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-rw-r--r--doc/guix.texi20
-rw-r--r--gnu/machine.scm12
-rw-r--r--gnu/machine/ssh.scm148
-rw-r--r--gnu/packages/admin.scm2
-rw-r--r--gnu/packages/audio.scm4
-rw-r--r--gnu/packages/bioconductor.scm20
-rw-r--r--gnu/packages/bioinformatics.scm32
-rw-r--r--gnu/packages/cran.scm319
-rw-r--r--gnu/packages/emulators.scm12
-rw-r--r--gnu/packages/geo.scm9
-rw-r--r--gnu/packages/image.scm9
-rw-r--r--gnu/packages/linux.scm20
-rw-r--r--gnu/packages/machine-learning.scm7
-rw-r--r--gnu/packages/mail.scm16
-rw-r--r--gnu/packages/maths.scm4
-rw-r--r--gnu/packages/perl.scm2
-rw-r--r--gnu/packages/statistics.scm139
-rw-r--r--gnu/packages/terminals.scm6
-rw-r--r--gnu/packages/video.scm32
-rw-r--r--gnu/packages/vpn.scm12
-rw-r--r--gnu/packages/wm.scm2
-rw-r--r--gnu/tests/reconfigure.scm32
-rw-r--r--guix/scripts/deploy.scm6
-rw-r--r--guix/scripts/system/reconfigure.scm20
24 files changed, 551 insertions, 334 deletions
diff --git a/doc/guix.texi b/doc/guix.texi
index cb60d5c7b7..734206a4b2 100644
--- a/doc/guix.texi
+++ b/doc/guix.texi
@@ -25510,7 +25510,7 @@ evaluates to. As an example, @var{file} might contain a definition like this:
%base-services))))
(list (machine
- (system %system)
+ (operating-system %system)
(environment managed-host-environment-type)
(configuration (machine-ssh-configuration
(host-name "localhost")
@@ -25530,12 +25530,28 @@ complex deployment may involve, for example, starting virtual machines through
a Virtual Private Server (VPS) provider. In such a case, a different
@var{environment} type would be used.
+Do note that you first need to generate a key pair on the coordinator machine
+to allow the daemon to export signed archives of files from the store
+(@pxref{Invoking guix archive}).
+
+@example
+# guix archive --generate-key
+@end example
+
+@noindent
+Each target machine must authorize the key of the master machine so that it
+accepts store items it receives from the coordinator:
+
+@example
+# guix archive --authorize < coordinator-public-key.txt
+@end example
+
@deftp {Data Type} machine
This is the data type representing a single machine in a heterogeneous Guix
deployment.
@table @asis
-@item @code{system}
+@item @code{operating-system}
The object of the operating system configuration to deploy.
@item @code{environment}
diff --git a/gnu/machine.scm b/gnu/machine.scm
index 0b79402b0a..30ae97f6ec 100644
--- a/gnu/machine.scm
+++ b/gnu/machine.scm
@@ -34,7 +34,7 @@
machine?
this-machine
- machine-system
+ machine-operating-system
machine-environment
machine-configuration
machine-display-name
@@ -85,14 +85,14 @@
make-machine
machine?
this-machine
- (system machine-system) ; <operating-system>
- (environment machine-environment) ; symbol
- (configuration machine-configuration ; configuration object
- (default #f))) ; specific to environment
+ (operating-system machine-operating-system) ; <operating-system>
+ (environment machine-environment) ; symbol
+ (configuration machine-configuration ; configuration object
+ (default #f))) ; specific to environment
(define (machine-display-name machine)
"Return the host-name identifying MACHINE."
- (operating-system-host-name (machine-system machine)))
+ (operating-system-host-name (machine-operating-system machine)))
(define (machine-remote-eval machine exp)
"Evaluate EXP, a gexp, on MACHINE. Ensure that all the elements EXP refers to
diff --git a/gnu/machine/ssh.scm b/gnu/machine/ssh.scm
index 552eafa9de..274d56db26 100644
--- a/gnu/machine/ssh.scm
+++ b/gnu/machine/ssh.scm
@@ -20,6 +20,9 @@
#:use-module (gnu machine)
#:autoload (gnu packages gnupg) (guile-gcrypt)
#:use-module (gnu system)
+ #:use-module (gnu system file-systems)
+ #:use-module (gnu system uuid)
+ #:use-module (guix diagnostics)
#:use-module (guix gexp)
#:use-module (guix i18n)
#:use-module (guix modules)
@@ -29,6 +32,7 @@
#:use-module (guix scripts system reconfigure)
#:use-module (guix ssh)
#:use-module (guix store)
+ #:use-module (guix utils)
#:use-module (ice-9 match)
#:use-module (srfi srfi-19)
#:use-module (srfi srfi-26)
@@ -100,6 +104,145 @@ an environment type of 'managed-host."
;;;
+;;; Safety checks.
+;;;
+
+(define (machine-check-file-system-availability machine)
+ "Raise a '&message' error condition if any of the file-systems specified in
+MACHINE's 'system' declaration do not exist on the machine."
+ (define file-systems
+ (filter (lambda (fs)
+ (and (file-system-mount? fs)
+ (not (member (file-system-type fs)
+ %pseudo-file-system-types))
+ (not (memq 'bind-mount (file-system-flags fs)))))
+ (operating-system-file-systems (machine-operating-system machine))))
+
+ (define (check-literal-file-system fs)
+ (define remote-exp
+ #~(catch 'system-error
+ (lambda ()
+ (stat #$(file-system-device fs))
+ #t)
+ (lambda args
+ (system-error-errno args))))
+
+ (mlet %store-monad ((errno (machine-remote-eval machine remote-exp)))
+ (when (number? errno)
+ (raise (condition
+ (&message
+ (message (format #f (G_ "device '~a' not found: ~a")
+ (file-system-device fs)
+ (strerror errno)))))))
+ (return #t)))
+
+ (define (check-labeled-file-system fs)
+ (define remote-exp
+ (with-imported-modules '((gnu build file-systems))
+ #~(begin
+ (use-modules (gnu build file-systems))
+ (find-partition-by-label #$(file-system-label->string
+ (file-system-device fs))))))
+
+ (mlet %store-monad ((result (machine-remote-eval machine remote-exp)))
+ (unless result
+ (raise (condition
+ (&message
+ (message (format #f (G_ "no file system with label '~a'")
+ (file-system-label->string
+ (file-system-device fs))))))))
+ (return #t)))
+
+ (define (check-uuid-file-system fs)
+ (define remote-exp
+ (with-imported-modules (source-module-closure
+ '((gnu build file-systems)
+ (gnu system uuid)))
+ #~(begin
+ (use-modules (gnu build file-systems)
+ (gnu system uuid))
+
+ (define uuid
+ (string->uuid #$(uuid->string (file-system-device fs))))
+
+ (find-partition-by-uuid uuid))))
+
+ (mlet %store-monad ((result (machine-remote-eval machine remote-exp)))
+ (unless result
+ (raise (condition
+ (&message
+ (message (format #f (G_ "no file system with UUID '~a'")
+ (uuid->string (file-system-device fs))))))))
+ (return #t)))
+
+ (mbegin %store-monad
+ (mapm %store-monad check-literal-file-system
+ (filter (lambda (fs)
+ (string? (file-system-device fs)))
+ file-systems))
+ (mapm %store-monad check-labeled-file-system
+ (filter (lambda (fs)
+ (file-system-label? (file-system-device fs)))
+ file-systems))
+ (mapm %store-monad check-uuid-file-system
+ (filter (lambda (fs)
+ (uuid? (file-system-device fs)))
+ file-systems))))
+
+(define (machine-check-initrd-modules machine)
+ "Raise a '&message' error condition if any of the modules needed by
+'needed-for-boot' file systems in MACHINE are not available in the initrd."
+ (define file-systems
+ (filter file-system-needed-for-boot?
+ (operating-system-file-systems (machine-operating-system machine))))
+
+ (define (missing-modules fs)
+ (define remote-exp
+ (let ((device (file-system-device fs)))
+ (with-imported-modules (source-module-closure
+ '((gnu build file-systems)
+ (gnu build linux-modules)
+ (gnu system uuid)))
+ #~(begin
+ (use-modules (gnu build file-systems)
+ (gnu build linux-modules)
+ (gnu system uuid))
+
+ (define dev
+ #$(cond ((string? device) device)
+ ((uuid? device) #~(find-partition-by-uuid
+ (string->uuid
+ #$(uuid->string device))))
+ ((file-system-label? device)
+ #~(find-partition-by-label
+ (file-system-label->string #$device)))))
+
+ (missing-modules dev '#$(operating-system-initrd-modules
+ (machine-operating-system machine)))))))
+ (mlet %store-monad ((missing (machine-remote-eval machine remote-exp)))
+ (return (list fs missing))))
+
+ (mlet %store-monad ((device (mapm %store-monad missing-modules file-systems)))
+ (for-each (match-lambda
+ ((fs missing)
+ (unless (null? missing)
+ (raise (condition
+ (&message
+ (message (format #f (G_ "~a missing modules ~{ ~a~}~%")
+ (file-system-device fs)
+ missing))))))))
+ device)
+ (return #t)))
+
+(define (check-deployment-sanity machine)
+ "Raise a '&message' error condition if it is clear that deploying MACHINE's
+'system' declaration would fail."
+ (mbegin %store-monad
+ (machine-check-file-system-availability machine)
+ (machine-check-initrd-modules machine)))
+
+
+;;;
;;; System deployment.
;;;
@@ -165,8 +308,9 @@ of MACHINE's system profile, ordered from most recent to oldest."
"Internal implementation of 'deploy-machine' for MACHINE instances with an
environment type of 'managed-host."
(maybe-raise-unsupported-configuration-error machine)
- (mlet %store-monad ((boot-parameters (machine-boot-parameters machine)))
- (let* ((os (machine-system machine))
+ (mlet %store-monad ((_ (check-deployment-sanity machine))
+ (boot-parameters (machine-boot-parameters machine)))
+ (let* ((os (machine-operating-system machine))
(eval (cut machine-remote-eval machine <>))
(menu-entries (map boot-parameters->menu-entry boot-parameters))
(bootloader-configuration (operating-system-bootloader os))
diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm
index c3b1e04901..393dcb21eb 100644
--- a/gnu/packages/admin.scm
+++ b/gnu/packages/admin.scm
@@ -2606,7 +2606,7 @@ buffers.")
`(#:tests? #f ; many of the tests try to load kernel modules
#:phases
(modify-phases %standard-phases
- (add-after 'unpack 'autogen
+ (replace 'bootstrap
(lambda _
;; Don't run configure in this phase.
(setenv "NOCONFIGURE" "1")
diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index c6c42f66c6..fc0d6f80db 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -3700,7 +3700,7 @@ library.")
(define-public faudio
(package
(name "faudio")
- (version "19.07")
+ (version "19.08")
(source
(origin
(method git-fetch)
@@ -3709,7 +3709,7 @@ library.")
(commit version)))
(file-name (string-append name "-" version "-checkout"))
(sha256
- (base32 "1wf6skc5agaikc9qgwk8bx56sad31fafs53lqqn4jmx8i76pl0lw"))))
+ (base32 "1v13kfhyr46241vb6a4dcb4gw5f149525sprwa9cj4rv6wlcqgm5"))))
(arguments
'(#:tests? #f ; No tests.
#:configure-flags '("-DFFMPEG=ON")))
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 74af02a47d..74620a2cbe 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1212,14 +1212,14 @@ determining dependencies between variables, code improvement suggestions.")
(define-public r-chippeakanno
(package
(name "r-chippeakanno")
- (version "3.18.1")
+ (version "3.18.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ChIPpeakAnno" version))
(sha256
(base32
- "1mwi5s600c3jxy8f1azfrndc3g06qvhbmrp9wqac9nwjbfx1kfji"))))
+ "0wzwdxvvr7wknz5jnan0wsp81c1gv4d2qx0mrb1yybqf4z068779"))))
(properties `((upstream-name . "ChIPpeakAnno")))
(build-system r-build-system)
(propagated-inputs
@@ -1521,14 +1521,14 @@ experiments.")
(define-public r-genomicinteractions
(package
(name "r-genomicinteractions")
- (version "1.18.0")
+ (version "1.18.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "GenomicInteractions" version))
(sha256
(base32
- "0ipvm3c1cqd46n60lsrqzf6fx4b3lwia57jyfx9wcqqg205qj73b"))))
+ "0hq2n5yfr9h2ayn10dy9lz08gd2q0awrm5cy2kqdmz4d8ss4r94p"))))
(properties
`((upstream-name . "GenomicInteractions")))
(build-system r-build-system)
@@ -3529,14 +3529,14 @@ position-specific scores within R and Bioconductor.")
(define-public r-atacseqqc
(package
(name "r-atacseqqc")
- (version "1.8.1")
+ (version "1.8.5")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ATACseqQC" version))
(sha256
(base32
- "0h5j3724hnd86w22vy3whqx6gkf0nf2dxd2clgzdvjzblbcd5s69"))))
+ "1i8f0vs0z4jbc2yvj1diay7jhcmb1a82zv96xllk771f25nvmmxp"))))
(properties `((upstream-name . "ATACseqQC")))
(build-system r-build-system)
(propagated-inputs
@@ -3621,14 +3621,14 @@ annotations and ontologies.")
