi-gstreamer-server)))
+         ("python" ,python-wrapper)
+         ("python-pygobject" ,python-pygobject)
+         ("python-pyyaml" ,python-pyyaml)
+         ("python-tornado" ,python-tornado)))
       (home-page "https://github.com/alumae/kaldi-gstreamer-server")
       (synopsis "Real-time full-duplex speech recognition server")
       (description "This is a real-time full-duplex speech recognition server,
-- 
cgit v1.2.3


From e979cea9052d45f2a3e703ebe4103f441190d087 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 28 Apr 2020 13:35:51 +0200
Subject: gnu: Remove python2-ws4py-for-kaldi-gstreamer-server.

* gnu/packages/python-web.scm (python2-ws4py-for-kaldi-gstreamer-server):
Remove variable.
---
 gnu/packages/python-web.scm | 26 --------------------------
 1 file changed, 26 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 6b77a9d949..30cd22fddb 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -3268,32 +3268,6 @@ (define-public python-ws4py
 Python.")
     (license license:bsd-3)))
 
-;; kaldi-gstreamer-server does not yet work with python-ws4py > 0.3.2
-(define-public python2-ws4py-for-kaldi-gstreamer-server
-  (package (inherit python-ws4py)
-    (name "python2-ws4py")
-    (version "0.3.2")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "ws4py" version))
-       (sha256
-        (base32
-         "12ys3dv98awhrxd570vla3hqgzq3avjhq4yafhghhq3a942y1928"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:python ,python-2
-       #:phases
-       (modify-phases %standard-phases
-         ;; We don't have a package for cherrypy.
-         (add-after 'unpack 'remove-cherrypy-support
-           (lambda _
-             (delete-file "ws4py/server/cherrypyserver.py")
-             #t)))))
-    (propagated-inputs
-     `(("python-gevent" ,python2-gevent)
-       ("python-tornado" ,python2-tornado)))))
-
 (define-public python-slugify
   (package
     (name "python-slugify")
-- 
cgit v1.2.3


From 27cb52a20b9c697131e3d51e7bf084d6af5b5a62 Mon Sep 17 00:00:00 2001
From: Raghav Gururajan <raghavgururajan@disroot.org>
Date: Fri, 10 Jan 2020 08:49:02 -0500
Subject: gnu: gnome-calendar: Propagate evolution-data-server.

* gnu/packages/gnome.scm (gnome-calendar)[inputs]: Move evolution-data-server
from here...
[propagated-inputs]: ...to here.

Fixes <https://bugs.gnu.org/40686>.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
---
 gnu/packages/gnome.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm
index d96a5f4643..e6b1942450 100644
--- a/gnu/packages/gnome.scm
+++ b/gnu/packages/gnome.scm
@@ -8094,13 +8094,14 @@ (define-public gnome-calendar
        ("gtk+-bin" ,gtk+ "bin")         ; For gtk-update-icon-cache
        ("pkg-config" ,pkg-config)))
     (inputs
-     `(("evolution-data-server" ,evolution-data-server)
-       ("gnome-online-accounts:lib" ,gnome-online-accounts "lib")
+     `(("gnome-online-accounts:lib" ,gnome-online-accounts "lib")
        ("gsettings-desktop-schemas" ,gsettings-desktop-schemas)
        ("libdazzle" ,libdazzle)
        ("libedataserverui" ,evolution-data-server)
        ("libgweather" ,libgweather)
        ("geoclue" ,geoclue)))
+    (propagated-inputs
+     `(("evolution-data-server" ,evolution-data-server)))
     (home-page "https://wiki.gnome.org/Apps/Calendar")
     (synopsis "GNOME's calendar application")
     (description
-- 
cgit v1.2.3


From 39a96b99fe66c2cf7ff8ff023f3839647332ebd9 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 29 Apr 2020 13:37:22 +0200
Subject: gnu: Add python-restructuredtext-lint.

* gnu/packages/python-xyz.scm (python-restructuredtext-lint): New variable.
---
 gnu/packages/python-xyz.scm | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 31cafd47d1..45789d7eb5 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -3212,6 +3212,38 @@ (define-public python2-docutils-0.14
                (base32
                 "0x22fs3pdmr42kvz6c654756wja305qv6cx1zbhwlagvxgr4xrji"))))))
 
+(define-public python-restructuredtext-lint
+  (package
+    (name "python-restructuredtext-lint")
+    (version "1.3.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "restructuredtext-lint" version))
+       (sha256
+        (base32
+         "026rdy5h82ng4vqxk8fnprii9d6qxf7hkygiv0a8afjvdlsxmcwp"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (delete 'check)
+         (add-after 'install 'check
+           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
+             (when tests?
+               (add-installed-pythonpath inputs outputs)
+               (invoke "nosetests" "-v"))
+             #t)))))
+    (propagated-inputs
+     `(("python-docutils" ,python-docutils)))
+    (native-inputs
+     `(("python-nose" ,python-nose)))
+    (home-page "https://github.com/twolfson/restructuredtext-lint")
+    (synopsis "reStructuredText linter")
+    (description "This package provides a linter for the reStructuredText
+format.")
+    (license license:unlicense)))
+
 (define-public python-pygments
   (package
     (name "python-pygments")
-- 
cgit v1.2.3


From d08782d16c21998a493e50e2c90a183a3d4a53bb Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 29 Apr 2020 13:38:22 +0200
Subject: gnu: Add python-port-for.

* gnu/packages/python-web.scm (python-port-for): New variable.
---
 gnu/packages/python-web.scm | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 30cd22fddb..c0be3fa5d1 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -3595,3 +3595,35 @@ (define-public grip
 appear.  Changes you make to the file will be instantly reflected in the browser
 without requiring a page refresh.")
       (license license:expat))))
+
+(define-public python-port-for
+  (package
+    (name "python-port-for")
+    (version "0.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "port-for" version))
+       (sha256
+        (base32
+         "1pncxlj25ggw99r0ijfbkq70gd7cbhqdx5ivsxy4jdp0z14cpda7"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'use-urllib3
+           (lambda _
+             (substitute* "port_for/_download_ranges.py"
+               (("urllib2") "urllib3"))
+             #t)))))
+    (propagated-inputs
+     `(("python-urllib3" ,python-urllib3)))
+    (native-inputs
+     `(("python-mock" ,python-mock)))
+    (home-page "https://github.com/kmike/port-for/")
+    (synopsis "TCP localhost port finder and association manager")
+    (description
+     "This package provides a utility that helps with local TCP ports
+management.  It can find an unused TCP localhost port and remember the
+association.")
+    (license license:expat)))
-- 
cgit v1.2.3


From d0e0b865e1e97679f718daf159e766c19bc09c91 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 29 Apr 2020 13:40:54 +0200
Subject: gnu: Add python-livereload.

* gnu/packages/python-web.scm (python-livereload): New variable.
---
 gnu/packages/python-web.scm | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index c0be3fa5d1..0dba566a77 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -3627,3 +3627,26 @@ (define-public python-port-for
 management.  It can find an unused TCP localhost port and remember the
 association.")
     (license license:expat)))
+
+(define-public python-livereload
+  (package
+    (name "python-livereload")
+    (version "2.6.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "livereload" version))
+       (sha256
+        (base32
+         "0rhggz185bxc3zjnfpmhcvibyzi86i624za1lfh7x7ajsxw4y9c9"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-six" ,python-six)
+       ("python-tornado" ,python-tornado)))
+    (home-page "https://github.com/lepture/python-livereload")
+    (synopsis "Python LiveReload")
+    (description
+     "Python LiveReload provides a command line utility, @command{livereload},
+for starting a web server in a directory.  It can trigger arbitrary commands
+and serve updated contents upon changes to the directory.")
+    (license license:bsd-3)))
-- 
cgit v1.2.3


From ff5ca61d15e979f1a91d77f950af13c76dd9b00a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 29 Apr 2020 13:41:13 +0200
Subject: gnu: Add python-doc8.

* gnu/packages/python-xyz.scm (python-doc8): New variable.
---
 gnu/packages/python-xyz.scm | 39 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 45789d7eb5..decc1ce8a6 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -3244,6 +3244,45 @@ (define-public python-restructuredtext-lint
 format.")
     (license license:unlicense)))
 
+(define-public python-doc8
+  (package
+    (name "python-doc8")
+    (version "0.8.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "doc8" version))
+       (sha256
+        (base32
+         "0hw5w8mpgsp51qg8nnq28p7y1jiksvz7a0axnn5bkgss3af9zy1d"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (delete 'check)
+         (add-after 'install 'check
+           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
+             (when tests?
+               (add-installed-pythonpath inputs outputs)
+               (invoke "pytest" "-v"))
+             #t)))))
+    (propagated-inputs
+     `(("python-chardet" ,python-chardet)
+       ("python-docutils" ,python-docutils)
+       ("python-restructuredtext-lint" ,python-restructuredtext-lint)
+       ("python-six" ,python-six)
+       ("python-stevedore" ,python-stevedore)))
+    (native-inputs
+     `(("python-testtools" ,python-testtools)
+       ("python-pytest" ,python-pytest)))
+    (home-page "https://launchpad.net/doc8")
+    (synopsis
+     "Style checker for Sphinx (or other) RST documentation")
+    (description
+     "Doc8 is an opinionated style checker for reStructured Text and plain
+text styles of documentation.")
+    (license license:asl2.0)))
+
 (define-public python-pygments
   (package
     (name "python-pygments")
-- 
cgit v1.2.3


From e9f93cd5f78ffa234263e049e594fc57cd1e94f7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 29 Apr 2020 13:41:52 +0200
Subject: gnu: Add python-sphinx-autobuild.

* gnu/packages/sphinx.scm (python-sphinx-autobuild): New variable.
---
 gnu/packages/sphinx.scm | 48 +++++++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 47 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/sphinx.scm b/gnu/packages/sphinx.scm
index ff5d8e5de7..f27f9d0176 100644
--- a/gnu/packages/sphinx.scm
+++ b/gnu/packages/sphinx.scm
@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2014 David Thompson <davet@gnu.org>
-;;; Copyright © 2015, 2017, 2019 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2017, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2015, 2016, 2017 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
 ;;; Copyright © 2016, 2017, 2018, 2019 Marius Bakke <mbakke@fastmail.com>
@@ -597,3 +597,49 @@ (define-public python-sphinx-intl
      "A utility tool that provides several features that make it easy to
 translate and to apply translation to Sphinx generated document.")
     (license license:bsd-2)))
+
+(define-public python-sphinx-autobuild
+  (package
+    (name "python-sphinx-autobuild")
+    (version "0.7.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "sphinx-autobuild" version))
+       (sha256
+        (base32
+         "0kn753dyh3b1s0h77lbk704niyqc7bamvq6v3s1f6rj6i20qyf36"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         ;; See https://github.com/GaretJax/sphinx-autobuild/pull/72
+         (add-after 'unpack 'use-later-port-for
+           (lambda _
+             (substitute* "requirements.txt"
+               (("port_for==.*") "port_for\n"))
+             #t))
+         (delete 'check)
+         (add-after 'install 'check
+           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
+             (when tests?
+               (add-installed-pythonpath inputs outputs)
+               (invoke "pytest" "-v"))
+             #t)))))
+    (propagated-inputs
+     `(("python-argh" ,python-argh)
+       ("python-livereload" ,python-livereload)
+       ("python-pathtools" ,python-pathtools)
+       ("python-port-for" ,python-port-for)
+       ("python-pyyaml" ,python-pyyaml)
+       ("python-tornado" ,python-tornado)
+       ("python-watchdog" ,python-watchdog)))
+    (native-inputs
+     `(("python-pytest" ,python-pytest)))
+    (home-page "https://github.com/GaretJax/sphinx-autobuild")
+    (synopsis "Rebuild Sphinx documentation when a change is detected")
+    (description
+     "This package lets you watch a Sphinx directory and rebuild the
+documentation when a change is detected.  It also includes a livereload
+enabled web server.")
+    (license license:expat)))
-- 
cgit v1.2.3


From 373c0dc95ce0dc65f378432d0cb1a29bda2f12e5 Mon Sep 17 00:00:00 2001
From: Masaya Tojo <masaya@tojo.tokyo>
Date: Wed, 29 Apr 2020 16:26:21 +0200
Subject: gnu: Add emacs-twittering-mode.

* gnu/packages/emacs-xyz.scm (emacs-twittering-mode): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
---
 gnu/packages/emacs-xyz.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm
index 2c61c4189d..650a573542 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -2632,6 +2632,27 @@ (define-public emacs-toml-mode
 Tom's Obvious, Minimal Language} data format.")
       (license license:gpl3+))))
 
+(define-public emacs-twittering-mode
+  (package
+    (name "emacs-twittering-mode")
+    (version "3.1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "mirror://sourceforge/twmode"
+                           "/twittering-mode-" version
+                           "/twittering-mode-" version ".tar.xz"))
+       (sha256
+        (base32 "02imis1gxz90lah0b5n37j2hlsaw5igss11d85vpsm5d1bgw8j28"))))
+    (build-system emacs-build-system)
+    (home-page "http://twmode.sourceforge.net")
+    (synopsis "Emacs major mode for Twitter")
+    (description
+     "Twittering mode is an Emacs major mode for Twitter.
+You can check timelines, tweet, mark posts as favorites and so on with
+Emacs.")
+    (license license:gpl2+)))
+
 (define-public emacs-f
   (package
     (name "emacs-f")
-- 
cgit v1.2.3


From 6d25f29143b8ebe7f627a32418a369a1c5f8625f Mon Sep 17 00:00:00 2001
From: pinoaffe <pinoaffe@airmail.cc>
Date: Wed, 29 Apr 2020 16:29:53 +0200
Subject: gnu: Add emacs-ryo-modal.

