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authorEfraim Flashner <efraim@flashner.co.il>2021-11-08 09:06:14 +0200
committerEfraim Flashner <efraim@flashner.co.il>2021-11-08 09:06:14 +0200
commit1c94392a13cbdf87e03a644633eb775bf45694a1 (patch)
tree74f11038dfc5f9d9db06660b1087253b28c5434f /gnu/packages
parentdd87bbb2b78b279248aaff15c0706fcd6d8cd7bb (diff)
parent9d25ee30b188f9202cc14f7cd25ba8a1c3ec1a72 (diff)
Merge remote-tracking branch 'origin/master' into core-updates-frozen
Diffstat (limited to 'gnu/packages')
-rw-r--r--gnu/packages/admin.scm5
-rw-r--r--gnu/packages/audio.scm32
-rw-r--r--gnu/packages/benchmark.scm61
-rw-r--r--gnu/packages/bioconductor.scm1552
-rw-r--r--gnu/packages/bioinformatics.scm16
-rw-r--r--gnu/packages/cdrom.scm22
-rw-r--r--gnu/packages/cran.scm511
-rw-r--r--gnu/packages/crates-io.scm2132
-rw-r--r--gnu/packages/cups.scm12
-rw-r--r--gnu/packages/databases.scm22
-rw-r--r--gnu/packages/diffoscope.scm4
-rw-r--r--gnu/packages/disk.scm5
-rw-r--r--gnu/packages/dns.scm11
-rw-r--r--gnu/packages/emacs-xyz.scm248
-rw-r--r--gnu/packages/file-systems.scm6
-rw-r--r--gnu/packages/games.scm202
-rw-r--r--gnu/packages/geo.scm8
-rw-r--r--gnu/packages/gnome.scm16
-rw-r--r--gnu/packages/graphics.scm26
-rw-r--r--gnu/packages/haskell-apps.scm4
-rw-r--r--gnu/packages/haskell-xyz.scm3
-rw-r--r--gnu/packages/linux.scm28
-rw-r--r--gnu/packages/mail.scm6
-rw-r--r--gnu/packages/markup.scm53
-rw-r--r--gnu/packages/messaging.scm119
-rw-r--r--gnu/packages/music.scm11
-rw-r--r--gnu/packages/ocaml.scm4
-rw-r--r--gnu/packages/patches/i3status-rust-enable-unstable-features.patch20
-rw-r--r--gnu/packages/patches/libblockdev-glib-compat.patch61
-rw-r--r--gnu/packages/protobuf.scm5
-rw-r--r--gnu/packages/python-web.scm77
-rw-r--r--gnu/packages/python-xyz.scm43
-rw-r--r--gnu/packages/rust-apps.scm77
-rw-r--r--gnu/packages/statistics.scm98
-rw-r--r--gnu/packages/vim.scm29
-rw-r--r--gnu/packages/web.scm14
-rw-r--r--gnu/packages/webkit.scm16
-rw-r--r--gnu/packages/zig.scm2
38 files changed, 4004 insertions, 1557 deletions
diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm
index 3062ddc874..f9eeffaa0b 100644
--- a/gnu/packages/admin.scm
+++ b/gnu/packages/admin.scm
@@ -2522,14 +2522,13 @@ of supported upstream metrics systems simultaneously.")
(define-public ansible-core
(package
(name "ansible-core")
- (version "2.11.4")
+ (version "2.11.6")
(source
(origin
(method url-fetch)
(uri (pypi-uri "ansible-core" version))
(sha256
- (base32
- "0jgahcv2pyc5ky0wir55a1h9q9d6rgqj60rqmvlpbj76vz1agsi2"))))
+ (base32 "0fih7nxszni8imi5sywsifd976v77ydhip43pzg7dd65qy1h5mck"))))
(build-system python-build-system)
(arguments
`(#:modules ((guix build python-build-system)
diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index f1540659c2..f4cfe18a87 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -15,7 +15,7 @@
;;; Copyright © 2018 Clément Lassieur <clement@lassieur.org>
;;; Copyright © 2018 Brett Gilio <brettg@gnu.org>
;;; Copyright © 2018, 2019 Marius Bakke <mbakke@fastmail.com>
-;;; Copyright © 2018 Thorsten Wilms <t_w_@freenet.de>
+;;; Copyright © 2018, 2021 Thorsten Wilms <t_w_@freenet.de>
;;; Copyright © 2018 Eric Bavier <bavier@member.fsf.org>
;;; Copyright © 2018 Brendan Tildesley <mail@brendan.scot>
;;; Copyright © 2019, 2021 Pierre Langlois <pierre.langlois@gmx.com>
@@ -616,7 +616,7 @@ streams from live audio.")
(define-public ardour
(package
(name "ardour")
- (version "6.8")
+ (version "6.9")
(source (origin
(method git-fetch)
(uri (git-reference
@@ -634,7 +634,7 @@ namespace ARDOUR { const char* revision = \"" version "\" ; const char* date = \
#t)))
(sha256
(base32
- "16x7bkzbrk0rgywq5vrkhf2z3jj08jw1bvaq9vwlf2b4h4sd7i4s"))
+ "0vlcbd70y0an881zv87kc3akmaiz4w7whsy3yaiiqqjww35jg1mm"))
(file-name (string-append name "-" version))))
(build-system waf-build-system)
(arguments
@@ -2207,14 +2207,14 @@ synchronous execution of all clients, and low latency operation.")
(define-public jalv
(package
(name "jalv")
- (version "1.6.4")
+ (version "1.6.6")
(source (origin
(method url-fetch)
(uri (string-append "https://download.drobilla.net/jalv-"
version ".tar.bz2"))
(sha256
(base32
- "1wwfn7yzbs37s2rdlfjgks63svd5g14yyzd2gdl7h0z12qncwsy2"))))
+ "05lycfq0f06zjp5xqvzjz9hx9kmqx72yng1lghh76hv63dw43lcj"))))
(build-system waf-build-system)
(arguments
`(#:tests? #f ; no check target
@@ -2612,14 +2612,14 @@ frequencies. This data is then formatted to MIDI and written to disk.")
(define-public lilv
(package
(name "lilv")
- (version "0.24.10")
+ (version "0.24.12")
(source (origin
(method url-fetch)
(uri (string-append "https://download.drobilla.net/lilv-"
version ".tar.bz2"))
(sha256
(base32
- "1565zy0yz46cf2f25pi46msdnzkj6bbhml9gfigdpjnsdlyskfyi"))))
+ "0qchfsyrsrp2pdpd59025kllycr04ddpzd03ha1iz70ci687g8r6"))))
(build-system waf-build-system)
(arguments
`(#:tests? #f ; no check target
@@ -2629,15 +2629,13 @@ frequencies. This data is then formatted to MIDI and written to disk.")
(lambda* (#:key outputs #:allow-other-keys)
(setenv "LDFLAGS"
(string-append "-Wl,-rpath="
- (assoc-ref outputs "out") "/lib"))
- #t))
+ (assoc-ref outputs "out") "/lib"))))
(add-after 'unpack 'full-store-path-to-shared-library
(lambda* (#:key outputs #:allow-other-keys)
(with-directory-excursion "bindings/python"
(substitute* "lilv.py"
(("liblilv-0.so") (string-append (assoc-ref outputs "out")
- "/lib/liblilv-0.so"))))
- #t)))))
+ "/lib/liblilv-0.so")))))))))
;; Required by lilv-0.pc.
(propagated-inputs
`(("lv2" ,lv2)
@@ -2658,14 +2656,14 @@ significantly faster and have minimal dependencies.")
(define-public lv2
(package
(name "lv2")
- (version "1.18.0")
+ (version "1.18.2")
(source (origin
(method url-fetch)
(uri (string-append "https://lv2plug.in/spec/lv2-"
version ".tar.bz2"))
(sha256
(base32
- "0gs7401xz23q9vajqr31aa2db8dvssgyh5zrvr4ipa6wig7yb8wh"))))
+ "0pp0n9x1rg8d4fw853z9cvfifjdi4bl85yjxxddqa1acfjy1z2af"))))
(build-system waf-build-system)
(arguments
`(#:tests? #f ; no check target
@@ -3316,7 +3314,7 @@ Suil currently supports every combination of Gtk, Qt, and X11.")
(define-public libebur128
(package
(name "libebur128")
- (version "1.2.4")
+ (version "1.2.6")
(source
(origin
(method git-fetch)
@@ -3325,7 +3323,7 @@ Suil currently supports every combination of Gtk, Qt, and X11.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "0n81rnm8dm1zmibkr2v3q79rsd609y0dbbsrbay18njcjva88p0g"))))
+ (base32 "0xkpz5rzz1j1srhprbh89669gw8z5f1njpvcnxqgf7qax69vd8sh"))))
(build-system cmake-build-system)
(arguments
`(;; Tests require proprietary .wav files. See
@@ -4921,7 +4919,7 @@ workstations as well as consumer software such as music players.")
(define-public redkite
(package
(name "redkite")
- (version "1.3.0") ;marked unmaintained as of Oct. 2021
+ (version "1.3.1") ;marked unmaintained as of Oct. 2021
(source
(origin
(method git-fetch)
@@ -4930,7 +4928,7 @@ workstations as well as consumer software such as music players.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "16j9zp5i7svq3g38rfb6h257qfgnd2brrxi7cjd2pdax9xxwj40y"))))
+ (base32 "1zb2k2a4m7z2ravqrjn8fq8lic20wbr2m8kja3p3113jsk7j9zvd"))))
(build-system cmake-build-system)
(arguments
`(#:tests? #f)) ;no tests included
diff --git a/gnu/packages/benchmark.scm b/gnu/packages/benchmark.scm
index dda0123d42..9741814c82 100644
--- a/gnu/packages/benchmark.scm
+++ b/gnu/packages/benchmark.scm
@@ -1,5 +1,5 @@
;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2016, 2017 Marius Bakke <mbakke@fastmail.com>
+;;; Copyright © 2016, 2017, 2021 Marius Bakke <marius@gnu.org>
;;; Copyright © 2017 Dave Love <fx@gnu.org>
;;; Copyright © 2018–2021 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
@@ -47,7 +47,6 @@
#:use-module (gnu packages python-science)
#:use-module (gnu packages python-web)
#:use-module (gnu packages python-xyz)
- #:use-module (gnu packages storage)
#:use-module (ice-9 match))
(define-public fio
@@ -63,55 +62,41 @@
"0ba9cnjrnm3nwcfbhh5x2sycr54j3yn1rqn76kjdyz40f3pdg3qm"))))
(build-system gnu-build-system)
(arguments
- '(#:test-target "test"
+ `(#:modules (,@%gnu-build-system-modules
+ (ice-9 textual-ports))
+ #:test-target "test"
+ #:configure-flags '("--disable-native") ;don't generate code for the build CPU
#:phases
(modify-phases %standard-phases
- (add-after
- 'unpack 'patch-paths
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (let ((out (assoc-ref outputs "out"))
- (gnuplot (search-input-file inputs "/bin/gnuplot")))
- (substitute* "tools/plot/fio2gnuplot"
- (("/usr/share/fio") (string-append out "/share/fio"))
- ;; FIXME (upstream): The 'gnuplot' executable is used inline
- ;; in various os.system() calls mixed with *.gnuplot filenames.
- (("; do gnuplot") (string-append "; do " gnuplot))
- (("gnuplot mymath") (string-append gnuplot " mymath"))
- (("gnuplot mygraph") (string-append gnuplot " mygraph"))))))
(replace 'configure
- (lambda* (#:key outputs #:allow-other-keys)
+ (lambda* (#:key (configure-flags ''()) outputs #:allow-other-keys)
;; The configure script doesn't understand some of the
- ;; GNU options, so we can't use #:configure-flags.
+ ;; GNU options, so we can't use the stock phase.
(let ((out (assoc-ref outputs "out")))
- (invoke "./configure"
- (string-append "--prefix=" out)))))
+ (apply invoke "./configure"
+ (string-append "--prefix=" out)
+ configure-flags))))
;; The main `fio` executable is fairly small and self contained.
- ;; Moving the auxiliary python and gnuplot scripts to a separate
- ;; output saves almost 400 MiB on the closure.
+ ;; Moving the auxiliary scripts to a separate output saves ~100 MiB
+ ;; on the closure.
(add-after 'install 'move-outputs
(lambda* (#:key outputs #:allow-other-keys)
(let ((oldbin (string-append (assoc-ref outputs "out") "/bin"))
- (newbin (string-append (assoc-ref outputs "utils") "/bin")))
+ (newbin (string-append (assoc-ref outputs "utils") "/bin"))
+ (script? (lambda* (file #:rest _)
+ (call-with-input-file file
+ (lambda (port)
+ (char=? #\# (peek-char port)))))))
(mkdir-p newbin)
(for-each (lambda (file)
- (let ((src (string-append oldbin "/" file))
- (dst (string-append newbin "/" file)))
- (link src dst)
- (delete-file src)))
- '("fio2gnuplot" "fiologparser_hist.py"
- "fiologparser.py"))
- ;; Make sure numpy et.al is found.
- (wrap-program (string-append newbin "/fiologparser_hist.py")
- `("GUIX_PYTHONPATH" ":" prefix (,(getenv "GUIX_PYTHONPATH"))))))))))
+ (link file (string-append newbin "/" (basename file)))
+ (delete-file file))
+ (find-files oldbin script?))))))))
(outputs '("out" "utils"))
(inputs
- `(("ceph" ,ceph "lib")
- ("libaio" ,libaio)
- ("gnuplot" ,gnuplot)
- ("zlib" ,zlib)
- ("python-numpy" ,python2-numpy)
- ("python-pandas" ,python2-pandas)
- ("python" ,python-2)))
+ `(("libaio" ,libaio)
+ ("python" ,python)
+ ("zlib" ,zlib)))
(home-page "https://github.com/axboe/fio")
(synopsis "Flexible I/O tester")
(description
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 90a0e1f288..47bfa11e68 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1055,13 +1055,13 @@ All datasets are restricted to protein coding genes.")
(define-public r-aneufinder
(package
(name "r-aneufinder")
- (version "1.20.0")
+ (version "1.22.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "AneuFinder" version))
(sha256
(base32
- "0m6wphlriq7y21ih1p2kzml5jzcic79jc52kkk59dkjj8j88yllk"))))
+ "0xn8952fkchhx7m8dam6gjy86j551xp1cs67510s1qrmfgzpkjp0"))))
(build-system r-build-system)
(native-inputs
`(("r-knitr" ,r-knitr)))
@@ -1401,14 +1401,14 @@ across the entire multi-'omics experiment.")
(define-public r-biocversion
(package
(name "r-biocversion")
- (version "3.13.1")
+ (version "3.14.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BiocVersion" version))
(sha256
(base32
- "0rsw8g4g1pcjw1zbx8x17yd3drhxqk4sx3cy3ddzy5731hl6mbfi"))))
+ "0qwzkh2alw7xhjprh719la0lg1q38pmjbipy3s2fy79m4xy8y8ik"))))
(properties `((upstream-name . "BiocVersion")))
(build-system r-build-system)
(home-page "https://bioconductor.org/packages/BiocVersion/")
@@ -1421,13 +1421,13 @@ of Bioconductor.")
(define-public r-biocgenerics
(package
(name "r-biocgenerics")
- (version "0.38.0")
+ (version "0.40.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BiocGenerics" version))
(sha256
(base32
- "1kv7lzmyki3hi771v01nml1v1hzz8pyhqqv0xcdzqy354mlgx4m6"))))
+ "0nr5x4r8f2krnfrxm7wrzgzr7nbljypi985cbwx5hxhn95zmfifh"))))
(properties
`((upstream-name . "BiocGenerics")))
(build-system r-build-system)
@@ -1441,13 +1441,13 @@ packages.")
(define-public r-coverageview
(package
(name "r-coverageview")
- (version "1.30.0")
+ (version "1.32.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "CoverageView" version))
(sha256
(base32
- "1xhirbjdw09cqm4xvysxqicvqjbahavwvs7shg4cb05gwyd2ha8g"))))
+ "0sb1h5qsk41c9xisq73agqh502wv6p2j1k45s32a4bkdynf696as"))))
(build-system r-build-system)
(propagated-inputs
`(("r-s4vectors" ,r-s4vectors)
@@ -1468,13 +1468,13 @@ how the coverage distributed across the genome.")
(define-public r-cummerbund
(package
(name "r-cummerbund")
- (version "2.34.0")
+ (version "2.36.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "cummeRbund" version))
(sha256
(base32
- "1avvmvrmldbscc7xd6a6k22xjykbzafvqf87wh5z9rx3qlzswsjx"))))
+ "0130hrlz2jabbshis1g11ndda8b8vlirzi7a004li3cgdghscxql"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
@@ -1498,13 +1498,13 @@ used visualizations.")
(define-public r-decipher
(package
(name "r-decipher")
- (version "2.20.0")
+ (version "2.22.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "DECIPHER" version))
(sha256
(base32
- "0mr7glkx2d37l9nszs52m0kycpm14vxl5gdp3z7i5j7yig1sw2nk"))))
+ "0a9k3f70jmd17kxf1zjmdzrfjs0dmwfad2zgz6wihxh5s1shc8qm"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biostrings" ,r-biostrings)
@@ -1522,13 +1522,13 @@ biological sequences.")
(define-public r-deepsnv
(package
(name "r-deepsnv")
- (version "1.38.0")
+ (version "1.40.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "deepSNV" version))
(sha256
(base32
- "0zz56hf417m7bgg2g2wpbaik30pi6h2nam1n5bviqgdn4mv8n0bs"))))
+ "1wi6j6yb6i9fs9yszfywqz3w50mhl85dkfmr4w3phwvkf0xkn81w"))))
(properties `((upstream-name . "deepSNV")))
(build-system r-build-system)
(propagated-inputs
@@ -1558,13 +1558,13 @@ bases such as COSMIC.")
(define-public r-delayedarray
(package
(name "r-delayedarray")
- (version "0.18.0")
+ (version "0.20.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "DelayedArray" version))
(sha256
(base32
- "0w632262dqzcnvq9s6jvc7naz93dayx51fsv05s0zb6cjwygbqjr"))))
+ "1cm6zh01mvhiq7zrik7q3dmgxinyjz1nyg6rfj93kpkvcb5d4wpj"))))
(properties
`((upstream-name . "DelayedArray")))
(build-system r-build-system)
@@ -1591,13 +1591,13 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns),
(define-public r-bluster
(package
(name "r-bluster")
- (version "1.2.1")
+ (version "1.4.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "bluster" version))
(sha256
(base32
- "128zd5vwlhmrkq0bpp1dxnkrcqfz1mjmdjlla4wqbjv7v6yyn6lg"))))
+ "1j24l12i3aga4qd827sj8b160yvrhlznggb4piddkmhjc0sppbjm"))))
(properties `((upstream-name . "bluster")))
(build-system r-build-system)
(propagated-inputs
@@ -1621,13 +1621,13 @@ and evaluate clustering results.")
(define-public r-ideoviz
(package
(name "r-ideoviz")
- (version "1.28.0")
+ (version "1.30.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "IdeoViz" version))
(sha256
(base32
- "17sx0v5lq2zmg098ps4ksj1h0yla3vlh6s2w1ahqsq0nvm193scm"))))
+ "0cclk2pcb2mvsfxhw0zq3qlnfkblb1gqxnn7xypmlf0bm6hcvl4g"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
@@ -1645,13 +1645,13 @@ arbitrary genomic intervals along chromosomal ideogram.")
(define-public r-iranges
(package
(name "r-iranges")
- (version "2.26.0")
+ (version "2.28.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "IRanges" version))
(sha256
(base32
- "0dzj8wqbjzilh2dsaj3ylx958xqrv0c688ayfq2r1z7rs75qy7kx"))))
+ "07zs231wbfwwc1c1165rhp711fbss40p9l8kyjjv9flzpr3hr1pg"))))
(properties
`((upstream-name . "IRanges")))
(build-system r-build-system)
@@ -1803,14 +1803,14 @@ performing parallel computations on multicore machines.")
(define-public r-affy
(package
(name "r-affy")
- (version "1.70.0")
+ (version "1.72.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "affy" version))
(sha256
(base32
- "0vz5y92gqcm0qk57qlba85bk683lzdr7vkmxv109rq6i17vdkkrm"))))
+ "0z66pyn2020h3x22xabkmnjxb20kbgblivvk7mqjk9134wvvf15a"))))
(build-system r-build-system)
(propagated-inputs
`(("r-affyio" ,r-affyio)
@@ -1831,14 +1831,14 @@ analysis.")
(define-public r-affycomp
(package
(name "r-affycomp")
- (version "1.68.0")
+ (version "1.70.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "affycomp" version))
(sha256
(base32
- "07my5scdh6h0y1bx1h9y5m4fa8bnmw389f83gkb7cf19w4vp36b2"))))
+ "0kawlfff82ikrbrfyyy38zm5wj5xdri2ii9wgwilnq50z5qc6r21"))))
(properties `((upstream-name . "affycomp")))
(build-system r-build-system)
(propagated-inputs `(("r-biobase" ,r-biobase)))
@@ -1852,14 +1852,14 @@ measures for Affymetrix Oligonucleotide Arrays.")
(define-public r-affycompatible
(package
(name "r-affycompatible")
- (version "1.52.0")
+ (version "1.54.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "AffyCompatible" version))
(sha256
(base32
- "1xwz22wf2smsvmd0d5lfadbsgscnl3fl9msypy2mml38k048p6vj"))))
+ "1qlfh1gcwa6akd5dhdqh260yaw1j6dap6a15ghwf74rchi5218sg"))))
(properties
`((upstream-name . "AffyCompatible")))
(build-system r-build-system)
@@ -1880,14 +1880,14 @@ Command Console} (AGCC)-compatible sample annotation files.")
(define-public r-affycontam
(package
(name "r-affycontam")
- (version "1.50.0")
+ (version "1.52.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "affyContam" version))
(sha256
(base32
- "0242ga68wrdk1kcmxfdbq73a0d3zhrzdlzkzphfg3q0zjbvg49jj"))))
+ "1vw3nxg9jvlw0zg9h70w2ww8l42qpyvgf12hsla9hyyfhj3m6i9f"))))
(properties `((upstream-name . "affyContam")))
(build-system r-build-system)
(propagated-inputs
@@ -1905,14 +1905,14 @@ problems in CEL-level data to help evaluate performance of quality metrics.")
(define-public r-affycoretools
(package
(name "r-affycoretools")
- (version "1.64.0")
+ (version "1.66.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "affycoretools" version))
(sha256
(base32
- "1dx861spr3kn1dxwhf43s5l1r7bmrq0h6538l3q64iiwzzc6krdh"))))
+ "1ccyaj129ii9f47r41qsy34y6ck4wna55j8vz3v3hbldddn93f40"))))
(properties `((upstream-name . "affycoretools")))
(build-system r-build-system)
(propagated-inputs
@@ -1947,14 +1947,14 @@ to streamline the more common analyses that a Biostatistician might see.")
(define-public r-affyio
(package
(name "r-affyio")
- (version "1.62.0")
+ (version "1.64.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "affyio" version))
(sha256
(base32
- "07kibqsm888g06qqqa4648ph877kriy74kprbri8nyx83y8aspjr"))))
+ "02lqdq8hcldkf9qbyhhllkm3smpqc51sn2d9gbkm74r96fx37lvm"))))
(build-system r-build-system)
(propagated-inputs
`(("r-zlibbioc" ,r-zlibbioc)))
@@ -1971,14 +1971,14 @@ CDF file formats.")
(define-public r-affxparser
(package
(name "r-affxparser")
- (version "1.64.1")
+ (version "1.66.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "affxparser" version))
(sha256
(base32
- "0lr0kmp087j2g4i5kd7rh8a038ymp6z82861lyql2fwk5dh80043"))))
+ "1bd0f8ifj6l7dx2m3wpmd0mji2gdf39mzgcjf9lbvvmbqnbxbcal"))))
(properties `((upstream-name . "affxparser")))
(build-system r-build-system)
(home-page "https://github.com/HenrikBengtsson/affxparser")
@@ -1999,14 +1999,14 @@ structure.")
(define-public r-annotate
(package
(name "r-annotate")
- (version "1.70.0")
+ (version "1.72.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "annotate" version))
(sha256
(base32
- "13ny596wh65sw7dbw0zd4h84d6k1w99g91c4sqy83mdzgpv73sz7"))))
+ "0p7q5hdk7003q72vg4hrgdzn463spybxhrkvcq3a6l6jkgy9sf84"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
@@ -2026,13 +2026,13 @@ microarrays.")
(define-public r-annotationdbi
(package
(name "r-annotationdbi")
- (version "1.54.1")
+ (version "1.56.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "AnnotationDbi" version))
(sha256
(base32
- "0fcammls431pgmp47r85k0zh3bz42bajbqdmafd31kpqncc1ijal"))))
+ "1svh5zcb7ymz463z5641l2cvzniswxasjjix2plfhqs0yqf1j9qg"))))
(properties
`((upstream-name . "AnnotationDbi")))
(build-system r-build-system)
@@ -2056,13 +2056,13 @@ annotation data packages using SQLite data storage.")
(define-public r-annotationfilter
(package
(name "r-annotationfilter")
- (version "1.16.0")
+ (version "1.18.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "AnnotationFilter" version))
(sha256
(base32
- "0799jja6v7l3jsi26wbjalkr5lriaxid05xb5g36iq93myhaj0sa"))))
+ "15fp1228yb06jm5cblvhw3qv9mlpbjfggaz2nvi3p46mby1vs64w"))))
(properties
`((upstream-name . "AnnotationFilter")))
(build-system r-build-system)
@@ -2082,14 +2082,14 @@ used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.")
(define-public r-annotationforge
(package
(name "r-annotationforge")
- (version "1.34.0")
+ (version "1.36.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "AnnotationForge" version))
(sha256
(base32
- "1by3diy0y4809k97cw97mp4j177gn1dzhqil8myij1r7b8sk7hax"))))
+ "02wvni5q560idi6677g5f4md73z4qzjl5yycxv5dbvgbl2picisz"))))
(properties
`((upstream-name . "AnnotationForge")))
(build-system r-build-system)
@@ -2114,14 +2114,14 @@ databases. Packages produced are intended to be used with AnnotationDbi.")
(define-public r-annotationhub
(package
(name "r-annotationhub")
- (version "3.0.1")
+ (version "3.2.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "AnnotationHub" version))
(sha256
(base32
- "12i8lafy1z97gs4knqi7r5l1hd7dr6j8a23qj4fkdpqsdpyz21z7"))))
+ "0ks8yzvvs2r66pb9687mkskf0n3wgvp7h92k83b0a1q32sca5wng"))))
(properties `((upstream-name . "AnnotationHub")))
(build-system r-build-system)
(propagated-inputs
@@ -2155,14 +2155,14 @@ by the user, helping with quick and reproducible access.")
(define-public r-aroma-light
(package
(name "r-aroma-light")
- (version "3.22.0")
+ (version "3.24.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "aroma.light" version))
(sha256
(base32
- "1yvq6l1p8cpijvlib4fn9y88ihn0gaalrmgx82jgrfmnszkqn3y5"))))
+ "12qa85hsp8d1xhgn27iymknbhpnp9bd7hsgqxwvp1i8kki06z5hp"))))
(properties `((upstream-name . "aroma.light")))
(build-system r-build-system)
(propagated-inputs
@@ -2182,14 +2182,14 @@ classes.")
(define-public r-bamsignals
(package
(name "r-bamsignals")
- (version "1.24.0")
+ (version "1.26.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "bamsignals" version))
(sha256
(base32
- "1ljrip0jlxjcljqac7vzvwqbcqil5v4f4s4bhpq4akvdkshas6mn"))))
+ "03m3yaagplh7j4q5hp3cfcdqwsnh1pwrlla9cv3ajnfd83s8ncqv"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
@@ -2212,13 +2212,13 @@ paired-end data.")
(define-public r-biobase
(package
(name "r-biobase")
- (version "2.52.0")
+ (version "2.54.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "Biobase" version))
(sha256
(base32
- "1sg8w8860zhlz9s1pf75xa8asd2hyqsj13fh5xc37hf5yqdfkavr"))))
+ "0kar2kgaayp5l7xv9zcxj61l01m8jlwnppql6qf01wsz36dacgww"))))
(properties
`((upstream-name . "Biobase")))
(build-system r-build-system)
@@ -2234,13 +2234,13 @@ on Bioconductor or which replace R functions.")
(define-public r-biomart
(package
(name "r-biomart")
- (version "2.48.3")
+ (version "2.50.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "biomaRt" version))
(sha256
(base32
- "096s243yzbhhz3wsm7azml5sznqczmcpi5g0gnb02mah1przczfx"))))
+ "069wqihm8pj3r41dizvdbj4jnw9bsc5jrz8czfrak5v69bgk5v5q"))))
(properties
`((upstream-name . "biomaRt")))
(build-system r-build-system)
@@ -2272,13 +2272,13 @@ powerful online queries from gene annotation to database mining.")
(define-public r-biocparallel
(package
(name "r-biocparallel")
- (version "1.26.2")
+ (version "1.28.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BiocParallel" version))
(sha256
(base32
- "1y459cygq21f3igsdlxz1zlyad8qbl2qlr5h2d2dpnvblykvf48i"))))
+ "0jqgbpjppwinzw100qhc42kc95znq6xanl26bi8m9cq7yggbpra6"))))
(properties
`((upstream-name . "BiocParallel")))
(build-system r-build-system)
@@ -2306,7 +2306,7 @@ powerful online queries from gene annotation to database mining.")
(("\\today") "later"))
;; Initialize the random number generator seed when building.
- (substitute* "R/internal_rng_stream.R"
+ (substitute* "R/rng.R"
(("\"L'Ecuyer-CMRG\"\\)" m)
(string-append
m "; if (!is.na(Sys.getenv(\"SOURCE_DATE_EPOCH\"))) {set.seed(100)}\n"))))))))
@@ -2327,13 +2327,13 @@ objects.")
(define-public r-biostrings
(package
(name "r-biostrings")
- (version "2.60.2")
+ (version "2.62.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "Biostrings" version))
(sha256
(base32
- "0ai0fg0w4l0a7avbafdbqjgjpg91myxalwrg2i3ixm1l2lyyfyah"))))
+ "11qkw863mkfz3mc55v2gmfr4w3xziqfb5pq3hmjqpn8vpw8ax3xq"))))
(properties
`((upstream-name . "Biostrings")))
(build-system r-build-system)
@@ -2355,14 +2355,14 @@ biological sequences or sets of sequences.")
(define-public r-biovizbase
(package
(name "r-biovizbase")
- (version "1.40.0")
+ (version "1.42.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "biovizBase" version))
(sha256
(base32
- "14jyyg3ggdhaqhp0j4qf6dapykh76fygbaa4lr7czqbc5mr0iw23"))))
+ "0kg71p7sqfvxal0c19zrws1ffaqgyi8p605l3z6mkq5ldi26pajz"))))
(properties `((upstream-name . "biovizBase")))
(build-system r-build-system)
(propagated-inputs
@@ -2397,13 +2397,13 @@ effort and encourages consistency.")
(define-public r-bsgenome
(package
(name "r-bsgenome")
- (version "1.60.0")
+ (version "1.62.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BSgenome" version))
(sha256
(base32
- "1jhissp9ad1rn2p0bzr3yslbn84yqbaqgnn5p9hyacwr7mr091cn"))))
+ "1b023dpy8ygq0kd6qy0mk97c66gzpf39y2s0n89kmv61z5sg0jyi"))))
(properties
`((upstream-name . "BSgenome")))
(build-system r-build-system)
@@ -2428,14 +2428,14 @@ genome data packages and support for efficient SNP representation.")
(define-public r-category
(package
(name "r-category")
- (version "2.58.0")
+ (version "2.60.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Category" version))
(sha256
(base32
- "0f76pb7h8qc51mca5pq00m9p02sbkcj6ywfzli20qai2ykpfr71x"))))
+ "164zp4la9rqnp5vpn2y2p6plc5yxyk2kmn0z3d2flla54zc1b427"))))
(properties `((upstream-name . "Category")))
(build-system r-build-system)
(propagated-inputs
@@ -2459,13 +2459,13 @@ analysis.")
(define-public r-chipseeker
(package
(name "r-chipseeker")
- (version "1.28.3")
+ (version "1.30.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "ChIPseeker" version))
(sha256
(base32
- "18hdgml80770c0xgd06zrl8px1ql9fa65rirfkq07z7rzpnd23rw"))))
+ "1x8px8ylc231g87rd48kmy9y36h26rldbmqjkcj4mgaldvbsj0rp"))))
(build-system r-build-system)
(native-inputs
`(("r-knitr" ,r-knitr)))
@@ -2506,14 +2506,14 @@ annotation, distance to TSS, and overlap of peaks or genes.")
(define-public r-chipseq
(package
(name "r-chipseq")
- (version "1.42.0")
+ (version "1.44.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "chipseq" version))
(sha256
(base32
- "078p9h0zghlhpd6cr54nww1mk7q97imx8yqfayw5m2yq4097ivbi"))))
+ "1jw209bfh1c22mqs9z44qx3pmca9m68rhxp0p9bvbmqsnqwrndi6"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
@@ -2532,20 +2532,19 @@ experiments.")
(define-public r-complexheatmap
(package
(name "r-complexheatmap")
- (version "2.8.0")
+ (version "2.10.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ComplexHeatmap" version))
(sha256
(base32
- "0jl96msj1njdrvngg68s50vmphvhi2lfwlv34x07pcdzgkjjs41f"))))
+ "124w74mk0zk035wyr7cimblzx5blags4n5c8f83mp7iimxcb4gcn"))))
(properties
`((upstream-name . "ComplexHeatmap")))
(build-system r-build-system)
(propagated-inputs
- `(("r-cairo" ,r-cairo)
- ("r-circlize" ,r-circlize)
+ `(("r-circlize" ,r-circlize)
("r-clue" ,r-clue)
("r-colorspace" ,r-colorspace)
("r-digest" ,r-digest)
@@ -2572,14 +2571,14 @@ self-defined annotation graphics.")