(define-public r-abaenrichment
(package
(name "r-abaenrichment")
- (version "1.14.0")
+ (version "1.14.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ABAEnrichment" version))
(sha256
(base32
- "0av1dysk7qa8c4a0pp7yq89k8c4y40d2gyvsb8f27slvv2i3aad2"))))
+ "1w322wsp6bd3gyfwzgdf088cvfmpq774knr57d0dj420ljf4xn48"))))
(properties `((upstream-name . "ABAEnrichment")))
(build-system r-build-system)
(propagated-inputs
@@ -4841,14 +4841,14 @@ annotations.")
(define-public r-rsubread
(package
(name "r-rsubread")
- (version "1.34.4")
+ (version "1.34.6")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Rsubread" version))
(sha256
(base32
- "1230p8nsakifmpsqfiaj8rpm7npa8ab903mfjmayfa71n6yzvcbs"))))
+ "0nnfh4hnrs5kd72m8c50cidbsxjz12szw2vynpmg8q0wpd99q550"))))
(properties `((upstream-name . "Rsubread")))
(build-system r-build-system)
(inputs `(("zlib" ,zlib)))
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index bcec9cd279..956257d7bb 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7458,13 +7458,13 @@ names in their natural, rather than lexicographic, order.")
(define-public r-edger
(package
(name "r-edger")
- (version "3.26.5")
+ (version "3.26.6")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "edgeR" version))
(sha256
(base32
- "0iba4krz30dx5b0s89n5cfkwn64867s7vmvvfqms9lbcr4kj439m"))))
+ "17vadhamjv4x0l4qqq2p2fi6j2bkllz5zd8dq761vgd5ic23zizm"))))
(properties `((upstream-name . "edgeR")))
(build-system r-build-system)
(propagated-inputs
@@ -7525,13 +7525,13 @@ coding changes and predict coding outcomes.")
(define-public r-limma
(package
(name "r-limma")
- (version "3.40.2")
+ (version "3.40.6")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "limma" version))
(sha256
(base32
- "1d4ig2b7fa9mwja52isxrwmprfdjdk1mlcf2skhdp51l24z6wbk7"))))
+ "166z8cdh6w90rldqqaar7hyaskwiy4smawjfbn4sn58clv6q3mp8"))))
(build-system r-build-system)
(home-page "http://bioinf.wehi.edu.au/limma")
(synopsis "Package for linear models for microarray and RNA-seq data")
@@ -7658,13 +7658,13 @@ annotation data packages using SQLite data storage.")
(define-public r-biomart
(package
(name "r-biomart")
- (version "2.40.1")
+ (version "2.40.3")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "biomaRt" version))
(sha256
(base32
- "1abl0c4qbhfqf9ixdp74183phm7s8rszrr5ldczm59b8vyng8rhx"))))
+ "022m1r44s00c5k9bmv0lr22lcn662nhc91aazvv0yyysxjamyf60"))))
(properties
`((upstream-name . "biomaRt")))
(build-system r-build-system)
@@ -7819,13 +7819,13 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns),
(define-public r-summarizedexperiment
(package
(name "r-summarizedexperiment")
- (version "1.14.0")
+ (version "1.14.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "SummarizedExperiment" version))
(sha256
(base32
- "1ypk63pdml89y81pr41i2zq0fimsaxsa5lgpg6xs5cwikyaq0pci"))))
+ "0bhwgzrdipr0qjzc4j0qspqprx3v1rvshmx4j6506dv43pqlgp3f"))))
(properties
`((upstream-name . "SummarizedExperiment")))
(build-system r-build-system)
@@ -7883,13 +7883,13 @@ alignments.")
(define-public r-rtracklayer
(package
(name "r-rtracklayer")
- (version "1.44.0")
+ (version "1.44.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "rtracklayer" version))
(sha256
(base32
- "161gcks9b12993g9k27gf7wfh8lgd8m8rr7x2slgfqqssk0yrmpd"))))
+ "03b4rfsbzjjf5kxcsjv7kq8hrsgcvz9rfzcn2v7fx3nr818pbb8s"))))
(build-system r-build-system)
(arguments
`(#:phases
@@ -7930,13 +7930,13 @@ as well as query and modify the browser state, such as the current viewport.")
(define-public r-genomicfeatures
(package
(name "r-genomicfeatures")
- (version "1.36.3")
+ (version "1.36.4")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomicFeatures" version))
(sha256
(base32
- "0zkd57i5qjxsravv0gbyckc0wrnqzgxd61ibh3jmhmrccrr9ihn3"))))
+ "0mzqv8pyxx5nwchyx3radym9ws2f9hb50xc9abjsjs4w4pv91j3k"))))
(properties
`((upstream-name . "GenomicFeatures")))
(build-system r-build-system)
@@ -8354,13 +8354,13 @@ paired-end data.")
(define-public r-rcas
(package
(name "r-rcas")
- (version "1.10.0")
+ (version "1.10.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "RCAS" version))
(sha256
(base32
- "1h4vf5gzilqbdrd8m9l3zc2m4sca8cir8366a7njgd558k7ld5kl"))))
+ "06z5zmdi34jblw37z6ff8hb6lvvi0chwr37acwqfn8d27ax9lakz"))))
(properties `((upstream-name . "RCAS")))
(build-system r-build-system)
(propagated-inputs
@@ -9418,14 +9418,14 @@ of mass spectrometry based proteomics data.")
(define-public r-msnid
(package
(name "r-msnid")
- (version "1.18.0")
+ (version "1.18.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MSnID" version))
(sha256
(base32
- "18mp8zacawhfapfwpq8czbswxix2ykvqhwjga54v0a99zg3k87h3"))))
+ "1n49l5mjdz7p4g2nwsbhm1jcj42sv6lsriq77n2imvacsvk0qfmb"))))
(properties `((upstream-name . "MSnID")))
(build-system r-build-system)
(propagated-inputs
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 3bd0d664da..4b998eb1fb 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -78,14 +78,14 @@
(define-public r-clipr
(package
(name "r-clipr")
- (version "0.6.0")
+ (version "0.7.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "clipr" version))
(sha256
(base32
- "0k9kimkmmj9k7290sxiqn4kd1vvm4w7q9a44wp0w30b7yjpavx2m"))))
+ "1qn2p13d0c1bpqss6mv9hk60980rzhznfqpyaf5x0fy65svy9903"))))
(build-system r-build-system)
(home-page "https://github.com/mdlincoln/clipr")
(synopsis "Read and write from the system clipboard")
@@ -97,14 +97,14 @@ the system clipboards.")
(define-public r-ellipsis
(package
(name "r-ellipsis")
- (version "0.2.0")
+ (version "0.2.0.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "ellipsis" version))
(sha256
(base32
- "0hdk79q4wn5nq52p8qd65kqz81l0b8gfzsbzyvmfais0p24qclib"))))
+ "0hx9l043433bwm1np9sypph77c7y9dddpz0wrhbkcv01x32jhr8f"))))
(build-system r-build-system)
(propagated-inputs
`(("r-rlang" ,r-rlang)))
@@ -370,14 +370,14 @@ such as copy/paste from an R session.")
(define-public r-callr
(package
(name "r-callr")
- (version "3.2.0")
+ (version "3.3.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "callr" version))
(sha256
(base32
- "1s5h2k7c1vgbry90xczin66q89cbkc6mvh4679l5rsz83087pd2b"))))
+ "0rvrlg86fxr5nadvqa0dr1iifqjs4d1rc32v76m3ccvx6m3xlq5z"))))
(build-system r-build-system)
(propagated-inputs
`(("r-r6" ,r-r6)
@@ -500,13 +500,13 @@ in systems and applications.")
(define-public r-servr
(package
(name "r-servr")
- (version "0.14")
+ (version "0.15")
(source (origin
(method url-fetch)
(uri (cran-uri "servr" version))
(sha256
(base32
- "0zjjnfgas9d16fihksyk24kgkkqswb4sd0rz51id2ni1ymdyasjk"))))
+ "199k9aghwk9rf1rm8pjg60xacqww25cza259h5dfj1ixil0m6dxi"))))
(build-system r-build-system)
(propagated-inputs
`(("r-httpuv" ,r-httpuv)
@@ -614,13 +614,13 @@ LaTeX.")
(define-public r-curl
(package
(name "r-curl")
- (version "3.3")
+ (version "4.0")
(source (origin
(method url-fetch)
(uri (cran-uri "curl" version))
(sha256
(base32
- "1gd5i25anzi28lg1f8p7g63z9d46xi0qaw4lxpml5p0f52lvkc0c"))))
+ "0wb1j87fa2nd4a9x1w2nmc453nzvx6qiq8dviwc4jr36hsf9ra89"))))
(build-system r-build-system)
(arguments
`(#:phases
@@ -1205,14 +1205,14 @@ including functions for geolocation and routing.")
(define-public r-haven
(package
(name "r-haven")
- (version "2.1.0")
+ (version "2.1.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "haven" version))
(sha256
(base32
- "0x5fwc4q2gdxwwp5sxdd6q17jhpisd769y9kv0xgnjcm0cdwz8f0"))))
+ "12h64r2v2451igyl7v4w2kg0hzw9rnanph0m7smffq29ybkv9g4h"))))
(build-system r-build-system)
(inputs
`(("zlib" ,zlib)))
@@ -1441,14 +1441,14 @@ processes. Most of its code is based on the @code{psutil} Python package.")
(define-public r-pkgbuild
(package
(name "r-pkgbuild")
- (version "1.0.3")
+ (version "1.0.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "pkgbuild" version))
(sha256
(base32
- "0k8zwa66rm1ncx19ld5mbaxcjxkswiczpdqyssy44vl8k6scwfn9"))))
+ "0prvx91dha5pvd0k4jca2arkngvi6vnfs2indmiy3kwwzyjyyd19"))))
(build-system r-build-system)
(propagated-inputs
`(("r-callr" ,r-callr)
@@ -1497,13 +1497,13 @@ you to rapidly iterate while developing a package.")
(define-public r-rcpp
(package
(name "r-rcpp")
- (version "1.0.1")
+ (version "1.0.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "Rcpp" version))
(sha256
- (base32 "015rmxns8mhmnd9wnz9bmma4iwx2sf4bcwkkp9hcgvdmblzf0vg7"))))
+ (base32 "170jlmjrs92z5qdv58badhxycjvfjpqwwpic7rm13pc9zkb3i4xd"))))
(build-system r-build-system)
(native-inputs
`(("r-knitr" ,r-knitr))) ; for vignettes
@@ -2230,14 +2230,14 @@ topics for ecologists (ISBN 978-0-691-12522-0).")
(define-public r-lpsolve
(package
(name "r-lpsolve")
- (version "5.6.13.1")
+ (version "5.6.13.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "lpSolve" version))
(sha256
(base32
- "1f10ywlaaldgjj84vs108ly0nsbkrdgbn5d6qj7nk93j1x1xrn3a"))))
+ "0fc5m259ayc880f5hvnq59ih6nb2rlp394n756n1khmxbjpw1w3m"))))
(properties `((upstream-name . "lpSolve")))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/lpSolve")
@@ -2315,14 +2315,14 @@ data). Weighted versions of MLE, MME and QME are available.")
(define-public r-energy
(package
(name "r-energy")
- (version "1.7-5")
+ (version "1.7-6")
(source
(origin
(method url-fetch)
(uri (cran-uri "energy" version))
(sha256
(base32
- "15k9dg0a82cs9ypm0wpcsff3il1hzhnnv86dv5ngby1r144czhi4"))))
+ "16m8bxfgr9sdisjy2qrv6fv5xxwcc9q890l0hpbwq6qzisrdn3lh"))))
(build-system r-build-system)
(propagated-inputs
`(("r-boot" ,r-boot)
@@ -2450,14 +2450,14 @@ available in a vignette.")
(define-public r-lava
(package
(name "r-lava")
- (version "1.6.5")
+ (version "1.6.6")
(source
(origin
(method url-fetch)
(uri (cran-uri "lava" version))
(sha256
(base32
- "13rlqdg42ylnz4hc932bl50xismrcr4d9ykcd9zs19cw5mckjx0f"))))
+ "0nfab5fgnmxh8cplg8rd8cp34fny5j0k5wn4baj51r6ck7fq9g3s"))))
(build-system r-build-system)
(propagated-inputs
`(("r-numderiv" ,r-numderiv)
@@ -2640,20 +2640,41 @@ to access PostgreSQL database systems.")
;; under the PostgreSQL license.
(license license:gpl2)))
+(define-public r-linprog
+ (package
+ (name "r-linprog")
+ (version "0.9-2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "linprog" version))
+ (sha256
+ (base32
+ "1ki14an0pmhs2mnmfjjvdzd76pshiyvi659zf7hqvqwj0viv4dw9"))))
+ (build-system r-build-system)
+ (propagated-inputs `(("r-lpsolve" ,r-lpsolve)))
+ (home-page "http://linprog.r-forge.r-project.org/")
+ (synopsis "Linear programming and optimization")
+ (description
+ "This package can be used to solve Linear Programming / Linear
+Optimization problems by using the simplex algorithm.")