* gnu/packages/emacs-xyz.scm (emacs-ryo-modal): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
---
 gnu/packages/emacs-xyz.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm
index 650a573542..56cd298c28 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -68,6 +68,7 @@
 ;;; Copyright © 2020 John Soo <jsoo1@asu.edu>
 ;;; Copyright © 2020 Jérémy Korwin-Zmijowski <jeremy@korwin-zmijowski.fr>
 ;;; Copyright © 2020 Alberto Eleuterio Flores Guerrero <barbanegra+guix@posteo.mx>
+;;; Copyright © 2020 pinoaffe <pinoaffe@airmail.cc>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -7312,6 +7313,30 @@ (define-public emacs-rainbow-mode
 names, e.g. #0000ff is displayed in white with a blue background.")
     (license license:gpl3+)))
 
+(define-public emacs-ryo-modal
+  ;; Package has no release.  Version is extracted from "Version:" keyword in
+  ;; main file.
+  (let ((commit "3a54312eea7023a86ca3f8eb3c03c872554bff2f")
+        (revision "0"))
+    (package
+      (name "emacs-ryo-modal")
+      (version (git-version "0.4" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/Kungsgeten/ryo-modal.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "1cyvp3bi6yhckbdnq98xvghmhdzghya5y9wd7hxjawibs75rza95"))))
+      (build-system emacs-build-system)
+      (home-page "http://github.com/Kungsgeten/ryo-modal")
+      (synopsis "Emacs minor mode for defining modal editing environments")
+      (description "RYO modal provides a convenient way of defining modal
+keybindings in Emacs, and does not come with any predefined bindings.")
+      (license license:expat))))
+
 (define-public emacs-visual-fill-column
   (package
     (name "emacs-visual-fill-column")
-- 
cgit v1.2.3


From 1cc9947a53adc36d0767c1854f54178d91eb872d Mon Sep 17 00:00:00 2001
From: pinoaffe <pinoaffe@airmail.cc>
Date: Wed, 29 Apr 2020 16:33:35 +0200
Subject: gnu: Add emacs-kakoune.

* gnu/packages/emacs-xyz.scm (emacs-kakoune): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
---
 gnu/packages/emacs-xyz.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm
index 56cd298c28..9200122b77 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -2479,6 +2479,37 @@ (define-public emacs-extempore-mode
 running Extempore process, and more.")
       (license license:bsd-2))))
 
+(define-public emacs-kakoune
+  ;; Package has no release.  Version is extracted from "Version:" keyword in
+  ;; main file.
+  (let ((commit "d73d14e69ea38076af50cc69f846808383ff539d")
+        (revision "0"))
+    (package
+      (name "emacs-kakoune")
+      (version (git-version "0.1" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/jmorag/kakoune.el.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "0nk6jdy1y5mc3ryd0smiqghrk6iv34d5grc7f7migmshlbq0np92"))))
+      (build-system emacs-build-system)
+      (propagated-inputs
+       `(("emacs-expand-region"    ,emacs-expand-region)
+         ("emacs-multiple-cursors" ,emacs-multiple-cursors)
+         ("emacs-ryo-modal"        ,emacs-ryo-modal)))
+      (home-page "https://github.com/jmorag/kakoune.el")
+      (synopsis "Emacs simple simulation, but not emulation, of Kakoune")
+      (description "This package provides many, but not all of the editing
+primitives in the Kakoune editor.  Unlike Evil mode for Vim, this is a very
+shallow emulation, which seeks to do as little work as possible, leveraging
+Emacs native editing commmands and the work of other packages wherever
+possible.")
+      (license license:expat))))
+
 (define-public emacs-keyfreq
   (package
     (name "emacs-keyfreq")
-- 
cgit v1.2.3


From 587ccf4c793973dcde1abd3ef207a9ee58b9f0e5 Mon Sep 17 00:00:00 2001
From: Oleg Pykhalov <go.wigust@gmail.com>
Date: Wed, 29 Apr 2020 19:36:30 +0300
Subject: gnu: emacs-vterm: Update to 0-1.e63bd65.

* gnu/packages/emacs-xyz.scm (emacs-vterm): Update to 0-1.e63bd65.
---
 gnu/packages/emacs-xyz.scm | 13 +++++--------
 1 file changed, 5 insertions(+), 8 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm
index 9200122b77..79f7126ed7 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -18241,7 +18241,7 @@ (define-public emacs-mpdel
 (define-public emacs-vterm
   (let ((version "0")
         (revision "1")
-        (commit "7d7381fa8104b55b70148cf147523d9ab7f01fcd"))
+        (commit "e63bd65eece7c5de3a534b7e2fdbe58256ec2da0"))
     (package
       (name "emacs-vterm")
       (version (git-version version revision commit))
@@ -18253,7 +18253,7 @@ (define-public emacs-vterm
                 (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "04a2jlhmr20ipgzpnba3yryw3ly7qdxjgaw10dwn9wxy1yqmapz1"))))
+                  "0iq857w54qmazxh23fipz85fb9i6dav3f63g0ghpmi6mybfp6i5v"))))
       (build-system emacs-build-system)
       (arguments
        `(#:modules ((guix build emacs-build-system)
@@ -18264,14 +18264,11 @@ (define-public emacs-vterm
                              (guix build cmake-build-system))
          #:phases
          (modify-phases %standard-phases
-           (add-before 'add-source-to-load-path 'remove-vterm-module-make
+           (add-before 'add-source-to-load-path 'substitute-vterm-module-path
              (lambda* (#:key outputs #:allow-other-keys)
-               ;; Remove the Emacs Lisp file.
-               (delete-file "vterm-module-make.el")
-               ;; Remove references to the removed file.
-               (make-file-writable "vterm.el")
+               (chmod "vterm.el" #o644)
                (emacs-substitute-sexps "vterm.el"
-                 ("(or (require 'vterm-module nil t)"
+                 ("(require 'vterm-module nil t)"
                   `(module-load
                     ,(string-append (assoc-ref outputs "out")
                                     "/lib/vterm-module.so"))))
-- 
cgit v1.2.3


From 19987f5efe0acb65918802681f3a18cbb6a07c2a Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 29 Apr 2020 16:57:09 +0200
Subject: gnu: foo2zjs: Update to 20200426.

* gnu/packages/cups.scm (foo2zjs): Update to 20200426.
---
 gnu/packages/cups.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cups.scm b/gnu/packages/cups.scm
index 1db2f101f1..f24ea6c02a 100644
--- a/gnu/packages/cups.scm
+++ b/gnu/packages/cups.scm
@@ -673,14 +673,14 @@ (define-public foomatic-filters
 (define-public foo2zjs
   (package
     (name "foo2zjs")
-    (version "20200207")
+    (version "20200426")
     (source (origin
               (method url-fetch)
               ;; XXX: This is an unversioned URL!
               (uri "http://foo2zjs.rkkda.com/foo2zjs.tar.gz")
               (sha256
                (base32
-                "0pf1sm29gnrhhpyvq95jskvr874h5r4kls9w10gc24z23fjmr5zx"))))
+                "0wwh29ddd59q18r1jpi3166lgnwr8zn9lry82vahc2g96l97isp7"))))
     (build-system gnu-build-system)
     (arguments
      '(#:phases (modify-phases %standard-phases
-- 
cgit v1.2.3


From f224a8bb79cc3c9e5960227ffea5524eb666d34a Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Tue, 28 Apr 2020 15:59:16 -0400
Subject: gnu: OpenLDAP: Update to 2.4.50 [fixes CVE-2019-{13057,13565}].

* gnu/packages/openldap.scm (openldap)[replacement]: Use openldap-2.4.50.
(openldap/fixed): Replace with ...
(openldap-2.4.50): ... new variable.
* gnu/packages/patches/openldap-CVE-2020-12243.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
---
 gnu/local.mk                                       |   1 -
 gnu/packages/openldap.scm                          |  16 ++-
 gnu/packages/patches/openldap-CVE-2020-12243.patch | 125 ---------------------
 3 files changed, 11 insertions(+), 131 deletions(-)
 delete mode 100644 gnu/packages/patches/openldap-CVE-2020-12243.patch

(limited to 'gnu/packages')

diff --git a/gnu/local.mk b/gnu/local.mk
index 67bf04547c..9426ee30a0 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1276,7 +1276,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/opencv-rgbd-aarch64-test-fix.patch	\
   %D%/packages/patches/openfoam-4.1-cleanup.patch			\
   %D%/packages/patches/openjdk-10-idlj-reproducibility.patch	\
-  %D%/packages/patches/openldap-CVE-2020-12243.patch		\
   %D%/packages/patches/openmpi-mtl-priorities.patch		\
   %D%/packages/patches/openocd-nrf52.patch			\
   %D%/packages/patches/openssl-runpath.patch			\
diff --git a/gnu/packages/openldap.scm b/gnu/packages/openldap.scm
index aa51520654..53c57e846f 100644
--- a/gnu/packages/openldap.scm
+++ b/gnu/packages/openldap.scm
@@ -58,8 +58,8 @@ (define-module (gnu packages openldap)
 
 (define-public openldap
   (package
-   (replacement openldap/fixed)
    (name "openldap")
+   (replacement openldap-2.4.50)
    (version "2.4.47")
    (source (origin
             (method url-fetch)
@@ -112,12 +112,18 @@ (define-public openldap
    (license openldap2.8)
    (home-page "https://www.openldap.org/")))
 
-(define openldap/fixed
+(define openldap-2.4.50
   (package
     (inherit openldap)
-    (source
-      (origin (inherit (package-source openldap))
-              (patches (search-patches "openldap-CVE-2020-12243.patch"))))))
+    (version "2.4.50")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://www.openldap.org/software/download/"
+                                  "OpenLDAP/openldap-release/openldap-" version
+                                  ".tgz"))
+              (sha256
+               (base32
+                "1f46nlfwmys110j36sifm7ah8m8f3s10c3vaiikmmigmifapvdaw"))))))
 
 (define-public nss-pam-ldapd
   (package
diff --git a/gnu/packages/patches/openldap-CVE-2020-12243.patch b/gnu/packages/patches/openldap-CVE-2020-12243.patch
deleted file mode 100644
index 6321998198..0000000000
--- a/gnu/packages/patches/openldap-CVE-2020-12243.patch
+++ /dev/null
@@ -1,125 +0,0 @@
-From 98464c11df8247d6a11b52e294ba5dd4f0380440 Mon Sep 17 00:00:00 2001
-From: Howard Chu <hyc@openldap.org>
-Date: Thu, 16 Apr 2020 01:08:19 +0100
-Subject: [PATCH] ITS#9202 limit depth of nested filters
-
-Using a hardcoded limit for now; no reasonable apps
-should ever run into it.
----
- servers/slapd/filter.c | 41 ++++++++++++++++++++++++++++++++---------
- 1 file changed, 32 insertions(+), 9 deletions(-)
-
-diff --git a/servers/slapd/filter.c b/servers/slapd/filter.c
-index 3252cf2a7..ed57bbd7b 100644
---- a/servers/slapd/filter.c
-+++ b/servers/slapd/filter.c
-@@ -37,11 +37,16 @@
- const Filter *slap_filter_objectClass_pres;
- const struct berval *slap_filterstr_objectClass_pres;
- 
-+#ifndef SLAPD_MAX_FILTER_DEPTH
-+#define SLAPD_MAX_FILTER_DEPTH	5000
-+#endif
-+
- static int	get_filter_list(
- 	Operation *op,
- 	BerElement *ber,
- 	Filter **f,
--	const char **text );
-+	const char **text,
-+	int depth );
- 
- static int	get_ssa(
- 	Operation *op,
-@@ -80,12 +85,13 @@ filter_destroy( void )
- 	return;
- }
- 
--int
--get_filter(
-+static int
-+get_filter0(
- 	Operation *op,
- 	BerElement *ber,
- 	Filter **filt,
--	const char **text )
-+	const char **text,
-+	int depth )
- {
- 	ber_tag_t	tag;
- 	ber_len_t	len;
-@@ -126,6 +132,11 @@ get_filter(
- 	 *
- 	 */
- 
-+	if( depth > SLAPD_MAX_FILTER_DEPTH ) {
-+		*text = "filter nested too deeply";
-+		return SLAPD_DISCONNECT;
-+	}
-+
- 	tag = ber_peek_tag( ber, &len );
- 
- 	if( tag == LBER_ERROR ) {
-@@ -221,7 +232,7 @@ get_filter(
- 
- 	case LDAP_FILTER_AND:
- 		Debug( LDAP_DEBUG_FILTER, "AND\n", 0, 0, 0 );
--		err = get_filter_list( op, ber, &f.f_and, text );
-+		err = get_filter_list( op, ber, &f.f_and, text, depth+1 );
- 		if ( err != LDAP_SUCCESS ) {
- 			break;
- 		}
-@@ -234,7 +245,7 @@ get_filter(
- 
- 	case LDAP_FILTER_OR:
- 		Debug( LDAP_DEBUG_FILTER, "OR\n", 0, 0, 0 );
--		err = get_filter_list( op, ber, &f.f_or, text );
-+		err = get_filter_list( op, ber, &f.f_or, text, depth+1 );
- 		if ( err != LDAP_SUCCESS ) {
- 			break;
- 		}
-@@ -248,7 +259,7 @@ get_filter(
- 	case LDAP_FILTER_NOT:
- 		Debug( LDAP_DEBUG_FILTER, "NOT\n", 0, 0, 0 );
- 		(void) ber_skip_tag( ber, &len );
--		err = get_filter( op, ber, &f.f_not, text );
-+		err = get_filter0( op, ber, &f.f_not, text, depth+1 );
- 		if ( err != LDAP_SUCCESS ) {
- 			break;
- 		}
-@@ -311,10 +322,22 @@ get_filter(
- 	return( err );
- }
- 
-+int
-+get_filter(
-+	Operation *op,
-+	BerElement *ber,
-+	Filter **filt,
-+	const char **text )
-+{
-+	return get_filter0( op, ber, filt, text, 0 );
-+}
-+
-+
- static int
- get_filter_list( Operation *op, BerElement *ber,
- 	Filter **f,
--	const char **text )
-+	const char **text,
-+	int depth )
- {
- 	Filter		**new;
- 	int		err;
-@@ -328,7 +351,7 @@ get_filter_list( Operation *op, BerElement *ber,
- 		tag != LBER_DEFAULT;
- 		tag = ber_next_element( ber, &len, last ) )
- 	{
--		err = get_filter( op, ber, new, text );
-+		err = get_filter0( op, ber, new, text, depth );
- 		if ( err != LDAP_SUCCESS )
- 			return( err );
- 		new = &(*new)->f_next;
--- 
-2.26.2
-
-- 
cgit v1.2.3