(define-public r-copywriter
(package
(name "r-copywriter")
- (version "2.24.0")
+ (version "2.26.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "CopywriteR" version))
(sha256
(base32
- "0pacs714d9b1fdz68pp9ca0x77d376s19lxb82np4l9fgx0rgkxp"))))
+ "0xm5gjzi4r1xzyn7r669blqxhyhmbk9rh9k2gn696j14hbhc1hcy"))))
(properties `((upstream-name . "CopywriteR")))
(build-system r-build-system)
(propagated-inputs
@@ -2643,14 +2642,14 @@ distribution.")
(define-public r-deseq2
(package
(name "r-deseq2")
- (version "1.32.0")
+ (version "1.34.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DESeq2" version))
(sha256
(base32
- "0r1brwmj7av0bj72jajn27vx3zs1bgg8qfbhf02fln6kf7im4kaz"))))
+ "0whk29zrmv9mrlc4w5ghy0fd29v8hfr8jccwgrn59mf3mkmfb2b9"))))
(properties `((upstream-name . "DESeq2")))
(build-system r-build-system)
(propagated-inputs
@@ -2681,14 +2680,14 @@ distribution.")
(define-public r-dexseq
(package
(name "r-dexseq")
- (version "1.38.0")
+ (version "1.40.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DEXSeq" version))
(sha256
(base32
- "1zywh30f4j4rj0f9w6yk5xr9mvdbg8gicy3wsb8yxdnamadyr7x4"))))
+ "1wd4bjd0a53s689yvb2lxzdiy0synh6ncfcly3cfw37kpdj8lds1"))))
(properties `((upstream-name . "DEXSeq")))
(build-system r-build-system)
(propagated-inputs
@@ -2726,14 +2725,14 @@ exploration of the results.")
(define-public r-dirichletmultinomial
(package
(name "r-dirichletmultinomial")
- (version "1.34.0")
+ (version "1.36.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DirichletMultinomial" version))
(sha256
(base32
- "0ikmj0300lfzj6q1vyahfyx5kwi5h59mds7ym4f2j1bbxqzy6ssl"))))
+ "06nallp9jj2vmaa7d18g6hiymjc109szdv8sp51r87n7s38bvyq6"))))
(properties
`((upstream-name . "DirichletMultinomial")))
(build-system r-build-system)
@@ -2755,14 +2754,14 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2):
(define-public r-edaseq
(package
(name "r-edaseq")
- (version "2.26.1")
+ (version "2.28.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "EDASeq" version))
(sha256
(base32
- "0pakcbkalhhqz3d9lpfx3hscf53k24mlmrywxxzfg43yq57srkql"))))
+ "1vygfdxbjcww7sqzc3j7sp7w13dx10vlzy9z31flf7345qp6blj7"))))
(properties `((upstream-name . "EDASeq")))
(build-system r-build-system)
(propagated-inputs
@@ -2795,13 +2794,13 @@ global-scaling and full-quantile normalization.")
(define-public r-edger
(package
(name "r-edger")
- (version "3.34.1")
+ (version "3.36.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "edgeR" version))
(sha256
(base32
- "0f6apsjq6cn794840ls9y2n0hix1gyhvkdgxch1v22qr4sq0c86k"))))
+ "1d18kdfi9vjhhw5kwfy5airrd3c16fh4wbwppbhwgawm038mwavk"))))
(properties `((upstream-name . "edgeR")))
(build-system r-build-system)
(propagated-inputs
@@ -2823,14 +2822,14 @@ CAGE.")
(define-public r-ensembldb
(package
(name "r-ensembldb")
- (version "2.16.4")
+ (version "2.18.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ensembldb" version))
(sha256
(base32
- "15yllkxr6sj5pfvkvv285nk3q5374nzq1iz8ywmnrq910k3xagd8"))))
+ "02rdbqp33g488w1df1rgp0dg63qrr6w2kmgigxzc8l9wmrvj0y1j"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
@@ -2868,14 +2867,14 @@ chromosome region or transcript models of lincRNA genes.")
(define-public r-fastseg
(package
(name "r-fastseg")
- (version "1.38.0")
+ (version "1.40.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "fastseg" version))
(sha256
(base32
- "006v7qs707xmnr35b7rw135pyvacrmhv55a3c53birkpsrjgkps0"))))
+ "1ds0hhc41nhfj3lmvld8nk2p547wd80b3yq7fjlf3dl3wfaxzy80"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
@@ -2898,14 +2897,14 @@ microarrays or GRanges for sequencing data.")
(define-public r-gage
(package
(name "r-gage")
- (version "2.42.0")
+ (version "2.44.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "gage" version))
(sha256
(base32
- "0z7hrwdm6my6p7z04bcpfhqk72pd0s1bdzvsiiym59qj79fbvb83"))))
+ "1spndmvl8wlz3z3wsvzi0fg9nzk81xi8c220pg2rf81j9181nkar"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
@@ -2929,14 +2928,14 @@ analysis using other methods.")
(define-public r-genefilter
(package
(name "r-genefilter")
- (version "1.74.0")
+ (version "1.76.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "genefilter" version))
(sha256
(base32
- "0dy9pmlb0pc9b4ks5fb9zgnmhc9f2mkqmsdlb7f5z88xmj68y4qk"))))
+ "05ba33m99dg414lasn36mjmkd9lvrxgpamy1qj2zvi31i9vkq6y2"))))
(build-system r-build-system)
(native-inputs
`(("gfortran" ,gfortran)
@@ -2957,13 +2956,13 @@ high-throughput sequencing experiments.")
(define-public r-geneoverlap
(package
(name "r-geneoverlap")
- (version "1.28.0")
+ (version "1.30.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GeneOverlap" version))
(sha256
(base32
- "1kfw3h68rvbafhklds6sfmviwv91nms8wk0ywzkjg5h3mmgxbsv9"))))
+ "18l5dc4xcy1xa2h3sfw92w9rq9v0mnclamjxmzs5fqi469y5mwmm"))))
(build-system r-build-system)
(propagated-inputs
`(("r-rcolorbrewer" ,r-rcolorbrewer)
@@ -2977,13 +2976,13 @@ and visualize the results.")
(define-public r-genomation
(package
(name "r-genomation")
- (version "1.24.0")
+ (version "1.26.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "genomation" version))
(sha256
(base32
- "0qa3b4mfd7l1sy4pw64zr2d90y5apah900krxjl4x39acygg0i2r"))))
+ "0ynwsrlnp98iyz4bl2s7plin0k9iy9zix4jy4v38lcqg6n4iz00j"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biostrings" ,r-biostrings)
@@ -3024,13 +3023,13 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.")
(define-public r-genomeinfodb
(package
(name "r-genomeinfodb")
- (version "1.28.4")
+ (version "1.30.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomeInfoDb" version))
(sha256
(base32
- "0fjpgvpvyvl8cqgh2annib6h0c5li3aqz1ajfh5z5k5d0avdm4w0"))))
+ "1r0wblz9w4hqxm15wdssz0invx7hxhg3bnblkia6w3aazh30s6ns"))))
(properties
`((upstream-name . "GenomeInfoDb")))
(build-system r-build-system)
@@ -3054,13 +3053,13 @@ names in their natural, rather than lexicographic, order.")
(define-public r-genomicalignments
(package
(name "r-genomicalignments")
- (version "1.28.0")
+ (version "1.30.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomicAlignments" version))
(sha256
(base32
- "00rq110jkh89nxgk05zh8kssxk8mb4dq0wjg3n7ivfmmm9wdwhp2"))))
+ "1jwksis94mk8bmdggk0w3kvxqwp4di6x78xgsjk6ij54710adyq9"))))
(properties
`((upstream-name . "GenomicAlignments")))
(build-system r-build-system)
@@ -3087,13 +3086,13 @@ alignments.")
(define-public r-genomicfeatures
(package
(name "r-genomicfeatures")
- (version "1.44.2")
+ (version "1.46.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomicFeatures" version))
(sha256
(base32
- "091p8xnf2xkqhind81vyv1rmy2fz2b3qalcbrsw4qnp24vgdv2am"))))
+ "1dm049r7k41m8zzp5b332fw3ah3jpzzgpcb21icxwhlg483ipjyv"))))
(properties
`((upstream-name . "GenomicFeatures")))
(build-system r-build-system)
@@ -3131,14 +3130,14 @@ extracting the desired features in a convenient format.")
(define-public r-genomicfiles
(package
(name "r-genomicfiles")
- (version "1.28.0")
+ (version "1.30.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "GenomicFiles" version))
(sha256
(base32
- "1plh14m7w6calw5yxcxp7g4bg8q00ax85m517wap78bni975k13y"))))
+ "0i5y6dk6z18yqj5k4zy756c6l57z9jq2w5a5dksh2di4qgdgjx3x"))))
(properties `((upstream-name . "GenomicFiles")))
(build-system r-build-system)
(propagated-inputs
@@ -3165,13 +3164,13 @@ provide added flexibility for data combination and manipulation.")
(define-public r-genomicranges
(package
(name "r-genomicranges")
- (version "1.44.0")
+ (version "1.46.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomicRanges" version))
(sha256
(base32
- "1qxc6dcwdlkan3hg0j9yfhz7gyi9qg671yj6zizsk6mzl7qqva0x"))))
+ "03fdmzcf8h17ksa3byc3k5mxc65pqrbcnw00myz1q53l01p3cnf2"))))
(properties
`((upstream-name . "GenomicRanges")))
(build-system r-build-system)
@@ -3196,14 +3195,14 @@ manipulating genomic intervals and variables defined along a genome.")
(define-public r-gostats
(package
(name "r-gostats")
- (version "2.58.0")
+ (version "2.60.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "GOstats" version))
(sha256
(base32
- "0jjswy6qmfgr2f6vk3y9pdvs9x91gn31h55qllgh0qb2cb26g9wa"))))
+ "1f8wqdl0swnvs59i6ljjcaglfqv314n8zxy4crpx806gbjzpn76z"))))
(properties `((upstream-name . "GOstats")))
(build-system r-build-system)
(propagated-inputs
@@ -3227,14 +3226,14 @@ testing and other simple calculations.")
(define-public r-gseabase
(package
(name "r-gseabase")
- (version "1.54.0")
+ (version "1.56.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "GSEABase" version))
(sha256
(base32
- "0946kkykms79mqnx262q20xzrrhv7cv723xh378335ff41qyf63n"))))
+ "1i8rryvagxk2pd8nl4a6yldwv82yx869nvv95jf8v00bna08f4d6"))))
(properties `((upstream-name . "GSEABase")))
(build-system r-build-system)
(propagated-inputs
@@ -3256,14 +3255,14 @@ Enrichment Analysis} (GSEA).")
(define-public r-hpar
(package
(name "r-hpar")
- (version "1.34.0")
+ (version "1.36.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "hpar" version))
(sha256
(base32
- "0q5pp04rq2gsh1kibvp8bvjkqc1kb46qpnj6agqp2vyqhrrfrm99"))))
+ "1inajapdhjxg0vwhsdnhfq22h3fv7ad7m1lv58y5v41p59av1w76"))))
(build-system r-build-system)
(native-inputs
`(("r-knitr" ,r-knitr)))
@@ -3276,14 +3275,14 @@ the Human Protein Atlas project.")
(define-public r-rhtslib
(package
(name "r-rhtslib")
- (version "1.24.0")
+ (version "1.26.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Rhtslib" version))
(sha256
(base32
- "0acpgv98529ic2i2k03knz05akb6h51wbz7sr5zgi8gk4nmawrlf"))))
+ "0pwmzwjf6agfp3bq6w8s3piwmzwjdd474qd8zmbzrm772qbadfr4"))))
(properties `((upstream-name . "Rhtslib")))
(build-system r-build-system)
;; Without this a temporary directory ends up in the Rhtslib.so binary,
@@ -3307,13 +3306,13 @@ of other R packages who wish to make use of HTSlib.")
(define-public r-impute
(package
(name "r-impute")
- (version "1.66.0")
+ (version "1.68.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "impute" version))
(sha256
(base32
- "0pprkv25avxhllddcssvqvy3nibmqkfwaq4xnlhka7858gyiyd1k"))))
+ "0k6dil8ljgp5qr87m7hxli4igb36fbxiwczaqc5pi8mlfh70fqj5"))))
(native-inputs
`(("gfortran" ,gfortran)))
(build-system r-build-system)
@@ -3327,14 +3326,14 @@ microarray data, using nearest neighbor averaging.")
(define-public r-interactivedisplaybase
(package
(name "r-interactivedisplaybase")
- (version "1.30.0")
+ (version "1.32.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "interactiveDisplayBase" version))
(sha256
(base32
- "00rgrrmglslgb6j7whp0m5dlyl4436r647br05rrpv8cxrmbs2iv"))))
+ "1pi887192k1jifb4k3pf2jn5hcl1xmmy6vwl22r9njsprdyb3kab"))))
(properties
`((upstream-name . "interactiveDisplayBase")))
(build-system r-build-system)
@@ -3354,14 +3353,14 @@ Shiny-based display methods for Bioconductor objects.")
(define-public r-keggrest
(package
(name "r-keggrest")
- (version "1.32.0")
+ (version "1.34.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "KEGGREST" version))
(sha256
(base32
- "15313d20v3ziyn52fhc6fbzcy1kxjkdx18124bxhdfd14f4aypcd"))))
+ "1np3i1k7rki9akh70156ggmid52yy0is9q5vd3s45ra7an0ap279"))))
(properties `((upstream-name . "KEGGREST")))
(build-system r-build-system)
(propagated-inputs
@@ -3380,13 +3379,13 @@ Shiny-based display methods for Bioconductor objects.")
(define-public r-limma
(package
(name "r-limma")
- (version "3.48.3")
+ (version "3.50.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "limma" version))
(sha256
(base32
- "0385ac0hvvml99krcgcpp6q7layjhzgp9xcxkcjrpfg5mjg1z4sx"))))
+ "05ypmax1s6y1nz42bxn61wxhzzw6185q633crzpdcbbz3dz4vgvy"))))
(build-system r-build-system)
(home-page "http://bioinf.wehi.edu.au/limma")
(synopsis "Package for linear models for microarray and RNA-seq data")
@@ -3399,13 +3398,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.")
(define-public r-methylkit
(package
(name "r-methylkit")
- (version "1.18.0")
+ (version "1.20.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "methylKit" version))
(sha256
(base32
- "147nag4rz2xpjkkf8rmhja9k4ixjj1hsb0lq3lw7mw6q67zxsvf3"))))
+ "02px46h2ynprss7kwll3i0jz0clrdg0bys70jacd432xw34nm2sx"))))
(properties `((upstream-name . "methylKit")))
(build-system r-build-system)
(propagated-inputs
@@ -3473,14 +3472,14 @@ throughput genetic sequencing data sets using regression methods.")
(define-public r-mutationalpatterns
(package
(name "r-mutationalpatterns")
- (version "3.2.0")
+ (version "3.4.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MutationalPatterns" version))
(sha256
(base32
- "0433i4xbz8hrfaj8fxgzps3x8dqrl5vgwzg7qmp4cy5sb1lw5wvs"))))
+ "1n9rakj57yf17hay1bzvwc2h761yijmlflb3crg1bzwvmn32yhsl"))))
(build-system r-build-system)
(native-inputs
`(("r-knitr" ,r-knitr)))
@@ -3503,6 +3502,7 @@ throughput genetic sequencing data sets using regression methods.")
("r-nmf" ,r-nmf)
("r-pracma" ,r-pracma)
("r-purrr" ,r-purrr)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)
("r-s4vectors" ,r-s4vectors)
("r-stringr" ,r-stringr)
("r-tibble" ,r-tibble)
@@ -3518,14 +3518,14 @@ in SNV base substitution data.")
(define-public r-msnbase
(package
(name "r-msnbase")
- (version "2.18.0")
+ (version "2.20.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MSnbase" version))
(sha256
(base32
- "1z7s17j6zgb70m0khyf9icqlnbnzlivca7vw7j0vxyw417ld9lkr"))))
+ "1r5igzb7xb5qcw37ffy0c3j6vlg9zffmksrc57rs1pmfnca773z5"))))
(properties `((upstream-name . "MSnbase")))
(build-system r-build-system)
(propagated-inputs
@@ -3563,14 +3563,14 @@ of mass spectrometry based proteomics data.")
(define-public r-msnid
(package
(name "r-msnid")
- (version "1.26.0")
+ (version "1.28.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MSnID" version))
(sha256
(base32
- "0r3vgigf4fk0xzfg8gcvad01jdh0fysh6x22m9qy77x6glyrxcj2"))))
+ "0dks5h3vp9ly8x24px2rl5blqicxybpxjnxvg2p1bwq8zvjkm38p"))))
(properties `((upstream-name . "MSnID")))
(build-system r-build-system)
(arguments
@@ -3620,14 +3620,14 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.")
(define-public r-mzid
(package
(name "r-mzid")
- (version "1.30.0")
+ (version "1.32.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "mzID" version))
(sha256
(base32
- "1wsy6frxa5602jqb1nlqv39mzgpid8wfyvb9m2jb6srv7p59rgys"))))
+ "0r001amd4m99cv0ixw38rpz0zv0xqb0qyvs16bz1i4a756391qri"))))
(properties `((upstream-name . "mzID")))
(build-system r-build-system)
(propagated-inputs
@@ -3651,14 +3651,14 @@ specific parser.")
(define-public r-mzr
(package
(name "r-mzr")
- (version "2.26.1")
+ (version "2.28.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "mzR" version))
(sha256
(base32
- "0z4cz6lir9gwzy0hxwv03wv36fkkfdb97p9wv4af020k0zkp3ipr"))
+ "1azq0wjjy6n5xc721gjz6afm43ajz15b4p34vgsdjzwg9qn1vrs1"))
(modules '((guix build utils)))
(snippet
'(begin
@@ -3681,7 +3681,7 @@ specific parser.")
#t)))))
(inputs
`(;; Our default boost package won't work here, unfortunately, even with
- ;; mzR version 2.26.1.
+ ;; mzR version 2.28.0.
("boost" ,boost-for-mysql) ; use this instead of the bundled boost sources
("zlib" ,zlib)))
(propagated-inputs
@@ -3708,14 +3708,14 @@ previously been used in XCMS.")
(define-public r-organismdbi
(package
(name "r-organismdbi")
- (version "1.34.0")
+ (version "1.36.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "OrganismDbi" version))
(sha256
(base32
- "0p8ccpdchdwci4kv9y07wdadzgms8nipvg6rm1rll35jcflnnkxi"))))
+ "0zp6x2iqhn9s3xp07yilnr6hn73acvkdai5xip4iiwjdlnfffj83"))))
(properties `((upstream-name . "OrganismDbi")))
(build-system r-build-system)
(propagated-inputs
@@ -3740,14 +3740,14 @@ the fact that each of these packages implements a select methods.")
(define-public r-pcamethods
(package
(name "r-pcamethods")
- (version "1.84.0")
+ (version "1.86.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "pcaMethods" version))
(sha256
(base32
- "1ccqsxn487dy92c2d1iffh9917z4zq5ia92zv2h6pi00jjc6ymb5"))))
+ "1fj2v6sna4lbw7ar9h93y2g4pzylqqp7760ih425gcai7s19xdrg"))))
(properties `((upstream-name . "pcaMethods")))
(build-system r-build-system)
(propagated-inputs
@@ -3770,14 +3770,14 @@ structure (pcaRes) to provide a common interface to the PCA results.")
(define-public r-protgenerics
(package
(name "r-protgenerics")
- (version "1.24.0")
+ (version "1.26.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ProtGenerics" version))
(sha256
(base32
- "1c79k8nc28782w5gxi7pkm8jmddq1hdw6khs9kgsp8dyk60ak6fq"))))
+ "0x53pk7h47gjza1q5pz7jb1qqhwa9z2rr5fr61qc92zl3mqk57m0"))))
(properties `((upstream-name . "ProtGenerics")))
(build-system r-build-system)
(home-page "https://github.com/lgatto/ProtGenerics")
@@ -3790,14 +3790,14 @@ proteomics packages.")
(define-public r-rbgl
(package
(name "r-rbgl")
- (version "1.68.0")
+ (version "1.70.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "RBGL" version))
(sha256
(base32
- "0l40ibf8g5s4ay83s92l198jjqc5l09hcmxqcjrpifvp5pjf9yy5"))))
+ "0k2p1lwdvix4n742a97lv988rx5kg8cvcmzgyzj0538n1nz0lxk0"))))
(properties `((upstream-name . "RBGL")))
(build-system r-build-system)
(propagated-inputs
@@ -3813,13 +3813,13 @@ the graph algorithms contained in the Boost library.")
(define-public r-rcas
(package
(name "r-rcas")
- (version "1.18.0")
+ (version "1.20.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "RCAS" version))
(sha256
(base32
- "0l92v870ndna8zjqwzf22fb9vyhkh6942v4gaiqr1yc4qr521p5p"))))
+ "02zwz7c8ljmdcfxj54xns0a31sj616x63q63wxhxa1nb4dhgmvk7"))))
(properties `((upstream-name . "RCAS")))
(build-system r-build-system)
(propagated-inputs
@@ -3863,14 +3863,14 @@ library implementing most of the pipeline's features.")
(define-public r-regioner
(package
(name "r-regioner")
- (version "1.24.0")
+ (version "1.26.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "regioneR" version))
(sha256
(base32
- "0xzzaz3cl6pyxfsg0d931v8k15wbd05s5mnsb7igxldc5qqg3nsl"))))
+ "0y1mawzfvxrympc47q3isk96sl9d1bc8kdsxpm8rnhqg5bmgwya6"))))
(properties `((upstream-name . "regioneR")))
(build-system r-build-system)
(propagated-inputs
@@ -3894,14 +3894,14 @@ region sets and other genomic features.")
(define-public r-reportingtools
(package
(name "r-reportingtools")
- (version "2.32.1")
+ (version "2.34.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ReportingTools" version))
(sha256
(base32
- "0wq9y649dh1am6djzz0xlz42428xsgw2bdx1dknhdw2xbydmmx47"))))
+ "06kwf87h84xgswkrm7brmgr9aj1nf6cxp24hrfymkzq2pha5y5j7"))))
(properties
`((upstream-name . "ReportingTools")))
(build-system r-build-system)
@@ -3944,13 +3944,13 @@ browser.")
(define-public r-rhdf5
(package
(name "r-rhdf5")
- (version "2.36.0")
+ (version "2.38.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "rhdf5" version))
(sha256
(base32
- "1a5kw9ry9cr258al0x3q0ss5xn1ymscdypx51vzzgzamhy7dqakz"))))
+ "13zm993l3i9f98gqdpxgsrzf9fgqppx2ajvrl0i3f7cvpifcgxqg"))))
(build-system r-build-system)
(propagated-inputs
`(("r-rhdf5filters" ,r-rhdf5filters)
@@ -3972,14 +3972,14 @@ the available RAM.")
(define-public r-rhdf5filters
(package
(name "r-rhdf5filters")
- (version "1.4.0")
+ (version "1.6.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "rhdf5filters" version))
(sha256
(base32
- "133v0s452acspi4dbf6gsa2xrr0qza86jdjjbpwhdv6zfd1djbgc"))))
+ "05b015pyp3g1crmm2d3ldsa7r5w0khmf87qbl4fv16r6pdggha78"))))
(properties `((upstream-name . "rhdf5filters")))
(build-system r-build-system)
(propagated-inputs
@@ -3998,13 +3998,13 @@ HDF5 datasets.")
(define-public r-rsamtools
(package
(name "r-rsamtools")
- (version "2.8.0")
+ (version "2.10.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "Rsamtools" version))
(sha256
(base32
- "0arhh5bbx3pmxmkh5sjgczcswqy83d35r7cjhd2knpczdvrixaq5"))))
+ "0v6b3j45ivd9f04fpfs1vjwby5pi30mf5683bjxim01vi2krj9yh"))))
(properties
`((upstream-name . "Rsamtools")))
(build-system r-build-system)
@@ -4067,13 +4067,13 @@ tab-delimited (tabix) files.")
(define-public r-rtracklayer
(package
(name "r-rtracklayer")
- (version "1.52.1")
+ (version "1.54.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "rtracklayer" version))
(sha256
(base32
- "11w6dx09pb49lin1gr9q88xn7ixh9jd5z6m9z27djchm0nw10lx9"))))
+ "11bh9khra2qdmicppi6ya43kf8f1z13ak92vkl6nr5f20k54cphc"))))
(build-system r-build-system)
(arguments
`(#:phases
@@ -4146,14 +4146,14 @@ differential expression analysis, RNAseq data and related problems.")
(define-public r-seqlogo
(package
(name "r-seqlogo")
- (version "1.58.0")
+ (version "1.60.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "seqLogo" version))
(sha256
(base32
- "1253sj1hc6bbrff0iv5xa3v9znqvisll0fy6fdjka9c778fn4mcp"))))
+ "013hwj2lp29nqa8mkvm25aliarg0k725crg4cpsbj0iiskyrs6rl"))))
(properties `((upstream-name . "seqLogo")))
(build-system r-build-system)
(native-inputs
@@ -4169,13 +4169,13 @@ Stephens (1990).")
(define-public r-seqpattern
(package
(name "r-seqpattern")
- (version "1.24.0")
+ (version "1.26.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "seqPattern" version))
(sha256
(base32
- "0h74z84zyvfzclsm0g13b95hirn99185wc6lp53jkzah9yyi59ay"))))
+ "1mik575qaxw9h9qyjn971207pfgbc8p1mx60jrb20jbrrihgg2na"))))
(properties
`((upstream-name . "seqPattern")))
(build-system r-build-system)
@@ -4196,14 +4196,14 @@ reference point and sorted by a user defined feature.")
(define-public r-shortread
(package
(name "r-shortread")
- (version "1.50.0")
+ (version "1.52.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ShortRead" version))
(sha256
(base32
- "0zqinw3c6h5v1c5nhzkiziirws16nbviccgw8nj2d22r33dbqwp3"))))
+ "1p17v15wd3v6w9ligpjjk28vy8k2ql57y2hhm8y6vnv9y3nagjsx"))))
(properties `((upstream-name . "ShortRead")))
(build-system r-build-system)
(inputs
@@ -4239,14 +4239,14 @@ ungapped alignment formats.")
(define-public r-simplifyenrichment
(package
(name "r-simplifyenrichment")
- (version "1.2.0")
+ (version "1.4.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "simplifyEnrichment" version))
(sha256
(base32
- "0rqa414kvyjjmj4932zk39rqa14z13b57rkrxdrf16jmq2r437vh"))))
+ "05d9yjd8s7q1q78qmnx5xfrz9ppswc2cpfmjj47d338w783lwk98"))))
(properties
`((upstream-name . "simplifyEnrichment")))
(build-system r-build-system)
@@ -4278,14 +4278,14 @@ and comparing the clusterings.")
(define-public r-trajectoryutils
(package
(name "r-trajectoryutils")
- (version "1.0.0")
+ (version "1.2.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "TrajectoryUtils" version))
(sha256
(base32
- "1b7mg3ypp1ay98cav47h9vn692lx0n9b5b0hpansgnkr5prb823b"))))
+ "0pzm1h69bg04a2v09r8c6pb3pix6f3n5dylvbv7wsp574qfaqyd1"))))
(properties
`((upstream-name . "TrajectoryUtils")))
(build-system r-build-system)
@@ -4308,13 +4308,13 @@ structures to hold pseudotime inference results.")
(define-public r-slingshot
(package
(name "r-slingshot")
- (version "2.0.0")
+ (version "2.2.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "slingshot" version))
(sha256
(base32
- "1aqsz2kxwax8d8d5iv3zk5hlyk5aya1wbxs1wky2rgccw4d35whx"))))
+ "081kp9b0lpw2xq9xvd2kykqqrqcj322mp7xa44xc3kf0nzsivqfa"))))
(build-system r-build-system)
(propagated-inputs
`(("r-igraph" ,r-igraph)
@@ -4340,13 +4340,13 @@ graph construction.")
(define-public r-structuralvariantannotation
(package
(name "r-structuralvariantannotation")
- (version "1.8.2")
+ (version "1.10.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "StructuralVariantAnnotation" version))
(sha256
- (base32 "04ac4mjh3pgdlws0aiacqg0vd7bhg890w44r7b90p947c3rk1mfw"))))
+ (base32 "1pw7d39944dwk5gw6q7igcn866zpqwz01ljaha2ih5dfvmhxka8n"))))
(build-system r-build-system)
(propagated-inputs
`(("r-assertthat" ,r-assertthat)
@@ -4377,13 +4377,13 @@ involving two separate genomic loci encoded as GRanges objects.")
(define-public r-summarizedexperiment
(package
(name "r-summarizedexperiment")
- (version "1.22.0")
+ (version "1.24.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "SummarizedExperiment" version))
(sha256
(base32
- "16np5ik6jgbi68mhlib6yskywwbaa50mlr7m3sh1hqk889whfn1g"))))
+ "0qpnx2aii9vs7fcp0ax5j77ysbhi4qhjhm35vnygs3isbrjn925a"))))
(properties
`((upstream-name . "SummarizedExperiment")))
(build-system r-build-system)
@@ -4411,14 +4411,14 @@ samples.")
(define-public r-sva
(package
(name "r-sva")
- (version "3.40.0")
+ (version "3.42.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "sva" version))
(sha256
(base32
- "12jkcybdfspabh7x124d44l9fj1hwwg3gvcqxvz5wpkiflc2vkji"))))
+ "0clzid9di2qfgc5bvnqx312k3inj1lc599ckqkllvr894wxb7mdj"))))
(build-system r-build-system)
(propagated-inputs
`(("r-edger" ,r-edger)
@@ -4442,44 +4442,30 @@ unmodeled, or latent sources of noise.")
(define-public r-systempiper
(package
(name "r-systempiper")
- (version "1.26.3")
+ (version "2.0.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "systemPipeR" version))
(sha256
(base32
- "01l35l5zj87qkarrbal9la6kshk3j7k8hy3iimv3gdnnz4axmvs7"))))
+ "0kibr47z7ml13hpl955qcr4wp2z4nq7gjiinyk30wivrwrng5sg1"))))
(properties `((upstream-name . "systemPipeR")))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotate" ,r-annotate)
- ("r-assertthat" ,r-assertthat)
- ("r-batchtools" ,r-batchtools)
+ `(("r-biocgenerics" ,r-biocgenerics)
("r-biostrings" ,r-biostrings)
("r-crayon" ,r-crayon)
- ("r-deseq2" ,r-deseq2)
- ("r-dot" ,r-dot)
- ("r-edger" ,r-edger)
- ("r-genomicfeatures" ,r-genomicfeatures)
("r-genomicranges" ,r-genomicranges)
("r-ggplot2" ,r-ggplot2)
- ("r-go-db" ,r-go-db)
- ("r-gostats" ,r-gostats)
- ("r-iranges" ,r-iranges)
- ("r-limma" ,r-limma)
+ ("r-htmlwidgets" ,r-htmlwidgets)
("r-magrittr" ,r-magrittr)
- ("r-pheatmap" ,r-pheatmap)
- ("r-rjson" ,r-rjson)
("r-rsamtools" ,r-rsamtools)
- ("r-rsvg" ,r-rsvg)
("r-s4vectors" ,r-s4vectors)
("r-shortread" ,r-shortread)
("r-stringr" ,r-stringr)
("r-summarizedexperiment" ,r-summarizedexperiment)
- ("r-testthat" ,r-testthat)
- ("r-yaml" ,r-yaml)
- ("r-variantannotation" ,r-variantannotation)))
+ ("r-yaml" ,r-yaml)))
(native-inputs
`(("r-knitr" ,r-knitr)))
(home-page "https://github.com/tgirke/systemPipeR")
@@ -4499,13 +4485,13 @@ annotation infrastructure.")
(define-public r-topgo
(package
(name "r-topgo")
- (version "2.44.0")
+ (version "2.46.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "topGO" version))
(sha256
(base32
- "1ggi7yrhkyi85p3sfj3yd95n9mzq1xpff28ixa4dl9yzasks1v5a"))))
+ "01vykf8bzwm2k7cfj09r6il6qaycjy10wpaxbn13f21p66r5nlm2"))))
(properties
`((upstream-name . "topGO")))
(build-system r-build-system)
@@ -4532,13 +4518,13 @@ dependencies between GO terms can be implemented and applied.")
(define-public r-tximport
(package
(name "r-tximport")
- (version "1.20.0")
+ (version "1.22.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "tximport" version))
(sha256
(base32
- "0ip2yr0zspf2aagskxl4dwncr48dw5qb90an3sswnnh2dqdb82if"))))
+ "0w6pr7s9j8l4fpn3przbfrsyxvzxc3ficgsychvhq3bami9np8g4"))))
(build-system r-build-system)
(native-inputs
`(("r-knitr" ,r-knitr)))
@@ -4556,13 +4542,13 @@ of gene-level counts.")
(define-public r-variantannotation
(package
(name "r-variantannotation")
- (version "1.38.0")
+ (version "1.40.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "VariantAnnotation" version))
(sha256
(base32
- "0c9r00j8a3bs6n0dv4wi17jc1ljzvr3r2bi4h9axhcsf2ip906rh"))))
+ "1r9kayp0hxcwls08lv2fh0cmf9ks0lqx3k31c1zn4asw4dyqpgva"))))
(properties
`((upstream-name . "VariantAnnotation")))
(propagated-inputs
@@ -4594,14 +4580,14 @@ coding changes and predict coding outcomes.")