+ (license license:gpl2+)))
+
(define-public r-geometry
(package
(name "r-geometry")
- (version "0.4.1")
+ (version "0.4.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "geometry" version))
(sha256
(base32
- "0v3ivaw8vbjyxg08dd573qk3kqfyknj5hli9503dza6p6xz0dzmm"))))
+ "0vq334115qi039vy198ggv1dsp6n1s6jwcm9ivipf5r8lbm287zz"))))
(build-system r-build-system)
(propagated-inputs
`(("r-magic" ,r-magic)
+ ("r-linprog" ,r-linprog)
("r-lpsolve" ,r-lpsolve)
("r-rcpp" ,r-rcpp)
("r-rcppprogress" ,r-rcppprogress)))
@@ -2871,14 +2892,14 @@ provides a one-row summary of model-level statistics.")
(define-public r-recipes
(package
(name "r-recipes")
- (version "0.1.5")
+ (version "0.1.6")
(source
(origin
(method url-fetch)
(uri (cran-uri "recipes" version))
(sha256
(base32
- "056zv4vhayyy8q9izcdknbb9hff2gxivg21g5mkssia78vw8g3mg"))))
+ "1ndz9h0zvdj141r63l8047wbhaj0x8fwzzyq7b8mh78pvrrdpq2i"))))
(build-system r-build-system)
(propagated-inputs
`(("r-dplyr" ,r-dplyr)
@@ -2890,7 +2911,6 @@ provides a one-row summary of model-level statistics.")
("r-magrittr" ,r-magrittr)
("r-matrix" ,r-matrix)
("r-purrr" ,r-purrr)
- ("r-rcpproll" ,r-rcpproll)
("r-rlang" ,r-rlang)
("r-tibble" ,r-tibble)
("r-tidyr" ,r-tidyr)
@@ -3056,14 +3076,14 @@ Laplace approximation and adaptive Gauss-Hermite quadrature.")
(define-public r-jomo
(package
(name "r-jomo")
- (version "2.6-8")
+ (version "2.6-9")
(source
(origin
(method url-fetch)
(uri (cran-uri "jomo" version))
(sha256
(base32
- "097zfdcqc3a45ay8xxbraqh8xsfyivskkdmc2b4ca4n979lx8vyb"))))
+ "16ychdhhv8cii8zrdfdf5gzgnvmfaq573bmi00xqdf323q3lf3xr"))))
(build-system r-build-system)
(propagated-inputs
`(("r-lme4" ,r-lme4)
@@ -3129,14 +3149,14 @@ analysis of multiply imputed data sets.")
(define-public r-mice
(package
(name "r-mice")
- (version "3.5.0")
+ (version "3.6.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "mice" version))
(sha256
(base32
- "0icydc312sbvzbp0r0mhs2r77a2ly2xvz5w5amirz3wdkvgyrk2g"))))
+ "0pgcxdmp77604h6f4x8hhs6j4xdjgf5b9zvnixyzdj8vcgdjpivv"))))
(build-system r-build-system)
(propagated-inputs
`(("r-broom" ,r-broom)
@@ -3212,14 +3232,14 @@ programming} (SQP) based solver).")
(define-public r-hardyweinberg
(package
(name "r-hardyweinberg")
- (version "1.6.2")
+ (version "1.6.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "HardyWeinberg" version))
(sha256
(base32
- "15i7b444hikkfgqmx2ki827998xwra38k9v7a7kavwz6zmq5mmv9"))))
+ "1irz44q6nf95h37av868f47aakwv3jgwgw217xfsfw0afkm7s25f"))))
(properties `((upstream-name . "HardyWeinberg")))
(build-system r-build-system)
(propagated-inputs
@@ -3289,14 +3309,14 @@ structure.")
(define-public r-vioplot
(package
(name "r-vioplot")
- (version "0.3.0")
+ (version "0.3.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "vioplot" version))
(sha256
(base32
- "1ddmmqq7qrnvr5q518afnysrl7ccr8am9njknv3dpwaqzcdr9akn"))))
+ "13kfjp747bnzksai8j39y2hyl3ljc6n53c2cfhaw78q3d63x0lbv"))))
(build-system r-build-system)
(propagated-inputs
`(("r-sm" ,r-sm)
@@ -3631,14 +3651,14 @@ constants, and control debugging of packages via environment variables.")
(define-public r-processx
(package
(name "r-processx")
- (version "3.3.1")
+ (version "3.4.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "processx" version))
(sha256
(base32
- "1bhbfacx2z2d97pz5bch45nvbvywhx2zp049czlfbdivkzgxn8v1"))))
+ "1g6ipcaxg9y94lyrnbp7kkbqfkcdh1fyrqjjclbjp3x7iysdvazi"))))
(build-system r-build-system)
(propagated-inputs
`(("r-ps" ,r-ps)
@@ -3839,18 +3859,19 @@ to variables on the left-hand side of the assignment.")
(define-public r-vctrs
(package
(name "r-vctrs")
- (version "0.1.0")
+ (version "0.2.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "vctrs" version))
(sha256
(base32
- "13w1r8zpalirpfaz5sykpn0mj4jmhxi2qkdcfq081ixlfjyzwa6c"))))
+ "05h0y8qzwc899qj84gkhg4jwzscd065as00d4d8smv42h4i8zkjv"))))
(build-system r-build-system)
(propagated-inputs
`(("r-backports" ,r-backports)
("r-digest" ,r-digest)
+ ("r-ellipsis" ,r-ellipsis)
("r-glue" ,r-glue)
("r-rlang" ,r-rlang)
("r-zeallot" ,r-zeallot)))
@@ -3877,14 +3898,14 @@ to variables on the left-hand side of the assignment.")
(define-public r-pillar
(package
(name "r-pillar")
- (version "1.4.1")
+ (version "1.4.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "pillar" version))
(sha256
(base32
- "0mcc09caxm69pghhz6b8vawj9ni63aijv5qba53pg4ph7rxclwgm"))))
+ "0988047mf0xdhdkqqmavzx4ifjhndjnxniyrrhrdq1nvnrvbpfms"))))
(build-system r-build-system)
(propagated-inputs
`(("r-cli" ,r-cli)
@@ -3923,14 +3944,14 @@ terminals.")
(define-public r-tinytex
(package
(name "r-tinytex")
- (version "0.14")
+ (version "0.15")
(source
(origin
(method url-fetch)
(uri (cran-uri "tinytex" version))
(sha256
(base32
- "0aab7ybc6kkxxk3lzdmbla8zcpp6nmlahchc33miv28cmnqw363w"))))
+ "145dmgq7h55mmqqlnnj153j484x2a9s1fbvjbjkdyqzpnz9qh2ax"))))
(build-system r-build-system)
(propagated-inputs
`(("r-xfun" ,r-xfun)))
@@ -4628,14 +4649,14 @@ files.")
(define-public r-shinyace
(package
(name "r-shinyace")
- (version "0.3.3")
+ (version "0.4.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "shinyAce" version))
(sha256
(base32
- "02q6wqw349nlyf3mbf18cxif1xv9cal5qzccrdlnv73szqn9jk7j"))))
+ "0hvih5g0pswlnz5rf3blx5yqw11ssxvm8w4klxddp1ap20ncbgl1"))))
(properties `((upstream-name . "shinyAce")))
(build-system r-build-system)
(propagated-inputs
@@ -4678,14 +4699,14 @@ systems.")
(define-public r-radiant-data
(package
(name "r-radiant-data")
- (version "0.9.9")
+ (version "1.0.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "radiant.data" version))
(sha256
(base32
- "17mgm0sggh4f7ihqmj9m3996p3pqc7h2cwx6ll1ha3kg5mx0znyn"))
+ "0b35jn4mcj10hqra18l8pi6s4pvj6fxipslbn6hkr4zza1z27gzw"))
(modules '((guix build utils)))
(snippet
'(begin
@@ -5140,14 +5161,14 @@ misclassification probabilities of different models.")
(define-public r-zip
(package
(name "r-zip")
- (version "2.0.2")
+ (version "2.0.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "zip" version))
(sha256
(base32
- "1xvgs7mhxi0sdp5ix4nisqm9lf8f75b7ip7b1hqpq9bzh0x6z8ix"))))
+ "0zii05jg9v9ljd0wd67g9x4bhlmpmsy5dzd093sbnc5n3vjbi32a"))))
(build-system r-build-system)
(home-page "https://github.com/gaborcsardi/zip")
(synopsis "Cross-platform Zip compression")
@@ -5298,14 +5319,14 @@ promises, but with a syntax that is idiomatic R.")
(define-public r-dosnow
(package
(name "r-dosnow")
- (version "1.0.16")
+ (version "1.0.18")
(source
(origin
(method url-fetch)
(uri (cran-uri "doSNOW" version))
(sha256
(base32
- "13ir4a8252h4yvp5ir9xnwack1kn58i4ny6sf2qdc12zspn3850n"))))
+ "0rj72z5505cprh6wykhhiz08l9bmd966srqh2qypwivf321bvrvh"))))
(properties `((upstream-name . "doSNOW")))
(build-system r-build-system)
(propagated-inputs
@@ -5431,14 +5452,14 @@ obtain a better initial configuration in non-metric MDS.")
(define-public r-reticulate
(package
(name "r-reticulate")
- (version "1.12")
+ (version "1.13")
(source
(origin
(method url-fetch)
(uri (cran-uri "reticulate" version))
(sha256
(base32
- "0pqr1rcs8yg9nlh729mvlws93cqhpmv49j9bcgarh7vxzkwyv0kb"))))
+ "1qwxh7zq9igl7dxl5g5qjbvv0mlac3w80djnkm0w8rxnaval3gmd"))))
(build-system r-build-system)
(inputs `(("python" ,python)))
(propagated-inputs
@@ -5548,14 +5569,14 @@ and adds the annotation to the plot.")
(define-public r-ggpubr
(package
(name "r-ggpubr")
- (version "0.2.1")
+ (version "0.2.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "ggpubr" version))
(sha256
(base32
- "0a4dv6a752hwvc7l31xs7bgqhfzfdy94xp6wgwaxf5dxm46na7k1"))))
+ "0r5knv3707pmpngmj60zn761y3bh8lj89dhh1b80ss083xnxr4qw"))))
(build-system r-build-system)
(propagated-inputs
`(("r-cowplot" ,r-cowplot)
@@ -5569,6 +5590,7 @@ and adds the annotation to the plot.")
("r-magrittr" ,r-magrittr)
("r-polynom" ,r-polynom)
("r-purrr" ,r-purrr)
+ ("r-rlang" ,r-rlang)
("r-scales" ,r-scales)
("r-tidyr" ,r-tidyr)))
(home-page "http://www.sthda.com/english/rpkgs/ggpubr")
@@ -5628,14 +5650,14 @@ clustering.")
(define-public r-factominer
(package
(name "r-factominer")
- (version "1.41")
+ (version "1.42")
(source
(origin
(method url-fetch)
(uri (cran-uri "FactoMineR" version))
(sha256
(base32
- "1h20hydav6l2b7bngqw1av4l5rrh0wk58nhailga1f4qw9lrv259"))))
+ "1yl16inb2m89l1czgaf0pgy9655dpr751hyx92yw6rqpd2ryznac"))))
(properties `((upstream-name . "FactoMineR")))
(build-system r-build-system)
(propagated-inputs
@@ -5918,20 +5940,19 @@ to help insert or delete content at a specific location in the document.")
(define-public r-abn
(package
(name "r-abn")
- (version "1.3")
+ (version "2.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "abn" version))
(sha256
(base32
- "1q9hzpxwg835711kxwygd0l2awal6f015f8s6fprwz7graz1wbbm"))))
+ "08jlvb6i5f7ry2dwm0jgrnn2w95vr0l67dpx13n9878lz9ld131b"))))
(build-system r-build-system)
(inputs
`(("gsl" ,gsl)))
(propagated-inputs
- `(("r-cairo" ,r-cairo)
- ("r-lme4" ,r-lme4)
+ `(("r-lme4" ,r-lme4)
("r-mass" ,r-mass)
("r-nnet" ,r-nnet)
("r-rcpp" ,r-rcpp)
@@ -6070,14 +6091,14 @@ other add-on packages.")
(define-public r-insight
(package
(name "r-insight")
- (version "0.3.0")
+ (version "0.4.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "insight" version))
(sha256
(base32
- "1r288hc01cpyrk3nias30fw783z2vw20qr1k67vr65anh7mwm7vb"))))
+ "1lw1r3mb97z5p9z25jfzlhs0sbnwp6v8kzysf0am01x4m7l3iz82"))))
(build-system r-build-system)
(home-page "https://easystats.github.io/insight/")
(synopsis "Easy access to model information for various model objects")
@@ -6527,14 +6548,14 @@ containing one or more SNPs that evolved under directional selection.")
(define-public r-proc
(package
(name "r-proc")
- (version "1.15.0")
+ (version "1.15.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "pROC" version))
(sha256
(base32
- "1dxxkwdhxfnj2znq4c5ggrr9m5klh5pmfxg17rz59vr2hfb73m24"))))
+ "1jx8af9p6sxbypqvj1cci7q9sbyaw310inbjxibjcr3acj59h45h"))))
(properties `((upstream-name . "pROC")))
(build-system r-build-system)
(propagated-inputs
@@ -6900,14 +6921,14 @@ used to teach mathematics, statistics, computation and modeling.")