From 4b800bff8039ca718aa70db814dc51b5de18da8e Mon Sep 17 00:00:00 2001
From: Lars-Dominik Braun <ldb@leibniz-psychology.org>
Date: Tue, 21 Apr 2020 10:34:30 +0200
Subject: gnu: python-aiosqlite: Update to 0.12.0.

* gnu/packages/databases.scm (python-aiosqlite): Update to 0.12.0.

Signed-off-by: Leo Famulari <leo@famulari.name>
---
 gnu/packages/databases.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 606594e005..bf5398d87b 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -2743,14 +2743,14 @@ (define-public python2-apsw
 (define-public python-aiosqlite
   (package
     (name "python-aiosqlite")
-    (version "0.11.0")
+    (version "0.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "aiosqlite" version))
        (sha256
         (base32
-         "1f3zdldp9zgrw6qz5fsp3wa5zw73cjf139pj4vf24ryv895320jg"))))
+         "1w8248yz85xyzvvh4jaxnc59fqil45aka6h82kn1rcih4rjxbnn1"))))
     (build-system python-build-system)
     (native-inputs
      `(("python-aiounittest" ,python-aiounittest)))
-- 
cgit v1.2.3


From 510472f865a9a21cce4ed8b1f16236ed513dbccc Mon Sep 17 00:00:00 2001
From: Lars-Dominik Braun <ldb@leibniz-psychology.org>
Date: Tue, 21 Apr 2020 10:35:33 +0200
Subject: gnu: python-pypika: Update to 0.37.2.

* gnu/packages/databases.scm (python-pypika): Update to 0.37.2.

Signed-off-by: Leo Famulari <leo@famulari.name>
---
 gnu/packages/databases.scm | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index bf5398d87b..57a5128e9e 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -3074,14 +3074,16 @@ (define-public python2-sql
 (define-public python-pypika
   (package
     (name "python-pypika")
-    (version "0.36.0")
+    (version "0.37.2")
     (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "PyPika" version))
-       (sha256
-        (base32
-         "0qzn5vygirg52dlizm6ayzdc5llq8p2krrx0kymr236lrz89wqp8"))))
+     (origin (method git-fetch)
+             (uri (git-reference
+                   (url "https://github.com/kayak/pypika.git")
+                   (commit (string-append "v" version))))
+             (file-name (git-file-name name version))
+             (sha256
+              (base32
+               "089z1c778q1fwhzsc88ws8j5gm2hgxknibabn4wpax8rz2bfs3ck"))))
     (build-system python-build-system)
     (native-inputs
      `(("python-parameterized" ,python-parameterized)))
-- 
cgit v1.2.3


From b9d96ed77343e3f158f7ee1c758270bf4f059a74 Mon Sep 17 00:00:00 2001
From: Lars-Dominik Braun <ldb@leibniz-psychology.org>
Date: Tue, 21 Apr 2020 10:36:29 +0200
Subject: gnu: python-tortoise-orm: Update to 0.16.7 [security fixes].

* gnu/packages/databases.scm (python-tortoise-orm)[source]: Update to 0.16.7.
[propagated-inputs]: Propagate python-ciso8601, which is required in setup.py.

Signed-off-by: Leo Famulari <leo@famulari.name>
---
 gnu/packages/databases.scm | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 57a5128e9e..23b8f14c54 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -2197,24 +2197,24 @@ (define-public python2-peewee
 (define-public python-tortoise-orm
   (package
     (name "python-tortoise-orm")
-    (version "0.16.3")
+    (version "0.16.7")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "tortoise-orm" version))
        (sha256
         (base32
-         "01hbvfyxs2qd1mjc96aipwsdxxhydw8ww686r4gsf87bl6f98dvz"))))
+         "0wr7p4v0b16ypm9fcpwpl99kf491m6w3jkd13xcsgq13fy73fbqc"))))
     (build-system python-build-system)
     ;; Disable tests for now. They pull in a lot of dependencies.
     (arguments `(#:tests? #f))
     (native-inputs
-     `(("python-ciso8601" ,python-ciso8601)
-       ("python-asynctest" ,python-asynctest)
+     `(("python-asynctest" ,python-asynctest)
        ("python-nose2" ,python-nose2)))
     (propagated-inputs
      `(("python-aiosqlite" ,python-aiosqlite)
        ("python-pypika" ,python-pypika)
+       ("python-ciso8601" ,python-ciso8601)
        ("python-typing-extensions"
         ,python-typing-extensions)))
     (home-page
-- 
cgit v1.2.3


From e118837ede3f96bc76c7db22f1fc2cc348099507 Mon Sep 17 00:00:00 2001
From: Marcin Karpezo <sirmacik@wioo.waw.pl>
Date: Wed, 29 Apr 2020 16:49:36 +0200
Subject: gnu: Add aspell-dict-pl.

* gnu/packages/aspell.scm (aspell-dict-pl): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
---
 gnu/packages/aspell.scm | 8 ++++++++
 1 file changed, 8 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/aspell.scm b/gnu/packages/aspell.scm
index b11a2dbe6b..689fe64ec1 100644
--- a/gnu/packages/aspell.scm
+++ b/gnu/packages/aspell.scm
@@ -8,6 +8,7 @@
 ;;; Copyright © 2016, 2017, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2019 Jens Mølgaard <jens@zete.tk>
 ;;; Copyright © 2020 Timotej Lazar <timotej.lazar@araneo.si>
+;;; Copyright © 2020 Marcin Karpezo <sirmacik@wioo.waw.pl>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -298,6 +299,13 @@ (define-public aspell-dict-nn
                      (base32
                       "0w2k5l5rbqpliripgqwiqixz5ghnjf7i9ggbrc4ly4vy1ia10rmc")))
 
+(define-public aspell-dict-pl
+  (aspell-dictionary "pl" "Polish"
+                     #:version "0.51-0"
+                     #:sha256
+                     (base32
+                      "1a3ccji6k5gys7l3ilr2lh5pzxgzb7ipc5vb737svl6nqgdy8757")))
+
 (define-public aspell-dict-pt-br
   (aspell-dictionary "pt_BR" "Brazilian Portuguese"
                      #:version "20131030-12-0"
-- 
cgit v1.2.3


From c5c25b39ebe68dd89bf3913d2766df3a8a77dff1 Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Wed, 29 Apr 2020 16:14:55 -0400
Subject: gnu: magic-wormhole-mailbox-server: Update to 0.4.1.

* gnu/packages/magic-wormhole.scm (magic-wormhole-mailbox-server): Update to
0.4.1.
---
 gnu/packages/magic-wormhole.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/magic-wormhole.scm b/gnu/packages/magic-wormhole.scm
index bdfc1162b6..85b25bc0e5 100644
--- a/gnu/packages/magic-wormhole.scm
+++ b/gnu/packages/magic-wormhole.scm
@@ -29,14 +29,14 @@ (define-module (gnu packages magic-wormhole)
 (define-public magic-wormhole-mailbox-server
   (package
     (name "magic-wormhole-mailbox-server")
-    (version "0.3.1")
+    (version "0.4.1")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "magic-wormhole-mailbox-server" version))
         (sha256
          (base32
-          "1q6zhbx8fcpk7rchclm7yqcxdsc1x97hki2ji61sa544r5xvxv55"))))
+          "1yw8i8jv5iv1kkz1aqimskw7fpichjn6ww0fq0czbalwj290bw8s"))))
     (build-system python-build-system)
     (arguments
      '(#:phases
-- 
cgit v1.2.3


From 718c8837f94f792d93b4fe1f8259f02718755f49 Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Wed, 29 Apr 2020 16:15:19 -0400
Subject: gnu: magic-wormhole-transit-relay: Update to 0.2.1.

* gnu/packages/magic-wormhole.scm (magic-wormhole-transit-relay): Update to
0.2.1.
---
 gnu/packages/magic-wormhole.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/magic-wormhole.scm b/gnu/packages/magic-wormhole.scm
index 85b25bc0e5..4456f95d99 100644
--- a/gnu/packages/magic-wormhole.scm
+++ b/gnu/packages/magic-wormhole.scm
@@ -68,14 +68,14 @@ (define-public magic-wormhole-mailbox-server
 (define-public magic-wormhole-transit-relay
   (package
     (name "magic-wormhole-transit-relay")
-    (version "0.1.2")
+    (version "0.2.1")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "magic-wormhole-transit-relay" version))
         (sha256
          (base32
-          "11w5gdc6am2ph5rns60x0694sx4zrlzxj540jljhn5cmnbx1ngxi"))))
+          "0ppsx2s1ysikns1h053x67z2zmficbn3y3kf52bzzslhd2s02j6b"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
-- 
cgit v1.2.3


From fb5bb6bd9e451aa672e67573bf2911a5fc7b4d6d Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Wed, 29 Apr 2020 16:15:40 -0400
Subject: gnu: Magic Wormhole: Update to 0.12.0.

* gnu/packages/magic-wormhole.scm (magic-wormhole): Update to 0.12.0.
---
 gnu/packages/magic-wormhole.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/magic-wormhole.scm b/gnu/packages/magic-wormhole.scm
index 4456f95d99..465e6aced6 100644
--- a/gnu/packages/magic-wormhole.scm
+++ b/gnu/packages/magic-wormhole.scm
@@ -107,14 +107,14 @@ (define-public magic-wormhole-transit-relay
 (define-public magic-wormhole
   (package
     (name "magic-wormhole")
-    (version "0.11.2")
+    (version "0.12.0")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "magic-wormhole" version))
         (sha256
          (base32
-          "01fr4bi6kc6fz9n3c4qq892inrc3nf6p2djy65yvm7xkvdxncydf"))))
+          "0q41j99718y7m95zg1vaybnsp31lp6lhyqkbv4yqz5ys6jixh3qv"))))
     (build-system python-build-system)
     (arguments
      '(#:phases
-- 
cgit v1.2.3


From fd65311cf4ee043290c594900b99ddeb9d8dff3a Mon Sep 17 00:00:00 2001
From: Marcin Karpezo <sirmacik@wioo.waw.pl>
Date: Wed, 29 Apr 2020 14:51:33 +0200
Subject: gnu: Add sbcl-stumpwm-pass.

* gnu/packages/wm.scm (sbcl-stumpwm-pass): New variable.

Signed-off-by: Oleg Pykhalov <go.wigust@gmail.com>
---
 gnu/packages/wm.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/wm.scm b/gnu/packages/wm.scm
index 4d1b6b3fd4..9f64f206af 100644
--- a/gnu/packages/wm.scm
+++ b/gnu/packages/wm.scm
@@ -34,6 +34,7 @@
 ;;; Copyright © 2020 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;; Copyright © 2020 Brice Waegeneire <brice@waegenei.re>
 ;;; Copyright © 2020 Boris A. Dekshteyn <harlequin78@gmail.com>
+;;; Copyright © 2020 Marcin Karpezo <sirmacik@wioo.waw.pl>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1730,6 +1731,36 @@ (define-public sbcl-stumpwm-ttf-fonts
 rendering.")
       (license (list license:gpl2+ license:gpl3+ license:bsd-2)))))
 
+(define-public sbcl-stumpwm-pass
+  (let ((commit "dd5b037923ec7d3cc27c55806bcec5a1b8cf4e91")
+        (revision "1"))
+    (package
+      (name "sbcl-pass")
+      (version (git-version "0.0.1" revision commit)) ;no upstream release
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/stumpwm/stumpwm-contrib.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "0ahxdj9f884afpzxczx6mx7l4nwg4kw6afqaq7lwhf7lxcwylldn"))))
+      (inputs
+       `(("stumpwm" ,stumpwm "lib")))
+      (build-system asdf-build-system/sbcl)
+      (arguments
+       '(#:phases
+         (modify-phases %standard-phases
+           (add-after 'unpack 'chdir
+             (lambda _
+               (chdir "util/pass"))))))
+      (home-page "https://github.com/stumpwm/stumpwm-contrib")
+      (synopsis "Integrate @code{pass} wih StumpWM")
+      (description "This package provides an interface which integrates
+password-store into StumpWM.")
+      (license (list license:gpl2+ license:gpl3+ license:bsd-2)))))
+
 (define-public sbcl-stumpwm-globalwindows
   (let ((commit "dd5b037923ec7d3cc27c55806bcec5a1b8cf4e91")
         (revision "1"))
-- 
cgit v1.2.3


From ad2736717a475fa696b4fe637d722f31ed520a8d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 28 Apr 2020 13:41:38 +0200
Subject: gnu: python-psutil: Update to 5.7.0.