(define-public r-vsn
(package
(name "r-vsn")
- (version "3.60.0")
+ (version "3.62.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "vsn" version))
(sha256
(base32
- "0nppph3kv8z83368snb8s3n4vcqj829yyi1kh4q09qvq18rhvssv"))))
+ "03p2wdjbjnrn1ddyz0fbn04mdxpsmv83qhh3apj6azshl0bs1j2x"))))
(build-system r-build-system)
(propagated-inputs
`(("r-affy" ,r-affy)
@@ -4630,13 +4616,13 @@ and specific in detecting differential transcription.")
(define-public r-xvector
(package
(name "r-xvector")
- (version "0.32.0")
+ (version "0.34.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "XVector" version))
(sha256
(base32
- "1cw34gd9iaspl0v737xl7rngq63zrj03a5ngai15ggrnv1sq2aqr"))))
+ "07r4qgmnifw9jk2srjg0cvl310j0f9y35jrg0zqhlvhmyhg6n2c0"))))
(properties
`((upstream-name . "XVector")))
(build-system r-build-system)
@@ -4666,13 +4652,13 @@ and specific in detecting differential transcription.")
(define-public r-zlibbioc
(package
(name "r-zlibbioc")
- (version "1.38.0")
+ (version "1.40.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "zlibbioc" version))
(sha256
(base32
- "1dv5bf12kzk1yzyfs3g5syim16sbi44kalvzj2i2xcnxnl6x60ip"))))
+ "0a0dl7z58zxdj6938zbxixphgljj1giylk1nd05bb7qsccmp0xhj"))))
(properties
`((upstream-name . "zlibbioc")))
(build-system r-build-system)
@@ -4682,17 +4668,49 @@ and specific in detecting differential transcription.")
libraries for systems that do not have these available via other means.")
(license license:artistic2.0)))
+(define-public r-zellkonverter
+ (package
+ (name "r-zellkonverter")
+ (version "1.4.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "zellkonverter" version))
+ (sha256
+ (base32 "1ihp2f23lpdfgf3qliy22vrq8czm353hyhqf74r5r712190k6pgg"))))
+ (properties `((upstream-name . "zellkonverter")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-basilisk" ,r-basilisk)
+ ("r-cli" ,r-cli)
+ ("r-delayedarray" ,r-delayedarray)
+ ("r-matrix" ,r-matrix)
+ ("r-reticulate" ,r-reticulate)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-singlecellexperiment" ,r-singlecellexperiment)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (native-inputs `(("r-knitr" ,r-knitr)))
+ (home-page "https://github.com/theislab/zellkonverter")
+ (synopsis "Conversion between AnnData and single-cell experiments objects")
+ (description
+ "This package provides methods to convert between Python AnnData objects
+and SingleCellExperiment objects. These are primarily intended for use by
+downstream Bioconductor packages that wrap Python methods for single-cell data
+analysis. It also includes functions to read and write H5AD files used for
+saving AnnData objects to disk.")
+ (license license:expat)))
+
(define-public r-geneplotter
(package
(name "r-geneplotter")
- (version "1.70.0")
+ (version "1.72.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "geneplotter" version))
(sha256
(base32
- "1d085lfa3yif5wkys1fb0zzgg0cqwd1y18vasgqqdr6rva075d4z"))))
+ "1b7ngp9l00vrymx3d3nsda546s7p4ifr90idn3x2v4ilf38rfhp8"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotate" ,r-annotate)
@@ -4710,14 +4728,14 @@ libraries for systems that do not have these available via other means.")
(define-public r-oligoclasses
(package
(name "r-oligoclasses")
- (version "1.54.0")
+ (version "1.56.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "oligoClasses" version))
(sha256
(base32
- "1nsfyfpj264h6y322pzz0i001b0m862j3skbq5rjwlrj1p8j2gi7"))))
+ "1ia2f19swiwb0552nfwkai4gl0av07cj75b6jwiviqa1bli09264"))))
(properties `((upstream-name . "oligoClasses")))
(build-system r-build-system)
(propagated-inputs
@@ -4745,14 +4763,14 @@ packages.")
(define-public r-oligo
(package
(name "r-oligo")
- (version "1.56.0")
+ (version "1.58.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "oligo" version))
(sha256
(base32
- "0fyq77im6s79havjwbchhqhnllxs134jsi98g6msxz66h16lj3al"))))
+ "1cmnnq0d5xsjsx8c8n8wcl6l9d31sbglb8yrsibykcvnhw15fsf6"))))
(properties `((upstream-name . "oligo")))
(build-system r-build-system)
(inputs `(("zlib" ,zlib)))
@@ -4781,14 +4799,14 @@ Affymetrix (CEL files) and NimbleGen arrays (XYS files).")
(define-public r-qvalue
(package
(name "r-qvalue")
- (version "2.24.0")
+ (version "2.26.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "qvalue" version))
(sha256
(base32
- "0xssanffh1hr7f48mnazcpwi25rdp7mxlyb9nbf4q2mp7m40jnpm"))))
+ "1mn2qmqn89lfsx7rg54d1lwz45bfx0b91q6ahf43a1yzrrhwn138"))))
(build-system r-build-system)
(propagated-inputs
`(("r-ggplot2" ,r-ggplot2)
@@ -4836,13 +4854,13 @@ integration with @code{Rcpp}.")
(define-public r-apeglm
(package
(name "r-apeglm")
- (version "1.14.0")
+ (version "1.16.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "apeglm" version))
(sha256
(base32
- "1xld6ar440achik4dbd7vhiw6jfj0sb96jm52n7hav5bv4gag3mh"))))
+ "11w4vyc1sllmm5lh42krhidazid78n4s3lhikpy9kk2l57jmifbr"))))
(properties `((upstream-name . "apeglm")))
(build-system r-build-system)
(propagated-inputs
@@ -4863,13 +4881,13 @@ posterior for individual coefficients.")
(define-public r-greylistchip
(package
(name "r-greylistchip")
- (version "1.24.0")
+ (version "1.26.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GreyListChIP" version))
(sha256
(base32
- "1g9ja8p90czx83ar0l9ran7m6aggvszdbqm714fq7z4rxq9b4hs3"))))
+ "1h7h27q6l9d8j0shklyrh135zrwx56v4zzmm21cj1b7dvmwvpbcv"))))
(properties `((upstream-name . "GreyListChIP")))
(build-system r-build-system)
(propagated-inputs
@@ -4890,14 +4908,14 @@ signal in the input, that lead to spurious peaks during peak calling.")
(define-public r-diffbind
(package
(name "r-diffbind")
- (version "3.2.7")
+ (version "3.4.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DiffBind" version))
(sha256
(base32
- "01jfxcj5c0088vvsi3pz8fs0ka6n12l2j8s1d0rpqwa1y0444x7z"))))
+ "15p4jd9k520va6kzizkgsl4a18kh5r8i50qfdkv7xazsfhvxjm3i"))))
(properties `((upstream-name . "DiffBind")))
(build-system r-build-system)
(propagated-inputs
@@ -4968,13 +4986,13 @@ processing to visualization and annotation.")
(define-public r-mbkmeans
(package
(name "r-mbkmeans")
- (version "1.8.0")
+ (version "1.10.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "mbkmeans" version))
(sha256
(base32
- "1k7ngpx4s50jplrsv19zzjr7izpdl9wwppb218ih5cp0ki1gcc2n"))))
+ "03hpj218s8fynmk1s50s0rinhsljikxdrff06yc8ysbyc6hyfb4k"))))
(build-system r-build-system)
(native-inputs
`(("r-knitr" ,r-knitr)))
@@ -5000,14 +5018,14 @@ large datasets, including support for on-disk data representation.")
(define-public r-multtest
(package
(name "r-multtest")
- (version "2.48.0")
+ (version "2.50.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "multtest" version))
(sha256
(base32
- "1wi15v4llgv11hpb2j9h4a35nrnawnmvbz5d5dvgy8lhqrlq8w9a"))))
+ "03z71r7g318nwwgiz0k8qwbhghw1hhdhh1an4qnb0nc62c5x9kns"))))
(build-system r-build-system)
(propagated-inputs
`(("r-survival" ,r-survival)
@@ -5038,13 +5056,13 @@ expressed genes in DNA microarray experiments.")
(define-public r-graph
(package
(name "r-graph")
- (version "1.70.0")
+ (version "1.72.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "graph" version))
(sha256
(base32
- "1i7s198d5kw4gk6nqqsd3vqaknj4493p822f2za8q95gv6x02rxa"))))
+ "0x31lz3qimxmng6w99xnqazaj943d94b04nbziad4jfv7c1bc2h0"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)))
@@ -5136,14 +5154,14 @@ determining dependencies between variables, code improvement suggestions.")
(define-public r-chippeakanno
(package
(name "r-chippeakanno")
- (version "3.26.4")
+ (version "3.28.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ChIPpeakAnno" version))
(sha256
(base32
- "1iqzm7pifl9zrw3s06i6h85n1p01pd06vh1a93izyfhgybxn262d"))))
+ "05fbq8zvww1nlyykrri0hf4248i1i7w5cr453giagmjq7lgg4v3b"))))
(properties `((upstream-name . "ChIPpeakAnno")))
(build-system r-build-system)
(propagated-inputs
@@ -5190,13 +5208,13 @@ enrichedGO (addGeneIDs).")
(define-public r-matrixgenerics
(package
(name "r-matrixgenerics")
- (version "1.4.3")
+ (version "1.6.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "MatrixGenerics" version))
(sha256
(base32
- "1yir3rwhz5vf0pdn3fpvlc57c75k98gvv8gapajbvymz3lyghijv"))))
+ "1s75p8rrmj24r0vcbaiyw8xg8y84j388mv6iawai7pypfcl8s1z3"))))
(properties
`((upstream-name . "MatrixGenerics")))
(build-system r-build-system)
@@ -5217,12 +5235,12 @@ incompatibilities.")
(define-public r-marray
(package
(name "r-marray")
- (version "1.70.0")
+ (version "1.72.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "marray" version))
(sha256
- (base32 "0wpmrhqpyv27h1hn31hzz21r74r7yqx79ljv8i8gn6ix8lf5ca56"))))
+ (base32 "1la805y8j522vpiazm1z6wpq4ibia9bib5fpiia5mxmpzmqg6gzz"))))
(build-system r-build-system)
(propagated-inputs
`(("r-limma" ,r-limma)))
@@ -5236,12 +5254,12 @@ normalization and quality checking.")
(define-public r-cghbase
(package
(name "r-cghbase")
- (version "1.52.0")
+ (version "1.54.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "CGHbase" version))
(sha256
- (base32 "1p87k4vw981k97d9bckmprrfg55jwd91658rgxzjj8hnschf28a4"))))
+ (base32 "1kfxw126bddfy67cmf8dca9qq4bg7fkxjf8iaikplhvs5hl7bp4d"))))
(properties `((upstream-name . "CGHbase")))
(build-system r-build-system)
(propagated-inputs
@@ -5256,12 +5274,12 @@ the @code{arrayCGH} packages.")
(define-public r-cghcall
(package
(name "r-cghcall")
- (version "2.54.0")
+ (version "2.56.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "CGHcall" version))
(sha256
- (base32 "1zik04y2q0anzy85l0b4ryzkxpfx2fnmpwp5s7akyk1jfl2r8gw7"))))
+ (base32 "1r4y8zakgmdbnpwgp14kwh4iwqgqcmjq2yg4nc7j37p09bw1c8zr"))))
(properties `((upstream-name . "CGHcall")))
(build-system r-build-system)
(propagated-inputs
@@ -5279,12 +5297,12 @@ the @code{arrayCGH} packages.")
(define-public r-qdnaseq
(package
(name "r-qdnaseq")
- (version "1.28.0")
+ (version "1.30.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "QDNAseq" version))
(sha256
- (base32 "1p4544xlarkbgs9kybrrawq3v7qr6ix62nrc6l7dcksh2ka69yzf"))))
+ (base32 "1sza9br8agpdz1k9fn5wisir44sj8v0rk4wbx35d2c2kp9q70pqj"))))
(properties `((upstream-name . "QDNAseq")))
(build-system r-build-system)
(propagated-inputs
@@ -5292,7 +5310,6 @@ the @code{arrayCGH} packages.")
("r-cghbase" ,r-cghbase)
("r-cghcall" ,r-cghcall)
("r-dnacopy" ,r-dnacopy)
- ("r-future" ,r-future)
("r-future-apply" ,r-future-apply)
("r-genomicranges" ,r-genomicranges)
("r-iranges" ,r-iranges)
@@ -5312,14 +5329,14 @@ respectively.")
(define-public r-bayseq
(package
(name "r-bayseq")
- (version "2.26.0")
+ (version "2.28.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "baySeq" version))
(sha256
(base32
- "0hyc0sl2nf18bz0jxbzim0v41zwh2rnnr7l3p6zkk9wnw5gn7bbc"))))
+ "1zgxwb287ccz4wqsjxmffknnzziv12l4yrw7df912dxz6yccvd8r"))))
(properties `((upstream-name . "baySeq")))
(build-system r-build-system)
(propagated-inputs
@@ -5338,14 +5355,14 @@ more complex hypotheses) via empirical Bayesian methods.")
(define-public r-chipcomp
(package
(name "r-chipcomp")
- (version "1.22.0")
+ (version "1.24.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ChIPComp" version))
(sha256
(base32
- "1kfxjh1mynrgqsy2q6byf03cbymqc8w7l7672iyd0wj5qzlif4h5"))))
+ "1wdy92y5l3wa3zgg59w69rd7gdwf4z1waa4i2cccniccz463p1xq"))))
(properties `((upstream-name . "ChIPComp")))
(build-system r-build-system)
(propagated-inputs
@@ -5372,14 +5389,14 @@ datasets.")
(define-public r-riboprofiling
(package
(name "r-riboprofiling")
- (version "1.22.0")
+ (version "1.24.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "RiboProfiling" version))
(sha256
(base32
- "1jmd8yrv7p7hn4gdibg3svmhqxjyrnfp7cgsqg8zv862lgd75zsl"))))
+ "1szlzvm8ggjc40k4z2fxxa2h28g6j9wj2g5aw480v9hgyvvdw5lx"))))
(properties `((upstream-name . "RiboProfiling")))
(build-system r-build-system)
(propagated-inputs
@@ -5413,14 +5430,14 @@ assessment, principal component analysis on codon coverage.")
(define-public r-riboseqr
(package
(name "r-riboseqr")
- (version "1.26.0")
+ (version "1.28.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "riboSeqR" version))
(sha256
(base32
- "1m5w2j35wr0lzwir4s58z757vrcsj5mglsqrkvs241k0hlmn06qa"))))
+ "0nnhjvjl4c9yyfzjf8kcj4yky5cdimicp7lz008sczy19jq4vjhd"))))
(properties `((upstream-name . "riboSeqR")))
(build-system r-build-system)
(propagated-inputs
@@ -5441,14 +5458,14 @@ parsing of genetic sequencing data from ribosome profiling experiments.")
(define-public r-interactionset
(package
(name "r-interactionset")
- (version "1.20.0")
+ (version "1.22.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "InteractionSet" version))
(sha256
(base32
- "034xidjmn67n1471fnpdmz7gjm6p05cj8sp9nssc3gxdzn54a6xb"))))
+ "19m2mpby73zanai68rlqvzx9zccli4dz4kix93acrw9755xp3bsw"))))
(properties
`((upstream-name . "InteractionSet")))
(build-system r-build-system)
@@ -5475,14 +5492,14 @@ experiments.")
(define-public r-genomicinteractions
(package
(name "r-genomicinteractions")
- (version "1.26.0")
+ (version "1.28.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "GenomicInteractions" version))
(sha256
(base32
- "0zjl7rp5fk14kqsx0bkbpq6hqahbkiyvwa9aggp4kfb8hnmz9qal"))))
+ "090kxq5jn1jfr9fgbkvbjr5g4bcxzgsaal3gc9yx1n7pgmhccfmb"))))
(properties
`((upstream-name . "GenomicInteractions")))
(build-system r-build-system)
@@ -5516,14 +5533,14 @@ information and producing various plots and statistics.")
(define-public r-ctc
(package
(name "r-ctc")
- (version "1.66.0")
+ (version "1.68.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ctc" version))
(sha256
(base32
- "1v8aysvy6a3r1iafc3xvk885c128kb3pb9zpcdhdjcn0by96k8hh"))))
+ "1yq5igwzcwfhxy49qf3pralpikiqq7sqr1cig8mkpjpaj5bbaayx"))))
(build-system r-build-system)
(propagated-inputs `(("r-amap" ,r-amap)))
(home-page "https://bioconductor.org/packages/ctc/")
@@ -5536,14 +5553,14 @@ trees and clusters to other programs.")
(define-public r-goseq
(package
(name "r-goseq")
- (version "1.44.0")
+ (version "1.46.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "goseq" version))
(sha256
(base32
- "07qrxssx4rb8r958r1smx8xfpzdxpp55hci3201hcmz3mxz77i0s"))))
+ "1psl9mqgx1d21kayaxvrxriw34fq30wnd57q5c1sk3p8iahg73g0"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
@@ -5562,14 +5579,14 @@ defined categories which are over/under represented in RNA-seq data.")
(define-public r-glimma
(package
(name "r-glimma")
- (version "2.2.0")
+ (version "2.4.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Glimma" version))
(sha256
(base32
- "0dsk8qmwimzmd1x4k4jwg9q11jm1ahn8cw0gzd6s2gmigfls4hsa"))))
+ "0qkbx9n2vb7kvb5f00csnbffy5bm7hhbdvkx2isgzi0wv0y59kx9"))))
(properties `((upstream-name . "Glimma")))
(build-system r-build-system)
(propagated-inputs
@@ -5595,14 +5612,14 @@ information.")
(define-public r-rots
(package
(name "r-rots")
- (version "1.20.0")
+ (version "1.22.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ROTS" version))
(sha256
(base32
- "18wyi73l95df182vg3m014sxwdbpggr61vsbazhyw4vyx2fnzmpl"))))
+ "0qhy984y83a3nf4zw54rasw3vn932q4zb3gljifkw701jnrzqmki"))))
(properties `((upstream-name . "ROTS")))
(build-system r-build-system)
(propagated-inputs
@@ -5619,14 +5636,14 @@ in omics data.")
(define-public r-plgem
(package
(name "r-plgem")
- (version "1.64.0")
+ (version "1.66.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "plgem" version))
(sha256
(base32
- "1rz5jk5bgpk7gjknx79jyslahjg46q2f4bx6dgd0vwmarc29a45z"))))
+ "06w8xlw4j1fc9ipdgw55dvhp07f04icmhr20lqzwwhqd5pskrra3"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
@@ -5644,14 +5661,14 @@ genes or proteins in these datasets.")
(define-public r-inspect
(package
(name "r-inspect")
- (version "1.22.0")
+ (version "1.24.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "INSPEcT" version))
(sha256
(base32
- "0jh5db9dv5pb6b50sg22x8q55m3h0h0nkmb9mivvvp22dhyrd82z"))))
+ "072kv5k3giyll1clzrg0anqhyl4qbi7cjnmkqz25zdl5bab9l7jk"))))
(properties `((upstream-name . "INSPEcT")))
(build-system r-build-system)
(propagated-inputs
@@ -5691,14 +5708,14 @@ modeling the rates that determines changes in mature mRNA levels.")
(define-public r-dnabarcodes
(package
(name "r-dnabarcodes")
- (version "1.22.0")
+ (version "1.24.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DNABarcodes" version))
(sha256
(base32
- "1wiqmzjcb7flp7ldcgbx91asxxrmm1rg9pcfljniab9xcsldhksp"))))
+ "07yaz98r18mjny1ilmfnjxcra7xpklnd183pw0kasvsri01ccwxg"))))
(properties `((upstream-name . "DNABarcodes")))
(build-system r-build-system)
(propagated-inputs
@@ -5720,14 +5737,14 @@ demultiplexed, i.e. assigned to their original reference barcode.")
(define-public r-ruvseq
(package
(name "r-ruvseq")
- (version "1.26.0")
+ (version "1.28.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "RUVSeq" version))
(sha256
(base32
- "1fy0k1p0m209lzjpd5jhfnifa22lrn63qq3a3kn5g0xhbbmijzac"))))
+ "1a19klscykdgsd7izcxyr45ml7g0gpdj65gvbaw124mal2p4zi9q"))))
(properties `((upstream-name . "RUVSeq")))
(build-system r-build-system)
(propagated-inputs
@@ -5748,14 +5765,14 @@ samples.")
(define-public r-biocneighbors
(package
(name "r-biocneighbors")
- (version "1.10.0")
+ (version "1.12.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BiocNeighbors" version))
(sha256
(base32
- "0cjidi18wjip9xzx83890wjk40vvjq06prf1ag4m2kac47w01r7v"))))
+ "04in8l6j7frgm0a5dzphazfhn9cm8w775z5yir712jxa37mh1agr"))))
(properties `((upstream-name . "BiocNeighbors")))
(build-system r-build-system)
(propagated-inputs
@@ -5780,14 +5797,14 @@ achieved for all methods using the BiocParallel framework.")
(define-public r-scaledmatrix
(package
(name "r-scaledmatrix")
- (version "1.0.0")
+ (version "1.2.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ScaledMatrix" version))
(sha256
(base32
- "1j96fvw1waqxbv5c8myfmhsidq370z03yz13yqmrs4nn1rpn1a06"))))
+ "0vz8441gl5gycy1ypybwhq97bnyvhhlg6gxpi1dsdy2c9b6d81kc"))))
(properties `((upstream-name . "ScaledMatrix")))
(build-system r-build-system)
(propagated-inputs
@@ -5808,14 +5825,14 @@ multiplication.")
(define-public r-treeio
(package
(name "r-treeio")
- (version "1.16.2")
+ (version "1.18.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "treeio" version))
(sha256
(base32
- "1y60yvg1rl21cab9xrkns0209pg44mwr90qj099dvk97wsjkx67g"))))
+ "03gz378qrp6b9fcriqanfnphibqv4bxhvz48rigzkidkzz71wfaj"))))
(properties `((upstream-name . "treeio")))
(build-system r-build-system)
(propagated-inputs
@@ -5840,14 +5857,14 @@ platform for merging tree with associated data and converting file formats.")
(define-public r-ggtree
(package
(name "r-ggtree")
- (version "3.0.4")
+ (version "3.2.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ggtree" version))
(sha256
(base32
- "0xf4b9vfdyzzivwgw4ymapl5bb4k9p04mmr53822kxgfd5qrs1zx"))))
+ "1c6b7kjh44k096v8mhn53abr181vpbn7s6ab7zk4phnsyfxsclxb"))))
(properties `((upstream-name . "ggtree")))
(build-system r-build-system)
(propagated-inputs
@@ -5877,14 +5894,14 @@ data.")
(define-public r-metapod
(package
(name "r-metapod")
- (version "1.0.0")
+ (version "1.2.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "metapod" version))
(sha256
(base32
- "1hbcwr6d8gyrf4azh0gi588xkrg6gz7gsb5hbvzqkhplbsp6shlv"))))
+ "1s8dfzpgbpxbn3jvx891gvw3jyn43nlxb73yv1vjn85brk9zbqpk"))))
(properties `((upstream-name . "metapod")))
(build-system r-build-system)
(propagated-inputs
@@ -5906,14 +5923,14 @@ missing values and weighting where appropriate.")
(define-public r-biocsingular
(package
(name "r-biocsingular")
- (version "1.8.1")
+ (version "1.10.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BiocSingular" version))
(sha256
(base32
- "16gkwq8fb8jdchpnlzq2hz3i74a6pzbnc1bf93282h11mp7qr58l"))))
+ "0dkh6a23qymjcynppmpp3k1mzpfadv8dqyz410pxkqsxig4ldd4n"))))
(properties `((upstream-name . "BiocSingular")))
(build-system r-build-system)
(propagated-inputs
@@ -5985,14 +6002,14 @@ maps.")
(define-public r-savr
(package
(name "r-savr")
- (version "1.30.0")
+ (version "1.32.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "savR" version))
(sha256
(base32
- "1ynp334hm76zf05j4f6vha6r16s5f2ncxx9yviq4rxidk9r723jq"))))
+ "0dwl94j5dm5ngn8lyyc4bd9ihd1nqincvq26najjn6lw0x55ciky"))))
(properties `((upstream-name . "savR")))
(build-system r-build-system)
(propagated-inputs
@@ -6011,14 +6028,14 @@ Viewer (SAV) files, access data, and generate QC plots.")
(define-public r-chipexoqual
(package
(name "r-chipexoqual")
- (version "1.16.0")
+ (version "1.18.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ChIPexoQual" version))
(sha256
(base32
- "0fbrf5s6pz115djm7xw95k1d0p7svi40aacbb3d52wmx5azwj424"))))
+ "1hh3mhfcngyx7cpzns8mjqviy8vfzrvxpv6nyizflpfmsr39mxfk"))))
(properties `((upstream-name . "ChIPexoQual")))
(build-system r-build-system)
(propagated-inputs
@@ -6051,13 +6068,13 @@ sequencing data.")
(define-public r-copynumber
(package
(name "r-copynumber")
- (version "1.32.0")
+ (version "1.34.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "copynumber" version))
(sha256
(base32
- "03pvjzjrcsbjfw3855s3whfzin45vaipy7cahnj6fywdysvh8hps"))))
+ "143ifvjkjz0392drm82xmpj1f8b5pc2dyyxyc9dkqmay8lf1n534"))))
(build-system r-build-system)
(propagated-inputs
`(("r-s4vectors" ,r-s4vectors)
@@ -6074,14 +6091,14 @@ penalized least squares regression method.")
(define-public r-dnacopy
(package
(name "r-dnacopy")
- (version "1.66.0")
+ (version "1.68.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DNAcopy" version))
(sha256
(base32
- "0mgq814f6c2271d2lxg763bsnv3ma4ari5xa4x1rbksv8yvcjc4d"))))
+ "19ax431i97r49gh1232vf8mgmkvc6k26lnq44j3g10n6q01czswm"))))
(properties `((upstream-name . "DNAcopy")))
(build-system r-build-system)
(native-inputs `(("gfortran" ,gfortran)))
@@ -6174,14 +6191,14 @@ and regression inferences from RNA-sequencing data.")
(define-public r-ebseq
(package
(name "r-ebseq")
- (version "1.32.0")
+ (version "1.34.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "EBSeq" version))
(sha256
(base32
- "0h5v3vrb90zim80bdnr3aw58g3h7zjqa4l9i0jwx5j19ywf54fdz"))))
+ "1p8i04v5h6mbc8zqbf3rifbwwylzzc1fqrkhh0a0mbcgq2nv7i9m"))))
(properties `((upstream-name . "EBSeq")))
(build-system r-build-system)
(propagated-inputs
@@ -6198,13 +6215,13 @@ gene and isoform level using RNA-seq data")
(define-public r-karyoploter
(package
(name "r-karyoploter")
- (version "1.18.0")
+ (version "1.20.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "karyoploteR" version))
(sha256
(base32
- "11sgxz2xz685pgm8mf0hzm6aryx4fj5g3dlffjzpqxh3awfqa19p"))))
+ "0x3mld9q55r2fy452wxq5sjzmms10zmpkzs71c3w1fdli5hwszdq"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
@@ -6236,14 +6253,14 @@ coordinates.")
(define-public r-lpsymphony
(package
(name "r-lpsymphony")
- (version "1.20.0")
+ (version "1.22.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "lpsymphony" version))
(sha256
(base32
- "0aw4b3p5z8ys7zlwy8s3bsqk03xwx42311yxr7q14w3f7sn3shzn"))))
+ "1bv28b1fgcazv6j0xw4nn6wljs37qnkyahqy7anrwissdpryhjfs"))))
(build-system r-build-system)
(inputs
`(("zlib" ,zlib)))
@@ -6266,14 +6283,14 @@ to install interface to SYMPHONY.")
(define-public r-ihw
(package
(name "r-ihw")
- (version "1.20.0")
+ (version "1.22.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "IHW" version))
(sha256
(base32
- "0b393a8ayzbnrgkk562w1dj7avacpb3wc7yq7awiki24wi5g2lfw"))))
+ "0vgij5zyaw3fh7arkg4jy1mizsqzbkcsjl05mh3ng2bqh30kyqqx"))))
(properties `((upstream-name . "IHW")))
(build-system r-build-system)
(propagated-inputs
@@ -6298,14 +6315,14 @@ independent of the p-value under the null hypothesis.")
(define-public r-icobra
(package
(name "r-icobra")
- (version "1.20.0")
+ (version "1.22.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "iCOBRA" version))
(sha256
(base32
- "190rkx3sivj68in36hhin5v535yd6fvlvm7l90w1bl38zpb7p6jn"))))
+ "0qg32g1rfvh6mx8wny1lrva9vc347288hzml7yb4rnrsx1hggkpa"))))
(properties `((upstream-name . "iCOBRA")))
(build-system r-build-system)
(propagated-inputs
@@ -6334,14 +6351,14 @@ interactive exploration of results.")
(define-public r-residualmatrix
(package
(name "r-residualmatrix")
- (version "1.2.0")
+ (version "1.4.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ResidualMatrix" version))
(sha256
(base32
- "0p7va19aw0j6anx7ck879kbi5cn7dy712h5ia94adr38ssismv1v"))))
+ "0xsn4fm34a7xpkgmx3a1j2xzdaxf2hyla1062wqn04kw0k9y29vg"))))
(properties
`((upstream-name . "ResidualMatrix")))
(build-system r-build-system)
@@ -6365,14 +6382,14 @@ multiplication and calculation of row/column sums or means.")
(define-public r-batchelor
(package
(name "r-batchelor")
- (version "1.8.1")
+ (version "1.10.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "batchelor" version))
(sha256
(base32
- "1bkk69b5llkmvmpsnhymwjm2szmzypgszfsw8mak1b5ms5zf8lr0"))))
+ "0axkic11bwjbw8apwxx6p51s7jvlwhq7xi1bdknn54k86axq84dr"))))
(properties `((upstream-name . "batchelor")))
(build-system r-build-system)
(propagated-inputs
@@ -6408,14 +6425,14 @@ the numbers of cells across batches.")
(define-public r-mast
(package
(name "r-mast")
- (version "1.18.0")
+ (version "1.20.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MAST" version))
(sha256
(base32
- "1gkpagam5rap36viyr3n4psa658x9vckrxap1h67jasiiyrcfz2d"))))
+ "14h6giny9lhzqjsx3h7gdhsm8wfwnvp5zsl4avrflip0jmsn45yy"))))
(properties `((upstream-name . "MAST")))
(build-system r-build-system)
(propagated-inputs
@@ -6443,14 +6460,14 @@ single cell assay data.")
(define-public r-monocle
(package
(name "r-monocle")
- (version "2.20.0")
+ (version "2.22.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "monocle" version))
(sha256
(base32
- "05j1vc51f39xalggdq27y7218gkr3zq7fh7jhzsb4jj7fpn837ry"))))
+ "0wb2c1jf502lrfx3d0amb09fvhalrwxvpsp99jsab162v4hddg85"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
@@ -6600,14 +6617,14 @@ several functions from the R igraph package.")
(define-public r-noiseq
(package
(name "r-noiseq")
- (version "2.36.0")
+ (version "2.38.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "NOISeq" version))
(sha256
(base32
- "18d51dv2ygsm7kkwal341f1wrwrazyns0045j00vld367kic8jiz"))))
+ "0mmvzf8y4gm84hgjdpf86b1y37237wp5mc3x1g6sdiz9qi8l356v"))))
(properties `((upstream-name . "NOISeq")))
(build-system r-build-system)
(propagated-inputs
@@ -6627,14 +6644,14 @@ assumptions.")
(define-public r-scdd
(package
(name "r-scdd")
- (version "1.16.0")
+ (version "1.18.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "scDD" version))
(sha256
(base32
- "1dw9m3m99apmbs32461c6lnmy81n5hxbhz3p8jk419gajkh4v1ji"))))
+ "0gjdjkpkm9zc9hzzb6r2mknl4zyg7s2lgqppmzzhgcnvlmgvm5b5"))))
(properties `((upstream-name . "scDD")))
(build-system r-build-system)
(propagated-inputs
@@ -6665,14 +6682,14 @@ distributions.")
(define-public r-scone
(package
(name "r-scone")
- (version "1.16.1")
+ (version "1.18.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "scone" version))
(sha256
(base32
- "0zw8g4mql7b02xqwhc1i0bnhm20c1q9xqc7yz84j98pqbi996vi5"))))
+ "1fqlwg195rzpwh35cj941vhmj2plzpn253skig6glr0z2sirr9r1"))))
(build-system r-build-system)
(propagated-inputs
`(("r-aroma-light" ,r-aroma-light)
@@ -6709,18 +6726,19 @@ high-throughput analyses.")
(define-public r-geoquery
(package
(name "r-geoquery")
- (version "2.60.0")
+ (version "2.62.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "GEOquery" version))
(sha256
(base32
- "0jhkdbcd03d5n8vn3xkad6f21xjkawyxc9rdwcj8vwc8alx730am"))))
+ "0fkx4jh1s76l015vwikkryarlx6iihb1z935nzpdhah3rpqx3b3z"))))
(properties `((upstream-name . "GEOquery")))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
+ ("r-data-table" ,r-data-table)
("r-dplyr" ,r-dplyr)
("r-httr" ,r-httr)
("r-limma" ,r-limma)
@@ -6742,14 +6760,14 @@ the bridge between GEO and BioConductor.")
(define-public r-illuminaio
(package
(name "r-illuminaio")
- (version "0.34.0")
+ (version "0.36.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "illuminaio" version))
(sha256
(base32
- "1sy0i3nbzsw4ymdxaiwpyx1vcg9yp3i8xfjcymqwhv95j3kyglv9"))))
+ "0icsp610am5vrd8x2h9c450phn4vl9c5wnzqmkix5hkqzrykk34m"))))
(build-system r-build-system)
(propagated-inputs
`(("r-base64" ,r-base64)))
@@ -6763,14 +6781,14 @@ files, including IDAT.")