(define-public r-raster
(package
(name "r-raster")
- (version "2.9-5")
+ (version "2.9-23")
(source
(origin
(method url-fetch)
(uri (cran-uri "raster" version))
(sha256
(base32
- "0ljrymsp4zzaxdj1l0mw0a6hi88m5h0h920ixfzrg0szbyxqd0yk"))))
+ "1brqigic8ygr223bp2hgk5qjz3q03r4sfglrv4an0ghy7fgfralh"))))
(build-system r-build-system)
(propagated-inputs
`(("r-rcpp" ,r-rcpp)
@@ -7468,14 +7489,14 @@ multiple-imputation datasets.")
(define-public r-magick
(package
(name "r-magick")
- (version "2.0")
+ (version "2.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "magick" version))
(sha256
(base32
- "18y465325mhf48x2jn3jz9khwq1z2aj13wfbdkv8k3hln1sd572m"))))
+ "1pz71maz05gx4ds1wfw0alggc8nn2w75lj12dg1zr72s3kybhkzg"))))
(build-system r-build-system)
(inputs
`(("imagemagick" ,imagemagick)
@@ -7857,14 +7878,14 @@ Hothorn, Westfall, 2010, CRC Press).")
(define-public r-emmeans
(package
(name "r-emmeans")
- (version "1.3.5.1")
+ (version "1.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "emmeans" version))
(sha256
(base32
- "0rgzjvmp3yqhwgfg96v17wi8gbafzbrmz134shj2jsf5bsmw6vbj"))))
+ "1ynf9hhbch83k63lwps69ijfch30fk5v0sc418ck264c5vih26dh"))))
(build-system r-build-system)
(propagated-inputs
`(("r-estimability" ,r-estimability)
@@ -8089,14 +8110,14 @@ differentiation.")
(define-public r-bayestestr
(package
(name "r-bayestestr")
- (version "0.2.2")
+ (version "0.2.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "bayestestR" version))
(sha256
(base32
- "09r654lrhwwnshn5h2s2fbx3c8wigv3j4sva5hmfnkwjg8cclhd9"))))
+ "08d3bsb6li59n17bx1zrqnlnvniyb3vls9kl856km4chx3b2ff82"))))
(properties `((upstream-name . "bayestestR")))
(build-system r-build-system)
(propagated-inputs
@@ -8114,14 +8135,14 @@ ROPE percentage and pd).")
(define-public r-performance
(package
(name "r-performance")
- (version "0.2.0")
+ (version "0.3.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "performance" version))
(sha256
(base32
- "1pzd6z7i1jxr2xi1shg3d0bxlbpmjl7kpmwgjnfys6syv57znd1z"))))
+ "13j74ffhx950kacs86ixx84nviq9qlwzr7hjnhkmzw2hspjxq99w"))))
(build-system r-build-system)
(propagated-inputs
`(("r-bayestestr" ,r-bayestestr)
@@ -8141,14 +8162,14 @@ effects models and Bayesian models.")
(define-public r-ggeffects
(package
(name "r-ggeffects")
- (version "0.10.0")
+ (version "0.11.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "ggeffects" version))
(sha256
(base32
- "0gmqzjk8k8q6j4q6asv9f3b1fv4qrw5w8xa48ha3y98shzm5np9k"))))
+ "1b0lxa8bljdh6h4lk7pql1lrhjlvh7p5c8qlgb8ac6ay8hb79vmi"))))
(build-system r-build-system)
(propagated-inputs
`(("r-dplyr" ,r-dplyr)
@@ -8175,14 +8196,14 @@ results using @code{ggplot2}.")
(define-public r-sjplot
(package
(name "r-sjplot")
- (version "2.6.3")
+ (version "2.7.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "sjPlot" version))
(sha256
(base32
- "0h1mkmp5mrkbf7y3zh6m4cnm737cpg1m5si0lrmal7j2ixqicwjy"))))
+ "1m0gy991fmxvqry91kkzdkdapyalhrwql25d0hg2a2naxgfw4zpk"))))
(properties `((upstream-name . "sjPlot")))
(build-system r-build-system)
(propagated-inputs
@@ -8192,6 +8213,7 @@ results using @code{ggplot2}.")
("r-forcats" ,r-forcats)
("r-ggeffects" ,r-ggeffects)
("r-ggplot2" ,r-ggplot2)
+ ("r-ggrepel" ,r-ggrepel)
("r-glmmtmb" ,r-glmmtmb)
("r-insight" ,r-insight)
("r-knitr" ,r-knitr)
@@ -8311,14 +8333,14 @@ terminals that do not support Unicode.")
(define-public r-usethis
(package
(name "r-usethis")
- (version "1.5.0")
+ (version "1.5.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "usethis" version))
(sha256
(base32
- "0pn6ka3726psaqlx573g6nxi90apf0rn5m4k2lz1jr66xdc19sag"))))
+ "07an5wbikilg7cb3q6x5aykw8dfqnjrc3wpfb7gjmy0d9fh20fcy"))))
(build-system r-build-system)
(propagated-inputs
`(("r-clipr" ,r-clipr)
@@ -8674,14 +8696,14 @@ analysing multivariate abundance data in community ecology.")
(define-public r-afex
(package
(name "r-afex")
- (version "0.23-0")
+ (version "0.24-1")
(source
(origin
(method url-fetch)
(uri (cran-uri "afex" version))
(sha256
(base32
- "0yv4s7461swn0116y4wq9v139p1br5rr6hhnq1cmkbvybmwj2vp7"))))
+ "14w7kcwr5hxmjcjmdm5ia9ka3bw1nl18pxlm1vpw62nmvicn3455"))))
(build-system r-build-system)
(propagated-inputs
`(("r-car" ,r-car)
@@ -8908,14 +8930,14 @@ Bioconductor packages.")
(define-public r-rgl
(package
(name "r-rgl")
- (version "0.100.24")
+ (version "0.100.26")
(source
(origin
(method url-fetch)
(uri (cran-uri "rgl" version))
(sha256
(base32
- "0nm3iyvhhmh0zlywkfmrq3vyh8z1l296xxfmcky0ifd2qnysfcqj"))))
+ "0h77akviwjd86j2qyx326xynbmwhypd6ydprzlwqnidd4ckrr271"))))
(build-system r-build-system)
(native-inputs
`(("pkg-config" ,pkg-config)))
@@ -9374,14 +9396,14 @@ maps.")
(define-public r-tidytree
(package
(name "r-tidytree")
- (version "0.2.4")
+ (version "0.2.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "tidytree" version))
(sha256
(base32
- "04bznlfs617plv258nmsyq2pywnijcnzy2pbn5b2fgjk2xqkp29w"))))
+ "0vfjv33352dmk9cr2qn0knzg761068rdk6jg32csd9vpmcma8awp"))))
(build-system r-build-system)
(propagated-inputs
`(("r-ape" ,r-ape)
@@ -9442,14 +9464,14 @@ giving it a description in the specific format.")
(define-public r-sparsesvd
(package
(name "r-sparsesvd")
- (version "0.1-4")
+ (version "0.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "sparsesvd" version))
(sha256
(base32
- "1yf373552wvdnd65r7hfcqa3v29dqn7jd4cn431mqd2acnqjrsam"))))
+ "1xm969fjq3fv1p2sqza2apz8picibj4s2agpwf1sx9nwn3b587qs"))))
(build-system r-build-system)
(propagated-inputs `(("r-matrix" ,r-matrix)))
(home-page "http://tedlab.mit.edu/~dr/SVDLIBC/")
@@ -9664,14 +9686,14 @@ diagnostics for controlling type-1 errors are also provided.")
(define-public r-flare
(package
(name "r-flare")
- (version "1.6.0")
+ (version "1.6.0.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "flare" version))
(sha256
(base32
- "0ygif9a7a99qwv0b488wymmmncp6f5ww9yz13s4qs6p8yf37x1r1"))))
+ "1ybrsx1djqldw0l5l1iz4pfh6xxb8ckkg1ric7wnsr51wm9ljlh5"))))
(build-system r-build-system)
(propagated-inputs
`(("r-igraph" ,r-igraph)
@@ -9764,14 +9786,14 @@ Touzet and Varre (2007).")
(define-public r-rnifti
(package
(name "r-rnifti")
- (version "0.11.0")
+ (version "0.11.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "RNifti" version))
(sha256
(base32
- "0zs8ffa6gpi9cygxk7xjin6k3vpvfgb540a506zlk50bf6kc5nlf"))))
+ "0jcgdg5k2swmi57aqj347kfi1fc4nvag7pxdfz61kc0vqqamm0wg"))))
(properties `((upstream-name . "RNifti")))
(build-system r-build-system)
(propagated-inputs `(("r-rcpp" ,r-rcpp)))
@@ -9787,14 +9809,14 @@ used by other packages.")
(define-public r-shades
(package
(name "r-shades")
- (version "1.3.1")
+ (version "1.4.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "shades" version))
(sha256
(base32
- "0v0xp9l1zyq4iysmkrbdwk4r1rksjj8p5c1726yrcgyg55mj59nv"))))
+ "1zg95sjhrfvbdlfc387g9p0vnb8nb6agdk1mb3wq3kwkm2da0bqj"))))
(build-system r-build-system)
(home-page "https://github.com/jonclayden/shades")
(synopsis "Simple color manipulation")
@@ -10143,23 +10165,51 @@ library.")
and manipulating sets of ontological terms.")
(license license:gpl2+)))
+(define-public r-gargle
+ (package
+ (name "r-gargle")
+ (version "0.3.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "gargle" version))
+ (sha256
+ (base32
+ "0vqgp4w03sdyj0q96gxkybqflzzbaw84zifsbi7pxk5y08fimj2v"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-fs" ,r-fs)
+ ("r-glue" ,r-glue)
+ ("r-httr" ,r-httr)
+ ("r-jsonlite" ,r-jsonlite)
+ ("r-rlang" ,r-rlang)
+ ("r-withr" ,r-withr)))
+ (home-page "https://gargle.r-lib.org")
+ (synopsis "Utilities for working with Google APIs")
+ (description
+ "This package provides utilities for working with Google APIs. This
+includes functions and classes for handling common credential types and for
+preparing, executing, and processing HTTP requests.")
+ (license license:expat)))
+
(define-public r-bigrquery
(package
(name "r-bigrquery")
- (version "1.1.1")
+ (version "1.2.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "bigrquery" version))
(sha256
(base32
- "1if39xkr231xmjq10fx2g7bgg4jgfd3wzx1p9g3pq4hbf2s6x0is"))))
+ "1ggh2gngr5x0g6y7d55y6kvn94anf7qi1bkc28cjmw61hxjq38fb"))))
(build-system r-build-system)
(propagated-inputs
`(("r-assertthat" ,r-assertthat)
("r-bit64" ,r-bit64)
("r-curl" ,r-curl)
("r-dbi" ,r-dbi)
+ ("r-gargle" ,r-gargle)
("r-glue" ,r-glue)
("r-httr" ,r-httr)
("r-jsonlite" ,r-jsonlite)
@@ -10167,6 +10217,7 @@ and manipulating sets of ontological terms.")
("r-progress" ,r-progress)
("r-rapidjsonr" ,r-rapidjsonr)
("r-rcpp" ,r-rcpp)
+ ("r-rlang" ,r-rlang)
("r-tibble" ,r-tibble)))
(home-page "https://github.com/rstats-db/bigrquery")
(synopsis "R interface to Google's BigQuery API")
@@ -10724,14 +10775,14 @@ covariance functions for large data sets.")
(define-public r-spatialextremes
(package
(name "r-spatialextremes")
- (version "2.0-7")
+ (version "2.0-7.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "SpatialExtremes" version))
(sha256
(base32
- "1y0h1pcfqp9ynxsr3yrfbihlwm25ypyb88jmm5k2g7xvm8h9g050"))))
+ "0aqq9ryxi4xsdqjhc1lhb7ai8szs7m2vys6nn0ygps1w3pm4xwj8"))))
(properties
`((upstream-name . "SpatialExtremes")))
(build-system r-build-system)
@@ -10994,14 +11045,14 @@ model with finite state space using the Aalen-Johansen estimator.")
(define-public r-epi
(package
(name "r-epi")
- (version "2.37")
+ (version "2.38")
(source
(origin
(method url-fetch)
(uri (cran-uri "Epi" version))
(sha256
(base32
- "1lanr9x0c6w22406p56j7cwk6wck8njq6pscb4gzc613d68zj1lk"))))
+ "0ald9fjynrlyah8nzwfs49a08j4myd3c5bm56zn61gg5pyyhi8hd"))))
(properties `((upstream-name . "Epi")))
(build-system r-build-system)
(propagated-inputs
@@ -11177,14 +11228,14 @@ them in distributed compute environments.")
(define-public r-future
(package
(name "r-future")
- (version "1.13.0")
+ (version "1.14.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "future" version))
(sha256
(base32
- "0h8ng2a6vg4axd5f75xcb3ip9d95zi22fa048dq2bzlnncwlznjz"))))
+ "1jyv2wlmpfqbk3hw269h4xg36na3wh1kd1lxmwdb40bsv4850lqa"))))
(build-system r-build-system)
(propagated-inputs
`(("r-digest" ,r-digest)
@@ -11237,14 +11288,14 @@ machine or distributed on a compute cluster.")