* gnu/packages/python-xyz.scm (python-psutil): Update to 5.7.0.
---
 gnu/packages/python-xyz.scm | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index decc1ce8a6..6f881161fd 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -412,16 +412,17 @@ (define-public python-pymediainfo
 (define-public python-psutil
   (package
     (name "python-psutil")
-    (version "5.6.5")
+    (version "5.7.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "psutil" version))
        (sha256
-        (base32 "0isil5jxwwd8awz54qk28rpgjg43i5l6yl70g40vxwa4r4m56lfh"))))
+        (base32 "03jykdi3dgf1cdal9bv4fq9zjvzj9l9bs99gi5ar81sdl5nc2pk8"))))
     (build-system python-build-system)
     (arguments
-     ;; FIXME: some tests does not return and times out.
+     ;; FIXME: some tests do not return and time out.  Some tests fail because
+     ;; some processes survive kill().
      '(#:tests? #f))
     (home-page "https://www.github.com/giampaolo/psutil")
     (synopsis "Library for retrieving information on running processes")
-- 
cgit v1.2.3


From 88f8a7c6100302e66e9a0058ae018042cdd27b62 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 29 Apr 2020 14:12:37 +0200
Subject: gnu: Add python-voluptuous.

* gnu/packages/python-xyz.scm (python-voluptuous): New variable.
---
 gnu/packages/python-xyz.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 6f881161fd..e6088bd6ce 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -19660,3 +19660,24 @@ (define-public python-osc
 dependencies.  It implements the @uref{http://opensoundcontrol.org/spec-1_0,
 Open Sound Control 1.0} specification.")
     (license license:unlicense)))
+
+(define-public python-voluptuous
+  (package
+    (name "python-voluptuous")
+    (version "0.11.7")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (pypi-uri "voluptuous" version))
+        (sha256
+          (base32
+            "0mplkcpb5d8wjf8vk195fys4y6a3wbibiyf708imw33lphfk9g1a"))))
+    (build-system python-build-system)
+    (native-inputs
+     `(("python-nose" ,python-nose)))
+    (home-page "https://github.com/alecthomas/voluptuous")
+    (synopsis "Python data validation library")
+    (description
+     "Voluptuous is a Python data validation library.  It is primarily
+intended for validating data coming into Python as JSON, YAML, etc.")
+    (license license:bsd-3)))
-- 
cgit v1.2.3


From 7e3ddb6904e27b18f364b7c3b161f2927017155c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 29 Apr 2020 14:12:49 +0200
Subject: gnu: Add python-cmd2.

* gnu/packages/python-xyz.scm (python-cmd2): New variable.
---
 gnu/packages/python-xyz.scm | 46 +++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 46 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index e6088bd6ce..c37ed2bfa0 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -19681,3 +19681,49 @@ (define-public python-voluptuous
      "Voluptuous is a Python data validation library.  It is primarily
 intended for validating data coming into Python as JSON, YAML, etc.")
     (license license:bsd-3)))
+
+(define-public python-cmd2
+  (package
+    (name "python-cmd2")
+    (version "1.0.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "cmd2" version))
+       (sha256
+        (base32
+         "1f18plbc9yyvhn0js3d2bii9yld8zfl775gxsaw9jza5pmlg9ss2"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-attrs" ,python-attrs)
+       ("python-colorama" ,python-colorama)
+       ("python-pyperclip" ,python-pyperclip)
+       ("python-wcwidth" ,python-wcwidth)))
+    (native-inputs
+     `(("python-codecov" ,python-codecov)
+       ("python-coverage" ,python-coverage)
+       ("python-doc8" ,python-doc8)
+       ("python-flake8" ,python-flake8)
+       ("python-invoke" ,python-invoke)
+       ("python-mock" ,python-mock)
+       ("python-pytest" ,python-pytest)
+       ("python-pytest-cov" ,python-pytest-cov)
+       ("python-pytest-mock" ,python-pytest-mock)
+       ("python-setuptools-scm" ,python-setuptools-scm)
+       ("python-sphinx" ,python-sphinx)
+       ("python-sphinx-autobuild" ,python-sphinx-autobuild)
+       ("python-sphinx-rtd-theme" ,python-sphinx-rtd-theme)
+       ("python-tox" ,python-tox)
+       ("python-twine" ,python-twine)
+       ("which" ,which)))
+    (home-page "https://github.com/python-cmd2/cmd2")
+    (synopsis "Tool for building interactive command line applications")
+    (description
+     "Cmd2 is a tool for building interactive command line applications in
+Python.  Its goal is to make it quick and easy for developers to build
+feature-rich and user-friendly interactive command line applications.  It
+provides a simple API which is an extension of Python's built-in @code{cmd}
+module.  @code{cmd2} provides a wealth of features on top of @code{cmd} to
+make your life easier and eliminates much of the boilerplate code which would
+be necessary when using @code{cmd}.")
+    (license license:expat)))
-- 
cgit v1.2.3


From 37130eccd23eccfdc6653c3e73321fea4000d51d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 29 Apr 2020 22:16:31 +0200
Subject: gnu: Remove python2-pyflakes-0.8.1.

* gnu/packages/python-xyz.scm (python2-pyflakes-0.8.1): Remove variable.
---
 gnu/packages/python-xyz.scm | 3 ---
 1 file changed, 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index c37ed2bfa0..c6c6bf2c3e 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -7454,9 +7454,6 @@ (define-public python-pyflakes-0.8.1
      ;; XXX Tests not compatible with Python 3.5.
      '(#:tests? #f))))
 
-(define-public python2-pyflakes-0.8.1
-  (package-with-python2 python-pyflakes-0.8.1))
-
 (define-public python-flake8
   (package
     (name "python-flake8")
-- 
cgit v1.2.3


From a6559240098d8b8ff7f799f57aecf96a53a88401 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 29 Apr 2020 22:19:25 +0200
Subject: gnu: Replace python-pyflakes-0.8.1 with python-pyflakes-1.2.

* gnu/packages/python-xyz.scm (python-pyflakes-0.8.1): Remove variable.
(python-pyflakes-1.2): New variable.
* gnu/packages/openstack.scm (python-hacking)[propagated-inputs]: Replace
python-pyflakes-0.8.1 with python-pyflakes-1.2.
---
 gnu/packages/openstack.scm  |  2 +-
 gnu/packages/python-xyz.scm | 37 +++++++++++++++++++++----------------
 2 files changed, 22 insertions(+), 17 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm
index 8dd8c1907c..6c81454150 100644
--- a/gnu/packages/openstack.scm
+++ b/gnu/packages/openstack.scm
@@ -144,7 +144,7 @@ (define-public python-hacking
        ("python-mccabe-0.2.1" ,python-mccabe-0.2.1)
        ("python-pbr" ,python-pbr)
        ("python-pep8-1.5.7" ,python-pep8-1.5.7)
-       ("python-pyflakes-0.8.1" ,python-pyflakes-0.8.1)
+       ("python-pyflakes-1.2" ,python-pyflakes-1.2)
        ("python-six" ,python-six)))
     (native-inputs
      `( ;; Tests
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index c6c6bf2c3e..80185f49e0 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -7380,6 +7380,27 @@ (define-public python-pyflakes
 (define-public python2-pyflakes
   (package-with-python2 python-pyflakes))
 
+;; Flake8 2.6 requires an older version of pyflakes.
+;; This should be removed ASAP.
+(define-public python-pyflakes-1.2
+  (package (inherit python-pyflakes)
+    (version "1.2.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "pyflakes" version))
+       (sha256
+        (base32
+         "17hkw8yd44cr8fz13phy4aih3r5j2p7ild4zlvqdh2c8dmiinjif"))))
+    (arguments
+     '(#:phases
+       (modify-phases %standard-phases
+         ;; This one test fails.
+         (replace 'check
+           (lambda _ (invoke "pytest" "-vv" "-k" "not test_f_string"))))))
+    (native-inputs
+     `(("python-pytest" ,python-pytest)))))
+
 (define-public python-mccabe
   (package
     (name "python-mccabe")
@@ -7438,22 +7459,6 @@ (define-public python-pep8-1.5.7
 (define-public python2-pep8-1.5.7
   (package-with-python2 python-pep8-1.5.7))
 
-;; Flake8 2.4.1 requires an older version of pyflakes.
-;; This should be removed ASAP.
-(define-public python-pyflakes-0.8.1
-  (package (inherit python-pyflakes)
-    (version "0.8.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "pyflakes" version))
-       (sha256
-        (base32
-         "0sbpq6pqm1i9wqi41mlfrsc5rk92jv4mskvlyxmnhlbdnc80ma1z"))))
-    (arguments
-     ;; XXX Tests not compatible with Python 3.5.
-     '(#:tests? #f))))
-
 (define-public python-flake8
   (package
     (name "python-flake8")
-- 
cgit v1.2.3


From 7fea8e076fd2405c0d53d7ee5d7a36936215ffcc Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 29 Apr 2020 22:23:19 +0200
Subject: gnu: Remove python2-flake8-2.5.

* gnu/packages/python-xyz.scm (python2-flake8-2.5): Remove variable.
(python-flake8-2.5)[properties]: Remove.
---
 gnu/packages/python-xyz.scm | 13 +------------
 1 file changed, 1 insertion(+), 12 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 80185f49e0..1110360afd 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -7519,18 +7519,7 @@ (define-public python-flake8-2.5
                 "1snylqwbmrylbx3r1wpz8ggk98f6bcag4441ag8mm2l7wyn58sij"))))
     (propagated-inputs
      `(("python-pep8" ,python-pep8)
-       ,@(package-propagated-inputs python-flake8)))
-    (properties `((python2-variant . ,(delay python2-flake8-2.5))))))
-
-(define-public python2-flake8-2.5
-  (package
-    (inherit python2-flake8)
-    (version (package-version python-flake8-2.5))
-    (source (origin
-              (inherit (package-source python-flake8-2.5))))
-    (propagated-inputs
-     `(("python2-pep8" ,python2-pep8)
-       ,@(package-propagated-inputs python2-flake8)))))
+       ,@(package-propagated-inputs python-flake8)))))
 
 (define-public python-flake8-polyfill
   (package
-- 
cgit v1.2.3


From 7b0e0fd5a2f963758d4c9161e9f2844e56289dad Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 29 Apr 2020 22:24:49 +0200
Subject: gnu: python-flake8-2.5: Update to 2.6.2.

* gnu/packages/python-xyz.scm (python-flake8-2.5): Update to 2.6.2; rename
it...
(python-flake8-2.6): ...to this.
[arguments]: Add phase "use-later-pycodestyles", and move "check" phase after
"install".
[propagated-inputs]: Explicitly list python-pycodestyle, python-entrypoints,
python-pyflakes-1.2, and python-mccabe.
---
 gnu/packages/python-xyz.scm | 29 ++++++++++++++++++++++++-----
 1 file changed, 24 insertions(+), 5 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 1110360afd..0f4351d152 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -7506,20 +7506,39 @@ (define-public python2-flake8
          ("python2-typing" ,python2-typing)
           ,@(package-propagated-inputs base))))))
 
-;; python-hacking requires flake8 <2.6.0.
-(define-public python-flake8-2.5
+;; python-hacking requires flake8 <2.7.0.
+(define-public python-flake8-2.6
   (package
     (inherit python-flake8)
-    (version "2.5.5")
+    (version "2.6.2")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "flake8" version))
               (sha256
                (base32
-                "1snylqwbmrylbx3r1wpz8ggk98f6bcag4441ag8mm2l7wyn58sij"))))
+                "0y57hzal0j84dh9i1g1g6dc4aywvrnhy2fjmmbglpv5ajihxh713"))))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'use-later-pycodestyles
+           (lambda __
+             (substitute* '("flake8.egg-info/requires.txt"
+                            "setup.py")
+               (("pycodestyle >= 2.0, < 2.1")
+                "pycodestyle >= 2.0"))
+             #t))
+         (delete 'check)
+         (add-after 'install 'check
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (add-installed-pythonpath inputs outputs)
+             (invoke "pytest" "-v")
+             #t)))))
     (propagated-inputs
      `(("python-pep8" ,python-pep8)
-       ,@(package-propagated-inputs python-flake8)))))
+       ("python-pycodestyle" ,python-pycodestyle)
+       ("python-entrypoints" ,python-entrypoints)
+       ("python-pyflakes" ,python-pyflakes-1.2)
+       ("python-mccabe" ,python-mccabe)))))
 
 (define-public python-flake8-polyfill
   (package
-- 
cgit v1.2.3


From 851a3a779a7173807683e0a3c4e118ef4d8eb0b7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 29 Apr 2020 22:28:07 +0200
Subject: gnu: python-hacking: Update to 1.1.0.