(define-public r-siggenes
(package
(name "r-siggenes")
- (version "1.66.0")
+ (version "1.68.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "siggenes" version))
(sha256
(base32
- "0lva0f255fcpy625frvij4n14q7nw4jcx8n2hlkxid4mgkfqwlhf"))))
+ "1fymp5ci1nwkk5yfj7hli464xqvvlvzf2a5j0w3qkxly9hrymix9"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
@@ -6789,14 +6807,14 @@ Bayes Analyses of Microarrays} (EBAM).")
(define-public r-bumphunter
(package
(name "r-bumphunter")
- (version "1.34.0")
+ (version "1.36.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "bumphunter" version))
(sha256
(base32
- "0wi38vwfi8qr10x4xifhylxx7vfc6fqvqs649iq7lf0y7islwq2v"))))
+ "0d5cz9xy7vhcaj5n3h4cfiv08sn7wn83458525pdwvdzzm449xgv"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
@@ -6823,14 +6841,14 @@ studies.")
(define-public r-minfi
(package
(name "r-minfi")
- (version "1.38.0")
+ (version "1.40.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "minfi" version))
(sha256
(base32
- "189lzppvrz6bw2kpppawgsfjyh2ahyy8bi9z8srpas67qf2r8jmj"))))
+ "0d5220nknwgi1020vhvf7408n5p80dmad66n85af5776qn84a6nx"))))
(build-system r-build-system)
(propagated-inputs
`(("r-beanplot" ,r-beanplot)
@@ -6874,14 +6892,14 @@ methylation arrays.")
(define-public r-methylumi
(package
(name "r-methylumi")
- (version "2.38.0")
+ (version "2.40.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "methylumi" version))
(sha256
(base32
- "1941rc524ssx8gwhmwk40mgfrhddfs6hgldvs7bi22r29gm4y7qj"))))
+ "1lfcsv8k9c4ndfwlbdk3vd7fq58100bfijyxklna41zf8m8kkkka"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotate" ,r-annotate)
@@ -6891,6 +6909,7 @@ methylation arrays.")
("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19)
("r-genefilter" ,r-genefilter)
("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicfeatures" ,r-genomicfeatures)
("r-genomicranges" ,r-genomicranges)
("r-ggplot2" ,r-ggplot2)
("r-illuminaio" ,r-illuminaio)
@@ -6920,14 +6939,14 @@ and Infinium HD arrays are also included.")
(define-public r-lumi
(package
(name "r-lumi")
- (version "2.44.0")
+ (version "2.46.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "lumi" version))
(sha256
(base32
- "0qjdxjdzfnnxcm07bf51v38388s5qf1i03l1sdb9jf3gxdh8yh02"))))
+ "0v33p66vn4alhx2il9wwdvc9sqvgasgj0s2gk85gjc76ad0017in"))))
(build-system r-build-system)
(propagated-inputs
`(("r-affy" ,r-affy)
@@ -6959,14 +6978,14 @@ especially Illumina Infinium methylation microarrays.")
(define-public r-linnorm
(package
(name "r-linnorm")
- (version "2.16.0")
+ (version "2.18.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Linnorm" version))
(sha256
(base32
- "035hrniycqadmkwg8rmzw8szv0amhy31390izy91rfrld31v2yy7"))))
+ "1bdnglznsfs1kdscqyjv595wiy09khcv9kxm4fmbnmksisqjz5qj"))))
(properties `((upstream-name . "Linnorm")))
(build-system r-build-system)
(propagated-inputs
@@ -7020,14 +7039,14 @@ evaluation of DEG analysis methods.")
(define-public r-ioniser
(package
(name "r-ioniser")
- (version "2.16.0")
+ (version "2.18.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "IONiseR" version))
(sha256
(base32
- "0fknlwdfd49v09zspg0337b0zzc8hqza3563yrw51viw3g35d6q3"))))
+ "1hdg446z5s616aaalzz49if1wp9nmzm2mbyva82m1vz8i7ih9m4h"))))
(properties `((upstream-name . "IONiseR")))
(build-system r-build-system)
(propagated-inputs
@@ -7117,13 +7136,13 @@ published results; and a routine for graphical display.")
(define-public r-tradeseq
(package
(name "r-tradeseq")
- (version "1.6.0")
+ (version "1.8.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "tradeSeq" version))
(sha256
(base32
- "0fgmb309pvqf3chdhqgbd4lzhahcj5g71sica33nzn98qhipldx7"))))
+ "1s5anbb38gi5sfkxy19zpvkj8d0ij7m6cd0z4gmx4f5pf7pz0m3j"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
@@ -7132,10 +7151,10 @@ published results; and a routine for graphical display.")
("r-ggplot2" ,r-ggplot2)
("r-igraph" ,r-igraph)
("r-magrittr" ,r-magrittr)
+ ("r-mass" ,r-mass)
("r-matrix" ,r-matrix)
("r-matrixstats" ,r-matrixstats)
("r-mgcv" ,r-mgcv)
- ("r-monocle" ,r-monocle)
("r-pbapply" ,r-pbapply)
("r-princurve" ,r-princurve)
("r-rcolorbrewer" ,r-rcolorbrewer)
@@ -7144,6 +7163,7 @@ published results; and a routine for graphical display.")
("r-slingshot" ,r-slingshot)
("r-summarizedexperiment" ,r-summarizedexperiment)
("r-tibble" ,r-tibble)
+ ("r-trajectoryutils" ,r-trajectoryutils)
("r-viridis" ,r-viridis)))
(native-inputs
`(("r-knitr" ,r-knitr)))
@@ -7187,14 +7207,14 @@ peak definition in combination with known profile characteristics.")
(define-public r-varianttools
(package
(name "r-varianttools")
- (version "1.34.0")
+ (version "1.36.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "VariantTools" version))
(sha256
(base32
- "1gpzrln2clfrja8rzxhsis6bi1xqglh3h2lhvqlnrx4lqxhbkv9c"))))
+ "0079dsgav4q03c4i0dhggc88iifd828n73kjv3sahim9akafdshl"))))
(properties `((upstream-name . "VariantTools")))
(build-system r-build-system)
(propagated-inputs
@@ -7227,14 +7247,14 @@ gmapR.")
(define-public r-heatplus
(package
(name "r-heatplus")
- (version "3.0.0")
+ (version "3.2.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Heatplus" version))
(sha256
(base32
- "0xwg3sxmihg3p6v3nxgrqy0nrqxi6razg3b3rjh2gcb2vv8gcqng"))))
+ "0yrnjrbfn8vjzvp2742lyxdqca4s18h73j44qxw7ib95x3p4lndf"))))
(properties `((upstream-name . "Heatplus")))
(build-system r-build-system)
(propagated-inputs
@@ -7252,14 +7272,14 @@ information about samples and features can be added to the plot.")
(define-public r-gosemsim
(package
(name "r-gosemsim")
- (version "2.18.1")
+ (version "2.20.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "GOSemSim" version))
(sha256
(base32
- "00dbgkiv9x7g2i0anzcxpycwqqqry0y7jl3ad93lhvi31qnqq1sm"))))
+ "15qi69kkgah7g25bymk9q1xf16hp1rd040fglg0svnydylg2d0ab"))))
(properties `((upstream-name . "GOSemSim")))
(build-system r-build-system)
(propagated-inputs
@@ -7281,14 +7301,14 @@ sets of GO terms, gene products and gene clusters.")
(define-public r-anota
(package
(name "r-anota")
- (version "1.40.0")
+ (version "1.42.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "anota" version))
(sha256
(base32
- "039bmcv5l44gszb6xapbihp3mfqdaaa8mfc05y702p78i7x93g5y"))))
+ "0agvcpb3lr9v55h53ywf662gpxayivxacv8dcm526cc8i8hdqa9f"))))
(build-system r-build-system)
(propagated-inputs
`(("r-multtest" ,r-multtest)
@@ -7312,14 +7332,14 @@ the data set is suitable for such analysis.")
(define-public r-sigpathway
(package
(name "r-sigpathway")
- (version "1.60.0")
+ (version "1.62.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "sigPathway" version))
(sha256
(base32
- "1xz5nbw5dzyah8az7mpwj8m27fsvpi2jjhfg3n27dsv8rvdncqi8"))))
+ "1c46m1gbgiygcj8m65h8iwzk3fkp6nynd6rk1f5qdh7kw5ap28f9"))))
(properties `((upstream-name . "sigPathway")))
(build-system r-build-system)
(home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
@@ -7334,17 +7354,19 @@ phenotype of interest.")
(define-public r-fcscan
(package
(name "r-fcscan")
- (version "1.6.0")
+ (version "1.8.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "fcScan" version))
(sha256
- (base32 "10fcz741dr3wbb9f63qywlrays4cnvfnsm6yw4bmkrwk6ccijg8h"))))
+ (base32 "0b161ayq4m9xxfs0lgw632lgygzabz8gjl0n75050pa7qaazknvd"))))
(properties `((upstream-name . "fcScan")))
(build-system r-build-system)
(propagated-inputs
- `(("r-genomicranges" ,r-genomicranges)
+ `(("r-doparallel" ,r-doparallel)
+ ("r-foreach" ,r-foreach)
+ ("r-genomicranges" ,r-genomicranges)
("r-iranges" ,r-iranges)
("r-plyr" ,r-plyr)
("r-rtracklayer" ,r-rtracklayer)
@@ -7365,14 +7387,14 @@ presence of additional sites within the allowed window size.")
(define-public r-fgsea
(package
(name "r-fgsea")
- (version "1.18.0")
+ (version "1.20.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "fgsea" version))
(sha256
(base32
- "1mhdgy46nxgv7v54bk9bqfy0vgjzl1law7zy718swdd762xn6g9d"))))
+ "10flcdm4b1kxnsvhl4k6mwkzb1vbai33k291j8nsrhj2cl5l8gm9"))))
(build-system r-build-system)
(propagated-inputs
`(("r-bh" ,r-bh)
@@ -7397,14 +7419,14 @@ to multiple hypothesis correction.")
(define-public r-dose
(package
(name "r-dose")
- (version "3.18.2")
+ (version "3.20.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DOSE" version))
(sha256
(base32
- "0kp6j42mpxrpd02cjrzqmrx3rvvpi90xiy4gc5km6ny3vxbhlaqw"))))
+ "0hj5hn54g8a3gj4q9200bffcy9m1mvkiwbg60ysv1hxxbpi57kmv"))))
(properties `((upstream-name . "DOSE")))
(build-system r-build-system)
(propagated-inputs
@@ -7432,17 +7454,17 @@ data.")
(define-public r-enrichplot
(package
(name "r-enrichplot")
- (version "1.12.2")
+ (version "1.14.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "enrichplot" version))
(sha256
(base32
- "194sfmcnjfi3fvvfpljg1f80f44vvvxiij336b8z1dgzki6bqa3r"))))
+ "0nsx96mkcg0hhg3x8jndzq3xvq9bq7m4yf1b3ry73b17ladx81ch"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-cowplot" ,r-cowplot)
+ `(("r-aplot" ,r-aplot)
("r-dose" ,r-dose)
("r-ggplot2" ,r-ggplot2)
("r-ggraph" ,r-ggraph)
@@ -7455,7 +7477,8 @@ data.")
("r-rcolorbrewer" ,r-rcolorbrewer)
("r-reshape2" ,r-reshape2)
("r-scatterpie" ,r-scatterpie)
- ("r-shadowtext" ,r-shadowtext)))
+ ("r-shadowtext" ,r-shadowtext)
+ ("r-yulab-utils" ,r-yulab-utils)))
(native-inputs
`(("r-knitr" ,r-knitr)))
(home-page "https://github.com/GuangchuangYu/enrichplot")
@@ -7469,14 +7492,14 @@ All the visualization methods are developed based on ggplot2 graphics.")
(define-public r-clusterprofiler
(package
(name "r-clusterprofiler")
- (version "4.0.5")
+ (version "4.2.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "clusterProfiler" version))
(sha256
(base32
- "1dccrl2ffhgmv3iqlmpln7z86ahpf0j9ma194fnknsgi3cd9rhrl"))))
+ "18y7482sw0awlhazikq13r2r0zid9ksk942rma87m448y1cq2fi5"))))
(properties
`((upstream-name . "clusterProfiler")))
(build-system r-build-system)
@@ -7506,13 +7529,13 @@ profiles (GO and KEGG) of gene and gene clusters.")
(define-public r-clusterexperiment
(package
(name "r-clusterexperiment")
- (version "2.12.0")
+ (version "2.14.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "clusterExperiment" version))
(sha256
(base32
- "1fhmayciwn1m124b4dcs3gzbghgk9f7a7qmjnvvxc958cywcwkx5"))))
+ "0riray1f841d5fx6mbcki5xmqz21kg5q5l0qz4pkgg9c1d9f7mbc"))))
(build-system r-build-system)
(native-inputs
`(("r-knitr" ,r-knitr)))
@@ -7552,14 +7575,14 @@ expression data sets.")
(define-public r-mlinterfaces
(package
(name "r-mlinterfaces")
- (version "1.72.0")
+ (version "1.74.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MLInterfaces" version))
(sha256
(base32
- "0ipzv7wdvfqhdyjiak956qq201igsdxm6dr6rh3dj6cssgsrnrpb"))))
+ "1nzy04fqwzb0ywiafgx3m3i2n1b0g4pcg8mlgh8yz5d3mmna4kag"))))
(properties `((upstream-name . "MLInterfaces")))
(build-system r-build-system)
(propagated-inputs
@@ -7594,14 +7617,14 @@ data in R and Bioconductor containers.")
(define-public r-annaffy
(package
(name "r-annaffy")
- (version "1.64.2")
+ (version "1.66.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "annaffy" version))
(sha256
(base32
- "03y633vgxprd2abhanj4sanmb4ymz7az5aiasxn6wjzawiqjdcb1"))))
+ "0crj37v571005brdd0ypfx2a7d1f829xxj2hahp2gy8aj9xm4s8l"))))
(build-system r-build-system)
(arguments
`(#:phases
@@ -7630,14 +7653,14 @@ It allows searching of biological metadata using various criteria.")
(define-public r-a4core
(package
(name "r-a4core")
- (version "1.40.0")
+ (version "1.42.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "a4Core" version))
(sha256
(base32
- "00fi753nsayv0xspavw8r9ni1sim8ng33hp3d3kj2b8ihygd1s10"))))
+ "074aa52y6c70417lxwrclk613gbs7zv3326g9ndbbzzs5pmnh1y0"))))
(properties `((upstream-name . "a4Core")))
(build-system r-build-system)
(propagated-inputs
@@ -7655,14 +7678,14 @@ arrays.")
(define-public r-a4classif
(package
(name "r-a4classif")
- (version "1.40.0")
+ (version "1.42.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "a4Classif" version))
(sha256
(base32
- "1lz85bys5dp5d1ir9c9c4wy85wkk62s14niyzzxaqrxpsji2p2iw"))))
+ "0q50d41n7drj5c9x6njyvzr6bj7glmkp1vpyz6cpj97j2v9nikwb"))))
(properties `((upstream-name . "a4Classif")))
(build-system r-build-system)
(propagated-inputs
@@ -7685,14 +7708,14 @@ Affymetrix arrays.")
(define-public r-a4preproc
(package
(name "r-a4preproc")
- (version "1.40.0")
+ (version "1.42.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "a4Preproc" version))
(sha256
(base32
- "1jibm2f5glzsrvl64hxc5sf59d4w6ry0f663p619hfr44mi1mpri"))))
+ "1qzr54w1qys1ppd71i5b57503dijfnnbn516a2mfk5l9l7wr728d"))))
(properties `((upstream-name . "a4Preproc")))
(build-system r-build-system)
(propagated-inputs
@@ -7710,14 +7733,14 @@ is used for preprocessing the arrays.")
(define-public r-a4reporting
(package
(name "r-a4reporting")
- (version "1.40.0")
+ (version "1.42.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "a4Reporting" version))
(sha256
(base32
- "09jjfby5znmg2fdkhpbinx2v21zrfa44qq7cylcn9ipffqx3pk86"))))
+ "1vyah71gm4ngsgy0y10cdxa9b1g810gqa5pbvb3krh5i6h35smwr"))))
(properties `((upstream-name . "a4Reporting")))
(build-system r-build-system)
(propagated-inputs
@@ -7734,14 +7757,14 @@ provides reporting features.")
(define-public r-a4base
(package
(name "r-a4base")
- (version "1.40.0")
+ (version "1.42.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "a4Base" version))
(sha256
(base32
- "101w4i0w8n7qhki22qr8l8wk8w6zalzmcywqm2g4238qv7xbnr8p"))))
+ "0rddxnflvbc6z4sj2h8js8yfh0zhrrwj8fk00wicaqp4rkr5yaxy"))))
(properties `((upstream-name . "a4Base")))
(build-system r-build-system)
(propagated-inputs
@@ -7765,14 +7788,14 @@ Affymetrix arrays.")
(define-public r-a4
(package
(name "r-a4")
- (version "1.40.0")
+ (version "1.42.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "a4" version))
(sha256
(base32
- "0bwn185admy5k99fkd2dhhvy7x1f75r0mqn5k24dbbg0paw6nnr8"))))
+ "0mkgim93441zxhn4wmbin9ydl94srsawis0xwx479l0byj88n07m"))))
(build-system r-build-system)
(propagated-inputs
`(("r-a4base" ,r-a4base)
@@ -7790,14 +7813,14 @@ Affymetrix arrays.")
(define-public r-abseqr
(package
(name "r-abseqr")
- (version "1.10.0")
+ (version "1.12.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "abseqR" version))
(sha256
(base32
- "1xvk84gd1lfq1icrfwwd6y79zywrisfnc3knprigzzax31aks32c"))))
+ "1v9g71x689ly107c0qmc5iv8qk63nn6lp7yd03jf7hlcafmvqsvz"))))
(properties `((upstream-name . "abseqR")))
(build-system r-build-system)
(inputs
@@ -7838,14 +7861,14 @@ further downstream analysis on its output.")
(define-public r-bacon
(package
(name "r-bacon")
- (version "1.20.0")
+ (version "1.22.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "bacon" version))
(sha256
(base32
- "1yp0675n1g8rxdjdd7w8al5c9jq96h0kfm8218mc50z0p2fasgbj"))))
+ "13dhma34j9ggryainn4x6qvd3hphpxks5gf0mysia00r9hhpwwlc"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biocparallel" ,r-biocparallel)
@@ -7865,14 +7888,14 @@ fitting a three-component normal mixture on z-scores.")
(define-public r-rgadem
(package
(name "r-rgadem")
- (version "2.40.0")
+ (version "2.42.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "rGADEM" version))
(sha256
(base32
- "05drbhjqn5kik6k4h03vr3d2b6pv5rm65lsnkyx4caxxcdii4jzm"))))
+ "1v8xgqqv7m2kyc38x9ppwsv87ivll5ppd6z76zcxj5yspkkrqw3v"))))
(properties `((upstream-name . "rGADEM")))
(build-system r-build-system)
(propagated-inputs
@@ -7923,12 +7946,12 @@ distributions, modules and filter motifs.")
(define-public r-motifdb
(package
(name "r-motifdb")
- (version "1.34.0")
+ (version "1.36.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "MotifDb" version))
(sha256
- (base32 "04cmgg5mw1cqbg95zyfc2imykmdxyff16w26rq97xghcxwiq2b3z"))))
+ (base32 "0a2zg26zzk7bj5c33mbwl8dx9lh1hns8q8kwp09rbfjdichv7425"))))
(properties `((upstream-name . "MotifDb")))
(build-system r-build-system)
(propagated-inputs
@@ -7950,12 +7973,12 @@ frequency matrices from nine public sources, for multiple organisms.")
(define-public r-motifbreakr
(package
(name "r-motifbreakr")
- (version "2.6.1")
+ (version "2.8.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "motifbreakR" version))
(sha256
- (base32 "1n6v8a7c27aswmbrlcwcpghf27aplkc6nn923imglc3c0sh2lkrz"))))
+ (base32 "0lrgy64sv2ma6kylp4lsbwkg6ci1kn6qkk0cvzw3m4k3bgia1npj"))))
(properties `((upstream-name . "motifbreakR")))
(build-system r-build-system)
(propagated-inputs
@@ -8001,14 +8024,14 @@ Bioconductor.")
(define-public r-motifstack
(package
(name "r-motifstack")
- (version "1.36.0")
+ (version "1.38.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "motifStack" version))
(sha256
(base32
- "0yn348kmw7v46iym913ncx4yh5nxzmba8bdys52s12ldgjja53gp"))))
+ "1ck6bbnrab8mbf70alfdsrcv6lq0fkvcy3klhcwyxxir7r9sgbaz"))))
(properties `((upstream-name . "motifStack")))
(build-system r-build-system)
(propagated-inputs
@@ -8032,14 +8055,14 @@ type and symbol colors.")
(define-public r-genomicscores
(package
(name "r-genomicscores")
- (version "2.4.0")
+ (version "2.6.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "GenomicScores" version))
(sha256
(base32
- "1b8982fj0r7igj749wljsdfn3c985w8n3d5gbhr5rw73llfb8x6w"))))
+ "18fzi2qi95851ci7qrzwpb7v6fhwp6xi1d1vk11xbygpbvql5mls"))))
(properties `((upstream-name . "GenomicScores")))
(build-system r-build-system)
(propagated-inputs
@@ -8069,14 +8092,14 @@ position-specific scores within R and Bioconductor.")
(define-public r-atacseqqc
(package
(name "r-atacseqqc")
- (version "1.16.0")
+ (version "1.18.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ATACseqQC" version))
(sha256
(base32
- "168g3xkhjzrfjpa1ynifdyfhsxx3rpyrbybsarlzr9kslw1cdkxl"))))
+ "0i1i3bfkp1xsjdl1nd56mlh66qz3aasd1hp09d4i31njz2f9znwn"))))
(properties `((upstream-name . "ATACseqQC")))
(build-system r-build-system)
(propagated-inputs
@@ -8116,14 +8139,14 @@ footprints.")
(define-public r-gofuncr
(package
(name "r-gofuncr")
- (version "1.12.0")
+ (version "1.14.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "GOfuncR" version))
(sha256
(base32
- "0lp2gmjlsk1yqxim5pi26i27iijw11lrcxmji7ynlag359yfnynd"))))
+ "08n1d03i4l2dl47axmrziiypi83yffndf0ww1b32skyjm2r0x127"))))
(properties `((upstream-name . "GOfuncR")))
(build-system r-build-system)
(propagated-inputs
@@ -8165,14 +8188,14 @@ annotations and ontologies.")
(define-public r-abaenrichment
(package
(name "r-abaenrichment")
- (version "1.22.0")
+ (version "1.24.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ABAEnrichment" version))
(sha256
(base32
- "15v5n6d3mnj9d86swkh9agfvrsd065dldaywm1adwmkhhk525wmd"))))
+ "1sp3f72rzlr822dxx42bswynrwwfx6f520hdhfdikqp13p2y4044"))))
(properties `((upstream-name . "ABAEnrichment")))
(build-system r-build-system)
(propagated-inputs
@@ -8222,14 +8245,14 @@ different identifieres using the Biocore Data Team data-packages (e.g.
(define-public r-annotationtools
(package
(name "r-annotationtools")
- (version "1.66.0")
+ (version "1.68.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "annotationTools" version))
(sha256
(base32
- "18dd8saqx17fplvv5sbfz4p9fy7ksy3n9348rd3qlczihcrh9i3w"))))
+ "0grdswbf8nj0qwl0n5pqsir9242dry85j6m688j81gwwjgmzidvh"))))
(properties
`((upstream-name . "annotationTools")))
(build-system r-build-system)
@@ -8247,14 +8270,14 @@ text files).")
(define-public r-allelicimbalance
(package
(name "r-allelicimbalance")
- (version "1.30.0")
+ (version "1.32.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "AllelicImbalance" version))
(sha256
(base32
- "1mn6975npncmfjlpjs3s2pgsrm32xgvnyl2vh1922l6vra97dkrc"))))
+ "1s6arjd0nxgxyqy7vhqcb78k0ss7vwrhv41pm346hs1nyr5dkzaq"))))
(properties
`((upstream-name . "AllelicImbalance")))
(build-system r-build-system)
@@ -8290,14 +8313,14 @@ investigation using RNA-seq data.")
(define-public r-aucell
(package
(name "r-aucell")
- (version "1.14.0")
+ (version "1.16.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "AUCell" version))
(sha256
(base32
- "0qdac3qalcki20r90k40cc8d0lfywzn9pffg9d719yvs7nrsfdjr"))))
+ "1lclf8hkhrm6g5fp8yhvjxnwgf8p0j9ffxsmcybz4rjvmwkiz5dp"))))
(properties `((upstream-name . "AUCell")))
(build-system r-build-system)
(propagated-inputs
@@ -8329,14 +8352,14 @@ needed.")
(define-public r-ebimage
(package
(name "r-ebimage")
- (version "4.34.0")
+ (version "4.36.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "EBImage" version))
(sha256
(base32
- "1z3cxxg593d66nczz5hh2hdj1d87wc0lxrzc5sn6bp43n351q8h3"))))
+ "030vpn55ppfqq4408c4db4w40d17x1yq6zajb11p2glikvm1q619"))))
(properties `((upstream-name . "EBImage")))
(build-system r-build-system)
(propagated-inputs
@@ -8368,14 +8391,14 @@ visualization with image data.")
(define-public r-yamss
(package
(name "r-yamss")
- (version "1.18.0")
+ (version "1.20.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "yamss" version))
(sha256
(base32
- "1al615x778h17jqiyhiyf6djaq9iygs1hlbrna6y4xc0f2kvgxld"))))
+ "141hbryifm6na5shjyrbjwwksqnl75kqp1m2zl03l9sjqm0kapab"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
@@ -8402,14 +8425,14 @@ analysis.")
(define-public r-gtrellis
(package
(name "r-gtrellis")
- (version "1.24.0")
+ (version "1.26.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "gtrellis" version))
(sha256
(base32
- "0l5271cpzjlm4m0v6xcdg2vxlbhn53x1fd59ynb9jwll93av5h1f"))))
+ "0q2lyb8p1xhqqhw4q1br4r8mwq06mjws8iwbbilkngvs3brbmrzl"))))
(build-system r-build-system)
(propagated-inputs
`(("r-circlize" ,r-circlize)
@@ -8431,14 +8454,14 @@ genomic categories and to add self-defined graphics in the plot.")
(define-public r-somaticsignatures
(package
(name "r-somaticsignatures")
- (version "2.28.0")
+ (version "2.30.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "SomaticSignatures" version))
(sha256
(base32
- "0jr11c9hz7m49xc8pi6xrr5fhbv68vafvqpzhr0pmm51vvr1vfs9"))))
+ "1dxzfkvljnydv7kfybfa52dwcbkkci2r8gjspjf90k2bxf10phql"))))
(properties
`((upstream-name . "SomaticSignatures")))
(build-system r-build-system)
@@ -8470,14 +8493,14 @@ decomposition algorithms.")
(define-public r-yapsa
(package
(name "r-yapsa")
- (version "1.18.0")
+ (version "1.19.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "YAPSA" version))
(sha256
(base32
- "1xfkgjlm0rxz82qcaqzx95cwirxifd9dsswjg3zcqmz03v7a0gz2"))))
+ "0fgcbskz96p5815nywsnqv2gzn7g93m438hpd5rpg85srg4wrpdj"))))
(properties `((upstream-name . "YAPSA")))
(build-system r-build-system)
(propagated-inputs
@@ -8519,14 +8542,14 @@ provided.")
(define-public r-gcrma
(package
(name "r-gcrma")
- (version "2.64.0")
+ (version "2.66.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "gcrma" version))
(sha256
(base32
- "1z4abw9s2hs3csnx25nli7fpvb3rh3l0swzl0wfqp087fcs78pxi"))))
+ "0h7dl4if6skbcqdjdzqyghyswhwpx7xvb54lffz4wdaxpabp3001"))))
(build-system r-build-system)
(propagated-inputs
`(("r-affy" ,r-affy)
@@ -8605,14 +8628,14 @@ chips with the MAQC reference datasets.")
(define-public r-quantro
(package
(name "r-quantro")
- (version "1.26.0")
+ (version "1.28.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "quantro" version))
(sha256
(base32
- "1fkma2ic448h2lrlza8ipg65gpfsz4fhlxcnjpmzhhmzp2xi2p4a"))))
+ "1r2wbsndc0ji22ap27gbr1wy8icj3cjxwqlz1x0gvxkaj69mwsfq"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
@@ -8638,14 +8661,14 @@ groups.")
(define-public r-yarn
(package
(name "r-yarn")
- (version "1.18.0")
+ (version "1.20.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "yarn" version))
(sha256
(base32
- "1x07l255x52z6cgdc2j8285shqszhr034xm5686rp6d35vah55ji"))))
+ "0nk4qzrwjiv8q39lgil9x25bm3gpzrnhd37d7754kpxhs2fsmw9d"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
@@ -8675,14 +8698,14 @@ large RNA-seq experiments.")
(define-public r-roar
(package
(name "r-roar")
- (version "1.28.0")
+ (version "1.30.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "roar" version))
(sha256
(base32
- "0vp0n90rvjm8rzwkbrxa3fasb9val56bz2srz72xwsl3jzb5yk6w"))))
+ "0hqh4vsnxl2sn1bf6s6wxl2nskb40rhvrysdvb6dr60zkih3g347"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
@@ -8743,14 +8766,14 @@ genes.")
(define-public r-massspecwavelet
(package
(name "r-massspecwavelet")
- (version "1.58.0")
+ (version "1.60.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MassSpecWavelet" version))
(sha256
(base32
- "1cs32sig1yvqn9xs0cvhfpmkh2lbllx7aab80sz58x03wnx8v60z"))))
+ "1icqyxkx5a9y3wahkxpxngw85c7l4hih1ym9nwwn9qy93pnw1zi4"))))
(properties
`((upstream-name . "MassSpecWavelet")))
(build-system r-build-system)
@@ -8767,14 +8790,14 @@ based on @dfn{Continuous Wavelet Transform} (CWT).")
(define-public r-xcms
(package
(name "r-xcms")
- (version "3.14.1")
+ (version "3.16.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "xcms" version))
(sha256
(base32
- "1g8k90p0sbcb3rdrbldj5bcjp2piy5ldni4jplyr78vjpmrmvqk7"))))
+ "0m6w68ndf2a4k148pbb0bbbgq57akzqgi9nf7k6ngkk22j3m7m95"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
@@ -8784,6 +8807,7 @@ based on @dfn{Continuous Wavelet Transform} (CWT).")
("r-lattice" ,r-lattice)
("r-massspecwavelet" ,r-massspecwavelet)
("r-mscoreutils" ,r-mscoreutils)
+ ("r-msfeatures" ,r-msfeatures)
("r-msnbase" ,r-msnbase)
("r-mzr" ,r-mzr)
("r-plyr" ,r-plyr)
@@ -8807,14 +8831,14 @@ data for high-throughput, untargeted analyte profiling.")
(define-public r-wrench
(package
(name "r-wrench")
- (version "1.10.0")
+ (version "1.12.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Wrench" version))
(sha256
(base32
- "0yssmqayaryrc0asjjqxdipqdfg309llrzldx38jrfgdsza6bvs0"))))
+ "1vzv7sswijgb8nq58yrc19wlw2nnpjvans86fqqzs4p8wvq8j06n"))))
(properties `((upstream-name . "Wrench")))
(build-system r-build-system)
(propagated-inputs
@@ -8833,14 +8857,14 @@ that arising from 16s metagenomic surveys.")
(define-public r-wiggleplotr
(package
(name "r-wiggleplotr")
- (version "1.16.0")
+ (version "1.18.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "wiggleplotr" version))
(sha256
(base32
- "13f3g6fcc29k0g21mhnypm3nc6qqjw867vamvfkdzynspsfb32ga"))))
+ "01y1rbmxjza7qx3q33k0r241if69hzkx9plgmj59wyji22lm7syi"))))
(build-system r-build-system)
(propagated-inputs
`(("r-assertthat" ,r-assertthat)
@@ -8867,14 +8891,14 @@ visualization of exonic read coverage.")
(define-public r-widgettools
(package
(name "r-widgettools")
- (version "1.70.0")
+ (version "1.72.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "widgetTools" version))
(sha256
(base32
- "186xgpgyfyi4angxhz6558lfpzvvszzlpyfr8xnbccs3gshk3db2"))))
+ "0jajfh78116wjfwbmzfvcbxswai4jj9ypzmfhs5j5iypaf8zff8j"))))
(properties `((upstream-name . "widgetTools")))
(build-system r-build-system)
(home-page "https://bioconductor.org/packages/widgetTools/")
@@ -8888,14 +8912,14 @@ widgets in R.")
(define-public r-webbioc
(package
(name "r-webbioc")
- (version "1.64.0")
+ (version "1.66.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "webbioc" version))
(sha256
(base32
- "1mpdw477j78s2nvlf2lzm6mdjcpamyyazjn060h9q3apawn6zajx"))))
+ "1r3rjvfhqbbzdhlslnc86kr2iip3xgvr81zpvcr8xv9mysgrln17"))))
(build-system r-build-system)
(inputs
`(("netpbm" ,netpbm)
@@ -8921,14 +8945,14 @@ Currently only Affymetrix oligonucleotide analysis is supported.")
(define-public r-zinbwave
(package
(name "r-zinbwave")
- (version "1.14.2")
+ (version "1.16.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "zinbwave" version))
(sha256
(base32
- "1y8krazz2qdn0wn8ijjs2gn5dl5l960v6bijbkvh0r8066l7viky"))))
+ "05w95bnq63a339d8x4932k81ycqf825s3qwn98vr52v5g2hv46fq"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biocparallel" ,r-biocparallel)
@@ -8954,14 +8978,14 @@ the data.")