(define-public r-rsvd
(package
(name "r-rsvd")
- (version "1.0.1")
+ (version "1.0.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "rsvd" version))
(sha256
(base32
- "1faskhf5j2bj9f971qljsmh182g3rnyilj1wwijz530a6skxidzz"))))
+ "0fia77y5fxnhwkcxlgp98ygb8fdfraky75x80hkf7kvvpwc5rzn8"))))
(build-system r-build-system)
(propagated-inputs
`(("r-matrix" ,r-matrix)))
@@ -11445,14 +11496,14 @@ identifying outliers.")
(define-public r-bayesm
(package
(name "r-bayesm")
- (version "3.1-1")
+ (version "3.1-3")
(source
(origin
(method url-fetch)
(uri (cran-uri "bayesm" version))
(sha256
(base32
- "0y30cza92s6kgvmxjpr6f5g0qbcck7hslqp89ncprarhxiym2m28"))))
+ "041ach2f2vrqzd5kz17v7wmkjz6z8cjjihpk4qvczm4cr9z85r2i"))))
(build-system r-build-system)
(propagated-inputs
`(("r-rcpp" ,r-rcpp)
@@ -11849,14 +11900,14 @@ probabilities from a standard bivariate normal CDF.")
(define-public r-lavaan
(package
(name "r-lavaan")
- (version "0.6-3")
+ (version "0.6-4")
(source
(origin
(method url-fetch)
(uri (cran-uri "lavaan" version))
(sha256
(base32
- "0hw856kv11zqn6nd4216rh19i6xbnc1rh044r7jvvxkhzgbqkyxz"))))
+ "1zf0sxpms35rhq2syb7r3sshhc8kjvc3pv97dk9x0gf4xl7pck4g"))))
(build-system r-build-system)
(propagated-inputs
`(("r-mass" ,r-mass)
@@ -12073,14 +12124,14 @@ running IRkernel session.")
(define-public r-irkernel
(package
(name "r-irkernel")
- (version "1.0.1")
+ (version "1.0.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "IRkernel" version))
(sha256
(base32
- "1gij59b068qp7sbn9d0b9ghmnhfks15a9anj7bp26acv0yvdsg3s"))))
+ "040qig675zaxsf81ranmvk293amrswi5098k69wyq0vgqyin6vwp"))))
(properties `((upstream-name . "IRkernel")))
(build-system r-build-system)
(arguments
@@ -12192,14 +12243,14 @@ R, enabling interactive analysis and visualization of genome-scale data.")
(define-public r-rematch2
(package
(name "r-rematch2")
- (version "2.0.1")
+ (version "2.1.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "rematch2" version))
(sha256
(base32
- "16k0i5p7fa3qfxv59ijyn638wpz8n4jrkrnilqmh5g9l8f8bn4h6"))))
+ "00cznm6rk33b53w7zybkz7549bnydc66znpi5mb0xd24pmqp0rvq"))))
(build-system r-build-system)
(propagated-inputs
`(("r-tibble" ,r-tibble)))
@@ -12541,14 +12592,14 @@ classes.")
(define-public r-classint
(package
(name "r-classint")
- (version "0.3-3")
+ (version "0.4-1")
(source
(origin
(method url-fetch)
(uri (cran-uri "classInt" version))
(sha256
(base32
- "0c2z6shlxa928xa20yl956r06lx20mji3mwipdvmj3f4z5g6hgm9"))))
+ "00q1bpgblrldckn1rk166q1b0hgap2sjjyfmfcyh6ydk6y73ziir"))))
(properties `((upstream-name . "classInt")))
(build-system r-build-system)
(propagated-inputs
@@ -12616,14 +12667,14 @@ sampling.")
(define-public r-deldir
(package
(name "r-deldir")
- (version "0.1-21")
+ (version "0.1-23")
(source
(origin
(method url-fetch)
(uri (cran-uri "deldir" version))
(sha256
(base32
- "03392pl6j8rm3n32xrfkyfx866k1vm5sj87pva70yyiwh70vrnmr"))))
+ "0790dwxb2mz1ffz8gd5vwdr0if2q76dzy3vab5rsykf9kz72n4g0"))))
(build-system r-build-system)
(native-inputs `(("gfortran" ,gfortran)))
(home-page "https://cran.r-project.org/web/packages/deldir")
@@ -12640,14 +12691,14 @@ tessellation.")
(define-public r-sf
(package
(name "r-sf")
- (version "0.7-4")
+ (version "0.7-7")
(source
(origin
(method url-fetch)
(uri (cran-uri "sf" version))
(sha256
(base32
- "0vnyr7xyfcl928kbrb1k8l4fkd0cjrfq486g6gxpvy5j0cc2h4i1"))))
+ "192hw52x1qlif8zyai1kff1wiyr3yl5f7jj1rk3k0nr8das0qy6i"))))
(build-system r-build-system)
(inputs
`(("gdal" ,gdal)
@@ -13022,18 +13073,19 @@ inbred lines, F2 intercrosses, and association mapping populations.")
(define-public r-ldheatmap
(package
(name "r-ldheatmap")
- (version "0.99-5")
+ (version "0.99-7")
(source
(origin
(method url-fetch)
(uri (cran-uri "LDheatmap" version))
(sha256
(base32
- "0il3g3n3bzv74lz7dlhyiwc2x2417v6yhx2g47pahxdzqa09kf4s"))))
+ "1r0j8bihi5z1x0sgaf7dwzpsw9i0nc1vylvipvc0cia2ka1lr9dc"))))
(properties `((upstream-name . "LDheatmap")))
(build-system r-build-system)
(propagated-inputs
`(("r-genetics" ,r-genetics)
+ ("r-rcpp" ,r-rcpp)
("r-snpstats" ,r-snpstats)))
(home-page "http://stat.sfu.ca/statgen/research/ldheatmap.html")
(synopsis "Graphical display of pairwise linkage disequilibria between SNPs")
@@ -13112,13 +13164,13 @@ SELECT or UPDATE queries to an end-point.")
(define-public r-bookdown
(package
(name "r-bookdown")
- (version "0.11")
+ (version "0.12")
(source (origin
(method url-fetch)
(uri (cran-uri "bookdown" version))
(sha256
(base32
- "0w4fkv5fqiaqgkx44p0s161imf29zir9742126xkz1pl1j25jn1r"))))
+ "1c2v0rpa1rrpbx8yb66sfvrf4gf57f6a8x7ydjqqbkbwhxdlrsrq"))))
(build-system r-build-system)
(propagated-inputs
`(("r-htmltools" ,r-htmltools)
@@ -13585,14 +13637,14 @@ package.")
(define-public r-ggplotify
(package
(name "r-ggplotify")
- (version "0.0.3")
+ (version "0.0.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "ggplotify" version))
(sha256
(base32
- "14hqlpvnaq5psz1ljcpw9isa06827rg3fm5c1dx159rsjfi56yby"))))
+ "0nv3wdmxnc5ww9m3xlgnb0jp30j45dg33nqc6gg3y36svg8anjcg"))))
(build-system r-build-system)
(propagated-inputs
`(("r-ggplot2" ,r-ggplot2)
@@ -14562,14 +14614,14 @@ engine (Salmon et al., 2011) as provided by the package @code{sitmo}.")
(define-public r-dalex
(package
(name "r-dalex")
- (version "0.4")
+ (version "0.4.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "DALEX" version))
(sha256
(base32
- "1mr8lqq8s4aacmh7xdhmkmv8vsjqjczlqlaw27xnsljgj2kgq87a"))))
+ "04i17ni8g595jj8dxdfwr9vsxmdn2kkam90ab68vlwws3ywqjl6r"))))
(properties `((upstream-name . "DALEX")))
(build-system r-build-system)
(propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
@@ -14588,14 +14640,14 @@ and model output.")
(define-public r-enrichr
(package
(name "r-enrichr")
- (version "1.0")
+ (version "2.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "enrichR" version))
(sha256
(base32
- "0lfdr45sdyqhvgz8q4qdbk12mpv86d6id665kq6aaslgr8jggfmn"))))
+ "056m6hksfss29fj7zvlk7pbh8g3gq84kjh3240isrsnhp9m1h9iz"))))
(properties `((upstream-name . "enrichR")))
(build-system r-build-system)
(propagated-inputs
@@ -14698,18 +14750,17 @@ into R and converted to @code{BibEntry} objects.")
(define-public r-citr
(package
(name "r-citr")
- (version "0.3.0")
+ (version "0.3.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "citr" version))
(sha256
(base32
- "0pik6s6xk5768s3kkppw2192dj455py53gsn6k2b7xgg96ircy0g"))))
+ "0p2sg0fl7cppxxmr20qyqzs2469kglmgpsvykynw4qx501as57rc"))))
(build-system r-build-system)
(propagated-inputs
`(("r-assertthat" ,r-assertthat)
- ("r-bibtex" ,r-bibtex)
("r-curl" ,r-curl)
("r-httr" ,r-httr)
("r-miniui" ,r-miniui)
@@ -14729,14 +14780,14 @@ the current document.")
(define-public r-xgboost
(package
(name "r-xgboost")
- (version "0.82.1")
+ (version "0.90.0.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "xgboost" version))
(sha256
(base32
- "0plhx63wcm4syslzmjfv6bdgaqn96fnav048hrj0vxk4dzgfp8sq"))))
+ "1gy9rzg43mjpfis893vf15drmbigfn0481zrzss9ajnmnk0q8194"))))
(build-system r-build-system)
(propagated-inputs
`(("r-data-table" ,r-data-table)
diff --git a/gnu/packages/emulators.scm b/gnu/packages/emulators.scm
index 8d0162a2d1..257591c8d3 100644
--- a/gnu/packages/emulators.scm
+++ b/gnu/packages/emulators.scm
@@ -119,8 +119,8 @@
;; Building from recent Git because the official 5.0 release no longer builds.
(define-public dolphin-emu
- (let ((commit "2c57e709d0f9e4010a4415de4192de887e37f187")
- (revision "5"))
+ (let ((commit "24718c1a389e4f51db974575cd15c372485b92e2")
+ (revision "6"))
(package
(name "dolphin-emu")
(version (git-version "5.0" revision commit))
@@ -146,7 +146,7 @@
#t))
(sha256
(base32
- "0aszfdfvs7yg4bmrd3qxwsiz7hx3mrj29f4aw86bz7h9j7hkh57f"))))
+ "1d92rhnw307j3m6swk6bycb8fyc7vw2hfgakd5hpsc4qw65vxfq8"))))
(build-system cmake-build-system)
(arguments
'(#:tests? #f
@@ -250,12 +250,6 @@ turbo speed, networked multiplayer, and graphical enhancements.")
(base32
"02i648i50dwicv1vaql15rccv4g8h5blf5g6inv67lrfxpbkvlf0"))))
(build-system gnu-build-system)
- (arguments
- `(#:phases (modify-phases %standard-phases
- (add-after
- 'unpack 'autogen.sh
- (lambda _
- (invoke "sh" "autogen.sh"))))))
(native-inputs
`(("autoconf" ,autoconf)
("automake" ,automake)))
diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index 8005c46129..edb3b49841 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -131,7 +131,12 @@ topology functions.")
(gi-typelib-path (getenv "GI_TYPELIB_PATH"))
(goa-path (string-append
(assoc-ref inputs "gnome-online-accounts")
+ "/lib:"
+ (assoc-ref inputs "gnome-online-accounts:lib")
"/lib"))
+ (geocode-glib-path (string-append
+ (assoc-ref inputs "geocode-glib")
+ "/lib"))
(webkitgtk-path (string-append
(assoc-ref inputs "webkitgtk")
"/lib")))
@@ -141,7 +146,8 @@ topology functions.")
;; There seems to be no way to embed the path of
;; libgoa-1.0.so.0, libwebkit2gtk-4.0.so.37 and
;; libjavascriptcoregtk-4.0.so.18.
- `("LD_LIBRARY_PATH" ":" prefix (,goa-path ,webkitgtk-path)))
+ `("LD_LIBRARY_PATH" ":" prefix
+ (,goa-path ,webkitgtk-path ,geocode-glib-path)))
#t))))))
(native-inputs
`(("gobject-introspection" ,gobject-introspection)
@@ -163,6 +169,7 @@ topology functions.")
("gjs" ,gjs)
("glib" ,glib)
("gnome-online-accounts" ,gnome-online-accounts)
+ ("gnome-online-accounts:lib" ,gnome-online-accounts "lib")
("gsettings-desktop-schemas" ,gsettings-desktop-schemas)
("rest" ,rest)
("webkitgtk" ,webkitgtk)))
diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm
index d4273c6fa1..6928246509 100644
--- a/gnu/packages/image.scm
+++ b/gnu/packages/image.scm
@@ -595,9 +595,6 @@ collection of tools for doing simple manipulations of TIFF images.")
(arguments
'(#:phases
(modify-phases %standard-phases
- (add-after 'unpack 'autogen
- (lambda _
- (invoke "sh" "autobuild")))
(add-after 'unpack 'patch-reg-wrapper
(lambda _
(substitute* "prog/reg_wrapper.sh"
@@ -1240,12 +1237,6 @@ ISO/IEC 15444-1).")