* gnu/packages/openstack.scm (python-hacking): Update to 1.1.0.
[arguments]: Add "delete-broken-test" phase.
[propagated-inputs]: Replace python-flake8-2.5 with python-flake8-2.6.
---
 gnu/packages/openstack.scm | 17 ++++++++++++++---
 1 file changed, 14 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm
index 6c81454150..a1e21d8872 100644
--- a/gnu/packages/openstack.scm
+++ b/gnu/packages/openstack.scm
@@ -4,6 +4,7 @@
 ;;; Copyright © 2016, 2017, 2019 Clément Lassieur <clement@lassieur.org>
 ;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
+;;; Copyright © 2020 Ricardo Wurmus <rekado@elephly.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -130,17 +131,27 @@ (define-public python2-debtcollector
 (define-public python-hacking
   (package
     (name "python-hacking")
-    (version "1.0.0")
+    (version "1.1.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "hacking" version))
        (sha256
         (base32
-         "0s9l99s64jsyvm28fa4hzllbdi21sb7jn4gzdf1pd5ckvy7p4b0k"))))
+         "1vlgh81v4vsw3q3cf7qggsp043vq16knp203lrll82h7l7rhd8r3"))))
     (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'delete-broken-test
+           (lambda _
+             ;; TODO: Just one test fails:
+             ;; hacking.tests.test_doctest.HackingTestCase.test_pycodestyle
+             ;;   (H403-hacking_docstring_multiline_end-line-5)
+             (delete-file "hacking/tests/test_doctest.py")
+             #t)))))
     (propagated-inputs
-     `(("python-flake8" ,python-flake8-2.5)
+     `(("python-flake8" ,python-flake8-2.6)
        ("python-mccabe-0.2.1" ,python-mccabe-0.2.1)
        ("python-pbr" ,python-pbr)
        ("python-pep8-1.5.7" ,python-pep8-1.5.7)
-- 
cgit v1.2.3


From 5bc78570b28806b12485dc9863cd7d2c06d5883a Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Wed, 29 Apr 2020 22:12:10 -0400
Subject: gnu: linux-libre@4.19: Update to 4.19.119.

* gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.119.
(linux-libre-4.19-pristine-source): Update hash.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 12cb39ff9b..b5400d8a83 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -385,10 +385,10 @@ (define-public linux-libre-5.4-pristine-source
                             (%upstream-linux-source version hash)
                             deblob-scripts-5.4)))
 
-(define-public linux-libre-4.19-version "4.19.118")
+(define-public linux-libre-4.19-version "4.19.119")
 (define-public linux-libre-4.19-pristine-source
   (let ((version linux-libre-4.19-version)
-        (hash (base32 "15lcq3xky59v88vb8vvnmgcsmm1fadz0m4jyrii6rynsz5jr6x49")))
+        (hash (base32 "1klvdzz8sndg2zsr1anfy9p5fc1aapjqvc249myrbndyf55bk91b")))
     (make-linux-libre-source version
                              (%upstream-linux-source version hash)
                              deblob-scripts-4.19)))
-- 
cgit v1.2.3


From 09b87e503d3af1db309fdb3ea5617986013751f3 Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Wed, 29 Apr 2020 22:13:15 -0400
Subject: gnu: linux-libre@5.6: Update to 5.6.8.

* gnu/packages/linux.scm (linux-libre-5.6-version): Update to 5.6.8.
(linux-libre-5.6-pristine-source): Update hash.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index b5400d8a83..dd16cdc17d 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -369,10 +369,10 @@ (define (%upstream-linux-source version hash)
     (sha256 hash)))
 
 
-(define-public linux-libre-5.6-version "5.6.7")
+(define-public linux-libre-5.6-version "5.6.8")
 (define-public linux-libre-5.6-pristine-source
   (let ((version linux-libre-5.6-version)
-        (hash (base32 "1jljcva3gxg1yc2kw3jjgmhzzdm16nylzxl63zbndjza547l5813")))
+        (hash (base32 "1pw2q9509jzp84b6qasaais2ws25v2wrjh072q0x3j520zzl5q8r")))
    (make-linux-libre-source version
                             (%upstream-linux-source version hash)
                             deblob-scripts-5.6)))
-- 
cgit v1.2.3


From 89ea0415b33bc3382ead3755fc2fc27c11920878 Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Wed, 29 Apr 2020 22:13:56 -0400
Subject: gnu: linux-libre: Update to 5.4.36.

* gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.36.
(linux-libre-5.4-pristine-source): Update hash.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index dd16cdc17d..70d2163fee 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -377,10 +377,10 @@ (define-public linux-libre-5.6-pristine-source
                             (%upstream-linux-source version hash)
                             deblob-scripts-5.6)))
 
-(define-public linux-libre-5.4-version "5.4.35")
+(define-public linux-libre-5.4-version "5.4.36")
 (define-public linux-libre-5.4-pristine-source
   (let ((version linux-libre-5.4-version)
-        (hash (base32 "1m06k19pbb3wz8z2dgf03jvzbbdh6q8jwwdz509s902a53vxasz1")))
+        (hash (base32 "13avfvimjyg4lhj9micgib9bb5qpx11cja5liypid0rf2acfmymr")))
    (make-linux-libre-source version
                             (%upstream-linux-source version hash)
                             deblob-scripts-5.4)))
-- 
cgit v1.2.3


From f03e5ca59f2f099693def2c8e6ff409e5b4ed40a Mon Sep 17 00:00:00 2001
From: Guillaume Le Vaillant <glv@posteo.net>
Date: Thu, 30 Apr 2020 10:09:15 +0200
Subject: gnu: gnuradio: Fix runtime python environment for plugins.

* gnu/packages/radio.scm (gnuradio)[native-search-paths]: Add PYTHONPATH.
  [native-inputs]: Move python ...
  [inputs]: ... here.
---
 gnu/packages/radio.scm | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm
index 935880780f..30567431bf 100644
--- a/gnu/packages/radio.scm
+++ b/gnu/packages/radio.scm
@@ -26,6 +26,7 @@ (define-module (gnu packages radio)
   #:use-module (guix packages)
   #:use-module (guix download)
   #:use-module (guix git-download)
+  #:use-module (guix utils)
   #:use-module (gnu packages algebra)
   #:use-module (gnu packages audio)
   #:use-module (gnu packages autotools)
@@ -266,7 +267,6 @@ (define-public gnuradio
        ("ghostscript" ,ghostscript)
        ("orc" ,orc)
        ("pkg-config" ,pkg-config)
-       ("python" ,python)
        ("python-cheetah" ,python-cheetah)
        ("python-mako" ,python-mako)
        ("python-pyzmq" ,python-pyzmq)
@@ -293,6 +293,7 @@ (define-public gnuradio
        ("log4cpp" ,log4cpp)
        ("pango" ,pango)
        ("portaudio" ,portaudio)
+       ("python" ,python)
        ("python-click" ,python-click)
        ("python-click-plugins" ,python-click-plugins)
        ("python-lxml" ,python-lxml)
@@ -364,9 +365,16 @@ (define-public gnuradio
                  `("GI_TYPELIB_PATH" ":" prefix ,(filter identity paths))))
              #t)))))
     (native-search-paths
+     ;; Variables required to find third-party plugins at runtime.
      (list (search-path-specification
             (variable "GRC_BLOCKS_PATH")
-            (files '("/share/gnuradio/grc/blocks")))))
+            (files '("share/gnuradio/grc/blocks")))
+           (search-path-specification
+            (variable "PYTHONPATH")
+            (files (list (string-append "lib/python"
+                                        (version-major+minor
+                                         (package-version python))
+                                        "/site-packages"))))))
     (synopsis "Toolkit for software-defined radios")
     (description
      "GNU Radio is a development toolkit that provides signal processing blocks
-- 
cgit v1.2.3


From 1b73fbdf5e3be0d1a90432b63c5eea2cde8c456d Mon Sep 17 00:00:00 2001
From: Eric Brown <ecbrown@ericcbrown.com>
Date: Wed, 22 Apr 2020 06:04:59 -0500
Subject: gnu: Add r-rserve.

* gnu/packages/cran.scm (r-rserve): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
---
 gnu/packages/cran.scm | 37 +++++++++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index baf1e0c18a..18829537e8 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -21633,3 +21633,40 @@ (define-public r-rxnat
 Archive Toolkit.  Rxnat uses the XNAT REST API to perform data queries and
 download images.")
     (license license:gpl2)))
+
+(define-public r-rserve
+  (package
+    (name "r-rserve")
+    (version "1.8-6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "http://www.rforge.net/Rserve/snapshot/Rserve_"
+                           version ".tar.gz"))
+       (sha256
+        (base32
+         "017kkzv9lxlz9qhg3gprrf1wcyflxrif6wjk27x9b4bdzylw6bsx"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-checkmate" ,r-checkmate)
+       ("r-mime" ,r-mime)
+       ("r-jsonlite" ,r-jsonlite)
+       ("r-knitr" ,r-knitr)
+       ("r-r6" ,r-r6)
+       ("r-rcpp" ,r-rcpp)
+       ("r-uuid" ,r-uuid)))
+    (inputs
+     `(("openssl" ,openssl)
+       ("zlib" ,zlib)))
+    (home-page "https://github.com/s-u/Rserve")
+    (synopsis
+     "Server providing access to R from many languages and systems")
+    (description
+     "Rserve acts as a socket server (TCP/IP or local sockets) which allows
+binary requests to be sent to R.  Every connection has a separate workspace
+and working directory.  Client-side implementations are available for popular
+languages such as C/C++ and Java, allowing any application to use facilities
+of R without the need of linking to R code.  Rserve supports remote
+connection, user authentication and file transfer.  A simple R client is
+included in this package as well.")
+    (license license:gpl2)))
-- 
cgit v1.2.3


From ed33317893812715bf37005fb0ba5192b651b14f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 30 Apr 2020 13:00:40 +0200
Subject: gnu: Add python2-weave.

* gnu/packages/python-science.scm (python2-weave): New variable.
---
 gnu/packages/python-science.scm | 35 ++++++++++++++++++++++++++++++++++-
 1 file changed, 34 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 530a2478f3..2f7516b9f6 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2015, 2016 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2016, 2020 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2015 Federico Beffa <beffa@fbengineering.ch>
 ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
 ;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
@@ -162,6 +162,39 @@ (define-public python2-scipy
         (base32
          "1cgvgin8fvckv96hjh3ikmwkra5rif51bdb75ifzf7xbil5iwcx4"))))))
 
+(define-public python2-weave
+  (package
+    (name "python2-weave")
+    (version "0.16.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "weave" version))
+       (sha256
+        (base32 "0jnm3584mfichgwgrd1gk5i42ll9c08nkw9716n947n4338f6ghs"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:python ,python-2
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           (lambda _
+             (invoke "nosetests" "-v"
+                     "--exclude"
+                     "test_(user|incorrect_ownership|char_fail|obj_fail)"))))))
+    (propagated-inputs
+     `(("python-numpy" ,python2-numpy)))
+    (native-inputs
+     `(("python-nose" ,python2-nose)))
+    (home-page "https://www.scipy.org/")
+    (synopsis "Tools for including C/C++ code within Python code")
+    (description "Weave is the stand-alone version of the obsolete Scipy
+submodule @code{scipy.weave}.  It is Python 2.x only, and is provided for
+users that need new versions of Scipy but have existing code that still
+depends on @code{scipy.weave}.  For new code, users are recommended to use
+Cython.")
+    (license license:bsd-3)))
+
 (define-public python-scikit-image
   (package
     (name "python-scikit-image")
-- 
cgit v1.2.3


From 4a148c6da37b55b22842ddbf0ec0ba56132c44ff Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 30 Apr 2020 13:00:50 +0200
Subject: gnu: python2-warpedlmm: Fix build.

* gnu/packages/bioinformatics.scm (python2-warpedlmm)[propagated-inputs]: Add
python2-weave.
[arguments]: Disable tests and add "use-weave" phase.
---
 gnu/packages/bioinformatics.scm | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index f90a0bf90c..740ed66972 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4942,14 +4942,24 @@ (define-public python2-warpedlmm
          "1agfz6zqa8nc6cw47yh0s3y14gkpa9wqazwcj7mwwj3ffnw39p3j"))))
     (build-system python-build-system)
     (arguments
-     `(#:python ,python-2))  ; requires Python 2.7
+     `(#:python ,python-2  ; requires Python 2.7
+       #:tests? #f ; test data are not included
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'use-weave
+           (lambda _
+             (substitute* "warpedlmm/util/linalg.py"
+               (("from scipy import linalg, weave")
+                "from scipy import linalg\nimport weave"))
+             #t)))))
     (propagated-inputs
      `(("python-scipy" ,python2-scipy)
        ("python-numpy" ,python2-numpy)
        ("python-matplotlib" ,python2-matplotlib)
        ("python-fastlmm" ,python2-fastlmm)
        ("python-pandas" ,python2-pandas)
-       ("python-pysnptools" ,python2-pysnptools)))
+       ("python-pysnptools" ,python2-pysnptools)
+       ("python-weave" ,python2-weave)))
     (native-inputs
      `(("python-mock" ,python2-mock)
        ("python-nose" ,python2-nose)
-- 
cgit v1.2.3


From 7395047017a6c210a47e9d0144fd3ebabf156da1 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 30 Apr 2020 13:03:52 +0200
Subject: gnu: Add python-tornado-6.