(define-public r-zfpkm
(package
(name "r-zfpkm")
- (version "1.14.0")
+ (version "1.16.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "zFPKM" version))
(sha256
(base32
- "1k7xaxr2gn26y8bps5l32g2axfhdn07nbk4q3qcx32d5jm75qkx2"))))
+ "0fk05vrmyyrhmkwi06lsi553mlpqj3fgwhk1kygz83iqv5z2vfw9"))))
(properties `((upstream-name . "zFPKM")))
(build-system r-build-system)
(propagated-inputs
@@ -8983,18 +9007,22 @@ This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
(define-public r-rbowtie2
(package
(name "r-rbowtie2")
- (version "1.14.0")
+ (version "2.0.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Rbowtie2" version))
(sha256
(base32
- "0r5yqjal48xlcv5cidi7p3zwygvsllmv2zzkwkc9kfq083l2i4ih"))))
+ "0xpvrx2ak9x913sym4l46ycwbnmpcdwb3bf3dfd2gsp0krv8vh1x"))))
(properties `((upstream-name . "Rbowtie2")))
(build-system r-build-system)
+ (propagated-inputs
+ `(("r-magrittr" ,r-magrittr)
+ ("r-rsamtools" ,r-rsamtools)))
(inputs
- `(("zlib" ,zlib)))
+ `(("samtools" ,samtools)
+ ("zlib" ,zlib)))
(native-inputs
`(("r-knitr" ,r-knitr)))
(home-page "https://bioconductor.org/packages/Rbowtie2/")
@@ -9008,14 +9036,14 @@ rapid adapter trimming, identification, and read merging.")
(define-public r-progeny
(package
(name "r-progeny")
- (version "1.14.0")
+ (version "1.16.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "progeny" version))
(sha256
(base32
- "10vpjvl4wps857xiy8rpzr82jzdfbc5rgwh3ir3my26lfws4hfz8"))))
+ "0zhr5i5v87akzqjb6wid67nhg2icrw6w0awdy87x848c6c1i6j9y"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
@@ -9038,14 +9066,14 @@ expression\".")
(define-public r-arrmnormalization
(package
(name "r-arrmnormalization")
- (version "1.32.0")
+ (version "1.34.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ARRmNormalization" version))
(sha256
(base32
- "0ni3vblcadhwxaq1pf1n9jn66cp3bqch68ww4c8zh19zagil2y7r"))))
+ "1ryqr3mpakjml0jhbk28k2z511sdl87wxdczxq1rwx98s0pc9mnh"))))
(properties
`((upstream-name . "ARRmNormalization")))
(build-system r-build-system)
@@ -9061,14 +9089,14 @@ Infinium HumanMethylation 450k assay.")
(define-public r-biocfilecache
(package
(name "r-biocfilecache")
- (version "2.0.0")
+ (version "2.2.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BiocFileCache" version))
(sha256
(base32
- "0ymg4hmabk233qgassld62achjylm12rnidxbakfkx4dvvlbhxxv"))))
+ "11qayqmgv274hc4h1v222sma07wkxjm8002fl6w3yvi225zq1qc1"))))
(properties `((upstream-name . "BiocFileCache")))
(build-system r-build-system)
(propagated-inputs
@@ -9094,14 +9122,14 @@ and data files used across sessions.")
(define-public r-iclusterplus
(package
(name "r-iclusterplus")
- (version "1.28.0")
+ (version "1.30.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "iClusterPlus" version))
(sha256
(base32
- "1haj25c4cmmjjvh181b41a9pvkh92f7k2w4ljn17iqg31vm45za1"))))
+ "0w6r2clk8wdnnnjmq3cspmxiq1c8vwprd66xmdrhcqzbjkpkdw2b"))))
(properties `((upstream-name . "iClusterPlus")))
(build-system r-build-system)
(native-inputs `(("gfortran" ,gfortran)))
@@ -9124,18 +9152,16 @@ Gaussian distributions.")
(define-public r-rbowtie
(package
(name "r-rbowtie")
- (version "1.32.0")
+ (version "1.34.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Rbowtie" version))
(sha256
(base32
- "0mfikbrs28q7r3lnsq0jma5x6nkrnm3q46242jh35w9c969jk5yy"))))
+ "0ardmryx6ac7v6n900a1klrrldvbmh7bxvy8ldz8rwid19h29ikr"))))
(properties `((upstream-name . "Rbowtie")))
(build-system r-build-system)
- (inputs
- `(("zlib" ,zlib)))
(native-inputs
`(("r-knitr" ,r-knitr)))
(home-page "https://bioconductor.org/packages/Rbowtie/")
@@ -9149,14 +9175,14 @@ alignment tool.")
(define-public r-sgseq
(package
(name "r-sgseq")
- (version "1.26.0")
+ (version "1.28.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "SGSeq" version))
(sha256
(base32
- "0i1yaw8h8gibakvaf1xd6nnjx2bsb2s9c0q74rbq9lm7haihivp6"))))
+ "15l0r6svs27k82dd472is26shwayz6rs5ylg5gpf3mldr7sa5kja"))))
(properties `((upstream-name . "SGSeq")))
(build-system r-build-system)
(propagated-inputs
@@ -9192,14 +9218,14 @@ interpretation.")
(define-public r-rhisat2
(package
(name "r-rhisat2")
- (version "1.8.0")
+ (version "1.10.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Rhisat2" version))
(sha256
(base32
- "1hqahh5h22mj2crqp6r9xnm111xmfgk39c100rcaziqrpdy5npk8"))))
+ "092rws9vjxgm2jpkbp6ign47zmillyyidnc7ylcbn4zr9j5lwv0y"))))
(properties `((upstream-name . "Rhisat2")))
(build-system r-build-system)
(arguments
@@ -9232,21 +9258,20 @@ index.")
(define-public r-quasr
(package
(name "r-quasr")
- (version "1.32.0")
+ (version "1.34.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "QuasR" version))
(sha256
(base32
- "1635ff11ahzjrh3cdcxrq5bgd100n444k7mc0maz0jx21vj8qqb1"))))
+ "0d292xgaq8d3cdpa9anabda03lis46xc29iw9c5k5i3sj7dcr4g5"))))
(properties `((upstream-name . "QuasR")))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
("r-biobase" ,r-biobase)
("r-biocgenerics" ,r-biocgenerics)
- ("r-biocmanager" ,r-biocmanager)
("r-biocparallel" ,r-biocparallel)
("r-biostrings" ,r-biostrings)
("r-bsgenome" ,r-bsgenome)
@@ -9275,14 +9300,14 @@ quantification of genomic regions of interest.")
(define-public r-rqc
(package
(name "r-rqc")
- (version "1.26.0")
+ (version "1.28.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Rqc" version))
(sha256
(base32
- "02hwj2vd003x0zf273ndnwh7kxy6wc3sz14d3kryp2w2aqjj826f"))))
+ "0hcxkrfja0gmd8r2llijdvaw2xiiplk037305inimz0qna6w2071"))))
(properties `((upstream-name . "Rqc")))
(build-system r-build-system)
(propagated-inputs
@@ -9318,14 +9343,14 @@ graphics.")
(define-public r-birewire
(package
(name "r-birewire")
- (version "3.24.0")
+ (version "3.26.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BiRewire" version))
(sha256
(base32
- "0p6mr67mkw54490sv4dvkyh8l0xkpjfbqy532vi8l41i40qg3gry"))))
+ "0ki4rcwjgbixzy5q9s30ajx5zhpl18q50znrb60fchvl4hj9h93w"))))
(properties `((upstream-name . "BiRewire")))
(build-system r-build-system)
(propagated-inputs
@@ -9376,14 +9401,14 @@ Markov-Chain-Monte-Carlo is applied to sample the activity states.")
(define-public r-multidataset
(package
(name "r-multidataset")
- (version "1.20.0")
+ (version "1.22.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MultiDataSet" version))
(sha256
(base32
- "1hyk40xgmy50rqxwdvc64d3pgz5vsg8vmlj5cp5m0n5m0adxcdfj"))))
+ "17asldnxqvp3sijx7nbi2lbbgnq4iq8z72qlg9080sm5lga1yy1s"))))
(properties `((upstream-name . "MultiDataSet")))
(build-system r-build-system)
(propagated-inputs
@@ -9413,14 +9438,14 @@ packages.")
(define-public r-ropls
(package
(name "r-ropls")
- (version "1.24.0")
+ (version "1.26.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ropls" version))
(sha256
(base32
- "1j99kdywyljqzdcns5ysh590w4w8iiwzpddpfk5c8d4whax7vk5b"))))
+ "0mz5lrdsihx66sgx9klnvpxvw1mjjcbijcsdbgxwaimzl9k1kr05"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
@@ -9451,14 +9476,14 @@ coefficients).")
(define-public r-biosigner
(package
(name "r-biosigner")
- (version "1.20.0")
+ (version "1.22.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "biosigner" version))
(sha256
(base32
- "159fbkymn92li7dinsm56nsacjp8wnhsljv7airgs9m82p8wd5sl"))))
+ "189018qahyw33dmg73wa7k4rp8nzrx6ai8f2dr6vhbpcdc1gnm0z"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
@@ -9484,14 +9509,14 @@ datasets.")
(define-public r-annotatr
(package
(name "r-annotatr")
- (version "1.18.1")
+ (version "1.20.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "annotatr" version))
(sha256
(base32
- "1ls1qdfppcxysggi3bghrnspb5a3s40pm2mj4x0whc7c40cf90mg"))))
+ "1ha2wn56cdab4p3wdwv4xlqjsgl7sd8phbx71qbclrbdwpq2mi7i"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
@@ -9525,14 +9550,14 @@ annotations.")
(define-public r-rsubread
(package
(name "r-rsubread")
- (version "2.6.4")
+ (version "2.8.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Rsubread" version))
(sha256
(base32
- "043m4512q73x6q529hqfgrap0fq5anvny4va085nafia06b805pi"))))
+ "09kd7vl2z9k82ppfzy679hs7d00c60z3w3n6a8wq4z3k3f4glc3s"))))
(properties `((upstream-name . "Rsubread")))
(build-system r-build-system)
(inputs `(("zlib" ,zlib)))
@@ -9551,14 +9576,14 @@ and to both short and long sequence reads.")
(define-public r-flowutils
(package
(name "r-flowutils")
- (version "1.56.0")
+ (version "1.58.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "flowUtils" version))
(sha256
(base32
- "1sdwgyvrsz0pp60zdfrcgb7bs8s87j7257p8ck813ydizc324x9w"))))
+ "0rgybkzbn8c3kpbz0ddghp1np0gka0cgiqvkk5jbnhlgf4s07161"))))
(properties `((upstream-name . "flowUtils")))
(build-system r-build-system)
(propagated-inputs
@@ -9577,14 +9602,14 @@ and to both short and long sequence reads.")
(define-public r-consensusclusterplus
(package
(name "r-consensusclusterplus")
- (version "1.56.0")
+ (version "1.58.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ConsensusClusterPlus" version))
(sha256
(base32
- "163nr50nyvwrsajmm0cgxp70pqk61mgw0k7ams694hcb42162j8b"))))
+ "13z43qbk9z7mvy8v8k185m6n020i6ahb18pm4q88rs75qlklzdkr"))))
(properties
`((upstream-name . "ConsensusClusterPlus")))
(build-system r-build-system)
@@ -9602,14 +9627,14 @@ cluster count and membership by stability evidence in unsupervised analysis.")
(define-public r-cytolib
(package
(name "r-cytolib")
- (version "2.4.0")
+ (version "2.6.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "cytolib" version))
(sha256
(base32
- "0wl7zqwv0i38dfzqfsz40n3mcbxi38ffn1rbd5pm9s7hq16zr4nv"))))
+ "01r5dfjil1i526kb5gj9c8x9agi90x0bh7lzykbpn0g6s2hznbzi"))))
(properties `((upstream-name . "cytolib")))
(build-system r-build-system)
(native-inputs
@@ -9631,14 +9656,14 @@ interact with gated cytometry data.")
(define-public r-flowcore
(package
(name "r-flowcore")
- (version "2.4.0")
+ (version "2.6.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "flowCore" version))
(sha256
(base32
- "13xpbkxi53rxmhvpdiy6bydmhicmxd2gi96d9c1qx4lkss2f14nc"))))
+ "0zbd2hrdbb6r0np6nd3ab8nlcf9l57vcwnnhbqkbas8y0c2i2mwp"))))
(properties `((upstream-name . "flowCore")))
(build-system r-build-system)
(propagated-inputs
@@ -9663,14 +9688,14 @@ with flow cytometry data.")
(define-public r-flowmeans
(package
(name "r-flowmeans")
- (version "1.52.0")
+ (version "1.54.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "flowMeans" version))
(sha256
(base32
- "1awskkq48qhv4v9glxgfqi0kgwqd62fbj641k4vvxfcwsf2c7bfg"))))
+ "0iy8hvi0inj1ylhdx6q4mya9k55iazprz6fdrnq1mxb2iyndzsl6"))))
(properties `((upstream-name . "flowMeans")))
(build-system r-build-system)
(propagated-inputs
@@ -9689,14 +9714,14 @@ change point detection.")
(define-public r-ncdfflow
(package
(name "r-ncdfflow")
- (version "2.38.0")
+ (version "2.40.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ncdfFlow" version))
(sha256
(base32
- "1lm88qnfv6rnnr7wmgbvwyj272imjjjn7h3agxqqzsbmn8vyrnf0"))))
+ "1c6wb2x24ydqp5nxrx6bhj6f13x9djfy9awkc7zn63xkag7mvvar"))))
(properties `((upstream-name . "ncdfFlow")))
(build-system r-build-system)
(propagated-inputs
@@ -9720,14 +9745,14 @@ manipulation of flow cytometry data.")
(define-public r-ggcyto
(package
(name "r-ggcyto")
- (version "1.20.0")
+ (version "1.22.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ggcyto" version))
(sha256
(base32
- "0jd6m84m4znnpix4bcgdby7mnflsn206f5x2vw9n8rxnwzx77wpg"))))
+ "17dnmsa92gc2za36c3klgd7rklqlxrhkzs5ksnrc1am6a4knc0p1"))))
(properties `((upstream-name . "ggcyto")))
(build-system r-build-system)
(propagated-inputs
@@ -9757,14 +9782,14 @@ statistics to the plot.")
(define-public r-flowviz
(package
(name "r-flowviz")
- (version "1.56.0")
+ (version "1.58.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "flowViz" version))
(sha256
(base32
- "17x04xwyw2pp5zkhgvrmxkb8cbrv9wql6xhjsfpq0n6yd9dxqc1v"))))
+ "039sh7qn25gp2b34khs8dyrdpxyapsjlprrvxlz8f7dl8gmggl04"))))
(properties `((upstream-name . "flowViz")))
(build-system r-build-system)
(propagated-inputs
@@ -9788,14 +9813,14 @@ statistics to the plot.")
(define-public r-flowclust
(package
(name "r-flowclust")
- (version "3.30.0")
+ (version "3.32.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "flowClust" version))
(sha256
(base32
- "03xsmprrkxwkaksjlaxwp54mqfb3zlg6dbqhp87w78fwscisv76b"))))
+ "0ch7mkq40qcnxwgzy51vjdlwyzx4bvp03vpdm6dwjc6qy8a6qfzi"))))
(properties `((upstream-name . "flowClust")))
(build-system r-build-system)
(arguments
@@ -9811,6 +9836,7 @@ statistics to the plot.")
("r-flowviz" ,r-flowviz)
("r-graph" ,r-graph)
("r-mnormt" ,r-mnormt)))
+ #;
(inputs
`(("gsl" ,gsl)))
(native-inputs
@@ -9828,14 +9854,14 @@ model with Box-Cox transformation.")
(define-public r-rprotobuflib
(package
(name "r-rprotobuflib")
- (version "2.4.0")
+ (version "2.6.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "RProtoBufLib" version))
(sha256
(base32
- "1hyds97ay4mn7nl830yh9v8mlasgsljsx5wsrhz2zsmbbyx6wbnb"))))
+ "04qlhbhdchpr35rdc6jc3y8fy6znnfrdlsb8am04agbrvpjgrx10"))))
(properties `((upstream-name . "RProtoBufLib")))
(build-system r-build-system)
(arguments
@@ -9857,14 +9883,14 @@ for other R packages to compile and link against.")
(define-public r-flowworkspace
(package
(name "r-flowworkspace")
- (version "4.4.0")
+ (version "4.6.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "flowWorkspace" version))
(sha256
(base32
- "1a9qb2dcvwgb3z0vdbbzn1rzy77d3da72kirs272344hdx9b2cx9"))))
+ "11ni7kgk9s1fz3lvg85s6r7x2fhk4m7cdpilji05ya12jsyr3fig"))))
(properties `((upstream-name . "flowWorkspace")))
(build-system r-build-system)
(propagated-inputs
@@ -9911,14 +9937,14 @@ matches the flowJo analysis.")
(define-public r-flowstats
(package
(name "r-flowstats")
- (version "4.4.0")
+ (version "4.6.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "flowStats" version))
(sha256
(base32
- "1yr5m7qmhmm52c70z3d0zy4zgf0hja7r2ig9yljv5w86bzm962x6"))))
+ "0jjfq66m4lbpkynwxaparkd05znhp3jl9ccj37gyghly294x3rm9"))))
(properties `((upstream-name . "flowStats")))
(build-system r-build-system)
(propagated-inputs
@@ -9947,14 +9973,14 @@ package.")
(define-public r-opencyto
(package
(name "r-opencyto")
- (version "2.4.0")
+ (version "2.6.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "openCyto" version))
(sha256
(base32
- "1par1d5pk1rjg15q7i5z5wqma7xg6fycb826a823wk8wr52a885x"))))
+ "11svr1lk383pkm4npwrnf3h37b3drjsmcwcgdbb45x8k2k95z2fm"))))
(properties `((upstream-name . "openCyto")))
(build-system r-build-system)
(propagated-inputs
@@ -9991,14 +10017,14 @@ sequential way to mimic the manual gating strategy.")
(define-public r-cytoml
(package
(name "r-cytoml")
- (version "2.4.0")
+ (version "2.6.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "CytoML" version))
(sha256
(base32
- "0ixy7mmnipk8wy61wz6qy7jfbc5zhs6p5iqaii8hdprjnb841ri7"))))
+ "16rgsc2dz5b8lm3ma8nh9wiknrdnvfjcsij7809rmcfs0gn1arcz"))))
(properties `((upstream-name . "CytoML")))
(build-system r-build-system)
(inputs
@@ -10044,14 +10070,14 @@ standard to exchange gated cytometry data with other software platforms.")
(define-public r-flowsom
(package
(name "r-flowsom")
- (version "2.0.0")
+ (version "2.2.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "FlowSOM" version))
(sha256
(base32
- "18h7p7g3w9imyd1c93jllgp4kd74z96cs85wcqfhmd26nx18hl82"))))
+ "062xrv8li2z849qa8mv5dhafqli6ziz099ikjfvi7v2fr7174p8f"))))
(properties `((upstream-name . "FlowSOM")))
(build-system r-build-system)
(propagated-inputs
@@ -10087,14 +10113,14 @@ self-organizing map clustering and minimal spanning trees.")
(define-public r-mixomics
(package
(name "r-mixomics")
- (version "6.16.3")
+ (version "6.17.26")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "mixOmics" version))
(sha256
(base32
- "1x6dbw4q6p9vngm256fr96r9fjxk5nik5ivkhbl5a9zqyq8wagpa"))))
+ "10ir4876sjmw2mw0cjvshwy3qyhsyz6g1ihyr3dycgzya0jcxw1x"))))
(properties `((upstream-name . "mixOmics")))
(build-system r-build-system)
(propagated-inputs
@@ -10133,14 +10159,14 @@ delete entire rows with missing data.")
(define-public r-depecher
(package ;Source/Weave error
(name "r-depecher")
- (version "1.8.0")
+ (version "1.10.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DepecheR" version))
(sha256
(base32
- "04vxc43p3kpsx0vksk2nwmy9p56h35z2mc8j9p2wm29zaz1y8j3p"))))
+ "1500jivij7zdycdd0i0b7mgp44w4z0hqnpzqbq8nhvzzdigic8x9"))))
(properties `((upstream-name . "DepecheR")))
(build-system r-build-system)
(propagated-inputs
@@ -10179,14 +10205,14 @@ data, to only emphasize the data that actually matters.")
(define-public r-rcistarget
(package
(name "r-rcistarget")
- (version "1.12.0")
+ (version "1.14.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "RcisTarget" version))
(sha256
(base32
- "1yh0l11vnslgr6zsbpgc8mc4aa32zy34f5yrz98hkcdl53iw5y7f"))))
+ "1qarr7xd71kz1haccj65x7sc7pc4v6xpqcfa3rkyp2bk240gigi7"))))
(properties `((upstream-name . "RcisTarget")))
(build-system r-build-system)
(propagated-inputs
@@ -10221,14 +10247,14 @@ genes in the gene-set that are ranked above the leading edge).")
(define-public r-chicago
(package
(name "r-chicago")
- (version "1.20.0")
+ (version "1.22.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Chicago" version))
(sha256
(base32
- "0dkwy6pfvzd7g4qmhjl24ypn92l78w1zy0ajhcxgg39f7zsq883x"))))
+ "0nz9v37p7zl8yw3ykdbsb3izcwgx349wvrhwfyyn9h3jxjfafngn"))))
(properties `((upstream-name . "Chicago")))
(build-system r-build-system)
(propagated-inputs
@@ -10247,14 +10273,14 @@ genes in the gene-set that are ranked above the leading edge).")
(define-public r-cicero
(package
(name "r-cicero")
- (version "1.10.1")
+ (version "1.12.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "cicero" version))
(sha256
(base32
- "1y34cm52bv1v2hr7sz8zjzxwd4wng7v75avz5wx45l0ld54z9l10"))))
+ "1fc69nkm2cwpr6gkfmra2ph0lrmw486chswp4pn8i70ia43fzdm7"))))
(build-system r-build-system)
(propagated-inputs
`(("r-assertthat" ,r-assertthat)
@@ -10314,14 +10340,14 @@ accessibility data.")
(define-public r-circrnaprofiler
(package
(name "r-circrnaprofiler")
- (version "1.6.0")
+ (version "1.8.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "circRNAprofiler" version))
(sha256
(base32
- "1hif40vfg2lkbyf6abbkxbdm3b1biw6gxnh6ca2sydvi3y5l2ys2"))))
+ "0l83r9idhrha1m21vpnw917m5dlldji49zvx4d25m5g3ia1pkhpf"))))
(properties
`((upstream-name . "circRNAprofiler")))
(build-system r-build-system)
@@ -10449,14 +10475,14 @@ cisTopics and explore the nature and regulatory proteins driving them.")
(define-public r-genie3
(package
(name "r-genie3")
- (version "1.14.0")
+ (version "1.16.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "GENIE3" version))
(sha256
(base32
- "1v54dzcz654wfm3npbp8gb55v49im0fm547cz3hvsidq4zhi3l1b"))))
+ "0ms769267pimrx3xwwkgjy03qilkxxs7xwhzfca01f65i4n3l6fw"))))
(properties `((upstream-name . "GENIE3")))
(build-system r-build-system)
(propagated-inputs
@@ -10474,17 +10500,17 @@ regulatory networks from expression data.")
(define-public r-roc
(package
(name "r-roc")
- (version "1.68.1")
+ (version "1.70.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ROC" version))
(sha256
(base32
- "1rmsrvn6hrg9ay7xfb05mfkxknnig78p3kbk9ghsd11lhx2fjm3s"))))
+ "1mgxpv5p6gnv04wzkcryrg5as5xrxvlqlkkcbv0k1bx9y6ykijy9"))))
(properties `((upstream-name . "ROC")))
(build-system r-build-system)
- (propagated-inputs
+ (native-inputs
`(("r-knitr" ,r-knitr)))
(home-page "https://www.bioconductor.org/packages/ROC/")
(synopsis "Utilities for ROC curves")
@@ -10522,14 +10548,14 @@ data.")
(define-public r-watermelon
(package
(name "r-watermelon")
- (version "1.36.0")
+ (version "2.0.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "wateRmelon" version))
(sha256
(base32
- "1qar8z0nf33bqr488swig0bfq8lnvcdjcxvw3q3b0hkkvybn27zw"))))
+ "1kzkg3cnm5pcs6blpw1qn7na6z3kar93v67680wsxa6qxxdiggk3"))))
(properties `((upstream-name . "wateRmelon")))
(build-system r-build-system)
(propagated-inputs
@@ -10542,6 +10568,8 @@ data.")
("r-matrixstats" ,r-matrixstats)
("r-methylumi" ,r-methylumi)
("r-roc" ,r-roc)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://bioconductor.org/packages/wateRmelon/")
(synopsis "Illumina 450 methylation array normalization and metrics")
(description
@@ -10559,14 +10587,14 @@ metrics, with methods for objects produced by the @code{methylumi} and
(define-public r-gdsfmt
(package
(name "r-gdsfmt")
- (version "1.28.1")
+ (version "1.30.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "gdsfmt" version))
(sha256
(base32
- "1w3z718q3bhh8bp71va9pbcd62pwbvgjw33ffg960jya40xssvc7"))
+ "147i33sb65n3cl3ibmjzgfm7i4ljy640k18mzknvc18v1906j9vp"))
(modules '((guix build utils)))
;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build
;; them and link with system libraries instead.
@@ -10617,14 +10645,14 @@ with multiple R processes supported by the package @code{parallel}.")
(define-public r-bigmelon
(package
(name "r-bigmelon")
- (version "1.18.0")
+ (version "1.20.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "bigmelon" version))
(sha256
(base32
- "061f0hc4m4nvdr6298pg3inpx1z2bpsm9nlxqs3v7n58q15xyzri"))))
+ "0ksbmybi8wsg515b4k9ij1xqqk9i90pyap2wq5w3c49qgc0pqali"))))
(properties `((upstream-name . "bigmelon")))
(build-system r-build-system)
(propagated-inputs
@@ -10632,6 +10660,7 @@ with multiple R processes supported by the package @code{parallel}.")
("r-biocgenerics" ,r-biocgenerics)
("r-gdsfmt" ,r-gdsfmt)
("r-geoquery" ,r-geoquery)
+ ("r-illuminaio" ,r-illuminaio)
("r-methylumi" ,r-methylumi)
("r-minfi" ,r-minfi)
("r-watermelon" ,r-watermelon)))
@@ -10645,14 +10674,14 @@ with multiple R processes supported by the package @code{parallel}.")
(define-public r-seqbias
(package
(name "r-seqbias")
- (version "1.40.0")
+ (version "1.42.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "seqbias" version))
(sha256
(base32
- "06w43plv4x1pafybq633n7adqp9yj3bvaaamq7vylmkfbcx3nl8k"))))
+ "1q608c1madij8l52ljl3w52vi3cssr6ikny84yj6n8s7yvpx5jpr"))))
(properties `((upstream-name . "seqbias")))
(build-system r-build-system)
(propagated-inputs
@@ -10709,14 +10738,14 @@ injected in that sequence).")
(define-public r-reqon
(package
(name "r-reqon")
- (version "1.38.0")
+ (version "1.40.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ReQON" version))
(sha256
(base32
- "1z13avbxwvvhh03arjfnaipznynifsi8k2hzw4kappz24f7lwmza"))))
+ "14v79vg3pmpkbzgn8xqd020jdwcs8g57d46bzl23yi3w1rsfbrb1"))))
(properties `((upstream-name . "ReQON")))
(build-system r-build-system)
(propagated-inputs
@@ -10734,14 +10763,14 @@ format.")
(define-public r-wavcluster
(package
(name "r-wavcluster")
- (version "2.26.0")
+ (version "2.28.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "wavClusteR" version))
(sha256
(base32
- "1sydzrqydfv1ik2h08xkxlx6xrv866bf0if6v5wch9l3krh0sych"))))
+ "1a1zhckrgq5yl51acj5piyh2hq70q6hhpym4cawzdssxhcbq70bk"))))
(properties `((upstream-name . "wavClusteR")))
(build-system r-build-system)
(propagated-inputs
@@ -10781,14 +10810,14 @@ procedures that induce nucleotide substitutions (e.g. BisSeq).")
(define-public r-timeseriesexperiment
(package
(name "r-timeseriesexperiment")
- (version "1.10.1")
+ (version "1.12.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "TimeSeriesExperiment" version))
(sha256
(base32
- "1095a2ynxcf9xiac5cjzslcbmjnjpbby0vy7d84qagdiq1w6mrhn"))))
+ "0fphnkkd3i7zf33a9lhw95n80vzv1z7fmn7mhrfb949yz4jdvk7d"))))
(properties
`((upstream-name . "TimeSeriesExperiment")))
(build-system r-build-system)
@@ -10822,14 +10851,14 @@ provides methods for retrieving enriched pathways.")
(define-public r-variantfiltering
(package
(name "r-variantfiltering")
- (version "1.28.0")
+ (version "1.30.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "VariantFiltering" version))
(sha256
(base32
- "0abhrk53csd9jz9sv4q1qr74jax9mbj2icbz1iilf1123nvnjypd"))))
+ "15js8xzi9rsgkjkqcshzk3r3g85kdnxn5v2hi6l5s4yxj9lnq12p"))))
(properties
`((upstream-name . "VariantFiltering")))
(build-system r-build-system)
@@ -10928,21 +10957,20 @@ arrays based on fast wavelet-based functional models.")
(define-public r-variancepartition
(package
(name "r-variancepartition")
- (version "1.22.0")
+ (version "1.24.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "variancePartition" version))
(sha256
(base32
- "1pqy2g9pg8pswmkrs2fzlkwwliw2r7f33h05bci5bz41b8ribpzj"))))
+ "0f5y61dpzwmr8v7npim18zvxa8n49rbzclb9j72haba0px6ibhvw"))))
(properties
`((upstream-name . "variancePartition")))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
("r-biocparallel" ,r-biocparallel)
- ("r-colorramps" ,r-colorramps)
("r-doparallel" ,r-doparallel)
("r-foreach" ,r-foreach)
("r-ggplot2" ,r-ggplot2)
@@ -10952,9 +10980,11 @@ arrays based on fast wavelet-based functional models.")
("r-lme4" ,r-lme4)
("r-lmertest" ,r-lmertest)
("r-mass" ,r-mass)
+ ("r-matrix" ,r-matrix)
("r-pbkrtest" ,r-pbkrtest)
("r-progress" ,r-progress)
("r-reshape2" ,r-reshape2)
+ ("r-rlang" ,r-rlang)
("r-scales" ,r-scales)))
(native-inputs
`(("r-knitr" ,r-knitr)))
@@ -10972,14 +11002,14 @@ measures.")
(define-public r-htqpcr
(package
(name "r-htqpcr")
- (version "1.46.0")
+ (version "1.48.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "HTqPCR" version))
(sha256
(base32
- "1y3ik5a9w66jby6682jfm8mn2883s8yfv4xw8a8v1f6q2d1j938l"))))
+ "1d7qj5yv6kzqmdrnp5pd8qv1yr4bg8cs39p8ib0i0k8b4wr97kq3"))))
(properties `((upstream-name . "HTqPCR")))
(build-system r-build-system)
(propagated-inputs
@@ -11006,14 +11036,14 @@ features (e.g. genes, microRNAs).")
(define-public r-unifiedwmwqpcr
(package
(name "r-unifiedwmwqpcr")
- (version "1.28.0")
+ (version "1.30.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "unifiedWMWqPCR" version))
(sha256
(base32
- "1clcz610sl3s0mjf84j21xgrmjhkxcc4h292ljwq5yzbkk68g896"))))
+ "0kw26bm2yyna38q5r4zb2alpa3j4gx7v970419mnjlif4g0hmggk"))))
(properties
`((upstream-name . "unifiedWMWqPCR")))
(build-system r-build-system)
@@ -11031,14 +11061,14 @@ data.")
(define-public r-universalmotif
(package
(name "r-universalmotif")
- (version "1.10.2")
+ (version "1.12.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "universalmotif" version))
(sha256
(base32
- "0hv2v2zgif5ihr5hxmdz32rln43jc1j0rslp44kd3rijjl45zysn"))))
+ "0d6zrwbc4i2npl29idm1icwa62wdx47z9s8yx7k662v3qagwpj16"))))
(properties
`((upstream-name . "universalmotif")))
(build-system r-build-system)
@@ -11145,14 +11175,14 @@ cellular organization in health and disease.")
(define-public r-bgmix
(package
(name "r-bgmix")
- (version "1.52.0")
+ (version "1.54.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BGmix" version))
(sha256
(base32
- "1gp40ddspblpszzm4k4r7ysgx883iwdfqc5ds23p2q1ml9idwgvv"))))
+ "0x1sx319yfxgkscr9r62msq00ddvmzryzn42wy4dh5pvjmgifkkn"))))
(properties `((upstream-name . "BGmix")))
(build-system r-build-system)
(propagated-inputs
@@ -11167,14 +11197,14 @@ gene expression.")
(define-public r-bgx
(package
(name "r-bgx")
- (version "1.58.0")
+ (version "1.60.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "bgx" version))
(sha256
(base32
- "18n6j2ihv85rhai5sf5k3mwf9nkc2nl2sinx3rrs6sbl529g4mw4"))))
+ "0z3isnpyf9s11807dprxmd105lb0k4l7r1sygad30ncjvpldifzm"))))
(properties `((upstream-name . "bgx")))
(build-system r-build-system)
(propagated-inputs
@@ -11192,14 +11222,14 @@ Affymetrix GeneChips.")
(define-public r-bhc
(package
(name "r-bhc")
- (version "1.44.0")
+ (version "1.46.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BHC" version))
(sha256
(base32
- "0aaawm7h3ppyyhd7hi14rpynagnxx4730f5vxizj5bpzwbclp6h9"))))
+ "09nw4ljc9sn7iw09ha0m614hmdjj193xhhav5x5p07l501kks6h2"))))
(properties `((upstream-name . "BHC")))
(build-system r-build-system)
(home-page "https://bioconductor.org/packages/BHC/")
@@ -11218,14 +11248,14 @@ algorithm which is more efficient for larger data sets.")