`(("autoconf" ,autoconf)
("automake" ,automake)
("libtool" ,libtool)))
- (arguments
- '(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'autogen
- (lambda _
- (invoke "sh" "autogen.sh"))))))
(synopsis "Scaling, colorspace conversion, and dithering library")
(description "Zimg implements the commonly required image processing basics
of scaling, colorspace conversion, and depth conversion. A simple API enables
diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 9f20d2bace..a5b9f6bfed 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -350,42 +350,42 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
"linux-" version ".tar.xz"))
(sha256 hash)))
-(define-public linux-libre-5.2-version "5.2.6")
+(define-public linux-libre-5.2-version "5.2.7")
(define-public linux-libre-5.2-pristine-source
(let ((version linux-libre-5.2-version)
- (hash (base32 "1whzgdz1wnjzkb78yqz4xs3mad02rv17ksmwaf4ykp4lfgxml45y")))
+ (hash (base32 "1aazhf0v8bv4py0wnqkdmiy80fchnix431l0hda2fkwsdf9njgnv")))
(make-linux-libre-source version
(%upstream-linux-source version hash)
deblob-scripts-5.2)))
-(define-public linux-libre-4.19-version "4.19.64")
+(define-public linux-libre-4.19-version "4.19.65")
(define-public linux-libre-4.19-pristine-source
(let ((version linux-libre-4.19-version)
- (hash (base32 "1gasmcdsrsk81dscslmrsxqsvkfp5xxdx3ay95izggpk7piqnvvs")))
+ (hash (base32 "1pyyhr2airxzk4c6n7140yl723dc7yw7igy5i5i2ih0nd4c3k6g5")))
(make-linux-libre-source version
(%upstream-linux-source version hash)
deblob-scripts-4.19)))
-(define-public linux-libre-4.14-version "4.14.136")
+(define-public linux-libre-4.14-version "4.14.137")
(define-public linux-libre-4.14-pristine-source
(let ((version linux-libre-4.14-version)
- (hash (base32 "0w6z5fhwqgpqnz2js8vj9j5dl6isx8n7rnzrm0vr9r8njaazz396")))
+ (hash (base32 "0a72pab0zxy28i02glnzj6avzcf0a4gxxnadbdd343rh549yky4k")))
(make-linux-libre-source version
(%upstream-linux-source version hash)
deblob-scripts-4.14)))
-(define-public linux-libre-4.9-version "4.9.187")
+(define-public linux-libre-4.9-version "4.9.188")
(define-public linux-libre-4.9-pristine-source
(let ((version linux-libre-4.9-version)
- (hash (base32 "1iyimwl4ysnk6m66m73sg0cnp4vac56d6yy174shfpnj5h2csjq1")))
+ (hash (base32 "08p2cfc9982b804vmkapfasgipf6969g625ih7z3062xn99rhlr7")))
(make-linux-libre-source version
(%upstream-linux-source version hash)
deblob-scripts-4.9)))
-(define-public linux-libre-4.4-version "4.4.187")
+(define-public linux-libre-4.4-version "4.4.188")
(define-public linux-libre-4.4-pristine-source
(let ((version linux-libre-4.4-version)
- (hash (base32 "1dlzb5yzcsicd41myj3q4dq2ql8xcc49brs5f7xjmc5ynvvjjgnc")))
+ (hash (base32 "1llxamm62kgqd7dig98n8m16qas8dd8rrkmwpfcdgyf8rag216ff")))
(make-linux-libre-source version
(%upstream-linux-source version hash)
deblob-scripts-4.4)))
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index dd5ee1e9ee..e48c91a2cf 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -193,7 +193,7 @@ classification.")
(uri (svn-reference
(url "http://svn.code.sf.net/p/ghmm/code/trunk")
(revision svn-revision)))
- (file-name (string-append name "-" version))
+ (file-name (string-append name "-" version "-checkout"))
(sha256
(base32
"0qbq1rqp94l530f043qzp8aw5lj7dng9wq0miffd7spd1ff638wq"))))
@@ -251,10 +251,7 @@ classification.")
(string-append indent
"@unittest.skip(\"Disabled by Guix\")\n"
line)))
- #t))
- (add-after 'disable-broken-tests 'autogen
- (lambda _
- (invoke "bash" "autogen.sh"))))))
+ #t)))))
(inputs
`(("python" ,python-2) ; only Python 2 is supported
("libxml2" ,libxml2)))
diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm
index 40fe7d9450..b81b15d80c 100644
--- a/gnu/packages/mail.scm
+++ b/gnu/packages/mail.scm
@@ -1051,7 +1051,7 @@ useful features.")
(arguments
'(#:phases
(modify-phases %standard-phases
- (add-after 'unpack 'autogen
+ (replace 'bootstrap
(lambda _
(setenv "NOCONFIGURE" "true")
(invoke "sh" "autogen.sh"))))
@@ -1365,12 +1365,7 @@ It supports mbox/Maildir and its own dbox/mdbox formats.")
`(#:tests? #f ;No tests exist.
#:configure-flags (list (string-append "--with-dovecot="
(assoc-ref %build-inputs "dovecot")
- "/lib/dovecot"))
- #:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'autogen
- (lambda _
- (invoke "sh" "autogen.sh"))))))
+ "/lib/dovecot"))))
(home-page "https://0xacab.org/riseuplabs/trees")
(synopsis "NaCL-based Dovecot email storage encryption plugin")
(description
@@ -1421,12 +1416,7 @@ using libsodium sealed boxes.
`(#:tests? #f ;No tests exist.
#:configure-flags (list (string-append "--with-dovecot="
(assoc-ref %build-inputs "dovecot")
- "/lib/dovecot"))
- #:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'autogen
- (lambda _
- (invoke "sh" "autogen.sh"))))))
+ "/lib/dovecot"))))
(home-page "https://github.com/LuckyFellow/dovecot-libsodium-plugin")
(synopsis "Libsodium password hashing schemes plugin for Dovecot")
(description
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index b204b314c6..e3c7d9ce91 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -4333,14 +4333,14 @@ are noisy or are discontinuous at the solution.")
(define-public r-desolve
(package
(name "r-desolve")
- (version "1.21")
+ (version "1.24")
(source
(origin
(method url-fetch)
(uri (cran-uri "deSolve" version))
(sha256
(base32
- "0qqc4mknw1jblzcmph1dg3k1p6w42yal0k1xjh8pqk7yb3a75hs5"))))
+ "0hkvspq0fp8j64l9zayab2l2nazazhwfgfym0jllh0xv5a12r99s"))))
(properties `((upstream-name . "deSolve")))
(build-system r-build-system)
(native-inputs
diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm
index 2a40b2c736..5628a4b93f 100644
--- a/gnu/packages/perl.scm
+++ b/gnu/packages/perl.scm
@@ -4082,7 +4082,7 @@ relic support.")
(base32
"0h3wfnpv5d4d3f9xzmwkchay6251nhzngdv3f6xia56mj4hxabs0"))))
(build-system perl-build-system)
- (inputs
+ (propagated-inputs
`(("perl-clone-choose" ,perl-clone-choose)))
(home-page "https://metacpan.org/release/Hash-Merge")
(synopsis "Merge arbitrarily deep hashes into a single hash")
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 6ed1e40108..f27f2229f7 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -75,6 +75,7 @@
#:use-module (gnu packages time)
#:use-module (gnu packages tls)
#:use-module (gnu packages base)
+ #:use-module (gnu packages version-control)
#:use-module (gnu packages web)
#:use-module (gnu packages xml)
#:use-module (gnu packages xorg)
@@ -396,14 +397,14 @@ available, greatly increasing its breadth and scope.")
(define-public r-boot
(package
(name "r-boot")
- (version "1.3-22")
+ (version "1.3-23")
(source
(origin
(method url-fetch)
(uri (cran-uri "boot" version))
(sha256
(base32
- "1z2dig1mi76b3b9ck6qlkh07l3hs478gaf70db5nv8x7w2qhq7yg"))))
+ "0bx07zbb5nfz2xfgnzbspg7r5vxz4bjdz1ry4d1vk434vlcrxj1h"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/boot")
(synopsis "Bootstrap functions for R")
@@ -501,14 +502,14 @@ code for possible problems.")
(define-public r-foreign
(package
(name "r-foreign")
- (version "0.8-71")
+ (version "0.8-72")
(source
(origin
(method url-fetch)
(uri (cran-uri "foreign" version))
(sha256
(base32
- "1mv04w3ycz0ymsszn8aa87k6k5sb8mg8lhf1b8w4zpfrphpkkliv"))))
+ "124c9229is44p2rv7xyh2q86nsfi7vzyyh5n3c5ihziqrp4ig723"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/foreign")
(synopsis "Read data stored by other statistics software")
@@ -587,14 +588,14 @@ and operations on them using LAPACK and SuiteSparse.")
(define-public r-nlme
(package
(name "r-nlme")
- (version "3.1-140")
+ (version "3.1-141")
(source
(origin
(method url-fetch)
(uri (cran-uri "nlme" version))
(sha256
(base32
- "0k9x5j34fx093a023da9ny3b3101lbwpmfm27mkvfj950l22z88x"))))
+ "0ml00g79bimjcl0sgn6h55l5b4gfmnsnc1vvmivggn0318k4c04i"))))
(build-system r-build-system)
(propagated-inputs
`(("r-lattice" ,r-lattice)))
@@ -803,13 +804,13 @@ effects of different types of color-blindness.")
(define-public r-digest
(package
(name "r-digest")
- (version "0.6.19")
+ (version "0.6.20")
(source
(origin
(method url-fetch)
(uri (cran-uri "digest" version))
(sha256
- (base32 "1x6cbj9qvkk7pxv9xdqibazw3x8psjp6x0m0ildx1jwyb2ymkl98"))))
+ (base32 "1irhk2jaj9cg57cxprgyn1if06x121xwcxh1fzzn3148bl5lnrq5"))))
(build-system r-build-system)
;; Vignettes require r-knitr, which requires r-digest, so we have to
;; disable them and the tests.
@@ -1602,18 +1603,19 @@ R packages that praise their users.")
(define-public r-testthat
(package
(name "r-testthat")
- (version "2.1.1")
+ (version "2.2.1")
(source (origin
(method url-fetch)
(uri (cran-uri "testthat" version))
(sha256
(base32
- "03jgr0hlr77yp0aib4v30yjyjrjsa8dczr02yk21m93vl25vqvkp"))))
+ "0y0bvggm4pzkzp6xn7b8cf3ybqp9ijxkhhyp3z49a9iipc90bvk7"))))
(build-system r-build-system)
(propagated-inputs
`(("r-cli" ,r-cli)
("r-crayon" ,r-crayon)
("r-digest" ,r-digest)
+ ("r-evaluate" ,r-evaluate)
("r-magrittr" ,r-magrittr)
("r-praise" ,r-praise)
("r-r6" ,r-r6)
@@ -1695,13 +1697,13 @@ and printing capabilities than traditional data frames.")
(define-public r-dplyr
(package
(name "r-dplyr")
- (version "0.8.1")
+ (version "0.8.3")
(source (origin
(method url-fetch)
(uri (cran-uri "dplyr" version))
(sha256
(base32
- "1nw12hzk1jcac5879nfmf1yp98jpb3i59qkb8sfpk2cd6zqgfgjz"))))
+ "032c89wa04g9rih9shyvwl3il0bsrv3xk489x6867sk9bb3amd38"))))
(build-system r-build-system)
(propagated-inputs
`(("r-assertthat" ,r-assertthat)
@@ -1978,13 +1980,13 @@ inference for statistical models.")
(define-public r-coda
(package
(name "r-coda")
- (version "0.19-2")
+ (version "0.19-3")
(source (origin
(method url-fetch)
(uri (cran-uri "coda" version))
(sha256
(base32
- "03fs3sdrrym3is92dgpa6ydk3m63gaihwy7bva4k0wm2hxm7x2k7"))))
+ "1mn50bshky968gn4nf6vnkaa768fnvm1xmhkms7szwdw9341zpyk"))))
(build-system r-build-system)
(propagated-inputs
`(("r-lattice" ,r-lattice)))
@@ -2020,14 +2022,14 @@ and environmental data in the framework of Euclidean exploratory methods.")
(define-public r-xml2
(package
(name "r-xml2")
- (version "1.2.0")
+ (version "1.2.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "xml2" version))
(sha256
(base32
- "154lmksfiwkhnlmryas25mjhfg6k4mmnnk7bbb29mnn5x5pr2yha"))))
+ "0186d7r36xw1z9f8ajz35a0dz4ch6hmrjl9536yc7vq78v4vn5an"))))
(build-system r-build-system)
(inputs
`(("libxml2" ,libxml2)
@@ -2135,14 +2137,14 @@ R version.")
(define-public r-checkmate
(package
(name "r-checkmate")
- (version "1.9.3")
+ (version "1.9.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "checkmate" version))
(sha256
(base32
- "15ccwvmw73c2zz1k10k5zdn8px0rrbnvs1b4nzvlb0iwj7cimhp4"))))
+ "08ddpgs4mv5d5y4j054pm8drmxkn7yvhfpbghwxlizjpnxa5g8ps"))))
(build-system r-build-system)
(propagated-inputs
`(("r-backports" ,r-backports)))
@@ -2332,14 +2334,14 @@ collation, and NAMESPACE files.")