* gnu/packages/python-web.scm (python-tornado-6): New variable.
---
 gnu/packages/python-web.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 0dba566a77..76a2c57701 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -869,6 +869,37 @@ (define-public python-tornado
     (license license:asl2.0)
     (properties `((python2-variant . ,(delay python2-tornado))))))
 
+(define-public python-tornado-6
+  (package
+    (name "python-tornado")
+    (version "6.0.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "tornado" version))
+       (sha256
+        (base32
+         "1p5n7sw4580pkybywg93p8ddqdj9lhhy72rzswfa801vlidx9qhg"))))
+    (build-system python-build-system)
+    (arguments
+     '(#:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           (lambda _
+             (invoke "python" "-m" "tornado.test.runtests")
+             #t)))))
+    (native-inputs
+     `(("python-certifi" ,python-certifi)))
+    (home-page "https://www.tornadoweb.org/")
+    (synopsis "Python web framework and asynchronous networking library")
+    (description
+     "Tornado is a Python web framework and asynchronous networking library,
+originally developed at FriendFeed.  By using non-blocking network I/O,
+Tornado can scale to tens of thousands of open connections, making it ideal
+for long polling, WebSockets, and other applications that require a long-lived
+connection to each user.")
+    (license license:asl2.0)))
+
 (define-public python2-tornado
   (let ((tornado (package-with-python2 (strip-python2-variant python-tornado))))
     (package (inherit tornado)
-- 
cgit v1.2.3


From cb44af24c8308dd7e17e991ed6ee803f3cb8a1c2 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 30 Apr 2020 13:03:59 +0200
Subject: gnu: kaldi-gstreamer-server: Use Tornado 6.

* gnu/packages/machine-learning.scm (kaldi-gstreamer-server)[inputs]: Replace
python-tornado with python-tornado-6.
---
 gnu/packages/machine-learning.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 425961ee14..df2943167d 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -1326,7 +1326,7 @@ (define-public kaldi-gstreamer-server
          ("python" ,python-wrapper)
          ("python-pygobject" ,python-pygobject)
          ("python-pyyaml" ,python-pyyaml)
-         ("python-tornado" ,python-tornado)))
+         ("python-tornado" ,python-tornado-6)))
       (home-page "https://github.com/alumae/kaldi-gstreamer-server")
       (synopsis "Real-time full-duplex speech recognition server")
       (description "This is a real-time full-duplex speech recognition server,
-- 
cgit v1.2.3


From 46d07f8472f09813be287fa5a10afb50c959dcb1 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 30 Apr 2020 13:04:55 +0200
Subject: gnu: kaldi-gstreamer-server: Fix bug.

* gnu/packages/machine-learning.scm (kaldi-gstreamer-server)[arguments]: Patch
master_server.py before build.
---
 gnu/packages/machine-learning.scm | 4 ++++
 1 file changed, 4 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index df2943167d..8c817d3e3b 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -1269,6 +1269,10 @@ (define-public kaldi-gstreamer-server
                ;; are reproducible.
                (setenv "PYTHONHASHSEED" "0")
                (with-directory-excursion "kaldigstserver"
+                 ;; See https://github.com/alumae/kaldi-gstreamer-server/issues/232
+                 (substitute* "master_server.py"
+                   (("\\.replace\\('\\\\.*") ")"))
+
                  ;; This is a Python 2 file
                  (delete-file "decoder_test.py")
                  (delete-file "test-buffer.py")
-- 
cgit v1.2.3


From cf1ae793753e9da0d774f4a5495648f15d400b49 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 30 Apr 2020 13:06:01 +0200
Subject: gnu: python2-pysnptools: Update to 0.4.11.

* gnu/packages/python-xyz.scm (python2-pysnptools): Update to 0.4.11;
implement in terms of...
(python-pysnptools): ...this new variable.
[propagated-inputs]: Add python-dill, python-h5py, and python-psutil.
---
 gnu/packages/python-xyz.scm | 34 ++++++++++++++++++++++++----------
 1 file changed, 24 insertions(+), 10 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 0f4351d152..74280befea 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -4876,27 +4876,38 @@ (define-public python-matplotlib-venn
 three-way Venn diagrams in @code{matplotlib}.")
     (license license:expat)))
 
-(define-public python2-pysnptools
+(define-public python-pysnptools
   (package
-    (name "python2-pysnptools")
-    (version "0.3.13")
+    (name "python-pysnptools")
+    (version "0.4.11")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pysnptools" version))
        (sha256
         (base32
-         "0lnis5xsl7bi0hz4f7gbicahzi5zlxkc21nk3g374xv8fb5hb3qm"))))
+         "0gxr0bjix307wvk0qh7vkafbxbzfpdmq0wlswpxyyaymy0fwcypv"))))
     (build-system python-build-system)
     (arguments
-     `(#:python ,python-2 ; only Python 2.7 is supported
-       #:tests? #f))      ; test files (e.g. examples/toydata.bim) not included
+     `(#:tests? #f ; no test data are included
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
+             (if tests?
+                 (begin
+                   (add-installed-pythonpath inputs outputs)
+                   (invoke "python3" "pysnptools/test.py"))
+                 #t))))))
     (propagated-inputs
-     `(("python2-numpy" ,python2-numpy)
-       ("python2-scipy" ,python2-scipy)
-       ("python2-pandas" ,python2-pandas)))
+     `(("python-dill" ,python-dill)
+       ("python-h5py" ,python-h5py)
+       ("python-numpy" ,python-numpy)
+       ("python-pandas" ,python-pandas)
+       ("python-psutil" ,python-psutil)
+       ("python-scipy" ,python-scipy)))
     (native-inputs
-     `(("python2-cython" ,python2-cython)))
+     `(("python-cython" ,python-cython)))
     (home-page "http://microsoftgenomics.github.io/PySnpTools/")
     (synopsis "Library for reading and manipulating genetic data")
     (description
@@ -4906,6 +4917,9 @@ (define-public python2-pysnptools
 operators such as union, intersection, and difference.")
     (license license:asl2.0)))
 
+(define-public python2-pysnptools
+  (package-with-python2 python-pysnptools))
+
 (define-public python-socksipy-branch
   (package
     (name "python-socksipy-branch")
-- 
cgit v1.2.3


From 61fc72d3ac949d0c65690ee25bb1daf01f39bb42 Mon Sep 17 00:00:00 2001
From: Nicolas Goaziou <mail@nicolasgoaziou.fr>
Date: Fri, 10 Apr 2020 14:58:47 +0200
Subject: gnu: Add zbackup.

* gnu/packages/backup.scm (zbackup): New variable.
---
 gnu/packages/backup.scm | 37 +++++++++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/backup.scm b/gnu/packages/backup.scm
index d80359f8f1..23860ec821 100644
--- a/gnu/packages/backup.scm
+++ b/gnu/packages/backup.scm
@@ -14,6 +14,7 @@
 ;;; Copyright © 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2019 Alex Vong <alexvong1995@gmail.com>
 ;;; Copyright © 2019 Marius Bakke <mbakke@fastmail.com>
+;;; Copyright © 2020 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -976,6 +977,42 @@ (define-public restic
 @end itemize")
     (license license:bsd-2)))
 
+(define-public zbackup
+  (package
+    (name "zbackup")
+    (version "1.4.4")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/zbackup/zbackup.git")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "14l1kyxg7pccpax3d6qcpmdycb70kn3fxp1a59w64hqy2493hngl"))))
+    (build-system cmake-build-system)
+    (arguments
+     `(#:tests? #f))                    ;no test
+    (inputs
+     `(("lzo" ,lzo)
+       ("libressl" ,libressl)
+       ("protobuf" ,protobuf)
+       ("xz" ,xz)
+       ("zlib" ,zlib)))
+    (home-page "http://zbackup.org")
+    (synopsis "Versatile deduplicating backup tool")
+    (description
+     "ZBackup is a globally-deduplicating backup tool, based on the
+ideas found in Rsync.  Feed a large @file{.tar} into it, and it will
+store duplicate regions of it only once, then compress and optionally
+encrypt the result.  Feed another @file{.tar} file, and it will also
+re-use any data found in any previous backups.  This way only new
+changes are stored, and as long as the files are not very different,
+the amount of storage required is very low.  Any of the backup files
+stored previously can be read back in full at any time.  The program
+is format-agnostic, so you can feed virtually any files to it.")
+    (license license:gpl2+)))
+
 (define-public burp
   (package
     (name "burp")
-- 
cgit v1.2.3


From 4ac399603616b1fa5e2639ba2c587219f366ef6e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 30 Apr 2020 14:41:53 +0200
Subject: gnu: Add missing module import.

This is a follow-up to commit 61fc72d3ac949d0c65690ee25bb1daf01f39bb42.

* gnu/packages/backup.scm: Add missing import of (guix build-system cmake).
---
 gnu/packages/backup.scm | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/backup.scm b/gnu/packages/backup.scm
index 23860ec821..692795ce11 100644
--- a/gnu/packages/backup.scm
+++ b/gnu/packages/backup.scm
@@ -11,7 +11,7 @@
 ;;; Copyright © 2017 Rutger Helling <rhelling@mykolab.com>
 ;;; Copyright © 2018 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2018 Oleg Pykhalov <go.wigust@gmail.com>
-;;; Copyright © 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2019 Alex Vong <alexvong1995@gmail.com>
 ;;; Copyright © 2019 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2020 Nicolas Goaziou <mail@nicolasgoaziou.fr>
@@ -37,6 +37,7 @@ (define-module (gnu packages backup)
   #:use-module (guix git-download)
   #:use-module (guix download)
   #:use-module (guix utils)
+  #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system go)
   #:use-module (guix build-system python)
-- 
cgit v1.2.3


From e17423186323829dff925d2f0fdbd8f494206a6e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 30 Apr 2020 14:44:45 +0200
Subject: gnu: Add one more missing module import.

This is a follow-up to commit 61fc72d3ac949d0c65690ee25bb1daf01f39bb42.

* gnu/packages/backup.scm: Add missing import of (gnu packages protobuf).
---
 gnu/packages/backup.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/backup.scm b/gnu/packages/backup.scm
index 692795ce11..00986a328d 100644
--- a/gnu/packages/backup.scm
+++ b/gnu/packages/backup.scm
@@ -65,6 +65,7 @@ (define-module (gnu packages backup)
   #:use-module (gnu packages pcre)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages protobuf)
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-crypto)
   #:use-module (gnu packages python-web)
-- 
cgit v1.2.3


From eca648b65b51d1154363dd63dd602ebb9797d478 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Thu, 30 Apr 2020 15:30:16 +0200
Subject: gnu: Add miniasm.

* gnu/packages/bioinformatics.scm (miniasm): New variable.
---
 gnu/packages/bioinformatics.scm | 36 ++++++++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 740ed66972..65b44568e0 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13312,6 +13312,42 @@ (define-public minimap2
 @end enumerate\n")
     (license license:expat)))
 
+(define-public miniasm
+  (package
+   (name "miniasm")
+   (version "0.3")
+   (source (origin
+            (method url-fetch)
+            (uri (string-append
+                  "https://github.com/lh3/miniasm/archive/v"
+                  version ".tar.gz"))
+            (file-name (string-append name "-" version ".tar.gz"))
+            (sha256
+               (base32
+                "0g89pa98dvh34idv7w1zv12bsbyr3a11c4qb1cdcz68gyda88s4v"))))
+   (build-system gnu-build-system)
+   (inputs
+    `(("zlib" ,zlib)))
+   (arguments
+    `(#:tests? #f ; There are no tests.
+      #:phases
+      (modify-phases %standard-phases
+        (delete 'configure)
+        (replace 'install
+          (lambda* (#:key inputs outputs #:allow-other-keys)
+            (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
+              (install-file "miniasm" bin)
+              (install-file "minidot" bin)))))))
+   (home-page "https://github.com/lh3/miniasm")
+   (synopsis "Ultrafast de novo assembly for long noisy reads")
+   (description "Miniasm is a very fast OLC-based de novo assembler for noisy
+long reads.  It takes all-vs-all read self-mappings (typically by minimap) as
+input and outputs an assembly graph in the GFA format.  Different from
+mainstream assemblers, miniasm does not have a consensus step.  It simply
+concatenates pieces of read sequences to generate the final unitig sequences.
+Thus the per-base error rate is similar to the raw input reads.")
+   (license license:expat)))
+
 (define-public r-circus
   (package
     (name "r-circus")
-- 
cgit v1.2.3


From 0590673090d5fd76074977451a7f7e800e1698c9 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 30 Apr 2020 15:25:32 +0200
Subject: gnu: r-pkgbuild: Update to 1.0.7.

* gnu/packages/cran.scm (r-pkgbuild): Update to 1.0.7.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 18829537e8..94bb1aa4bc 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -1771,13 +1771,13 @@ (define-public r-ps
 (define-public r-pkgbuild
   (package
     (name "r-pkgbuild")
-    (version "1.0.6")
+    (version "1.0.7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "pkgbuild" version))
        (sha256
-        (base32 "0xnlz6ivhkbmncg9hfw5p69lm4rjy3wn5lyxmygxyf4rrfnnqwxx"))))
+        (base32 "0wd9678yp6yi73n92f58wi9jc19gdq5cmbj65l6pifh2haikifr9"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-callr" ,r-callr)
-- 
cgit v1.2.3


From 0ec790f82d0afe1baab5d24a0c94fbd77dc006ab Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 30 Apr 2020 15:25:45 +0200
Subject: gnu: r-proxy: Update to 0.4-24.