(define-public r-bicare
(package
(name "r-bicare")
- (version "1.50.0")
+ (version "1.52.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BicARE" version))
(sha256
(base32
- "0j3gs4xcdgaca2c62jf2h86skbbxm1c9g2khs5bsa8fmkskr6vl9"))))
+ "1g8vrsc05cysb36gsw8sfmr6dgbh4aji37vcq9qwkmkv3jgvnlf6"))))
(properties `((upstream-name . "BicARE")))
(build-system r-build-system)
(propagated-inputs
@@ -11242,14 +11272,14 @@ results.")
(define-public r-bifet
(package
(name "r-bifet")
- (version "1.12.0")
+ (version "1.14.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BiFET" version))
(sha256
(base32
- "1fwy7ws0bn67557s0kcw8pbln2jg834n6kfbs8297ps07nxr0lpj"))))
+ "0vidypvphnj76g4ra5ijrgqx2dnzw0fmvdvz35gsqswrr3k20jkk"))))
(properties `((upstream-name . "BiFET")))
(build-system r-build-system)
(propagated-inputs
@@ -11272,14 +11302,14 @@ the read count and GC content bias.")
(define-public r-rsbml
(package
(name "r-rsbml")
- (version "2.50.0")
+ (version "2.52.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "rsbml" version))
(sha256
(base32
- "017xwra6ms7kx6sg3ksw1vr9zn23imc2qjgpmjikx7mgbak125xh"))))
+ "0mdyr637sgasc156cv8i2s2mpl1hdvilfwwkhvw7l95pl90gnsh2"))))
(properties `((upstream-name . "rsbml")))
(build-system r-build-system)
(inputs
@@ -11299,14 +11329,14 @@ validating output, provides an S4 SBML DOM, converts SBML to R graph objects.")
(define-public r-hypergraph
(package
(name "r-hypergraph")
- (version "1.64.0")
+ (version "1.66.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "hypergraph" version))
(sha256
(base32
- "01knpd964m2g9vwd7c72qnc8g2p2pzhvk7lin4mhvcmb3pvsdlh7"))))
+ "0xnyl9qh5p32ifvzkcl5g4a38zbnwykqzrp8gwz076a0ksiqqdxf"))))
(properties `((upstream-name . "hypergraph")))
(build-system r-build-system)
(propagated-inputs
@@ -11321,14 +11351,14 @@ manipulating hypergraphs.")
(define-public r-hyperdraw
(package
(name "r-hyperdraw")
- (version "1.44.0")
+ (version "1.46.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "hyperdraw" version))
(sha256
(base32
- "1qkxixkgvvfha0ii8rwwcbrbjmbbxsy8afv5ymcq01k3hbykx44r"))))
+ "1lkiqrk01hshms9ghsfynxwj69zr3463r3rg8rn7hkwn3bj8xyzj"))))
(properties `((upstream-name . "hyperdraw")))
(build-system r-build-system)
(inputs `(("graphviz" ,graphviz)))
@@ -11345,14 +11375,14 @@ manipulating hypergraphs.")
(define-public r-biggr
(package
(name "r-biggr")
- (version "1.28.0")
+ (version "1.30.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BiGGR" version))
(sha256
(base32
- "1y9659pxm65w51zvrz36girb3qvfc64zijjkxmg6xn4pbc8vv1wf"))))
+ "1g01666wwznk148776s4vr1hfi3dfl448dhgk4d1qy2wv6sxh9kr"))))
(properties `((upstream-name . "BiGGR")))
(build-system r-build-system)
(propagated-inputs
@@ -11409,14 +11439,14 @@ a file-backed matrix with factor properties.")
(define-public r-bigpint
(package
(name "r-bigpint")
- (version "1.8.0")
+ (version "1.10.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "bigPint" version))
(sha256
(base32
- "0yrg9x1a92zmz7j5hk77cph1jg82mkpr7k7qi9fdr6z5nqq6fgz6"))))
+ "0b0l0v9p7a5da3x18d0pqn41ilgxfyzapjaawgsshcfm5mjq5d7q"))))
(properties `((upstream-name . "bigPint")))
(build-system r-build-system)
(propagated-inputs
@@ -11452,14 +11482,14 @@ visualizing RNA-sequencing datasets and differentially expressed genes.")
(define-public r-chemminer
(package
(name "r-chemminer")
- (version "3.44.0")
+ (version "3.46.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ChemmineR" version))
(sha256
(base32
- "1z59npqk7hnqzhjdnry6lfqlyxfzwqprp7bmbdzs4rp22pzcv1v8"))))
+ "069xd7if7fs69afmamgl6wrkzpnk97ic6z5ix4vvlzkb078dm0p8"))))
(properties `((upstream-name . "ChemmineR")))
(build-system r-build-system)
(propagated-inputs
@@ -11471,11 +11501,13 @@ visualizing RNA-sequencing datasets and differentially expressed genes.")
("r-dt" ,r-dt)
("r-ggplot2" ,r-ggplot2)
("r-gridextra" ,r-gridextra)
+ ("r-jsonlite" ,r-jsonlite)
("r-png" ,r-png)
("r-rcpp" ,r-rcpp)
("r-rcurl" ,r-rcurl)
("r-rjson" ,r-rjson)
- ("r-rsvg" ,r-rsvg)))
+ ("r-rsvg" ,r-rsvg)
+ ("r-stringi" ,r-stringi)))
(native-inputs
`(("r-knitr" ,r-knitr)))
(home-page "https://github.com/girke-lab/ChemmineR")
@@ -11493,14 +11525,14 @@ structures.")
(define-public r-bioassayr
(package
(name "r-bioassayr")
- (version "1.30.0")
+ (version "1.32.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "bioassayR" version))
(sha256
(base32
- "1mlv80w8a7l8cii3dfqvanvh0qdqvcg8c1iiq4xlyvkjxfs64ka1"))))
+ "1nfp1alva6qim5rbhg9j9w97p2n4z21ghr4j489lqklkcs4d030f"))))
(properties `((upstream-name . "bioassayR")))
(build-system r-build-system)
(propagated-inputs
@@ -11528,14 +11560,14 @@ available bioactivity data.")
(define-public r-biobroom
(package
(name "r-biobroom")
- (version "1.24.0")
+ (version "1.26.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "biobroom" version))
(sha256
(base32
- "1ybyhmrcvj6k1laxw9bc8jbn533frkzh9k8kl1ibd5pi368rfqzn"))))
+ "034gbywrscv23kk1qnk7sc7dxdckmf60wh29fz65v1n28mkf180r"))))
(properties `((upstream-name . "biobroom")))
(build-system r-build-system)
(propagated-inputs
@@ -11560,14 +11592,14 @@ visualize bioinformatics analyses.")
(define-public r-graphite
(package
(name "r-graphite")
- (version "1.38.0")
+ (version "1.40.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "graphite" version))
(sha256
(base32
- "11bgz6951nfygxp3fm0190gf2bb5zplis1bc0am4757liw4qybhf"))))
+ "0wmdv4j6dinszxwpz2jddshkh1ahbhm2fxh6vhjsk4grw38i1lfr"))))
(properties `((upstream-name . "graphite")))
(build-system r-build-system)
(propagated-inputs
@@ -11576,8 +11608,6 @@ visualize bioinformatics analyses.")
("r-graph" ,r-graph)
("r-httr" ,r-httr)
("r-rappdirs" ,r-rappdirs)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
(home-page "https://bioconductor.org/packages/graphite/")
(synopsis "Networks from pathway databases")
(description
@@ -11589,14 +11619,14 @@ symbols).")
(define-public r-reactomepa
(package
(name "r-reactomepa")
- (version "1.36.0")
+ (version "1.38.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ReactomePA" version))
(sha256
(base32
- "1293z89ai766c559axgr7mz5x4564gyl9xqzf6s8s0aj1xb35gqf"))))
+ "1f4kd5cql7knnqaq3ba48kkypw8p60lkfdsnpqxcabdj30gqp55b"))))
(properties `((upstream-name . "ReactomePA")))
(build-system r-build-system)
(propagated-inputs
@@ -11621,14 +11651,14 @@ enrichment analysis and several functions for visualization.")
(define-public r-ebarrays
(package
(name "r-ebarrays")
- (version "2.56.0")
+ (version "2.58.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "EBarrays" version))
(sha256
(base32
- "1k1kl0m7wzaqpv7i20pfav2a6jf93bhri4w7qdikmvkf011n9422"))))
+ "10dw6c93rmpknzf4cnhw3y7lb27q4xq7x7wirl2a7qywdj0yj2g6"))))
(properties `((upstream-name . "EBarrays")))
(build-system r-build-system)
(propagated-inputs
@@ -11667,13 +11697,13 @@ monograph.")
(define-public r-bioccheck
(package
(name "r-bioccheck")
- (version "1.28.0")
+ (version "1.30.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BiocCheck" version))
(sha256
(base32
- "1h0l5w33c9jpc20pynq634qmx8jbfa802d7jslmf4haljmrxm4a1"))))
+ "0w9ddicyp9i8rxf92n9pghd9s6bb8jdjikaylrmkydhb7jbhan0y"))))
(properties
`((upstream-name . "BiocCheck")))
(build-system r-build-system)
@@ -11697,14 +11727,14 @@ checks on R packages that are to be submitted to the Bioconductor repository.")
(define-public r-biocgraph
(package
(name "r-biocgraph")
- (version "1.54.0")
+ (version "1.56.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "biocGraph" version))
(sha256
(base32
- "12bmj9kdlylp02cfwviak7y323ndccl2694rvi4cdg4vsx7v3ya3"))))
+ "0c7r0c1kx22dlwi6d1ldbkkbf53yi0p3vmgbwzrbkn3cina7bcxq"))))
(properties `((upstream-name . "biocGraph")))
(build-system r-build-system)
(propagated-inputs
@@ -11722,13 +11752,13 @@ different graph related packages produced by Bioconductor.")
(define-public r-biocstyle
(package
(name "r-biocstyle")
- (version "2.20.2")
+ (version "2.22.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BiocStyle" version))
(sha256
(base32
- "0p2wdq5vrx63ndghl9ww428z2lwnv5y88xmcr51by2g6vcj3brcf"))))
+ "0xx6xr01sb5wig94515zxgw24r9fv0g962ajy87741civhq32lbd"))))
(properties
`((upstream-name . "BiocStyle")))
(build-system r-build-system)
@@ -11750,13 +11780,13 @@ functionality.")
(define-public r-biocviews
(package
(name "r-biocviews")
- (version "1.60.0")
+ (version "1.62.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "biocViews" version))
(sha256
(base32
- "0pc5ll59vm8a9s1nrdc7p9wk11a52rrz669fsrrqd8qapa8p6wfd"))))
+ "1v6himzp546dpb990vv0nlya21w8x2x30137rsmahjzg942nzs9r"))))
(properties
`((upstream-name . "biocViews")))
(build-system r-build-system)
@@ -11778,14 +11808,14 @@ also known as views, in a controlled vocabulary.")
(define-public r-experimenthub
(package
(name "r-experimenthub")
- (version "2.0.0")
+ (version "2.2.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ExperimentHub" version))
(sha256
(base32
- "1mzmw3100lf33yhz27nbxncrjk5bprlackrjcwf8xdhcaidg40p4"))))
+ "15las4qmqvrn81hczxa3ylikqh54kp1lg9r8rcyfvrx5l0kgwlfq"))))
(properties `((upstream-name . "ExperimentHub")))
(build-system r-build-system)
(propagated-inputs
@@ -11812,14 +11842,14 @@ access.")
(define-public r-grohmm
(package
(name "r-grohmm")
- (version "1.26.0")
+ (version "1.28.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "groHMM" version))
(sha256
(base32
- "1h63vg1iskw79ijg5h1b9097ams8pp3kvnlawlfci6xfli07xpkj"))))
+ "1jcj29df4prknqwbydca1jb9w6njacjhwwk9jp0r5mvb88xrm60s"))))
(properties `((upstream-name . "groHMM")))
(build-system r-build-system)
(propagated-inputs
@@ -11839,14 +11869,14 @@ access.")
(define-public r-multiassayexperiment
(package
(name "r-multiassayexperiment")
- (version "1.18.0")
+ (version "1.20.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MultiAssayExperiment" version))
(sha256
(base32
- "0l0arf3q1f6zy6pdgsy3h5n523sg1hlilv7lj7snr5814idgdj51"))))
+ "1h3b8vqlbd04amjprxd1814zksdrbi01a0xn3906vkbqi43hfyn9"))))
(properties
`((upstream-name . "MultiAssayExperiment")))
(build-system r-build-system)
@@ -11874,14 +11904,14 @@ rownames.")
(define-public r-bioconcotk
(package
(name "r-bioconcotk")
- (version "1.12.1")
+ (version "1.14.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BiocOncoTK" version))
(sha256
(base32
- "1ix09a39z7y2cj0y8qsd66ka8a8y8q79w08l4jv1yhhn9h4va89s"))))
+ "1h5s6wbc5n5x5d28rynxpcmaklxdhf72g9gg9fy8cg77niipvxd9"))))
(properties `((upstream-name . "BiocOncoTK")))
(build-system r-build-system)
(propagated-inputs
@@ -11919,14 +11949,14 @@ tools for genome-scale analysis of cancer studies.")
(define-public r-biocor
(package
(name "r-biocor")
- (version "1.16.0")
+ (version "1.18.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BioCor" version))
(sha256
(base32
- "135rga7mwpzy8ypvriqpbmlh9l5yf61s9s1sa9615qfab14jh06b"))))
+ "0ii4g7438lb34ykidkbxw3v3k289k662rgbgayf9gak5avpkb2cq"))))
(properties `((upstream-name . "BioCor")))
(build-system r-build-system)
(propagated-inputs
@@ -11948,14 +11978,14 @@ gene selection, testing relationships, and so on.")
(define-public r-biocpkgtools
(package
(name "r-biocpkgtools")
- (version "1.10.2")
+ (version "1.12.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BiocPkgTools" version))
(sha256
(base32
- "1sfp1nxlwbbbpx2iwvyk9p10jdy2vxhgn2b5fy5blayzjjlb3d80"))))
+ "13m6h35938407ajj7fakl50g4p2wsvinkg0r2mwl1zwq88735arg"))))
(properties `((upstream-name . "BiocPkgTools")))
(build-system r-build-system)
(propagated-inputs
@@ -11996,14 +12026,14 @@ analytics on packages.")
(define-public r-biocset
(package
(name "r-biocset")
- (version "1.6.1")
+ (version "1.8.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BiocSet" version))
(sha256
(base32
- "0nmrg9cgq8l9w467y364jghnvym05abpj8pyj90grmrib2xc5sj2"))))
+ "0ysm68gcalg3d91jx6vmdzra01vc6kvzqnvz557g3rnm0wkx12q6"))))
(properties `((upstream-name . "BiocSet")))
(build-system r-build-system)
(propagated-inputs
@@ -12034,14 +12064,14 @@ accessing web references for elements/sets are also available in BiocSet.")
(define-public r-biocworkflowtools
(package
(name "r-biocworkflowtools")
- (version "1.18.0")
+ (version "1.20.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BiocWorkflowTools" version))
(sha256
(base32
- "1a32bwgnxaw0gv2gij2p4rm0a6l06jjhidvfz2v4k900pz1w79av"))))
+ "1j9s8w5y8savcmh70npkanxacq1kipxnwk1wsiw5hwnp1p13ldaa"))))
(properties
`((upstream-name . "BiocWorkflowTools")))
(build-system r-build-system)
@@ -12067,14 +12097,14 @@ Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.")
(define-public r-biodist
(package
(name "r-biodist")
- (version "1.64.0")
+ (version "1.66.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "bioDist" version))
(sha256
(base32
- "1y1x9q9aa76gbhsyfn638rxp5icjvq30fv3a4205xh7g5jwlf6yw"))))
+ "0y35c9sdq5x4q64ip0wgqz59mh01l71k1pp6n8vqbr667nwg0gdp"))))
(properties `((upstream-name . "bioDist")))
(build-system r-build-system)
(propagated-inputs
@@ -12090,14 +12120,14 @@ distance measures.")
(define-public r-pcatools
(package
(name "r-pcatools")
- (version "2.4.0")
+ (version "2.6.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "PCAtools" version))
(sha256
(base32
- "11idi9fwvyhkakbm63qxcdhkany8gbskis04z0p5a39lppq8ks31"))))
+ "10kfhsxhsjpzal3yvcqg769h5fz99cqqjq217cj9jip3jfh2m2h4"))))
(properties `((upstream-name . "PCAtools")))
(build-system r-build-system)
(propagated-inputs
@@ -12136,14 +12166,14 @@ dimensional mass cytometry data.")
(define-public r-rgreat
(package
(name "r-rgreat")
- (version "1.24.0")
+ (version "1.26.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "rGREAT" version))
(sha256
(base32
- "0ads9c9i8b39wvjih057zlyivj8zpsqjxf6r97yflz4sbi1jmcji"))))
+ "0kr61mhxp9phn1136fci450zwfhsipchmlm8d5rgib4lh0zbxrhl"))))
(properties `((upstream-name . "rGREAT")))
(build-system r-build-system)
(propagated-inputs
@@ -12164,14 +12194,14 @@ user's input and automatically retrieving results from GREAT web server.")
(define-public r-m3c
(package
(name "r-m3c")
- (version "1.14.0")
+ (version "1.16.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "M3C" version))
(sha256
(base32
- "17gj4haa4ywc6bmppm342jzppl3inqa94235yspikij6c098vrmc"))))
+ "0jsql5wd58hs5mnn9wq5b4kl3z57y6amykirfb3k047zpyi8ijnh"))))
(properties `((upstream-name . "M3C")))
(build-system r-build-system)
(propagated-inputs
@@ -12197,14 +12227,14 @@ hypothesis @code{K=1}.")
(define-public r-icens
(package
(name "r-icens")
- (version "1.64.0")
+ (version "1.66.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Icens" version))
(sha256
(base32
- "1rzgwxx4w2bqsaz0xmkhi4w9zsxgms80xf59zg1xp1camyhaihlz"))))
+ "08jd7g28mazvwd3qbq8y26czmkz45avp4vy8l7i5d6qajwzqzgzs"))))
(properties `((upstream-name . "Icens")))
(build-system r-build-system)
(propagated-inputs
@@ -12222,14 +12252,14 @@ truncated data.")
(define-public r-interval
(package
(name "r-interval")
- (version "1.1-0.7")
+ (version "1.1-0.8")
(source
(origin
(method url-fetch)
(uri (cran-uri "interval" version))
(sha256
(base32
- "1b31lh0sv7lzy76230djipahxa10lblbr37kdiigr6hp3dd1xmz9"))))
+ "0g0k9nri19p3y3s70ic1w3i3sxq8fbsxaikd7c4d6afqzr8hk2nl"))))
(properties `((upstream-name . "interval")))
(build-system r-build-system)
(propagated-inputs
@@ -12327,14 +12357,14 @@ generated.")
(define-public r-preprocesscore
(package
(name "r-preprocesscore")
- (version "1.54.0")
+ (version "1.56.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "preprocessCore" version))
(sha256
(base32
- "17a00blz4kvhmsk92bp5alj9kdpy7h1id7nk4vqxakhkb2jabr20"))))
+ "1i93vdqa6pwzamiryp3lv6cyvhx9shs01is0q6vbmdvcbii2vf3x"))))
(properties
`((upstream-name . "preprocessCore")))
(build-system r-build-system)
@@ -12348,13 +12378,13 @@ routines.")
(define-public r-s4vectors
(package
(name "r-s4vectors")
- (version "0.30.1")
+ (version "0.32.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "S4Vectors" version))
(sha256
(base32
- "103sw0fmmm4f3hprrsn7dwg0kmmr9mcmb46dcwwb6p5np0al2sfx"))))
+ "1zm1xlqrq1f9xa81j3ij2p78g3aywq7izsk3h40z94fjggahvc09"))))
(properties
`((upstream-name . "S4Vectors")))
(build-system r-build-system)
@@ -12415,14 +12445,14 @@ data manipulation and visualization.")
(define-public r-rgraphviz
(package
(name "r-rgraphviz")
- (version "2.36.0")
+ (version "2.38.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Rgraphviz" version))
(sha256
(base32
- "0d0xq1vgr4b165cn4wg7zmfjyc1d9ir4amgs196j4cgrhpmrnl8s"))))
+ "0fyv1ybpahkwz3fawzxgxfnshi8y7c18262rgdmqwdl5662vv1p7"))))
(properties `((upstream-name . "Rgraphviz")))
(build-system r-build-system)
(arguments
@@ -12453,13 +12483,13 @@ objects from the @code{graph} package.")
(define-public r-fithic
(package
(name "r-fithic")
- (version "1.18.0")
+ (version "1.20.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "FitHiC" version))
(sha256
(base32
- "1p8a6lis5yswaj647bjw89harlarnsxmvjzz63fn1l6gxrwhh8bx"))))
+ "0a3d2bxp98lmbf3i864zgfwxwvxyqfcrh75z9yz7ra7y44pkjr4y"))))
(properties `((upstream-name . "FitHiC")))
(build-system r-build-system)
(propagated-inputs
@@ -12479,13 +12509,13 @@ assays such as Hi-C.")
(define-public r-hitc
(package
(name "r-hitc")
- (version "1.36.0")
+ (version "1.38.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "HiTC" version))
(sha256
(base32
- "0s3kfqs3zlmq61hxdmxpmi9gfs9w3byckw7xzp1hrhdbsl46yvgq"))))
+ "1ckiwqfq86k8p3y36iwr7k3y6g4z80n8hb047c0i2491lrn23rhx"))))
(properties `((upstream-name . "HiTC")))
(build-system r-build-system)
(propagated-inputs
@@ -12508,14 +12538,14 @@ provided.")
(define-public r-hdf5array
(package
(name "r-hdf5array")
- (version "1.20.0")
+ (version "1.22.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "HDF5Array" version))
(sha256
(base32
- "1718hplz5qlbwxwb87509bl7lir9kilvn1s7p2haz551pg48zvrc"))))
+ "13h6qr4zkynir0ck2aiasjvlid7hrk3m2lzkjyhpvbg1a15r8zi9"))))
(properties `((upstream-name . "HDF5Array")))
(build-system r-build-system)
(inputs
@@ -12539,14 +12569,14 @@ block processing.")
(define-public r-rhdf5lib
(package
(name "r-rhdf5lib")
- (version "1.14.2")
+ (version "1.16.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Rhdf5lib" version))
(sha256
(base32
- "1cwynbcaaxmbh45fc0d264liqdj0wbjlj7k2bsq3qfjbnh6kkam5"))
+ "0yly9s3wdnhd9ci2jxfkql38ibv35yzs38a6g6ashbg1m5kgwd9p"))
(modules '((guix build utils)))
(snippet
'(begin
@@ -12622,14 +12652,14 @@ packages.")
(define-public r-beachmat
(package
(name "r-beachmat")
- (version "2.8.1")
+ (version "2.10.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "beachmat" version))
(sha256
(base32
- "06bpfpddsl49csxrs8hlx5pv0absc2wdcparchf8qqaqydazwci2"))))
+ "1l8c9q35mf90ckb366bcfqa0v2gw7ahs2h362j7cwv8fp39h4mpb"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
@@ -12651,13 +12681,13 @@ matrices.")
(define-public r-cner
(package
(name "r-cner")
- (version "1.28.0")
+ (version "1.30.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "CNEr" version))
(sha256
- (base32 "13w0gsfm7k29dp5nb0c9sb2ix506ph6dixsjis6xxcz6acq7lg2k"))))
+ (base32 "0w4iqmyyhsb6l9bi8c6qwdh4j6z2i1i5fi85ia9069fpl9d0hpl2"))))
(properties `((upstream-name . "CNEr")))
(build-system r-build-system)
(inputs `(("zlib" ,zlib)))
@@ -12699,14 +12729,14 @@ advanced visualization of sets of conserved noncoding elements.")
(define-public r-tfbstools
(package
(name "r-tfbstools")
- (version "1.30.0")
+ (version "1.32.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "TFBSTools" version))
(sha256
(base32
- "1avgjv2nyr28cla0z9dvh3v0hr1f561sz2as1k53a42irbjk0var"))))
+ "0j5gv145fczzdspwhbywlg47y05pgnkra9jg7bn4wa1k0cf5pr9g"))))
(properties `((upstream-name . "TFBSTools")))
(build-system r-build-system)
(propagated-inputs
@@ -12745,14 +12775,14 @@ provides a wrapper of de novo motif discovery software.")
(define-public r-motifmatchr
(package
(name "r-motifmatchr")
- (version "1.14.0")
+ (version "1.16.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "motifmatchr" version))
(sha256
(base32
- "1vif3dp4lv4jz1pxsq0ig791ir8q65jmrlqmkyfxpfxfj5alqnbm"))))
+ "0f7j54zdn51h1gcn81vqs8avmschjwqprjcfpvsi00q4fna3fg7z"))))
(properties `((upstream-name . "motifmatchr")))
(build-system r-build-system)
(propagated-inputs
@@ -12779,13 +12809,13 @@ This package wraps C++ code from the MOODS motif calling library.")
(define-public r-chromvar
(package
(name "r-chromvar")
- (version "1.14.0")
+ (version "1.16.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "chromVAR" version))
(sha256
- (base32 "1birmwvcvl2hb5ygbsb3wvbdfayqqs53j1bks46cbkq7ybigfyar"))))
+ (base32 "0ylsfr540l763bh010irbcavlskahyb1769pppimdgn22gyr3spk"))))
(properties `((upstream-name . "chromVAR")))
(build-system r-build-system)
(propagated-inputs
@@ -12826,14 +12856,14 @@ sequence (@code{DNAse-seq}) experiments.")
(define-public r-singlecellexperiment
(package
(name "r-singlecellexperiment")
- (version "1.14.1")
+ (version "1.16.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "SingleCellExperiment" version))
(sha256
(base32
- "1bwdhx0ss0s8f4xdgwd7x48apn849x4dyb5hbyglcz31r5vh1qgz"))))
+ "01075vbs8hy399pxalav9rbkz4djvl84ip559jkz51fypd0m4i39"))))
(properties
`((upstream-name . "SingleCellExperiment")))
(build-system r-build-system)
@@ -12857,14 +12887,14 @@ libraries.")
(define-public r-scuttle
(package
(name "r-scuttle")
- (version "1.2.1")
+ (version "1.4.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "scuttle" version))
(sha256
(base32
- "015k879gg2r39lp6mz26jwmysa56k0ial6v74zzmbi8hnz9zic3i"))))
+ "1dbdb6yc6wk01dljy1vy6f0lf44crc5rxxnc4bhjk8i4iljz8467"))))
(properties `((upstream-name . "scuttle")))
(build-system r-build-system)
(propagated-inputs
@@ -12892,13 +12922,13 @@ of other packages.")
(define-public r-scater
(package
(name "r-scater")
- (version "1.20.1")
+ (version "1.22.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "scater" version))
(sha256
(base32
- "1046fgf93dda3y2z5ilrjdczz7klj67ag63p4p1h03965wpj9vfn"))))
+ "0k4i9pwmwxcr5a40ljl27wriccwn5vc52xy48yjjh8ppl5dbggdg"))))
(build-system r-build-system)
(propagated-inputs
`(("r-beachmat" ,r-beachmat)
@@ -12910,6 +12940,7 @@ of other packages.")
("r-delayedmatrixstats" ,r-delayedmatrixstats)
("r-ggbeeswarm" ,r-ggbeeswarm)
("r-ggplot2" ,r-ggplot2)
+ ("r-ggrepel" ,r-ggrepel)
("r-gridextra" ,r-gridextra)
("r-matrix" ,r-matrix)
("r-rcolorbrewer" ,r-rcolorbrewer)
@@ -12932,14 +12963,14 @@ quality control.")
(define-public r-scran
(package
(name "r-scran")
- (version "1.20.1")
+ (version "1.22.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "scran" version))
(sha256
(base32
- "0ilzp6ngw9pq88gk79iic2zxfh5jaic6lnq3xfwc9a269bjylff0"))))
+ "1nyvbss4914giwzp5wiw9g4z5b6lr5iprbjrqlg4vpgnf1hz8k7l"))))
(build-system r-build-system)
(propagated-inputs
`(("r-beachmat" ,r-beachmat)
@@ -12975,14 +13006,14 @@ variable and significantly correlated genes.")
(define-public r-sparsematrixstats
(package
(name "r-sparsematrixstats")
- (version "1.4.2")
+ (version "1.6.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "sparseMatrixStats" version))
(sha256
(base32
- "0b22kzg751zlkcbs8pi0bcqrsj3imsg35qfvxfrqb7gav7qznc8v"))))
+ "0ifqj4a6mn4749sr62gq3dwd6mmbbzdx5mh5b5663vcgl1kw96x1"))))
(properties
`((upstream-name . "sparseMatrixStats")))
(build-system r-build-system)
@@ -13003,14 +13034,14 @@ data in the column sparse format.")
(define-public r-delayedmatrixstats
(package
(name "r-delayedmatrixstats")
- (version "1.14.3")
+ (version "1.16.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DelayedMatrixStats" version))
(sha256
(base32
- "1zxs2wjnsq9w1cl4andsd7y9xsdnl1an55khw9viaq758m7hhbcn"))))
+ "1pqwkk39rfhcnhmgchk0gfmm4jgasl19yq0nhhwsfj45y2vk6kjk"))))
(properties
`((upstream-name . "DelayedMatrixStats")))
(build-system r-build-system)
@@ -13039,14 +13070,14 @@ memory usage and processing time is minimized.")
(define-public r-mscoreutils
(package
(name "r-mscoreutils")
- (version "1.4.0")
+ (version "1.6.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MsCoreUtils" version))
(sha256
(base32
- "13g8a726vsyjs6m1kd42vf8avdnmhykxhl6z3j2njzkp2jg17pd8"))))
+ "1w8d1v2r3plwwcz23zhbpvklhapf2a6x3xmglyh4sh6sy9ynkgrv"))))
(properties `((upstream-name . "MsCoreUtils")))
(build-system r-build-system)
(propagated-inputs
@@ -13068,17 +13099,49 @@ well as misc helper functions, that are used across high-level data structure
within the R for Mass Spectrometry packages.")
(license license:artistic2.0)))
+(define-public r-msfeatures
+ (package
+ (name "r-msfeatures")
+ (version "1.2.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "MsFeatures" version))
+ (sha256
+ (base32 "020ifrijlzdd3qk4bhd9z4knj5d87ildrkl3wcmxvwkvs9rbh8rq"))))
+ (properties `((upstream-name . "MsFeatures")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-mscoreutils" ,r-mscoreutils)
+ ("r-protgenerics" ,r-protgenerics)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://github.com/RforMassSpectrometry/MsFeatures")
+ (synopsis "Functionality for mass spectrometry features")
+ (description
+ "The MsFeature package defines functionality for Mass Spectrometry
+features. This includes functions to group (LC-MS) features based on some of
+their properties, such as retention time (coeluting features), or correlation
+of signals across samples. This packge hence allows to group features, and
+its results can be used as an input for the @code{QFeatures} package which
+allows to aggregate abundance levels of features within each group. This
+package defines concepts and functions for base and common data types,
+implementations for more specific data types are expected to be implemented in
+the respective packages (such as e.g. @code{xcms}).")
+ (license license:artistic2.0)))
+
(define-public r-biocio
(package
(name "r-biocio")
- (version "1.2.0")
+ (version "1.4.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BiocIO" version))
(sha256
(base32
- "0skwnpxl6fkqihidpqrfzzh7b05x11j6jwkiinmhggmv0ggjb5ph"))))
+ "1qg6v961sbj7qwyjx4z720f6h0kq693p7gc8q99my7gqkbbcxrfr"))))
(properties `((upstream-name . "BiocIO")))
(build-system r-build-system)
(propagated-inputs
@@ -13105,14 +13168,14 @@ as well as local access. Developers can register a file extension, e.g.,
(define-public r-msmseda
(package
(name "r-msmseda")
- (version "1.30.0")
+ (version "1.32.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "msmsEDA" version))
(sha256
(base32
- "0555a3riyp781mlffmnf93igfq8vl8wjk51pa9qb48qkdn6y8pfc"))))
+ "1jammjkjjkcqad2ki02l2pdf4jybyh71hv463aya2ylmzsin5vi9"))))
(properties `((upstream-name . "msmsEDA")))
(build-system r-build-system)
(propagated-inputs
@@ -13131,14 +13194,14 @@ experiments, and visualize de influence of the involved factors.")
(define-public r-msmstests
(package
(name "r-msmstests")
- (version "1.30.0")
+ (version "1.32.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "msmsTests" version))
(sha256
(base32
- "11vhy1l6za73dpdj85q4ksaghgd8vb2h8v9iirmsn2vpajqrvgjh"))))
+ "0xmjgd8rqpb8i7d46pvnj7da2di8bwfdncr48b8hgylkc98ghznb"))))
(properties `((upstream-name . "msmsTests")))
(build-system r-build-system)
(propagated-inputs
@@ -13163,14 +13226,14 @@ relevant, and the minimum expression of the most abundant condition.")
(define-public r-catalyst
(package
(name "r-catalyst")
- (version "1.16.2")
+ (version "1.18.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "CATALYST" version))
(sha256
(base32
- "1vw8x54hwgcyn29k81zcvawawy2iy2qgp49gjpb830q04gx6yc6h"))))
+ "15lah45lf16zh1ankbpjvz8zp38lldvq074nmvb99rhhqys2gbgi"))))
(properties `((upstream-name . "CATALYST")))
(build-system r-build-system)
(propagated-inputs
@@ -13221,14 +13284,14 @@ standards, ii) single-cell deconvolution, and iii) bead-based compensation.")