(define-public r-openssl
(package
(name "r-openssl")
- (version "1.4")
+ (version "1.4.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "openssl" version))
(sha256
(base32
- "0mh4xwb9wnn5j2n1zzmjldqjqv2nn4wdidiixxciaqrqsi0l9834"))))
+ "1ihz2qi33lhngl19xdanq0pbmfaacy63794mg8ll7z2lab3yryzp"))))
(build-system r-build-system)
(inputs
`(("libressl" ,libressl)))
@@ -2365,13 +2367,13 @@ integers.")
(define-public r-httr
(package
(name "r-httr")
- (version "1.4.0")
+ (version "1.4.1")
(source (origin
(method url-fetch)
(uri (cran-uri "httr" version))
(sha256
(base32
- "0j6vknwyvkjpjsxwch4q02aik4dnm3h4l0wc7dgzc555bm1g2cyn"))))
+ "0mp1il13q6n49n2hv1p2p8x6avjan6dr5az19ql4hb78pc3pwp37"))))
(build-system r-build-system)
(propagated-inputs
`(("r-curl" ,r-curl)
@@ -2391,20 +2393,16 @@ functions make it easy to control additional request components.")
(define-public r-git2r
(package
(name "r-git2r")
- (version "0.25.2")
+ (version "0.26.1")
(source (origin
(method url-fetch)
(uri (cran-uri "git2r" version))
(sha256
(base32
- "15kpvz6ry2r8ii5hzinjwkggc5kgmkbcpsdwzahsf8gha52w80p0"))))
+ "0dbl845sahv2i641ncaf06w06djravwc5wknp9syzx0ad8l0kmhk"))))
(build-system r-build-system)
- ;; This R package contains modified sources of libgit2. This modified
- ;; version of libgit2 is built as the package is built. Hence libgit2 is
- ;; not among the inputs of this package.
(inputs
- `(("libssh2" ,libssh2) ; for SSH transport
- ("openssl" ,openssl)
+ `(("libgit2" ,libgit2)
("zlib" ,zlib)))
(native-inputs
`(("pkg-config" ,pkg-config)))
@@ -2437,13 +2435,13 @@ informative error messages when it's not available.")
(define-public r-devtools
(package
(name "r-devtools")
- (version "2.0.2")
+ (version "2.1.0")
(source (origin
(method url-fetch)
(uri (cran-uri "devtools" version))
(sha256
(base32
- "028pppj39ng7q17k27531s8k00lmw982vz5krn74n9b8f2azm8lr"))))
+ "0393v7nr22gr5g9afgrhq4ab3lwbqy6fd3shnmlhdpqam5357xy1"))))
(build-system r-build-system)
(propagated-inputs
`(("r-callr" ,r-callr)
@@ -2456,9 +2454,11 @@ informative error messages when it's not available.")
("r-pkgbuild" ,r-pkgbuild)
("r-pkgload" ,r-pkgload)
("r-rcmdcheck" ,r-rcmdcheck)
+ ("r-roxygen2" ,r-roxygen2)
("r-remotes" ,r-remotes)
("r-rstudioapi" ,r-rstudioapi)
("r-sessioninfo" ,r-sessioninfo)
+ ("r-testthat" ,r-testthat)
("r-usethis" ,r-usethis)
("r-withr" ,r-withr)))
(home-page "https://github.com/hadley/devtools")
@@ -2489,18 +2489,19 @@ were originally a part of the r-devtools package.")
(define-public r-hms
(package
(name "r-hms")
- (version "0.4.2")
+ (version "0.5.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "hms" version))
(sha256
(base32
- "1g6hslk3z0xga38r71irxq802wskg6nv804mp8y9f7i2wfrj0y55"))))
+ "06snfqdczr0x0nbp7qnvwhlp2pw0wx9c2y3xb4gr1wrvbik74y58"))))
(build-system r-build-system)
(propagated-inputs
`(("r-rlang" ,r-rlang)
- ("r-pkgconfig" ,r-pkgconfig)))
+ ("r-pkgconfig" ,r-pkgconfig)
+ ("r-vctrs" ,r-vctrs)))
(home-page "https://github.com/rstats-db/hms")
(synopsis "Pretty time of day")
(description
@@ -2596,13 +2597,13 @@ well as additional utilities such as panel and axis annotation functions.")
(define-public r-rcpparmadillo
(package
(name "r-rcpparmadillo")
- (version "0.9.500.2.0")
+ (version "0.9.600.4.0")
(source (origin
(method url-fetch)
(uri (cran-uri "RcppArmadillo" version))
(sha256
(base32
- "1lyvpb7n54ijlqns29qiixqr39334knf67cnixvlic58945glrhv"))))
+ "07jg2667xyhmp1fbcdi5nnhmkk81da76s9rlswfq4k2sjsmbfmr0"))))
(properties `((upstream-name . "RcppArmadillo")))
(build-system r-build-system)
;; All needed for vignettes
@@ -2694,14 +2695,14 @@ certain criterion, e.g., it contains a certain regular file.")
(define-public r-rmarkdown
(package
(name "r-rmarkdown")
- (version "1.13")
+ (version "1.14")
(source
(origin
(method url-fetch)
(uri (cran-uri "rmarkdown" version))
(sha256
(base32
- "1vv3b8nlw8ra19492rjg3na42lwh3xr5a2jy2ia81fvvs846pywn"))))
+ "0qfw5rkvwqpgix32g6qy9xrr50awmm146aqbm836xravih2b2dpn"))))
(properties `((upstream-name . "rmarkdown")))
(build-system r-build-system)
(propagated-inputs
@@ -2787,17 +2788,18 @@ that package, other packages are unaffected.")
(define-public r-blob
(package
(name "r-blob")
- (version "1.1.1")
+ (version "1.2.0")
(source (origin
(method url-fetch)
(uri (cran-uri "blob" version))
(sha256
(base32
- "0lsg91hk508dd95ivig2lwg62qafwnarjw68110kx63cfk4zkjxc"))))
+ "08z071jzac4gasgfgab0y5g3ilfmlw08ln813wphxg07hsiczw8s"))))
(build-system r-build-system)
(propagated-inputs
`(("r-prettyunits" ,r-prettyunits)
- ("r-tibble" ,r-tibble)))
+ ("r-rlang" ,r-rlang)
+ ("r-vctrs" ,r-vctrs)))
(home-page "https://github.com/hadley/blob")
(synopsis "Simple S3 Class for representing vectors of binary data")
(description "Raw vectors in R are useful for storing a single binary
@@ -2809,13 +2811,13 @@ a column in data frame.")
(define-public r-rsqlite
(package
(name "r-rsqlite")
- (version "2.1.1")
+ (version "2.1.2")
(source (origin
(method url-fetch)
(uri (cran-uri "RSQLite" version))
(sha256
(base32
- "1giwk4335sc6yhj3rs8h070g1mwy38kyqyqv6vcfxvskykj7vp6z"))))
+ "1inrhap5cs0wry2jbw42fx9wwxb3qdzlpy0ba4f6a29bs8jx9nk6"))))
(properties `((upstream-name . "RSQLite")))
(build-system r-build-system)
(propagated-inputs
@@ -3068,14 +3070,14 @@ standard R subsetting and Kronecker products.")
(define-public r-iterators
(package
(name "r-iterators")
- (version "1.0.10")
+ (version "1.0.12")
(source
(origin
(method url-fetch)
(uri (cran-uri "iterators" version))
(sha256
(base32
- "1s3iykfvccpnzs73z90rx18qvbvgw2dgl4nfcrvm5m1850qb5qd9"))))
+ "0jwzxaa3jm1xzgfv5pn0xqkk7rhm0xwvgn85w7xaw8xx1vb33gwn"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/iterators")
(synopsis "Iterator construct for R")
@@ -3088,14 +3090,14 @@ data.")
(define-public r-foreach
(package
(name "r-foreach")
- (version "1.4.4")
+ (version "1.4.7")
(source
(origin
(method url-fetch)
(uri (cran-uri "foreach" version))
(sha256
(base32
- "0j2yj0rn0d5nbzz9nq5rqqgnxhp9pbd92q4klsarl2xpsn8119y0"))))
+ "0q7iyniw5iri4hl57bhil3r69s5wnaijzn0q0x4h3z42245jqqwm"))))
(build-system r-build-system)
(propagated-inputs
`(("r-codetools" ,r-codetools)
@@ -3116,14 +3118,14 @@ parallel.")
(define-public r-doparallel
(package
(name "r-doparallel")
- (version "1.0.14")
+ (version "1.0.15")
(source
(origin
(method url-fetch)
(uri (cran-uri "doParallel" version))
(sha256
(base32
- "01qjs4iw9f1kgymcypj0m2s4pvgqhxaycpli0fb8lq3dc0vpzfyb"))))
+ "0vnqbha3gig3awbfvsfx3ni5jir398md1n7xmsb8jihnjsk7xbbi"))))
(properties `((upstream-name . "doParallel")))
(build-system r-build-system)
(propagated-inputs
@@ -3139,14 +3141,14 @@ using the parallel package.")
(define-public r-domc
(package
(name "r-domc")
- (version "1.3.5")
+ (version "1.3.6")
(source
(origin
(method url-fetch)
(uri (cran-uri "doMC" version))
(sha256
(base32
- "1vfrykvfvsyq12mypd266867ml1dcwc3rj5k9c3wrn5bddcm88kr"))))
+ "1cn9gxavhvjswip8pwvkpi7q6wpzdllcsdjabga8akf55nggqxr9"))))
(properties `((upstream-name . "doMC")))
(build-system r-build-system)
(propagated-inputs
@@ -3162,13 +3164,13 @@ using the multicore functionality of the parallel package.")
(define-public r-dt
(package
(name "r-dt")
- (version "0.7")
+ (version "0.8")
(source (origin
(method url-fetch)
(uri (cran-uri "DT" version))
(sha256
(base32
- "0b6ywgzk9b35y5f69zwfz3vv7qwqqj3xsmy0xymf7nfcvrqg3qqx"))))
+ "08cfmv3d5awvd9h8648bvidcg2ak5pvl2p6vqwqwy1l82ia506ch"))))
(properties
`((upstream-name . "DT")))
(build-system r-build-system)
@@ -3176,6 +3178,7 @@ using the multicore functionality of the parallel package.")
`(("r-crosstalk" ,r-crosstalk)
("r-htmltools" ,r-htmltools)
("r-htmlwidgets" ,r-htmlwidgets)
+ ("r-jsonlite" ,r-jsonlite)
("r-magrittr" ,r-magrittr)
("r-promises" ,r-promises)))
(home-page "http://rstudio.github.io/DT")
@@ -3314,14 +3317,14 @@ package registries.")
(define-public r-rngtools
(package
(name "r-rngtools")
- (version "1.3.1.1")
+ (version "1.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "rngtools" version))
(sha256
(base32
- "0k1nlcxggflq0043m15dfclnqnzchkpw2ik7jk82h4dqwvysiqcr"))))
+ "1kivj594bn774lbn29ws2rmzy2km99sza0j3jqvhal6hwmk27a9s"))))
(build-system r-build-system)
(propagated-inputs
`(("r-digest" ,r-digest)
@@ -4565,19 +4568,19 @@ Farebrother's algorithm or Liu et al.'s algorithm.")
(define-public r-cowplot
(package
(name "r-cowplot")
- (version "0.9.4")
+ (version "1.0.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "cowplot" version))
(sha256
(base32
- "0yvalwalvyddyqk0q66y8361nxlh2cvp3ssazax9g5q89lghjmzv"))))
+ "19cqdhgfyr1wj0fz0c5ly8f0aiy9sfgzq6lzb78hkx0hdp2agybh"))))
(build-system r-build-system)
(propagated-inputs
`(("r-ggplot2" ,r-ggplot2)
("r-gtable" ,r-gtable)
- ("r-plyr" ,r-plyr)
+ ("r-rlang" ,r-rlang)
("r-scales" ,r-scales)))
(home-page "https://github.com/wilkelab/cowplot")
(synopsis "Streamlined plot theme and plot annotations for ggplot2")
@@ -4639,14 +4642,14 @@ regression.")
(define-public r-fastica
(package
(name "r-fastica")
- (version "1.2-1")
+ (version "1.2-2")
(source
(origin
(method url-fetch)
(uri (cran-uri "fastICA" version))
(sha256
(base32
- "108z2ymby5y4h8l4l2krqwm28rya93gq09yylgilnm3afvfrfabg"))))
+ "1zpijqcipm0aa3rxj0mys06lskqy4dbppjpxr1aby0j16y9ka8ij"))))
(properties `((upstream-name . "fastICA")))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/fastICA")
@@ -4748,14 +4751,14 @@ models, generalized linear models and model-based clustering.")
(define-public r-mclust
(package
(name "r-mclust")
- (version "5.4.4")
+ (version "5.4.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "mclust" version))
(sha256
(base32
- "039ymr57bq5327gypizw0v2qb81j6bkqhjdh8yj23qa5sh51phyc"))))
+ "0whandnda1fnjn5k3hgxdbp3b0xr7nlzy1j37saqb536h8q9dwkm"))))
(build-system r-build-system)
(native-inputs
`(("gfortran" ,gfortran)))
@@ -4918,14 +4921,14 @@ generally.")
(define-public r-robust
(package
(name "r-robust")
- (version "0.4-18")
+ (version "0.4-18.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "robust" version))
(sha256
(base32
- "1b7qh1aff500nd6dh4y2ipmjgdiq8991shflb63pc39vpc0ny6g4"))))
+ "0xs098pfw5zdcdk3rsxkylfl6d2pyp566s5v92bzhgl7h8c90cfy"))))
(build-system r-build-system)
(propagated-inputs
`(("r-fit-models" ,r-fit-models)
@@ -5024,14 +5027,14 @@ VGLMs can be loosely thought of as multivariate generalised linear models.")