* gnu/packages/cran.scm (r-proxy): Update to 0.4-24.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 94bb1aa4bc..f581cf462b 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2272,14 +2272,14 @@ (define-public r-ggally
 (define-public r-proxy
   (package
     (name "r-proxy")
-    (version "0.4-23")
+    (version "0.4-24")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "proxy" version))
        (sha256
         (base32
-         "17b6qfllqrhzrxqgx7dccffgybnkcria5a68ap5ly3plg04ypm4x"))))
+         "0z4wdnpv5x135nssxnmkkba7fivd5xgbpaabqjkl2na76vq9pzwc"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/proxy")
     (synopsis "Distance and similarity measures")
-- 
cgit v1.2.3


From 78b686824d8b5605a6203d0da760288f601b8f37 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 30 Apr 2020 15:25:50 +0200
Subject: gnu: r-rootsolve: Update to 1.8.2.1.

* gnu/packages/cran.scm (r-rootsolve): Update to 1.8.2.1.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index f581cf462b..ddab6c9830 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -7084,14 +7084,14 @@ (define-public r-proc
 (define-public r-rootsolve
   (package
     (name "r-rootsolve")
-    (version "1.8.2")
+    (version "1.8.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rootSolve" version))
        (sha256
         (base32
-         "0rj7c4zcrzgz7sb0vgvh7swpfafnw4040cxp7ypas3s8fnihn54l"))))
+         "0c9hhgq1pgqdg80a6n2ssfbj5nyaf97y4iiya7j7l6b34qc53128"))))
     (properties `((upstream-name . "rootSolve")))
     (build-system r-build-system)
     (native-inputs `(("gfortran" ,gfortran)))
-- 
cgit v1.2.3


From b5ea7affcfd6bfaa7a9f62862f5379f6f1bbda0e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 30 Apr 2020 15:25:57 +0200
Subject: gnu: r-usethis: Update to 1.6.1.

* gnu/packages/cran.scm (r-usethis): Update to 1.6.1.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index ddab6c9830..99d1c416d1 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -8920,14 +8920,14 @@ (define-public r-clisymbols
 (define-public r-usethis
   (package
     (name "r-usethis")
-    (version "1.6.0")
+    (version "1.6.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "usethis" version))
        (sha256
         (base32
-         "12iyimqyza752anj29wpfisl8nz5r25kfcqbssybg24nb4wyy146"))))
+         "0vwxsnq615mwc706a4a71gyy0hmvnllbh249gzm7vl3ym5cr0cv0"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-cli" ,r-cli)
-- 
cgit v1.2.3


From 1514fa85e49f3a31a75e7174a34678cb799efb8d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 30 Apr 2020 15:26:03 +0200
Subject: gnu: r-arm: Update to 1.11-1.

* gnu/packages/cran.scm (r-arm): Update to 1.11-1.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 99d1c416d1..304cddca83 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -9655,14 +9655,14 @@ (define-public r-feature
 (define-public r-arm
   (package
     (name "r-arm")
-    (version "1.10-1")
+    (version "1.11-1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "arm" version))
        (sha256
         (base32
-         "0vvp90jygajd6ydky57z66wqjq9msfbl88irj5jbsray574mh4bg"))))
+         "0i2lnm09bqy1qw0ms5pw0rzw196xmnk5dxha3g8lc58lqpldp0kv"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-abind" ,r-abind)
-- 
cgit v1.2.3


From 7d1e02c872fe5dd6dc3180dc50b0bd8288f033b0 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 30 Apr 2020 15:26:07 +0200
Subject: gnu: r-dalex: Update to 1.2.1.

* gnu/packages/cran.scm (r-dalex): Update to 1.2.1.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 304cddca83..a0ee26e8b5 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -15435,14 +15435,14 @@ (define-public r-ibreakdown
 (define-public r-dalex
   (package
     (name "r-dalex")
-    (version "1.2.0")
+    (version "1.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "DALEX" version))
        (sha256
         (base32
-         "0mfcci54622gnk8al9fl2jhs9i2vfly7lam04y5rdacbyiam49j6"))))
+         "0lx8nasm1zgh1ckz8nw3ysp6xjv3dsj39hzhr6k3xhh6i8pm9rxk"))))
     (properties `((upstream-name . "DALEX")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 8dfa9ab05a4fe4bde615d569486396a1c0d3a8fb Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 30 Apr 2020 15:26:13 +0200
Subject: gnu: r-ggfortify: Update to 0.4.10.

* gnu/packages/cran.scm (r-ggfortify): Update to 0.4.10.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index a0ee26e8b5..55ffb2787a 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -15510,14 +15510,14 @@ (define-public r-plot3d
 (define-public r-ggfortify
   (package
     (name "r-ggfortify")
-    (version "0.4.9")
+    (version "0.4.10")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ggfortify" version))
        (sha256
         (base32
-         "1p6knrbyaynaqwd939w09hpf1zz1gn95cb46sfgppl8l98krb2h5"))))
+         "0wmcwp63h90v3f00ixszvis4z28im621jickvc0wgi6qvjvnayq0"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-dplyr" ,r-dplyr)
-- 
cgit v1.2.3


From aa180e9e031a001228c74c34fe6516e75bcb719f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 30 Apr 2020 15:26:18 +0200
Subject: gnu: r-systemfonts: Update to 0.2.1.

* gnu/packages/cran.scm (r-systemfonts): Update to 0.2.1.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 55ffb2787a..1eddb459fe 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -16026,14 +16026,14 @@ (define-public r-covr
 (define-public r-systemfonts
   (package
     (name "r-systemfonts")
-    (version "0.2.0")
+    (version "0.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "systemfonts" version))
        (sha256
         (base32
-         "1aba07djvxqdmnsdbwvzcsbm2fddnhrssa54xyrlviiwsv2c1qsd"))))
+         "0dna00xai0pw76b4830yy4r5j1hq7f7kla67v0iz39cjm4rq4ygq"))))
     (properties `((upstream-name . "systemfonts")))
     (build-system r-build-system)
     (inputs
-- 
cgit v1.2.3


From d7a29bd586bf4d8f7af926ef9287f4e88890ff2e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 30 Apr 2020 15:26:24 +0200
Subject: gnu: r-graphlayouts: Update to 0.7.0.

* gnu/packages/cran.scm (r-graphlayouts): Update to 0.7.0.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 1eddb459fe..92902d0a73 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -16055,14 +16055,14 @@ (define-public r-systemfonts
 (define-public r-graphlayouts
   (package
     (name "r-graphlayouts")
-    (version "0.6.0")
+    (version "0.7.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "graphlayouts" version))
        (sha256
         (base32
-         "1la016m37kp79zk8p1yx9kaha8y6d4w52w39h0mzv1mfsi6d75w0"))))
+         "17lc75k8i3c696hfj44zj7j1a5sb0nap8spc5r98v7vd6xh4nii0"))))
     (properties `((upstream-name . "graphlayouts")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 2a749c859633c314a5b29f75b1d96836cda2fa2f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 30 Apr 2020 15:26:30 +0200
Subject: gnu: r-univoutl: Update to 0.2.

* gnu/packages/cran.scm (r-univoutl): Update to 0.2.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 92902d0a73..6d1cc8dbfe 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -18795,14 +18795,14 @@ (define-public r-adagio
 (define-public r-univoutl
   (package
     (name "r-univoutl")
-    (version "0.1-5")
+    (version "0.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "univOutl" version))
        (sha256
         (base32
-         "193wrpkvgmlrx43nag8w3ivrlqm37nm6g86wcvd3bgw3hchs70gi"))))
+         "0rlc3w7cx2hfxacpjs9kmjzv5p8v9wxnlpxi3rh276wiy5zdr91v"))))
     (properties `((upstream-name . "univOutl")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From c54b41093dd02254517df5b12cd059ab4ebad510 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 30 Apr 2020 15:26:35 +0200
Subject: gnu: r-kutils: Update to 1.70.

* gnu/packages/cran.scm (r-kutils): Update to 1.70.
[propagated-inputs]: Remove r-lavaan.
---
 gnu/packages/cran.scm | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 6d1cc8dbfe..965ab2949d 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -20219,19 +20219,18 @@ (define-public r-openmx
 (define-public r-kutils
   (package
     (name "r-kutils")
-    (version "1.69")
+    (version "1.70")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "kutils" version))
        (sha256
         (base32
-         "12pg26a85h0jxlfcyai68dbh4bq1gnq8v1ngi8k9qvafbrpc6gx8"))))
+         "06jk66wbq3jmdf2jdhqns6r3yk36l2x7c907x977zv80sqxa1l37"))))
     (properties `((upstream-name . "kutils")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-foreign" ,r-foreign)
-       ("r-lavaan" ,r-lavaan)
        ("r-openxlsx" ,r-openxlsx)
        ("r-plyr" ,r-plyr)
        ("r-runit" ,r-runit)
-- 
cgit v1.2.3


From 1b6434a324f7ad8fca4d63107b28fa95de6017a4 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 30 Apr 2020 15:26:52 +0200
Subject: gnu: r-boot: Update to 1.3-25.

* gnu/packages/statistics.scm (r-boot): Update to 1.3-25.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 6bf952734c..a599e2f432 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -407,14 +407,14 @@ (define-public rmath-standalone
 (define-public r-boot
   (package
     (name "r-boot")
-    (version "1.3-24")
+    (version "1.3-25")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "boot" version))
        (sha256
         (base32
-         "0yv0l55kjmlfdx1xhgyjdi0bskxhfal74wr5jxaib1qj99nmkm49"))))
+         "1gpvi1h3nqhnnsfy96rlhakdpj84iqqsxr29rr3261sknky3aj26"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/boot")
     (synopsis "Bootstrap functions for R")
-- 
cgit v1.2.3


From b2c95239e0d7ebb61b3bf5b056556517308ef99b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 30 Apr 2020 15:27:01 +0200
Subject: gnu: r-mass: Update to 7.3-51.6.

* gnu/packages/statistics.scm (r-mass): Update to 7.3-51.6.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index a599e2f432..d8be4fbade 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -428,14 +428,14 @@ (define-public r-boot
 (define-public r-mass
   (package
     (name "r-mass")
-    (version "7.3-51.5")
+    (version "7.3-51.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "MASS" version))
        (sha256
         (base32
-         "1k0m7pa4gb5apzrrkb5kx5d7bmkm2pl5g15vwb6j067hrqahck26"))))
+         "1viyxy22qp8abzzzlbck55b0i81rrdygim1dq2pm52s2v13mq0z2"))))
     (properties `((upstream-name . "MASS")))
     (build-system r-build-system)
     (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
-- 
cgit v1.2.3


From 175ec5eff4cdb92c01213de45c600eb5f2fd1742 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 30 Apr 2020 15:27:09 +0200
Subject: gnu: r-class: Update to 7.3-17.

* gnu/packages/statistics.scm (r-class): Update to 7.3-17.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index d8be4fbade..059747d031 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -449,14 +449,14 @@ (define-public r-mass
 (define-public r-class
   (package
     (name "r-class")
-    (version "7.3-16")
+    (version "7.3-17")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "class" version))
        (sha256
         (base32
-         "1jpdgj0lsi60q0mqbhfw809w8d66whix27y6wpdzll6775g3j3ll"))))
+         "04qk8qia0qr8893fizmkbd5hsqn6m8383c0cyn9xnmkmvyv8a7xy"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-mass" ,r-mass)))
-- 
cgit v1.2.3


From 1cf9a5cd759bed08b65d40e9cbdbe406c6565430 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 30 Apr 2020 15:27:15 +0200
Subject: gnu: r-foreign: Update to 0.8-79.

* gnu/packages/statistics.scm (r-foreign): Update to 0.8-79.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 059747d031..e749afd4b3 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -512,14 +512,14 @@ (define-public r-codetools
 (define-public r-foreign
   (package
     (name "r-foreign")
-    (version "0.8-78")
+    (version "0.8-79")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "foreign" version))
        (sha256
         (base32
-         "01anirfbfa3ip5pyqv72cg4x7p0jsppmbvxrllw7bm28fl1hgiyq"))))
+         "1d5rk4k3khjrir1b4ciridd6vdpcgzi35r7p7ra4ky7vbaabcdmg"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/foreign")
     (synopsis "Read data stored by other statistics software")
-- 
cgit v1.2.3


From 9c313889f10b8f877fbf12a743a940e825c27ffe Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 30 Apr 2020 15:27:19 +0200
Subject: gnu: r-kernsmooth: Update to 2.23-17.

* gnu/packages/statistics.scm (r-kernsmooth): Update to 2.23-17.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index e749afd4b3..8d8e2dacbb 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -532,14 +532,14 @@ (define-public r-foreign
 (define-public r-kernsmooth
   (package
     (name "r-kernsmooth")
-    (version "2.23-16")
+    (version "2.23-17")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "KernSmooth" version))
        (sha256
         (base32
-         "1acrkbdn3a74y4dndkcdl1njnpfqz7gk3bsz03g8lfj8l7z53hmq"))))
+         "11g6b0q67vasxag6v9m4px33qqxpmnx47c73yv1dninv2pz76g9b"))))
     (properties `((upstream-name . "KernSmooth")))
     (build-system r-build-system)
     (native-inputs
-- 
cgit v1.2.3


From aad9233c1dded6618c10228e8c21fa6ca550b4b9 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 30 Apr 2020 15:27:24 +0200
Subject: gnu: r-nnet: Update to 7.3-14.