(define-public r-erma
(package
(name "r-erma")
- (version "1.8.0")
+ (version "1.10.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "erma" version))
(sha256
(base32
- "02a9702sasgighwb0f9ii8n30ngfx1hjnppaay1f5zsigr8vqalz"))))
+ "0pb9ar1wy613vg6sfdmn8n4cfv1328m8bagnigsjdb3hc3hbir4z"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
@@ -13261,14 +13324,14 @@ by Ernst and Kellis.")
(define-public r-ggbio
(package
(name "r-ggbio")
- (version "1.40.0")
+ (version "1.42.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ggbio" version))
(sha256
(base32
- "0k3dxacrwgyrkvm7ggc2s1s1pbfs6c0a7ngykkj7jnc73czvnilx"))))
+ "1svmjaa3gisi39sl52337drvd54havcy5pjmwrykgykz5flid2m7"))))
(build-system r-build-system)
(arguments
`(#:phases
@@ -13429,14 +13492,14 @@ family of feature/genome hypotheses.")
(define-public r-gviz
(package
(name "r-gviz")
- (version "1.36.2")
+ (version "1.38.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Gviz" version))
(sha256
(base32
- "0lp0k8jd4dfsfn10706124graaqnzcyv1siblvm8dn2ykw2rc6vl"))))
+ "0nqa7m300d7gpsayb6c6rv64d3y8c390wvwgz7v29zs9c025s9a8"))))
(properties `((upstream-name . "Gviz")))
(build-system r-build-system)
(propagated-inputs
@@ -13478,14 +13541,14 @@ with your data.")
(define-public r-gwascat
(package
(name "r-gwascat")
- (version "2.24.0")
+ (version "2.26.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "gwascat" version))
(sha256
(base32
- "0109cxsviq1sk5hfwkjzd0y1kpm934287asjjd0j8jhh4b0ah2b2"))))
+ "0s67jgk3gnfiyfjwhq4r5xlfnip29blis4fg75kn4qmvjv5j2pxx"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
@@ -13512,13 +13575,13 @@ EMBL-EBI GWAS catalog.")
(define-public r-kegggraph
(package
(name "r-kegggraph")
- (version "1.52.0")
+ (version "1.54.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "KEGGgraph" version))
(sha256
- (base32 "0zxdph5hzr3kzj2g1mjqpiviwa189a5sq4bw7wiry6r79fdnklqs"))))
+ (base32 "1qqvbv1sq9j570syb2802ya2ffg1k8f1w986wr6ksqkwxb9qbbm4"))))
(properties `((upstream-name . "KEGGgraph")))
(build-system r-build-system)
(propagated-inputs
@@ -13539,14 +13602,14 @@ functionalities including parsing, graph operation, visualization and etc.")
(define-public r-ldblock
(package
(name "r-ldblock")
- (version "1.22.1")
+ (version "1.24.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ldblock" version))
(sha256
(base32
- "16vp5psmigxdkkd6fbivb6s8mvd7rsnm771wsbjvayl2y7ig7kq4"))))
+ "1v9b372d5hpwwik6956mfwc9b3bibygz042i4nydsklnbwm5vcmg"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
@@ -13665,13 +13728,13 @@ other functional sequencing data.")
(define-public r-pathview
(package
(name "r-pathview")
- (version "1.32.0")
+ (version "1.34.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "pathview" version))
(sha256
- (base32 "1fank0qavv9ikmzxvms8mky2wbzny02rfqkvsqzma26r3vl4r1g1"))))
+ (base32 "1jdl81lvrsz03b1nws90nssf2clipipzaqvwm1pq57mvshnlnkjr"))))
(properties `((upstream-name . "pathview")))
(build-system r-build-system)
(propagated-inputs
@@ -13699,14 +13762,14 @@ large-scale and fully automated analysis.")
(define-public r-snpstats
(package
(name "r-snpstats")
- (version "1.42.0")
+ (version "1.44.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "snpStats" version))
(sha256
(base32
- "11vvih5y9kvyjfp2navkfpp4xiyfgwlv4r0x3p52hkj92pc2pg3g"))))
+ "0ha34b5cg26940xihgky45adns1nflrgq2qjq77w4bncxpaacsqq"))))
(properties `((upstream-name . "snpStats")))
(build-system r-build-system)
(inputs `(("zlib" ,zlib)))
@@ -13726,14 +13789,14 @@ the earlier snpMatrix package, allowing for uncertainty in genotypes.")
(define-public r-chromstar
(package
(name "r-chromstar")
- (version "1.18.0")
+ (version "1.19.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "chromstaR" version))
(sha256
(base32
- "09cqzylci4x4i7wn4ckcqhdlljbzfrp08wdvkkc5vrdldnj9pq5h"))))
+ "0z511l26fhz00qn8h2yybylk8c3ws8hj1hp8hq9qj9mfczwiqy3j"))))
(properties `((upstream-name . "chromstaR")))
(build-system r-build-system)
(propagated-inputs
@@ -13764,14 +13827,14 @@ analyses.")
(define-public r-guitar
(package
(name "r-guitar")
- (version "2.8.0")
+ (version "2.10.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Guitar" version))
(sha256
(base32
- "1q4m6c5181dw12lvdp324jlk78c9jgcsg6b9hk87zjadp6j0gfr6"))))
+ "082yja4mmsq77sllv3c88agxjbb6jxwil2krb8fkfsijvyyx11c9"))))
(properties `((upstream-name . "Guitar")))
(build-system r-build-system)
(propagated-inputs
@@ -13796,13 +13859,13 @@ starting site, start codon, stop codon and transcription ending site.")
(define-public r-sushi
(package
(name "r-sushi")
- (version "1.30.0")
+ (version "1.31.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "Sushi" version))
(sha256
(base32
- "1m5l0nflhcynb3gz7b8qzvknb0s6xhds8z1yl3mbv8ic9qn2knv4"))))
+ "1cj4palsq99vnwihp6z9mw0f8w9qj2vq8zwnabf3bgg0l1wpsc7c"))))
(properties `((upstream-name . "Sushi")))
(build-system r-build-system)
(propagated-inputs
@@ -13818,14 +13881,14 @@ visualizations for publication-quality multi-panel figures.")
(define-public r-ballgown
(package
(name "r-ballgown")
- (version "2.24.0")
+ (version "2.26.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ballgown" version))
(sha256
(base32
- "0ff8z4pfgzai2q4aafclg36bhsi9jwl9xhh1p9fqhmikisscq7i1"))))
+ "0fiky82arvgzgxrm4bqn74m5kngqpdaqf6ks4cr89nlnhfq0v6rf"))))
(properties `((upstream-name . "ballgown")))
(build-system r-build-system)
(propagated-inputs
@@ -13852,14 +13915,14 @@ to annotation.")
(define-public r-megadepth
(package
(name "r-megadepth")
- (version "1.2.3")
+ (version "1.4.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "megadepth" version))
(sha256
(base32
- "0grgj7bzyqnxby0sx5ic1h9bzmx19xwl0a5b3v6wbnwqcla2i3kg"))))
+ "0mg7n3990qv65rg624473ssccka0yjpgc20glrdc5saci891j44r"))))
(properties `((upstream-name . "megadepth")))
(build-system r-build-system)
(inputs `(("megadepth" ,megadepth)))
@@ -13885,14 +13948,14 @@ regions or annotations of your choice from BigWig files.")
(define-public r-beclear
(package
(name "r-beclear")
- (version "2.8.0")
+ (version "2.10.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BEclear" version))
(sha256
(base32
- "0w18livng2gcmjgvws7pix3gsnj237rs34sgwxsfmn8p5vfx8b30"))))
+ "1njb1lfd4wmsrfw06jc8z8vdk14nmcw9lwyvbxr7z1zg4h8v6c29"))))
(properties `((upstream-name . "BEclear")))
(build-system r-build-system)
(propagated-inputs
@@ -13918,14 +13981,14 @@ real numbers.")
(define-public r-bgeecall
(package
(name "r-bgeecall")
- (version "1.8.0")
+ (version "1.10.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BgeeCall" version))
(sha256
(base32
- "1byciy7vzbdkdgaim10s9qb7zlxsywbhcsrka31gm0rm9ljqc665"))))
+ "0rbbl8m48qcvl26lnf27jq108p7pi84m9ac3qcpjc0ax5wywbv16"))))
(properties `((upstream-name . "BgeeCall")))
(build-system r-build-system)
(propagated-inputs
@@ -13954,14 +14017,14 @@ all RNA-Seq libraries of each species integrated in Bgee.")
(define-public r-bgeedb
(package
(name "r-bgeedb")
- (version "2.18.1")
+ (version "2.20.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BgeeDB" version))
(sha256
(base32
- "1ziq180yfpdqwhjdzkwjjhwzn3kb0gkj6q0a26c7a30mcfb50w11"))))
+ "0pjymal01sjl5dc37g66wykgxnksarlbvwnbvhg7w0i7y92zavqk"))))
(properties `((upstream-name . "BgeeDB")))
(build-system r-build-system)
(propagated-inputs
@@ -13988,14 +14051,14 @@ anatomical terms, mapped to genes by expression patterns.")
(define-public r-biobtreer
(package
(name "r-biobtreer")
- (version "1.4.0")
+ (version "1.6.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "biobtreeR" version))
(sha256
(base32
- "0pynx4ps1qxsn13ba6zyg6h5dqlp2y7qish67m7sdjns079zh061"))))
+ "0m9gx2g5ishbbh7aqp09mpknhr7q1v5ap0s6xp6ccj01pz2gkk8s"))))
(properties `((upstream-name . "biobtreeR")))
(build-system r-build-system)
(propagated-inputs
@@ -14015,14 +14078,14 @@ mappings functionalities.")
(define-public r-minet
(package
(name "r-minet")
- (version "3.50.0")
+ (version "3.52.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "minet" version))
(sha256
(base32
- "0bir2zr4r2wawkdvdhrk2hcyxmgkrkfvx36jj85fcm24axlqrzzb"))))
+ "0nhgvgci4r9pjfsnvxyj2q8im1wvig4zmfx2kidw8f63x2ip2rbd"))))
(properties `((upstream-name . "minet")))
(build-system r-build-system)
(propagated-inputs
@@ -14037,14 +14100,14 @@ information networks from data.")
(define-public r-genetclassifier
(package
(name "r-genetclassifier")
- (version "1.32.0")
+ (version "1.34.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "geNetClassifier" version))
(sha256
(base32
- "1i1cavbbvxzqgqxfmikghnls18jrq12hb953mjrwa95lkhzdxm2d"))))
+ "1phyphdc1i55ab1a05633b0p41q8n7w0byp1plgcav2s3h8mk1km"))))
(properties
`((upstream-name . "geNetClassifier")))
(build-system r-build-system)
@@ -14065,14 +14128,14 @@ interface to query the classifier.")
(define-public r-dir-expiry
(package
(name "r-dir-expiry")
- (version "1.0.0")
+ (version "1.2.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "dir.expiry" version))
(sha256
(base32
- "05mk7iwzay1xrgvssbz7nyl5d1n03syalbk18lmjmbx05dy0cjik"))))
+ "1bwmlxmizhmim2l0mk406hxfr5mnmsg5zbqkjyygaipa971m9s00"))))
(properties `((upstream-name . "dir.expiry")))
(build-system r-build-system)
(propagated-inputs `(("r-filelock" ,r-filelock)))
@@ -14089,14 +14152,14 @@ eliminating obsolete caches generated by old versions of packages.")
(define-public r-basilisk-utils
(package
(name "r-basilisk-utils")
- (version "1.4.0")
+ (version "1.6.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "basilisk.utils" version))
(sha256
(base32
- "0qbm6rj6h059hakflbwz4j4f59311jhbk5dnpx11kyixh5pgjk7v"))))
+ "0578rq2yz24sv7anb7vp0a0y35944ag1l8ca6haanb03wl97wm99"))))
(properties
`((upstream-name . "basilisk.utils")))
(build-system r-build-system)
@@ -14113,14 +14176,14 @@ package, primarily for creation of the underlying Conda instance.")
(define-public r-basilisk
(package
(name "r-basilisk")
- (version "1.4.0")
+ (version "1.6.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "basilisk" version))
(sha256
(base32
- "1nzbn3f2jzvg3a3m6wgksi4cvamqas2q7csdk4ir7fcirasf536v"))))
+ "1cdkpngv9qybd9yxc3i2201p433vkkahs71v28x6lgs5l2wz3m1a"))))
(properties `((upstream-name . "basilisk")))
(build-system r-build-system)
(propagated-inputs
@@ -14141,16 +14204,21 @@ Python environments in a single R session.")
(define-public r-biocthis
(package
(name "r-biocthis")
- (version "1.2.0")
+ (version "1.4.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "biocthis" version))
(sha256
(base32
- "08awghsg7q22csb0j9dr8dpb1vkn9gcs9qnhhljxifkw2ahbqia4"))))
+ "0kh5lmv992v4r5r58x29403cll0zxr9fx4ar81nrzvnch5668v39"))))
(properties `((upstream-name . "biocthis")))
(build-system r-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'set-HOME
+ (lambda _ (setenv "HOME" "/tmp"))))))
(propagated-inputs
`(("r-biocmanager" ,r-biocmanager)
("r-fs" ,r-fs)
@@ -14170,14 +14238,14 @@ Bioconductor-friendly.")
(define-public r-biocdockermanager
(package
(name "r-biocdockermanager")
- (version "1.4.0")
+ (version "1.6.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BiocDockerManager" version))
(sha256
(base32
- "0dh1flm5chsdcihljrg6znjskqkp0qyjh39hsv4zq0frf1rm97j7"))))
+ "1kpdmpcngnl667bfffp9bkf8c31ipmhsncq0h9bf3a4k8b83pi0w"))))
(properties
`((upstream-name . "BiocDockerManager")))
(build-system r-build-system)
@@ -14200,18 +14268,19 @@ the Bioconductor project.")
(define-public r-biodb
(package
(name "r-biodb")
- (version "1.0.4")
+ (version "1.2.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "biodb" version))
(sha256
(base32
- "1apnbr5p619nsrhd2drm6arj69sw0wijv8ap7dfrndqkffrpbfmx"))))
+ "0q343zbx341xdy634p50k7bj6byv8v2rqzy50nw75a79206pajl4"))))
(properties `((upstream-name . "biodb")))
(build-system r-build-system)
(propagated-inputs
- `(("r-chk" ,r-chk)
+ `(("r-biocfilecache" ,r-biocfilecache)
+ ("r-chk" ,r-chk)
("r-jsonlite" ,r-jsonlite)
("r-lgr" ,r-lgr)
("r-lifecycle" ,r-lifecycle)
@@ -14244,14 +14313,14 @@ separate published packages.")
(define-public r-biomformat
(package
(name "r-biomformat")
- (version "1.20.0")
+ (version "1.22.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "biomformat" version))
(sha256
(base32
- "1wgshkddxbmpsihpkm0dp7vqp59ns6iqbx574y80n2pxb8dx8sy9"))))
+ "0xf99j4lhf8kh9h1317hrbzxdv6rljs1fn68r8s40x6y4db3l817"))))
(properties `((upstream-name . "biomformat")))
(build-system r-build-system)
(propagated-inputs
@@ -14276,14 +14345,14 @@ as extensions of common core functions/methods.")
(define-public r-mvcclass
(package
(name "r-mvcclass")
- (version "1.66.0")
+ (version "1.68.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MVCClass" version))
(sha256
(base32
- "1di7y10mr7caacd6igwxnr62cm4v1x877yi4a2i5jqz1058jqni7"))))
+ "088gzh33vjkjf78xczqfs89pyg0k7c3533yfvijqxl84ni2ky78z"))))
(properties `((upstream-name . "MVCClass")))
(build-system r-build-system)
(home-page "https://bioconductor.org/packages/MVCClass")
@@ -14296,14 +14365,14 @@ design.")
(define-public r-biomvcclass
(package
(name "r-biomvcclass")
- (version "1.60.0")
+ (version "1.62.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BioMVCClass" version))
(sha256
(base32
- "04pld93nffbci47dnf0awmcmhlfzv599ggcd7hvq78w41ac60qv8"))))
+ "0jqgazwz35gz11a7vzanyy2yalzalx0z0rw6y18nmk8dbv01nv2j"))))
(properties `((upstream-name . "BioMVCClass")))
(build-system r-build-system)
(propagated-inputs
@@ -14321,14 +14390,14 @@ design.")
(define-public r-biomvrcns
(package
(name "r-biomvrcns")
- (version "1.32.0")
+ (version "1.34.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "biomvRCNS" version))
(sha256
(base32
- "0wyzj422smr4m9mswzn9inc1sn86pnia7jmd6k28nd2a7fjyrm16"))))
+ "01nhjhfyzs67p97bk9bjqdxk239ckl8sgfj55azk1zmw92aw2hfy"))))
(properties `((upstream-name . "biomvRCNS")))
(build-system r-build-system)
(propagated-inputs
@@ -14349,14 +14418,14 @@ using aCGH or sequencing.")
(define-public r-bionero
(package
(name "r-bionero")
- (version "1.0.4")
+ (version "1.2.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BioNERO" version))
(sha256
(base32
- "1yj0pavyfrj2gsvaj1dkgmznibm2appxjx9rk5qjslhslmm5b05b"))))
+ "0ddrzv1g46hvm52dzrcj5nbyyw9a16cqk8zg20wnkrh3qw1h4d9p"))))
(properties `((upstream-name . "BioNERO")))
(build-system r-build-system)
(propagated-inputs
@@ -14405,14 +14474,14 @@ networks.")
(define-public r-bionet
(package
(name "r-bionet")
- (version "1.52.0")
+ (version "1.54.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BioNet" version))
(sha256
(base32
- "15rk1jfv4h1mxvr5bs0qmq6fdnza7zcmksigqxb46fs7f6znr3yi"))))
+ "05rj14jn4gn0hfn57amf19b8fqwkd3y2ji3mg7m1yg1w7n4qxqsg"))))
(properties `((upstream-name . "BioNet")))
(build-system r-build-system)
(propagated-inputs
@@ -14438,14 +14507,14 @@ scoring subnetwork.")
(define-public r-bionetstat
(package
(name "r-bionetstat")
- (version "1.12.0")
+ (version "1.14.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BioNetStat" version))
(sha256
(base32
- "16xlfng9m8xvm831c2x6zmjc0gavlfiy9pnza55hdv86888fcnbg"))))
+ "13br8x4809hrr4ibz6iy5qjza9j6cazmkpvfikvw6bs588csxwf8"))))
(properties `((upstream-name . "BioNetStat")))
(build-system r-build-system)
(propagated-inputs
@@ -14480,14 +14549,14 @@ network and metabolic pathways view.")
(define-public r-bioqc
(package
(name "r-bioqc")
- (version "1.20.0")
+ (version "1.22.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BioQC" version))
(sha256
(base32
- "04akp94p0d0zid55m1b1k3qlw7iq914pcg57lihgj3pa92n1sc5l"))))
+ "190336qk0plg79gzvfn6wfplsi8nq0nj8508g7m0w3z6bdgwy407"))))
(properties `((upstream-name . "BioQC")))
(build-system r-build-system)
(propagated-inputs
@@ -14508,14 +14577,14 @@ optimised for high performance.")
(define-public r-biotip
(package
(name "r-biotip")
- (version "1.6.0")
+ (version "1.8.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BioTIP" version))
(sha256
(base32
- "1i6r8px0fmdjx8frpljppwql74mhx08ibvhs9y3qk91ck5h3f0js"))))
+ "0xmy5c4i9gf6d04gara6lbnnldqmzjaascb2pd2ih60jw2mvl4ys"))))
(properties `((upstream-name . "BioTIP")))
(build-system r-build-system)
(propagated-inputs
@@ -14538,24 +14607,22 @@ help unravel disease regulatory trajectory.")
(define-public r-biotmle
(package
(name "r-biotmle")
- (version "1.16.0")
+ (version "1.18.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "biotmle" version))
(sha256
(base32
- "01smkmbv40yprgrgi2gjnmi8ncqyrlkfdxsh33ki20amcx32nc7f"))))
+ "0p3iavf9059qa8qvfvqzskfc5gki3z0ivkkqdwg5anvf0wv2k47g"))))
(properties `((upstream-name . "biotmle")))
(build-system r-build-system)
(propagated-inputs
`(("r-assertthat" ,r-assertthat)
("r-biocgenerics" ,r-biocgenerics)
("r-biocparallel" ,r-biocparallel)
- ("r-dofuture" ,r-dofuture)
("r-dplyr" ,r-dplyr)
("r-drtmle" ,r-drtmle)
- ("r-future" ,r-future)
("r-ggplot2" ,r-ggplot2)
("r-ggsci" ,r-ggsci)
("r-limma" ,r-limma)
@@ -14582,14 +14649,14 @@ ensemble machine learning for the estimation of nuisance functions.")
(define-public r-bsseq
(package
(name "r-bsseq")
- (version "1.28.0")
+ (version "1.30.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "bsseq" version))
(sha256
(base32
- "1xpv85hr681kkkilsnasndkszwmzbzq11y0lff4na2ilsm7sqmmi"))))
+ "1i30zf6457a0qd64s89x9l544y1h0hj9rfgf1m8l4krd487a9b9d"))))
(properties `((upstream-name . "bsseq")))
(build-system r-build-system)
(propagated-inputs
@@ -14628,14 +14695,14 @@ visualizing bisulfite sequencing data.")
(define-public r-dmrseq
(package
(name "r-dmrseq")
- (version "1.12.0")
+ (version "1.14.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "dmrseq" version))
(sha256
(base32
- "1jbbjifjsnk9261wqmdwkbzj1w52g6vaanpk4w816ri0fap587m4"))))
+ "1d6y6rbvcgprmzqkdzxg5csf0yv845d9vw10pcd1pzyndrama1vd"))))
(properties `((upstream-name . "dmrseq")))
(build-system r-build-system)
(propagated-inputs
@@ -14674,13 +14741,13 @@ interest on transformed methylation proportions.")
(define-public r-omnipathr
(package
(name "r-omnipathr")
- (version "3.0.4")
+ (version "3.2.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "OmnipathR" version))
(sha256
- (base32 "0rbq3h3cp5dgpy5ifmbnfm6z8w4jv45wjzyl1f4qacgrbyf2l30a"))))
+ (base32 "1q89mxnp8cig9r1499g7fb9p9x9ryz1dmc3w6ps5ww9n6rl8jqk8"))))
(properties `((upstream-name . "OmnipathR")))
(build-system r-build-system)
(arguments
@@ -14690,6 +14757,7 @@ interest on transformed methylation proportions.")
(lambda _ (setenv "HOME" "/tmp"))))))
(propagated-inputs
`(("r-checkmate" ,r-checkmate)
+ ("r-crayon" ,r-crayon)
("r-curl" ,r-curl)
("r-digest" ,r-digest)
("r-dplyr" ,r-dplyr)
@@ -14725,14 +14793,14 @@ for ligand activity prediction from transcriptomics data.")
(define-public r-biscuiteer
(package
(name "r-biscuiteer")
- (version "1.6.0")
+ (version "1.8.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "biscuiteer" version))
(sha256
(base32
- "0f4kk4v2c5diq0fbvyvgwjd1kjk9izr6n9wfrlrr7wbx4pz3c3h6"))))
+ "16ds322b21g8ys5c3lkrvi70i82f9rxvnknbiqx4sp6f2l01j5yj"))))
(properties `((upstream-name . "biscuiteer")))
(build-system r-build-system)
(propagated-inputs
@@ -14776,14 +14844,14 @@ estimates, etc.")
(define-public r-tximeta
(package
(name "r-tximeta")
- (version "1.10.0")
+ (version "1.12.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "tximeta" version))
(sha256
(base32
- "0ipgpcl93cac4qff6lp9x2l3gav5kb1x1d56g32h09hlm797rvvh"))))
+ "03fbz6pka7bcbhd0bblgckyxsqhzp4n8qp2dcpdb3sr01lyw4bc5"))))
(properties `((upstream-name . "tximeta")))
(build-system r-build-system)
(propagated-inputs
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 3ddb91714a..12533c9efa 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -528,14 +528,26 @@ BED, GFF/GTF, VCF.")
'(#:test-target "test"
#:phases
(modify-phases %standard-phases
+ (add-after 'unpack 'compatibility
+ (lambda _
+ (substitute* "src/utils/fileType/FileRecordTypeChecker.h"
+ (("static const float PERCENTAGE")
+ "static constexpr float PERCENTAGE"))
+ (substitute* "src/utils/general/DualQueue.h"
+ (("template <class T, template<class T> class CompareFunc>")
+ "template <class T, template<class U> class CompareFunc>"))))
(delete 'configure)
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
(for-each (lambda (file)
(install-file file bin))
- (find-files "bin" ".*")))
- #t)))))))
+ (find-files "bin" ".*"))))))))
+ (native-inputs
+ `(("python" ,python-wrapper)))
+ (inputs
+ `(("samtools" ,samtools)
+ ("zlib" ,zlib)))))
(define-public pbbam
(package
diff --git a/gnu/packages/cdrom.scm b/gnu/packages/cdrom.scm
index 8faeedcfe9..76f713385b 100644
--- a/gnu/packages/cdrom.scm
+++ b/gnu/packages/cdrom.scm
@@ -419,16 +419,14 @@ or @command{xorrisofs} to create ISO 9660 images.")
(define-public dvdisaster
(package
(name "dvdisaster")
- (version "0.79.5")
+ (version "0.79.9")
(source
(origin
(method url-fetch)
- ;; Update this (and update HOME-PAGE) when/if one reappears.
- (uri (string-append "https://web.archive.org/web/20180428070843/"
- "http://dvdisaster.net/downloads/dvdisaster-"
+ (uri (string-append "https://dvdisaster.jcea.es/downloads/dvdisaster-"
version ".tar.bz2"))
(sha256
- (base32 "0f8gjnia2fxcbmhl8b3qkr5b7idl8m855dw7xw2fnmbqwvcm6k4w"))))
+ (base32 "1hz3fvqfdrwb7dn6ggqkpcgyjag37ivm1layw27ncjz9glklxjbr"))))
(build-system gnu-build-system)
(inputs
`(("gtk+" ,gtk+-2)))
@@ -447,8 +445,7 @@ or @command{xorrisofs} to create ISO 9660 images.")
(with-directory-excursion "regtest"
(substitute* "common.bash"
(("ISODIR=/var/tmp/regtest") "ISODIR=/tmp"))
- (for-each invoke (find-files "." "rs.*\\.bash")))
- #t))
+ (for-each invoke (find-files "." "rs.*\\.bash")))))
(add-after 'install 'install-desktop
(lambda* (#:key outputs #:allow-other-keys)
(let* ((datadir (string-append (assoc-ref outputs "out") "/share")))
@@ -468,10 +465,13 @@ or @command{xorrisofs} to create ISO 9660 images.")
(find-files "contrib" "dvdisaster[0-9]*\\.png"))
(mkdir-p (string-append datadir "/pixmaps"))
(copy-file "contrib/dvdisaster48.xpm"
- (string-append datadir "/pixmaps/dvdisaster.xpm"))
- #t))))))
- (home-page (string-append "https://web.archive.org/web/20180428070843/"
- "http://dvdisaster.net/en/index.html"))
+ (string-append datadir "/pixmaps/dvdisaster.xpm")))))
+ (add-after 'install 'remove-uninstall-script
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out")))
+ (delete-file
+ (string-append out "/bin/dvdisaster-uninstall.sh"))))))))
+ (home-page "https://dvdisaster.jcea.es/")
(synopsis "Error correcting codes for optical media images")
(description "Optical media (CD,DVD,BD) keep their data only for a
finite time (typically for many years). After that time, data loss develops
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 0280a51be5..4c4530deb9 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -188,14 +188,14 @@ etc.")
(define-public r-datawizard
(package
(name "r-datawizard")
- (version "0.2.0.1")
+ (version "0.2.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "datawizard" version))
(sha256
(base32
- "15q491qix4a9b10wkb5bm9jnnr62smjw4qdrw4bd51i1kgvd6kl5"))))
+ "062phzfcvn79npn4s58gz1m5ignyvr4q2zlqnyxla4p7l760djl9"))))
(properties `((upstream-name . "datawizard")))
(build-system r-build-system)
(propagated-inputs
@@ -213,14 +213,14 @@ wrangling backend for the packages in the @code{easystats} ecosystem.")
(define-public r-diffobj
(package
(name "r-diffobj")
- (version "0.3.4")
+ (version "0.3.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "diffobj" version))
(sha256
(base32
- "1z4yhfasjpi9rxl1lh9bny7yvs947a6hhc768azc1wwad748mk9q"))))
+ "0q6gwd9pqh41f6j5p9jl92aji4p8kx9inffpha93d7jc3ndsfq6q"))))
(properties `((upstream-name . "diffobj")))
(build-system r-build-system)
(propagated-inputs `(("r-crayon" ,r-crayon)))
@@ -1233,13 +1233,13 @@ single step.")
(define-public r-rvest
(package
(name "r-rvest")
- (version "1.0.1")
+ (version "1.0.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "rvest" version))
(sha256
- (base32 "1v99bpp2077s4y5phvkzpgjyr8cs9axifm1c3npw6jmh8x9j91h8"))))
+ (base32 "1905vxgnj3q09l1wf6rwxpbpydznp06nbkrclnc05j2415z4gfw9"))))
(build-system r-build-system)
(propagated-inputs
`(("r-httr" ,r-httr)
@@ -1686,13 +1686,13 @@ applications.")
(define-public r-htmltable
(package
(name "r-htmltable")
- (version "2.2.1")
+ (version "2.3.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "htmlTable" version))
(sha256
- (base32 "05zy9acx4s80dr880q69i4rcjqgmbz18gn7pyazda9gsnm981j96"))))
+ (base32 "0xx5fza40six81mkfjsja6a8j6cg1mlzg0cxfgv084riyq79l387"))))
(properties `((upstream-name . "htmlTable")))
(build-system r-build-system)
(propagated-inputs
@@ -1973,14 +1973,14 @@ language, which is stable, powerful, and CSS compatible.")
(define-public r-bslib
(package
(name "r-bslib")
- (version "0.3.0")
+ (version "0.3.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "bslib" version))
(sha256
(base32
- "0zfjavz5jw4lfbrmc3rgsivcrxq2ia9jwmfbcrdxnxlmyri8qinr"))
+ "0jcqklry1nkibz0sydsz5xdsnb4wnrrhvmyr9ji3k45bbipbap2z"))
(snippet
'(for-each delete-file
'("inst/lib/bs-a11y-p/plugins/js/bootstrap-accessibility.min.js"
@@ -2263,36 +2263,35 @@ supports interactive trees, to enable rich, editable trees in Shiny.")
(define-public r-shinydashboard
(package
(name "r-shinydashboard")
- (version "0.7.1")
+ (version "0.7.2")
(source (origin
(method url-fetch)
(uri (cran-uri "shinydashboard" version))
(sha256
(base32
- "0khac8b27q3swdw07kl609hm0fjfjsjv591b388q99mqqr2rk92i"))))
+ "0hrqkwlpb8rnmp5j74p134g4c4cl16icmwc2ip6k1634fa2y8vm5"))))
(build-system r-build-system)
;; The directory inst/AdminLTE/ contains a minified JavaScript file.
;; Regenerate it from the included sources.
(arguments
- `(#:modules ((guix build utils)
- (guix build r-build-system)
- (ice-9 popen))
- #:phases
+ `(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'generate-minified-javascript
(lambda _
(with-directory-excursion "inst/AdminLTE"
- (delete-file "app.min.js")
- (let ((minified (open-pipe* OPEN_READ "uglifyjs" "app.js")))
- (call-with-output-file "app.min.js"
- (lambda (port)
- (dump-port minified port))))))))))
+ (let ((target "app.min.js")
+ (source "app.js"))
+ (format #t "Processing ~a --> ~a~%"
+ source target)
+ (delete-file target)
+ (invoke "esbuild" source "--minify"
+ (string-append "--outfile=" target)))))))))
(propagated-inputs
`(("r-htmltools" ,r-htmltools)
("r-promises" ,r-promises)
("r-shiny" ,r-shiny)))
(native-inputs
- `(("uglifyjs" ,node-uglify-js)))
+ `(("esbuild" ,esbuild)))
(home-page "https://rstudio.github.io/shinydashboard/")
(synopsis "Create dashboards with shiny")
(description "This package provides an extension to the Shiny web
@@ -2798,14 +2797,14 @@ coordinates.")
(define-public r-geosphere
(package
(name "r-geosphere")
- (version "1.5-10")
+ (version "1.5-14")
(source
(origin
(method url-fetch)
(uri (cran-uri "geosphere" version))
(sha256
(base32
- "15xlgsmn0vwky1l13n6acdz6jn2b2na3gf6x367y3qh1f5w4zkan"))))
+ "0bg4vfmrw140j2ax0p6bflvb77w03ir39wa87l96rj473jpa9hzj"))))
(build-system r-build-system)
(propagated-inputs `(("r-sp" ,r-sp)))
(home-page "https://cran.r-project.org/web/packages/geosphere")
@@ -3213,14 +3212,14 @@ is configured appropriately so R can use them.")
(define-public r-pkgload
(package
(name "r-pkgload")
- (version "1.2.2")
+ (version "1.2.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "pkgload" version))
(sha256
(base32
- "0yxvik8kij0mqlki46hf6xnbfvmxwk0r2a3zwjpg0fwcd2s835a8"))))
+ "0jdkaj5cl0viy0i0hkcm4n2wlg1mfv3camr7f385njfararfanhh"))))
(build-system r-build-system)
(propagated-inputs
`(("r-cli" ,r-cli)
@@ -4249,14 +4248,14 @@ functions from LINPACK.")