(define-public r-pbapply
(package
(name "r-pbapply")
- (version "1.4-0")
+ (version "1.4-1")
(source
(origin
(method url-fetch)
(uri (cran-uri "pbapply" version))
(sha256
(base32
- "0bn7a9ni36xy5acnrl9ky3gd1k8jr5kxgazzh3pzd1q6bri1nx7k"))))
+ "1bbws9n90cqnnp5k58hp852jwmm6513jnhn4vzhl9f8x314k6qxk"))))
(build-system r-build-system)
(home-page "https://github.com/psolymos/pbapply")
(synopsis "Adding progress bar to apply functions")
@@ -5137,14 +5140,14 @@ using modular prediction and response module classes.")
(define-public r-quantreg
(package
(name "r-quantreg")
- (version "5.41")
+ (version "5.42.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "quantreg" version))
(sha256
(base32
- "110ax3ngn6i94h7iw7ha67kfsmj94hycp7lk62nmyvkp34vpfykh"))))
+ "1aycnghci329yqw63kybv7sfjjx5whq3xs7xzic4wsaj7j4b1hjc"))))
(build-system r-build-system)
(native-inputs
`(("gfortran" ,gfortran)))
diff --git a/gnu/packages/terminals.scm b/gnu/packages/terminals.scm
index df8d1e4b79..9077d295db 100644
--- a/gnu/packages/terminals.scm
+++ b/gnu/packages/terminals.scm
@@ -57,6 +57,7 @@
#:use-module (gnu packages golang)
#:use-module (gnu packages gtk)
#:use-module (gnu packages image)
+ #:use-module (gnu packages libcanberra)
#:use-module (gnu packages libevent)
#:use-module (gnu packages linux)
#:use-module (gnu packages ncurses)
@@ -954,7 +955,7 @@ tmux.")
(define-public kitty
(package
(name "kitty")
- (version "0.14.2")
+ (version "0.14.3")
(home-page "https://sw.kovidgoyal.net/kitty/")
(source
(origin
@@ -965,7 +966,7 @@ tmux.")
(file-name (git-file-name name version))
(sha256
(base32
- "15iv3k7iryf10n8n67d37x24pzcarq97a3dr42lbld00k1lx19az"))
+ "0wi6b6b1nyp16rcpcghk6by62wy6qsamv1xdymyn0zbqgd8h9n6b"))
(modules '((guix build utils)))
(snippet
'(begin
@@ -984,6 +985,7 @@ tmux.")
`(("python" ,python)
("harfbuzz" ,harfbuzz)
("zlib" ,zlib)
+ ("libcanberra" ,libcanberra)
("libpng" ,libpng)
("freetype" ,freetype)
("fontconfig" ,fontconfig)
diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm
index 04715a5ce1..eda5b8fc39 100644
--- a/gnu/packages/video.scm
+++ b/gnu/packages/video.scm
@@ -792,17 +792,18 @@ operate properly.")
(define-public ffmpeg
(package
(name "ffmpeg")
- (version "4.1.4")
+ (version "4.2")
(source (origin
(method url-fetch)
(uri (string-append "https://ffmpeg.org/releases/ffmpeg-"
version ".tar.xz"))
(sha256
(base32
- "1qd7a10gs12ifcp31gramcgqjl77swskjfp7cijibgyg5yl4kw7i"))))
+ "1mgcxm7sqkajx35px05szsmn9mawwm03cfpmk3br7bcp3a1i0gq2"))))
(build-system gnu-build-system)
(inputs
- `(("fontconfig" ,fontconfig)
+ `(("dav1d" ,dav1d)
+ ("fontconfig" ,fontconfig)
("freetype" ,freetype)
("frei0r-plugins" ,frei0r-plugins)
("gnutls" ,gnutls)
@@ -901,6 +902,7 @@ operate properly.")
"--enable-libbluray"
"--enable-libcaca"
"--enable-libcdio"
+ "--enable-libdav1d"
"--enable-libfreetype"
"--enable-libmp3lame"
"--enable-libopus"
@@ -983,9 +985,10 @@ audio/video codec library.")
(arguments
(substitute-keyword-arguments (package-arguments ffmpeg)
((#:configure-flags flags)
- `(delete "--enable-libaom" ,flags))))
- (inputs (alist-delete "libaom"
- (package-inputs ffmpeg)))))
+ `(delete "--enable-libdav1d" (delete "--enable-libaom"
+ ,flags)))))
+ (inputs (alist-delete "dav1d" (alist-delete "libaom"
+ (package-inputs ffmpeg))))))
(define-public ffmpeg-for-stepmania
(hidden-package
@@ -2063,12 +2066,6 @@ capabilities.")
("libass" ,libass)
("tesseract-ocr" ,tesseract-ocr)
("zimg" ,zimg)))
- (arguments
- '(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'autogen
- (lambda _
- (invoke "sh" "autogen.sh"))))))
(home-page "http://www.vapoursynth.com/")
(synopsis "Video processing framework")
(description "VapourSynth is a C++ library and Python module for video
@@ -2511,12 +2508,6 @@ Other features include a live preview and live streaming.")
(base32
"18yfkr70lr1x1hc8snn2ldnbzdcc7b64xmkqrfk8w59gpg7sl1xn"))))
(build-system gnu-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'autogen.sh
- (lambda _
- (invoke "sh" "autogen.sh"))))))
(native-inputs
`(("autoconf" ,autoconf)
("automake" ,automake)))
@@ -2896,10 +2887,7 @@ practically any type of media.")
(add-after 'unpack 'change-to-build-dir
(lambda _
(chdir "Project/GNU/Library")
- #t))
- (add-after 'change-to-build-dir 'autogen
- (lambda _
- (invoke "sh" "autogen.sh"))))))
+ #t)))))
(home-page "https://mediaarea.net/en/MediaInfo")
(synopsis "Library for retrieving media metadata")
(description "MediaInfo is a library used for retrieving technical
diff --git a/gnu/packages/vpn.scm b/gnu/packages/vpn.scm
index c7046b7f50..d1a7248536 100644
--- a/gnu/packages/vpn.scm
+++ b/gnu/packages/vpn.scm
@@ -3,7 +3,7 @@
;;; Copyright © 2013, 2016, 2018, 2019 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2014 Eric Bavier <bavier@member.fsf.org>
;;; Copyright © 2015 Jeff Mickey <j@codemac.net>
-;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2017, 2019 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2016, 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2017 Julien Lepiller <julien@lepiller.eu>
;;; Copyright © 2018 Pierre Langlois <pierre.langlois@gmx.com>
@@ -227,11 +227,6 @@ the entire VPN in a network namespace accessible only through SSH.")
("automake" ,automake)))
(inputs
`(("libevent" ,libevent)))
- (arguments
- '(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'autogen
- (lambda _ (invoke "sh" "autogen.sh"))))))
(home-page "https://github.com/cernekee/ocproxy")
(synopsis "OpenConnect proxy")
(description
@@ -252,11 +247,12 @@ the user specifically asks to proxy, so the @dfn{VPN} interface no longer
(sha256 (base32
"1wlypi68kqqg2mdck8wvf6aanhrmf9i7z6lngyxvcrp23jdzz34h"))))
(build-system gnu-build-system)
- (inputs
+ (propagated-inputs
`(("libxml2" ,libxml2)
("gnutls" ,gnutls)
- ("vpnc-scripts" ,vpnc-scripts)
("zlib" ,zlib)))
+ (inputs
+ `(("vpnc-scripts" ,vpnc-scripts)))
(native-inputs
`(("gettext" ,gettext-minimal)
("pkg-config" ,pkg-config)))
diff --git a/gnu/packages/wm.scm b/gnu/packages/wm.scm
index c56cf406ee..160c267882 100644
--- a/gnu/packages/wm.scm
+++ b/gnu/packages/wm.scm
@@ -290,8 +290,6 @@ Despite the name it should work with any X11 window manager.")
(arguments
`(#:make-flags (list "CC=gcc" (string-append "PREFIX=" %output))
#:phases (modify-phases %standard-phases
- (add-after 'unpack 'autogen
- (lambda _ (invoke "sh" "autogen.sh")))
(add-after 'install 'install-doc
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
diff --git a/gnu/tests/reconfigure.scm b/gnu/tests/reconfigure.scm
index 3a2f0a2e53..fb11e6164e 100644
--- a/gnu/tests/reconfigure.scm
+++ b/gnu/tests/reconfigure.scm
@@ -19,8 +19,10 @@
(define-module (gnu tests reconfigure)
#:use-module (gnu bootloader)
#:use-module (gnu services shepherd)
- #:use-module (gnu system vm)
#:use-module (gnu system)
+ #:use-module (gnu system accounts)
+ #:use-module (gnu system shadow)
+ #:use-module (gnu system vm)
#:use-module (gnu tests)
#:use-module (guix derivations)
#:use-module (guix gexp)
@@ -43,7 +45,13 @@
generation of the system profile."
(define os
(marionette-operating-system
- (simple-operating-system)
+ (operating-system
+ (inherit (simple-operating-system))
+ (users (cons (user-account
+ (name "jakob")
+ (group "users")
+ (home-directory "/home/jakob"))
+ %base-user-accounts)))
#:imported-modules '((gnu services herd)
(guix combinators))))
@@ -84,7 +92,25 @@ generation of the system profile."
(test-equal "script created new generation"
(length (system-generations marionette))
- (1+ (length generations-prior))))
+ (1+ (length generations-prior)))
+
+ (test-assert "script activated the new generation"
+ (and (eqv? 'symlink
+ (marionette-eval
+ '(stat:type (lstat "/run/current-system"))
+ marionette))
+ (string= #$os
+ (marionette-eval
+ '(readlink "/run/current-system")
+ marionette))))
+
+ (test-assert "script activated user accounts"
+ (marionette-eval
+ '(string-contains (call-with-input-file "/etc/passwd"
+ (lambda (port)
+ (get-string-all port)))
+ "jakob")
+ marionette)))
(test-end)
(exit (= (test-runner-fail-count (test-runner-current)) 0)))))
diff --git a/guix/scripts/deploy.scm b/guix/scripts/deploy.scm
index 52bba3f3bf..ebc99e52cc 100644
--- a/guix/scripts/deploy.scm
+++ b/guix/scripts/deploy.scm
@@ -19,6 +19,7 @@
(define-module (guix scripts deploy)
#:use-module (gnu machine)
+ #:use-module (guix discovery)
#:use-module (guix scripts)
#:use-module (guix scripts build)
#:use-module (guix store)
@@ -74,7 +75,10 @@ Perform the deployment specified by FILE.\n"))
(define (load-source-file file)
"Load FILE as a user module."
- (let ((module (make-user-module '((gnu) (gnu machine) (gnu machine ssh)))))
+ (let* ((guix-path (dirname (search-path %load-path "guix.scm")))
+ (environment-modules (scheme-modules* guix-path "gnu/machine"))
+ (module (make-user-module (append '((gnu) (gnu machine))
+ environment-modules))))
(load* file module)))
(define (guix-deploy . args)
diff --git a/guix/scripts/system/reconfigure.scm b/guix/scripts/system/reconfigure.scm
index dee0c24bd2..579b7fffbe 100644
--- a/guix/scripts/system/reconfigure.scm
+++ b/guix/scripts/system/reconfigure.scm
@@ -195,21 +195,31 @@ BOOTLOADER-PACKAGE."
(srfi srfi-34)
(srfi srfi-35))
(let* ((gc-root (string-append #$target %gc-roots-directory "/bootcfg"))
- (temp-gc-root (string-append gc-root ".new")))
- (switch-symlinks temp-gc-root gc-root)
- (install-boot-config #$bootcfg #$bootcfg-file #$target)
+ (new-gc-root (string-append gc-root ".new")))
+ ;; #$bootcfg has dependencies.
+ ;; The bootloader magically loads the configuration from
+ ;; (string-append #$target #$bootcfg-file) (for example
+ ;; "/boot/grub/grub.cfg").
+ ;; If we didn't do something special, the garbage collector
+ ;; would remove the dependencies of #$bootcfg.
+ ;; Register #$bootcfg as a GC root.
;; Preserve the previous activation's garbage collector root
;; until the bootloader installer has run, so that a failure in
;; the bootloader's installer script doesn't leave the user with
;; a broken installation.
+ (switch-symlinks new-gc-root #$bootcfg)
+ (install-boot-config #$bootcfg #$bootcfg-file #$target)
(when #$installer
(catch #t
(lambda ()
(#$installer #$bootloader-package #$device #$target))
(lambda args
- (delete-file temp-gc-root)
+ (delete-file new-gc-root)
(apply throw args))))
- (rename-file temp-gc-root gc-root)))))))
+ ;; We are sure that the installation of the bootloader
+ ;; succeeded, so we can replace the old GC root by the new
+ ;; GC root now.
+ (rename-file new-gc-root gc-root)))))))
(define* (install-bootloader eval configuration bootcfg
#:key
generated by cgit v1.2.3 (git 2.44.0) at 2024-07-04 13:19:44 +0000