* gnu/packages/statistics.scm (r-nnet): Update to 7.3-14.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 8d8e2dacbb..15098331e0 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -643,14 +643,14 @@ (define-public r-mgcv
 (define-public r-nnet
   (package
     (name "r-nnet")
-    (version "7.3-13")
+    (version "7.3-14")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "nnet" version))
        (sha256
         (base32
-         "1z0rj5cm4ycw1y0gd5wwwg8c2298v90iybgqdqh17967jbi2125f"))))
+         "1bzl62p5awva5kxcncs6lrdrkqp9ljd993zia731ckfpcjbrw6sx"))))
     (build-system r-build-system)
     (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
     (synopsis "Feed-forward neural networks and multinomial log-linear models")
-- 
cgit v1.2.3


From 599f2b50dee740af8cbc37f59726ba1ecf14b0ec Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 30 Apr 2020 15:27:30 +0200
Subject: gnu: r-spatial: Update to 7.3-12.

* gnu/packages/statistics.scm (r-spatial): Update to 7.3-12.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 15098331e0..030701a22f 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -681,14 +681,14 @@ (define-public r-rpart
 (define-public r-spatial
   (package
     (name "r-spatial")
-    (version "7.3-11")
+    (version "7.3-12")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "spatial" version))
        (sha256
         (base32
-         "04aw8j533sn63ybyrf4hyhrqm4058vfcb7yhjy07kq92mk94hi32"))))
+         "0qrdhzd5r78iwi46nk8jr56dzz5l5imkflxjw64d0ys0wyg06fbn"))))
     (build-system r-build-system)
     (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
     (synopsis "Functions for kriging and point pattern analysis")
-- 
cgit v1.2.3


From 0ffd9701f583a05db92e7cc883a20d1c4b3a1c17 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 30 Apr 2020 15:27:40 +0200
Subject: gnu: r-rcpparmadillo: Update to 0.9.870.2.0.

* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.9.870.2.0.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 030701a22f..18eb38ff29 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -2588,13 +2588,13 @@ (define-public r-latticeextra
 (define-public r-rcpparmadillo
   (package
     (name "r-rcpparmadillo")
-    (version "0.9.860.2.0")
+    (version "0.9.870.2.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "RcppArmadillo" version))
               (sha256
                (base32
-                "1rg9ak0zbv8d9cyj10jq52nrcbk1pvfz28kbkhpx79mpjhrl7pb5"))))
+                "1r7iajxvbyvslsy16rqacc95azmjciw9lvcq31xl97fl09kmsq5v"))))
     (properties `((upstream-name . "RcppArmadillo")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 24599740e7e0910fdc2b859d2e0eff0411abbc3a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 30 Apr 2020 15:27:45 +0200
Subject: gnu: r-vgam: Update to 1.1-3.

* gnu/packages/statistics.scm (r-vgam): Update to 1.1-3.
[inputs]: Move gfortran from here...
[native-inputs]: ...to here.
---
 gnu/packages/statistics.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 18eb38ff29..00b648a54c 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -4957,16 +4957,16 @@ (define-public r-fpc
 (define-public r-vgam
   (package
     (name "r-vgam")
-    (version "1.1-2")
+    (version "1.1-3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "VGAM" version))
        (sha256
-        (base32 "0kyan3a4ys2xbg9kf167cyf1gk7g963id62cjm2ij4i7y4wi61zq"))))
+        (base32 "1hwlrdx3nhdp83pvy1h23i16vbbhi4kizdhr58c8nvg7kqdzb7qc"))))
     (properties `((upstream-name . "VGAM")))
     (build-system r-build-system)
-    (inputs
+    (native-inputs
      `(("gfortran" ,gfortran)))
     (home-page "https://www.stat.auckland.ac.nz/~yee/VGAM")
     (synopsis "Vector generalized linear and additive models")
-- 
cgit v1.2.3


From 192177b04974f456a081e7cb9177e7d9147f822c Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Thu, 30 Apr 2020 16:56:44 +0200
Subject: gnu: sbcl-osicat: Fix library path.

* gnu/packages/lisp-xyz.scm (sbcl-osicat)[arguments]: Replace 'cleanup phase
  to preserve the location of libosicat.so so that it can be found when
  loading the system.
---
 gnu/packages/lisp-xyz.scm | 24 +++++++++++-------------
 1 file changed, 11 insertions(+), 13 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm
index c2029d940e..b032346a30 100644
--- a/gnu/packages/lisp-xyz.scm
+++ b/gnu/packages/lisp-xyz.scm
@@ -11533,21 +11533,19 @@ (define-public sbcl-osicat
       (arguments
        `(#:phases
          (modify-phases %standard-phases
-           (add-before 'validate-runpath 'cleanup-files
+           ;; The cleanup phase moves files around but we need to keep the
+           ;; directory structure for the grovel-generated library.
+           (replace 'cleanup
              (lambda* (#:key outputs #:allow-other-keys)
                (let* ((out (assoc-ref outputs "out"))
-                      (lib (string-append out "/lib/sbcl")))
-                 (for-each
-                  delete-file
-                  (filter (lambda (file)
-                            (not (member (basename file)
-                                         '("basic-unixint__grovel"
-                                           "libosicat.so"
-                                           "osicat--system.fasl"
-                                           "osicat.asd"
-                                           "unixint__grovel"))))
-                          (find-files lib ".*")))
-                 #t))))))
+                      (lib (string-append out "/lib/sbcl/")))
+                 (delete-file-recursively (string-append lib "src"))
+                 (delete-file-recursively (string-append lib "tests"))
+                 (for-each delete-file
+                           (filter (lambda (file)
+                                     (not (member (basename file) '("libosicat.so"))))
+                                   (find-files (string-append lib "posix") ".*"))))
+               #t)))))
       (inputs
        `(("alexandria" ,sbcl-alexandria)
          ("cffi" ,sbcl-cffi)
-- 
cgit v1.2.3


From 194cb75d85a2d282419b2a618c8e124f140859f3 Mon Sep 17 00:00:00 2001
From: Simon Josefsson <simon@josefsson.org>
Date: Thu, 30 Apr 2020 11:02:08 +0200
Subject: gnu: libntlm: Update to 1.6 [fixes CVE-2019-17455].

* gnu/packages/gsasl.scm (libntlm): Update to 1.6.

Signed-off-by: Leo Famulari <leo@famulari.name>
---
 gnu/packages/gsasl.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/gsasl.scm b/gnu/packages/gsasl.scm
index a796f9aa82..98acc3c756 100644
--- a/gnu/packages/gsasl.scm
+++ b/gnu/packages/gsasl.scm
@@ -35,14 +35,14 @@ (define-module (gnu packages gsasl)
 (define-public libntlm
   (package
     (name "libntlm")
-    (version "1.5")
+    (version "1.6")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://www.nongnu.org/libntlm/releases/"
                                   "libntlm-" version ".tar.gz"))
               (sha256
                (base32
-                "1gcvv7f9rggpxay81qv6kw5hr6gd4qiyzkbwhzz02fx9jvv9kmsk"))))
+                "08b83nss16jsn213j326yhn1vnrz10k15fwq6jm5b1vdn23nndzj"))))
     (build-system gnu-build-system)
     (synopsis "Library that implements NTLM authentication")
     (description
-- 
cgit v1.2.3


From 2a94f72adef710af481a5abefdddb6cde04b5526 Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Thu, 30 Apr 2020 14:17:32 -0400
Subject: gnu: MPD: Update to 0.21.23.

* gnu/packages/mpd.scm (mpd): Update to 0.21.23.
---
 gnu/packages/mpd.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/mpd.scm b/gnu/packages/mpd.scm
index 303af32983..755fa5d482 100644
--- a/gnu/packages/mpd.scm
+++ b/gnu/packages/mpd.scm
@@ -92,7 +92,7 @@ (define-public libmpdclient
 (define-public mpd
   (package
     (name "mpd")
-    (version "0.21.22")
+    (version "0.21.23")
     (source (origin
               (method url-fetch)
               (uri
@@ -101,7 +101,7 @@ (define-public mpd
                               "/mpd-" version ".tar.xz"))
               (sha256
                (base32
-                "18lvyv3crijki5nxjdhf1byayyavdvj07dk6rm856n4vi78qfmjn"))))
+                "18q72b9baj5cdpq0yn60qm7q4g8vwqqyqndl9xg3f3w0m4n557s3"))))
     (build-system meson-build-system)
     (arguments
      `(#:configure-flags '("-Ddocumentation=true"))) ;the default is 'false'...
-- 
cgit v1.2.3


From ac4fefb2983aff5e5972b4279aee5296a08aab6a Mon Sep 17 00:00:00 2001
From: Vagrant Cascadian <vagrant@reproducible-builds.org>
Date: Thu, 30 Apr 2020 18:46:30 +0000
Subject: gnu: diffoscope: Update to 143.

* gnu/packages/diffoscope (diffoscope): Update to 143.
  [native-inputs]: Add openssl and python-h5py.
  [arguments] Add openssl to add-known-tools phase.
  [arguments] Remove hdf5 from add-known-tools phase, added upstream.
---
 gnu/packages/diffoscope.scm | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/diffoscope.scm b/gnu/packages/diffoscope.scm
index 71c0039dfb..1df8552a30 100644
--- a/gnu/packages/diffoscope.scm
+++ b/gnu/packages/diffoscope.scm
@@ -57,6 +57,7 @@ (define-module (gnu packages diffoscope)
   #:use-module (gnu packages ssh)
   #:use-module (gnu packages statistics)
   #:use-module (gnu packages textutils)
+  #:use-module (gnu packages tls)
   #:use-module (gnu packages video)
   #:use-module (gnu packages vim)
   #:use-module (gnu packages web)
@@ -69,7 +70,7 @@ (define-module (gnu packages diffoscope)
   #:use-module (ice-9 match))
 
 (define-public diffoscope
-  (let ((version "141"))
+  (let ((version "143"))
     (package
       (name "diffoscope")
       (version version)
@@ -81,7 +82,7 @@ (define-public diffoscope
                 (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "0pls2jryx394ysaz0g8h959lhrsdqak9bkxjd5r6sdckgiikplkj"))))
+                  "0j58dqdk8ln8y0bcnfy37ljs37nkl56lzxqns396300ysln0qiwm"))))
       (build-system python-build-system)
       (arguments
        `(#:phases (modify-phases %standard-phases
@@ -96,8 +97,8 @@ (define-public diffoscope
                     (add-after 'unpack 'add-known-tools
                       (lambda _
                         (substitute* "diffoscope/external_tools.py"
-                          (("'debian': 'hdf5-tools'")
-                           "'debian': 'hdf5-tools', 'guix': 'hdf5'"))))
+                          (("'debian': 'openssl'")
+                           "'debian': 'openssl', 'guix': 'openssl'"))))
                     ;; This test is broken because our `file` package has a
                     ;; bug in berkeley-db file type detection.
                     (add-after 'unpack 'remove-berkeley-test
@@ -161,6 +162,7 @@ (define-public diffoscope
       (native-inputs `(("python-pytest" ,python-pytest)
                        ("python-chardet" ,python-chardet)
                        ("python-binwalk" ,python-binwalk)
+                       ("python-h5py" ,python-h5py)
                        ("python-pypdf2" ,python-pypdf2)
                        ("python-progressbar33" ,python-progressbar33)
                        ;; test suite skips tests when tool is missing
@@ -205,6 +207,7 @@ (define-public diffoscope
                        ("ocaml" ,ocaml)
                        ("odt2txt" ,odt2txt)
                        ("openssh" ,openssh)
+                       ("openssl" ,openssl)
                        ("pgpdump" ,pgpdump)
                        ("poppler" ,poppler)
                        ("python-jsbeautifier" ,python-jsbeautifier)
-- 
cgit v1.2.3


From 229f4fa9522fb56b014ee9c0d8111e8fb6da764d Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Thu, 30 Apr 2020 23:31:53 +0200
Subject: gnu: emacs-toml-mode: Fix syntax error in description.

* gnu/packages/emacs-xyz.scm (emacs-toml-mode)[description]: Replace usage of
@acronym with @dfn to work around a Guile Texinfo limitation.
---
 gnu/packages/emacs-xyz.scm | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm
index 79f7126ed7..776dcbb897 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -2660,8 +2660,11 @@ (define-public emacs-toml-mode
       (home-page "https://github.com/dryman/toml-mode.el")
       (synopsis "Emacs major mode for editing TOML files")
       (description
-       "This package provides a major mode for editing files in @acronym{TOML,
-Tom's Obvious, Minimal Language} data format.")
+       ;; XXX: Ideally we'd use @acronym for "TOML", but Guile's Texinfo
+       ;; parser does not currently support @comma{}, making it impossible
+       ;; to use commas in the @acronym arguments.
+       "This package provides a major mode for editing files in @dfn{TOML}
+(Tom's Obvious, Minimal Language) data format.")
       (license license:gpl3+))))
 
 (define-public emacs-twittering-mode
-- 
cgit v1.2.3