(define-public r-fitdistrplus
(package
(name "r-fitdistrplus")
- (version "1.1-5")
+ (version "1.1-6")
(source
(origin
(method url-fetch)
(uri (cran-uri "fitdistrplus" version))
(sha256
(base32
- "1p9rvvh05zqb9vzhcyzdh7i8lbmb53nj8nyn0gqcmp7wafg9cd1f"))))
+ "1glnbcm1gghzgvzpxcfsmn7dp2f9jqyx39n3ydwp9fx38409khhp"))))
(build-system r-build-system)
(propagated-inputs
`(("r-mass" ,r-mass)
@@ -4611,14 +4610,14 @@ the RMariaDB package.")
(define-public r-rpostgresql
(package
(name "r-rpostgresql")
- (version "0.7")
+ (version "0.7-3")
(source
(origin
(method url-fetch)
(uri (cran-uri "RPostgreSQL" version))
(sha256
(base32
- "1bqfdbs09f65ssc6bx4z3kkmia8ja6qbnijxizw63p0fbcakq2q4"))))
+ "1fbixmnjp1kh6yiv8zhg8zi5ryvdf5j2jxv4agq5gcxf541s3g5x"))))
(properties `((upstream-name . "RPostgreSQL")))
(build-system r-build-system)
(inputs
@@ -4890,14 +4889,14 @@ provides a one-row summary of model-level statistics.")
(define-public r-recipes
(package
(name "r-recipes")
- (version "0.1.16")
+ (version "0.1.17")
(source
(origin
(method url-fetch)
(uri (cran-uri "recipes" version))
(sha256
(base32
- "1mayfdbn6q775d4gbdjrrhdbmpsxga57kwh0h7bwv8rk0vmvik23"))))
+ "0gbdc5kvbn14s5zrf4vrdjvkfajs00p7vvb433ii0lqnl07bl87d"))))
(build-system r-build-system)
(propagated-inputs
`(("r-dplyr" ,r-dplyr)
@@ -4916,6 +4915,7 @@ provides a one-row summary of model-level statistics.")
("r-tidyr" ,r-tidyr)
("r-tidyselect" ,r-tidyselect)
("r-timedate" ,r-timedate)
+ ("r-vctrs" ,r-vctrs)
("r-withr" ,r-withr)))
(native-inputs
`(("r-knitr" ,r-knitr)))
@@ -5160,14 +5160,14 @@ clustered data.")
(define-public r-mitml
(package
(name "r-mitml")
- (version "0.4-2")
+ (version "0.4-3")
(source
(origin
(method url-fetch)
(uri (cran-uri "mitml" version))
(sha256
(base32
- "0zrmchsk012linw3m5rda6hj8xpxpwzbf4alq0nc1pzvl99aa558"))))
+ "00i18nnvrdrg91crgcp2a431xs71cawaip3xkqk2myv0iav3xga9"))))
(build-system r-build-system)
(propagated-inputs
`(("r-haven" ,r-haven)
@@ -5446,14 +5446,14 @@ where possible.")
(define-public r-laeken
(package
(name "r-laeken")
- (version "0.5.1")
+ (version "0.5.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "laeken" version))
(sha256
(base32
- "199rjkhjjygpr6cjzab87as46acb5npi44m4yycvk7lnd0blma8s"))))
+ "1p3ccbaydlr52p8qmgmm2l6kryvq6jjjx7mqn2vv0gpjaxqhyy92"))))
(build-system r-build-system)
(propagated-inputs
`(("r-boot" ,r-boot)
@@ -5468,14 +5468,14 @@ modeling for empirical income distributions.")
(define-public r-vcd
(package
(name "r-vcd")
- (version "1.4-8")
+ (version "1.4-9")
(source
(origin
(method url-fetch)
(uri (cran-uri "vcd" version))
(sha256
(base32
- "030yyhpzsj4ivwrla7p9kgvmyjh6b8fr7czf678ykxjj64ccnvr3"))))
+ "13sn77qdcyll9lz7nab0bxzfvpgj8f5rl2cq5ylpz8pibynj1d55"))))
(build-system r-build-system)
(propagated-inputs
`(("r-colorspace" ,r-colorspace)
@@ -5754,14 +5754,14 @@ timeout. It can also poll several processes at once.")
(define-public r-tsp
(package
(name "r-tsp")
- (version "1.1-10")
+ (version "1.1-11")
(source
(origin
(method url-fetch)
(uri (cran-uri "TSP" version))
(sha256
(base32
- "0z1v6m0vqjzxc4az3zyjaayygx0jr3mdmc56jjd421iqh0b9z5s4"))))
+ "0gdwxbj2gria7jhsswmfvc32r43sdd63z3lyy21gbvmfcakvb8j9"))))
(properties `((upstream-name . "TSP")))
(build-system r-build-system)
(propagated-inputs `(("r-foreach" ,r-foreach)))
@@ -5841,14 +5841,14 @@ Markdown documents.")
(define-public r-seriation
(package
(name "r-seriation")
- (version "1.3.0")
+ (version "1.3.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "seriation" version))
(sha256
(base32
- "1vl0zfdvxdccvda8lwkjhg5rivj2q5gjm4qvkqwny6asm06x80ny"))))
+ "08c37n3xxc4n4vbkw38k3l3hdlmck8drqpl6z274vkgi2sqv8qyf"))))
(build-system r-build-system)
(propagated-inputs
`(("r-cluster" ,r-cluster)
@@ -5873,13 +5873,13 @@ iVAT).")
(define-public r-xfun
(package
(name "r-xfun")
- (version "0.26")
+ (version "0.27")
(source
(origin
(method url-fetch)
(uri (cran-uri "xfun" version))
(sha256
- (base32 "1997s00dzkyj15xk9w1r2h6i49srpgqzvhhyvd5pk1kwkd4809ly"))))
+ (base32 "11alh3kasiizfar0f667m5sj3s5443fggjv0541ghmxwlqrvyxf7"))))
(build-system r-build-system)
;; knitr itself depends on xfun
#;
@@ -5977,14 +5977,14 @@ to variables on the left-hand side of the assignment.")
(define-public r-pillar
(package
(name "r-pillar")
- (version "1.6.3")
+ (version "1.6.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "pillar" version))
(sha256
(base32
- "1ica4zjr3kmcpqh2668nmsv5dbvm4yri5952vcxja4djsgfnry3j"))))
+ "17m13rzgwdddwa0n3gpmax6wmfaphbg71l13ffhw5vnxf6i94fh3"))))
(build-system r-build-system)
(propagated-inputs
`(("r-cli" ,r-cli)
@@ -6046,14 +6046,14 @@ packages that work with genomic data.")
(define-public r-tinytex
(package
(name "r-tinytex")
- (version "0.33")
+ (version "0.34")
(source
(origin
(method url-fetch)
(uri (cran-uri "tinytex" version))
(sha256
(base32
- "10lqn704dqv5k5v6y964l8c77rwy4ilrc1hcb99j4vxpx3p4nd43"))))
+ "16z6v06pmvg02rbxkqyiidasg1dryy759zabnqjw6y85nybr618x"))))
(build-system r-build-system)
(propagated-inputs
`(("r-xfun" ,r-xfun)))
@@ -6340,14 +6340,14 @@ provides some missing S-PLUS functionality in R.")
(define-public r-ifultools
(package
(name "r-ifultools")
- (version "2.0-22")
+ (version "2.0-23")
(source
(origin
(method url-fetch)
(uri (cran-uri "ifultools" version))
(sha256
(base32
- "0f95vqc47dgssqngznk0rclr72ndbyxc7gdq2cmbksvq7qpn3gg1"))))
+ "16a7rbvlym3bnfm93ikr5kl0l86ppk0s41fva6idvcx765g3fqkk"))))
(build-system r-build-system)
(propagated-inputs
`(("r-mass" ,r-mass)
@@ -6796,14 +6796,14 @@ powerful and convenient features.")
(define-public r-heatmaply
(package
(name "r-heatmaply")
- (version "1.2.1")
+ (version "1.3.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "heatmaply" version))
(sha256
(base32
- "0hspfkninwy62sf8gkdcsvwnvl66bbnjs2dpah9rr95a3rsgdp9d"))))
+ "1w8yyzb68laxd4zxycvgmpqj5wnyidjgv1vbzbxndp9p92f2cp8a"))))
(build-system r-build-system)
(propagated-inputs
`(("r-assertthat" ,r-assertthat)
@@ -7920,14 +7920,14 @@ Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.")
(define-public r-rastervis
(package
(name "r-rastervis")
- (version "0.50.3")
+ (version "0.51.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "rasterVis" version))
(sha256
(base32
- "10njks2kwyh5rp2b6sf2hffxzzwwhskb8m98l73p8yrvsdri1gyj"))))
+ "1gkn5na7cspnh3qpmi4k5n65crmp8c2s106g8hh51lsdvm5369aj"))))
(properties `((upstream-name . "rasterVis")))
(build-system r-build-system)
(propagated-inputs
@@ -8549,14 +8549,14 @@ functions.")
(define-public r-rjags
(package
(name "r-rjags")
- (version "4-11")
+ (version "4-12")
(source
(origin
(method url-fetch)
(uri (cran-uri "rjags" version))
(sha256
(base32
- "0vs86jji4h26y8aczy8r08jiq7ax0idlrm87mmvaa5sxlqmqa705"))))
+ "041y4zfr50y96g0kl857jcba0a3gpdpk8qfn9fj8zxzbz71k87xr"))))
(build-system r-build-system)
(propagated-inputs
`(("r-coda" ,r-coda)))
@@ -8575,14 +8575,14 @@ hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.")
(define-public r-rbibutils
(package
(name "r-rbibutils")
- (version "2.2.3")
+ (version "2.2.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "rbibutils" version))
(sha256
(base32
- "1rzc2icik26qlnrbq58c24lc9m0grl83p0hyr70whallqfipa174"))))
+ "15yyihk0dgz3yyqz28r5nc6m99zcywpabnabf18phbs7rb87p7mv"))))
(properties `((upstream-name . "rbibutils")))
(build-system r-build-system)
(home-page "https://geobosh.github.io/rbibutils/")
@@ -8709,14 +8709,14 @@ reduced-bias estimates.")
(define-public r-entropy
(package
(name "r-entropy")
- (version "1.3.0")
+ (version "1.3.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "entropy" version))
(sha256
(base32
- "0fhhsy8ci9c73xwr2b167dfix0b7kqsk6kf46qqv1lmvbv11vxqa"))))
+ "1f0j8jsn6pzf4gi5g0akixx6x5vc69ci5f4m2vnwp40frvsqjnkg"))))
(properties `((upstream-name . "entropy")))
(build-system r-build-system)
(home-page "https://www.strimmerlab.org/software/entropy/")
@@ -8849,14 +8849,14 @@ other add-on packages.")
(define-public r-insight
(package
(name "r-insight")
- (version "0.14.4")
+ (version "0.14.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "insight" version))
(sha256
(base32
- "0h63nr337zbczbj9izyb7g5dlzwail5w70hbbn45paq6vybkqks3"))))
+ "10kc72g2hfsiipba4kalda1wxsb01nq2ax2yim386bkk0vjszwfx"))))
(build-system r-build-system)
(native-inputs
`(("r-knitr" ,r-knitr)))
@@ -8985,14 +8985,14 @@ functions.")
(define-public r-flextable
(package
(name "r-flextable")
- (version "0.6.8")
+ (version "0.6.9")
(source
(origin
(method url-fetch)
(uri (cran-uri "flextable" version))
(sha256
(base32
- "1b4hyrarxbk4d1ma5gy162b13nm5r5ysi049bxgcfim50rh40igs"))))
+ "15lba98wnci2nsndj86gx3k94q9lfxhp5nr5xlhgcnycyj1c9zjx"))))
(build-system r-build-system)
(propagated-inputs
`(("r-base64enc" ,r-base64enc)
@@ -9137,14 +9137,14 @@ matches version and feature constraints.")
(define-public r-argparse
(package
(name "r-argparse")
- (version "2.1.1")
+ (version "2.1.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "argparse" version))
(sha256
(base32
- "1k6v35g3bppcr896h4v39zh1sxxia1bxxh29xv0mhad1nvmv25j9"))))
+ "1cz5qlxw3v8smd5vb00wlzy02mx5i0infm5hnq55hnakffd3b5wr"))))
(build-system r-build-system)
(inputs `(("python" ,python)))
(propagated-inputs
@@ -9370,14 +9370,14 @@ bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.")
(define-public r-rootsolve
(package
(name "r-rootsolve")
- (version "1.8.2.2")
+ (version "1.8.2.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "rootSolve" version))
(sha256
(base32
- "1p7nh09g2815vqpvi6c5vvjshkwjn00nx5d3gdyjs304q5312q0a"))))
+ "182bb727sgqi5f3pzmw8jnn328wdjrgj9lfvg49gv8s22rjd3cxm"))))
(properties `((upstream-name . "rootSolve")))
(build-system r-build-system)
(native-inputs `(("gfortran" ,gfortran)))
@@ -9446,13 +9446,13 @@ based on index arrays and simple triplet representations, respectively.")
(define-public r-manipulatewidget
(package
(name "r-manipulatewidget")
- (version "0.11.0")
+ (version "0.11.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "manipulateWidget" version))
(sha256
- (base32 "0iysgl6ab8fvg1xxdx6hr3swqwbkfqzjkk4x5sbvmawbl2a395gj"))))
+ (base32 "1dpgzmiv08afm57yxr017b014lfn9h3pa4w65prk5k3dgn6p4wsv"))))
(properties
`((upstream-name . "manipulateWidget")))
(build-system r-build-system)
@@ -9549,14 +9549,14 @@ from the @code{stats} package (plus some extra parameters).")
(define-public r-cmplot
(package
(name "r-cmplot")
- (version "3.6.2")
+ (version "3.7.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "CMplot" version))
(sha256
(base32
- "13y05j5gsdc712fn7yvcz5nx2pbcdvl201hfb6jzpvl86qx2l0j1"))))
+ "0d6ww8pdrawdg5acbhiyi2jpmapf2ghixy9mi4kmsq8yg36pksfh"))))
(properties `((upstream-name . "CMplot")))
(build-system r-build-system)
(home-page "https://github.com/YinLiLin/CMplot")
@@ -9981,14 +9981,14 @@ data with multiple data types.")
(define-public r-qualv
(package
(name "r-qualv")
- (version "0.3-3")
+ (version "0.3-4")
(source
(origin
(method url-fetch)
(uri (cran-uri "qualV" version))
(sha256
(base32
- "1yyqk223ydcc0125gsn33a4mcdp8bd76fpn8kj9bfz9g78b8dqmx"))))
+ "0rkjzva2h158d5c631jmjjh7qjibbyisl0503san80rk9fgxl45b"))))
(properties `((upstream-name . "qualV")))
(build-system r-build-system)
(propagated-inputs
@@ -10121,18 +10121,19 @@ used to teach mathematics, statistics, computation and modeling.")
(define-public r-raster
(package
(name "r-raster")
- (version "3.4-13")
+ (version "3.5-2")
(source
(origin
(method url-fetch)
(uri (cran-uri "raster" version))
(sha256
(base32
- "120k4bkgwddrx8ijgdhsgjz8g8dxcwp9bx3kfzrhw00q1b289hir"))))
+ "0wixw1ixnmcmkwczpj8m90c76727zira2rl4ighashggydkm2mlr"))))
(build-system r-build-system)
(propagated-inputs
`(("r-rcpp" ,r-rcpp)
- ("r-sp" ,r-sp)))
+ ("r-sp" ,r-sp)
+ ("r-terra" ,r-terra)))
(home-page "https://www.rspatial.org/")
(synopsis "Geographic data analysis and modeling")
(description
@@ -11013,13 +11014,13 @@ series.")
(define-public r-acceptancesampling
(package
(name "r-acceptancesampling")
- (version "1.0-6")
+ (version "1.0-7")
(source
(origin
(method url-fetch)
(uri (cran-uri "AcceptanceSampling" version))
(sha256
- (base32 "1z3rmln63ki2kik9kinbwr9qhr32ggbmh4mm3xqy6di119n47ca9"))))
+ (base32 "13k3zczjycw24n5yp0qmrm233id5j8h6fvra57f1n6js7ljxiiq2"))))
(properties
`((upstream-name . "AcceptanceSampling")))
(build-system r-build-system)
@@ -11111,19 +11112,21 @@ cross-sectional, time series, clustered, panel, and longitudinal data.")
(define-public r-th-data
(package
(name "r-th-data")
- (version "1.0-10")
+ (version "1.1-0")
(source
(origin
(method url-fetch)
(uri (cran-uri "TH.data" version))
(sha256
(base32
- "0mgz7aj2d9abbmdr65zgmg1ddp3fdbs3mfj83r5xadh5ldkir2k1"))))
+ "0ghihfpk5d8gsdlzf6phw7dwwz3adx64pxk82vlmlqx53ljpxcr1"))))
(properties `((upstream-name . "TH.data")))
(build-system r-build-system)
(propagated-inputs
`(("r-mass" ,r-mass)
("r-survival" ,r-survival)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://cran.r-project.org/web/packages/TH.data/")
(synopsis "Shared data sets")
(description
@@ -11162,20 +11165,19 @@ Hothorn, Westfall, 2010, CRC Press).")
(define-public r-emmeans
(package
(name "r-emmeans")
- (version "1.6.3")
+ (version "1.7.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "emmeans" version))
(sha256
(base32
- "1mwcq3hvpx04qnn5k0bv1mikjgm9mk6m83i8hj350s1c1a0mi40n"))))
+ "1ig94mjifhhygznv2xv1gl8hdvk618w5fcmkaj1xmpwpc64m9dnl"))))
(build-system r-build-system)
(propagated-inputs
`(("r-estimability" ,r-estimability)
("r-mvtnorm" ,r-mvtnorm)
("r-numderiv" ,r-numderiv)
- ("r-plyr" ,r-plyr)
("r-xtable" ,r-xtable)))
(native-inputs
`(("r-knitr" ,r-knitr)))
@@ -11213,13 +11215,13 @@ Cohen (1988).")
(define-public r-libcoin
(package
(name "r-libcoin")
- (version "1.0-8")
+ (version "1.0-9")
(source
(origin
(method url-fetch)
(uri (cran-uri "libcoin" version))
(sha256
- (base32 "0izgnr4zdrbz3a05b0s28xfly4izp2zslgh282l9ads4skrmj3hl"))))
+ (base32 "1syrcdj5qg5m3zd3dlxgpfklswbalfg42w058dr09hnzqsvx0z9d"))))
(build-system r-build-system)
(propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
(home-page "https://cran.r-project.org/web/packages/libcoin")
@@ -11232,14 +11234,14 @@ and permutation inference in the framework of Strasser and Weber (1999).")
(define-public r-coin
(package
(name "r-coin")
- (version "1.4-1")
+ (version "1.4-2")
(source
(origin
(method url-fetch)
(uri (cran-uri "coin" version))
(sha256
(base32
- "15xvhnbyg34aacn6jfz4bsa1f7wq2ci0hslj8mgymql90k50x1qi"))))
+ "1cpv7jx840inzg98bkhrb5yscx0gpag6br237r5qpnc2gbrd2ikm"))))
(build-system r-build-system)
(propagated-inputs
`(("r-libcoin" ,r-libcoin)
@@ -11294,14 +11296,14 @@ Bayesian modeling.")
(define-public r-tmb
(package
(name "r-tmb")
- (version "1.7.21")
+ (version "1.7.22")
(source
(origin
(method url-fetch)
(uri (cran-uri "TMB" version))
(sha256
(base32
- "1lf9vf28l48xhw2irxfxl4vsqzj7skzblydw32p18zddzpapl0z9"))))
+ "116k7ffgadhkqq4lckfd4403qvybcls1hcs1ap1b7lkylghjahf2"))))
(properties `((upstream-name . "TMB")))
(build-system r-build-system)
(propagated-inputs
@@ -11426,14 +11428,14 @@ ROPE percentage and pd).")
(define-public r-performance
(package
(name "r-performance")
- (version "0.7.3")
+ (version "0.8.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "performance" version))
(sha256
(base32
- "03qdsdl4x3hwqlbs7hlqb73xypd13p5zj519y0zcydqkf25391sp"))))
+ "1xjjnhqmwfflm5yfgjhycjn0fj0manvsvkk2ppifn0373bajp5n2"))))
(build-system r-build-system)
(propagated-inputs
`(("r-bayestestr" ,r-bayestestr)
@@ -11484,20 +11486,22 @@ results using @code{ggplot2}.")
(define-public r-effectsize
(package
(name "r-effectsize")
- (version "0.4.5")
+ (version "0.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "effectsize" version))
(sha256
(base32
- "0rp0r75p8q467lmrsr1gl9wjpib9jz7ksx5rm6c7q2lfg9b9zrjf"))))
+ "0w7m3hzmwral9cycpvknrkbdvgk230b3vg5sxbm84x72mw534hnh"))))
(properties `((upstream-name . "effectsize")))
(build-system r-build-system)
(propagated-inputs
`(("r-bayestestr" ,r-bayestestr)
+ ("r-datawizard" ,r-datawizard)
("r-insight" ,r-insight)
- ("r-parameters" ,r-parameters)))
+ ("r-parameters" ,r-parameters)
+ ("r-performance" ,r-performance)))
(native-inputs
`(("r-knitr" ,r-knitr)))
(home-page "https://github.com/easystats/effectsize")
@@ -11749,14 +11753,14 @@ User credentials are shared with command line git through the
(define-public r-usethis
(package
(name "r-usethis")
- (version "2.0.1")
+ (version "2.1.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "usethis" version))
(sha256
(base32
- "1j6nzzrm2m6vi1gq0d5kxnnr9d8cy88wpmgigz3inych65x9w9pg"))))
+ "1s40rbr2z9bilsldp8pv5abrr7n0ixyxi2qqbf4hfhs14rhigncy"))))
(build-system r-build-system)
(propagated-inputs
`(("r-cli" ,r-cli)
@@ -11764,6 +11768,7 @@ User credentials are shared with command line git through the
("r-crayon" ,r-crayon)
("r-curl" ,r-curl)
("r-desc" ,r-desc)
+ ("r-ellipsis" ,r-ellipsis)
("r-fs" ,r-fs)
("r-gert" ,r-gert)
("r-gh" ,r-gh)
@@ -11813,14 +11818,14 @@ more information about packages, and where they were installed from.")
(define-public r-remotes
(package
(name "r-remotes")
- (version "2.4.0")
+ (version "2.4.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "remotes" version))
(sha256
(base32
- "048lihmwksl72fg4fdmhihblj9ipxl22x9wfpgwsbsv79zjc7rfd"))))
+ "0xij8x4ga0r7rp2lxx9hw1zlzv48mfg56v8nf03gsw0dw6r7gmym"))))
(build-system r-build-system)
(native-inputs
`(("r-knitr" ,r-knitr)))
@@ -11857,19 +11862,19 @@ directories or URLs with their associated programs.")
(define-public r-rcmdcheck
(package
(name "r-rcmdcheck")
- (version "1.3.3")
+ (version "1.4.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "rcmdcheck" version))
(sha256
(base32
- "1d4kzgfqy72r6b7bn1j4znyksrycgypx1jjvpv9lrmvn37mpkdhs"))))
+ "1l696byn3kjq2xvz4wxybzaj6ink85h4lz3a35v2132ba5yyzm5v"))))
(build-system r-build-system)
(propagated-inputs
`(("r-callr" ,r-callr)
("r-cli" ,r-cli)
- ("r-crayon" ,r-crayon)
+ ("r-curl" ,r-curl)
("r-desc" ,r-desc)
("r-digest" ,r-digest)
("r-pkgbuild" ,r-pkgbuild)
@@ -12066,13 +12071,13 @@ and related methods.")
(define-public r-rcppgsl
(package
(name "r-rcppgsl")
- (version "0.3.9")
+ (version "0.3.10")
(source
(origin
(method url-fetch)
(uri (cran-uri "RcppGSL" version))
(sha256
- (base32 "0zhfkn3w5q2k2ggizrikz9an8hm90g6mr60paq0z8xgp5hpkrlk6"))))
+ (base32 "0lalz51q31qqy0cr227vc3msi0h47p111lzy4zs93drgl1yhh4l6"))))
(properties `((upstream-name . "RcppGSL")))
(build-system r-build-system)
(propagated-inputs
@@ -12497,14 +12502,14 @@ to colexicographical order.")
(define-public r-misc3d
(package
(name "r-misc3d")
- (version "0.9-0")
+ (version "0.9-1")
(source
(origin
(method url-fetch)
(uri (cran-uri "misc3d" version))
(sha256
(base32
- "10jf5r1x588vi54bzaqgi9mgcqlkiga2c3jvmqmk3lavc8fjksd1"))))
+ "0r9x57s63kx9f6dgam2nhbziq8nrs9wd8pk7g76hds2kw46vnyx0"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/misc3d/")
(synopsis "Miscellaneous 3D Plots")
@@ -12576,19 +12581,18 @@ features (e.g. local modes).")
(define-public r-arm
(package
(name "r-arm")
- (version "1.11-2")
+ (version "1.12-2")
(source
(origin
(method url-fetch)
(uri (cran-uri "arm" version))
(sha256
(base32
- "1grb27vayr2vhyalzfqbhx6p278r7c3l4pzi5nrz3dmnyqrbx1c3"))))
+ "0pagrc1vkaz460d0lvrgb4xj6gcd920f4mrc8zpzw07c3v1s2sw1"))))
(build-system r-build-system)
(propagated-inputs
`(("r-abind" ,r-abind)
("r-coda" ,r-coda)
- ("r-hmisc" ,r-hmisc)
("r-lme4" ,r-lme4)
("r-mass" ,r-mass)
("r-matrix" ,r-matrix)
@@ -12759,14 +12763,14 @@ Anderson-Darling Distribution\".")
(define-public r-sodium
(package
(name "r-sodium")
- (version "1.1")
+ (version "1.2.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "sodium" version))
(sha256
(base32
- "1zxzi8xvxnhgcd5qrylf08nz1cdq3aslrswjas440qg63ypmbf6w"))))
+ "0x4jb3cf1nv1spz1jc9xp8hly2b4a7nj48xr4s33jnfcpdjkmn5q"))))
(properties `((upstream-name . "sodium")))
(build-system r-build-system)
(inputs
@@ -13015,13 +13019,13 @@ manipulate tree data.")
(define-public r-rvcheck
(package
(name "r-rvcheck")
- (version "0.2.0")
+ (version "0.2.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "rvcheck" version))
(sha256
- (base32 "09gx29q882vh4q1qbb8z8lc3pgmpn7bk8skzcm85mrf3x3vgvkpa"))))
+ (base32 "09khjklvzbafd7r55496by01a9g3y291d87hpy43w44dmz9fzn9a"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biocmanager" ,r-biocmanager)
@@ -13502,13 +13506,13 @@ creating color scales and calculating color distances.")
(define-public r-ore
(package
(name "r-ore")
- (version "1.6.3")
+ (version "1.7.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "ore" version))
(sha256
- (base32 "1vh6w3arrhgkfjjjw7ci91xmz4wpfr3cmwd5zkqch89dgn07skkv"))))
+ (base32 "0qhbv7bynisr0prv7h0yxsxff7qdxfqza7i06xi4vn360kxx6w9g"))))
(build-system r-build-system)
(home-page "https://github.com/jonclayden/ore")
(synopsis "R interface to the Onigmo regular expression library")
@@ -13573,14 +13577,14 @@ handling.")
(define-public r-grimport
(package
(name "r-grimport")
- (version "0.9-3")
+ (version "0.9-4")
(source
(origin
(method url-fetch)
(uri (cran-uri "grImport" version))
(sha256
(base32
- "109mrdvq06xq3zgn9ngz0c7zzgqkv5zbpvsb2i636vmlk6y4dpkd"))))
+ "0y9lsvfp1350das5v5d5pkv10z0n1crc7k4zn9inr94f9s4kjjr5"))))
(properties `((upstream-name . "grImport")))
(build-system r-build-system)
(inputs
@@ -13935,14 +13939,14 @@ limitations\" using the GNU Multiple Precision library.")
(define-public r-rmpfr
(package
(name "r-rmpfr")
- (version "0.8-4")
+ (version "0.8-5")
(source
(origin
(method url-fetch)
(uri (cran-uri "Rmpfr" version))
(sha256
(base32
- "0xaqbgkpnjg53zcp56c59cz5dh3jvvwqnzvyxqzy77c6yvkwy3hx"))))
+ "1a37zaahcyccb5kgad98z4dh9n75vffmiziv4al8axvihxqs5hjn"))))
(properties `((upstream-name . "Rmpfr")))
(build-system r-build-system)
(inputs
@@ -15494,45 +15498,36 @@ to easily call your own custom JavaScript functions from R.")
(define-public r-colourpicker
(package
(name "r-colourpicker")
- (version "1.1.0")
+ (version "1.1.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "colourpicker" version))
(sha256
(base32
- "1qjispj7i12m02js5cm5xlgn5lyff0kc5ybz6lbknz8q5lkbdyrd"))))
+ "1q1wi3g403fbzp4ys3gsjbwdc86x770cx323qgi47ca8n219kl50"))))
(build-system r-build-system)
(arguments
- `(#:modules ((guix build utils)
- (guix build r-build-system)
- (srfi srfi-1)
- (ice-9 popen))
- #:phases
+ `(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'process-javascript
(lambda* (#:key inputs #:allow-other-keys)
(with-directory-excursion "inst"
- (call-with-values
- (lambda ()
- (unzip2
+ (let ((mapping
`((,(assoc-ref inputs "js-salvattore")
- "examples/colourInput/www/salvattore.min.js")
+ . "examples/colourInput/www/salvattore.min.js")
(,(assoc-ref inputs "js-jquery")
- "htmlwidgets/lib/jquery/jquery.min.js")
+ . "htmlwidgets/lib/jquery/jquery.min.js")
("www/shared/colourpicker/js/colourpicker.js"
- "www/shared/colourpicker/js/colourpicker.min.js"))))
- (lambda (sources targets)
- (for-each (lambda (source target)
- (format #t "Processing ~a --> ~a~%"
- source target)
- (delete-file target)
- (let ((minified (open-pipe* OPEN_READ "uglifyjs" source)))
- (call-with-output-file target
- (lambda (port)
- (dump-port minified port)))))
- sources targets))))
- #t)))))
+ . "www/shared/colourpicker/js/colourpicker.min.js"))))
+ (for-each (lambda (source target)
+ (format #true "Processing ~a --> ~a~%"
+ source target)
+ (delete-file target)
+ (invoke "esbuild" source "--minify"
+ (string-append "--outfile=" target)))
+ (map car mapping)
+ (map cdr mapping)))))))))
(propagated-inputs
`(("r-ggplot2" ,r-ggplot2)
("r-htmltools" ,r-htmltools)
@@ -15542,15 +15537,14 @@ to easily call your own custom JavaScript functions from R.")
("r-shiny" ,r-shiny)
("r-shinyjs" ,r-shinyjs)))
(native-inputs
- `(("r-knitr" ,r-knitr)
- ("uglifyjs" ,node-uglify-js)
+ `(("esbuild" ,esbuild)
("js-jquery"
,(origin
(method url-fetch)
- (uri "https://code.jquery.com/jquery-3.3.1.js")
+ (uri "https://code.jquery.com/jquery-1.11.3.js")
(sha256
(base32
- "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
+ "1v956yf5spw0156rni5z77hzqwmby7ajwdcd6mkhb6zvl36awr90"))))
("js-salvattore"
,(origin
(method url-fetch)
@@ -16207,14 +16201,14 @@ additional utilities for genomic regions processing.")
(define-public r-sets
(package
(name "r-sets")
- (version "1.0-18")
+ (version "1.0-19")
(source
(origin
(method url-fetch)
(uri (cran-uri "sets" version))
(sha256
(base32
- "16v7650p47khqrbbw0z98llmwmmhswqmhri0n7nrfhdqwmby1lbl"))))
+ "18185rm458nlifzrp73fjrjvksmm5dvn5ygs949kdzdln1myb4xf"))))
(properties `((upstream-name . "sets")))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/sets")
@@ -16469,14 +16463,14 @@ univariate class intervals for mapping or other graphics purposes.")
(define-public r-spdata
(package
(name "r-spdata")
- (version "0.3.10")
+ (version "2.0.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "spData" version))
(sha256
(base32
- "0c3kg2daz65znnmcaf5l108c88anzlfrsjlnmv2kxqr1lx8z9zl5"))))
+ "1z4hp5ivwzyvl8mkp98j2ng1cl1xksqbjxv85vdlqfqjwpia6df6"))))
(properties `((upstream-name . "spData")))
(build-system r-build-system)
(propagated-inputs
@@ -16522,14 +16516,14 @@ sampling.")
(define-public r-deldir
(package
(name "r-deldir")
- (version "0.2-10")
+ (version "1.0-6")
(source
(origin
(method url-fetch)
(uri (cran-uri "deldir" version))
(sha256
(base32
- "08ij6zb6id71zk6gzs9z779y49y41c2gpi7p7mljnlw7py92g8k5"))))
+ "1igq0l2knsbhizncgydcsidgkvvlwwlkrifbcdyhnzk0bhrdixkd"))))
(build-system r-build-system)
(native-inputs `(("gfortran" ,gfortran)))
(home-page "https://cran.r-project.org/web/packages/deldir")
@@ -16572,14 +16566,14 @@ high-performance functions are provided here.")
(define-public r-s2
(package
(name "r-s2")
- (version "1.0.6")
+ (version "1.0.7")
(source
(origin
(method url-fetch)
(uri (cran-uri "s2" version))
(sha256
(base32
- "1xd42bpbm090dqlldavbn6c1h1mfwhlws9536avan00w3szlxk56"))))
+ "0gwydn6wdl675ydkcckrci6ylcx30qn8nfhmrp4qx4r9mv3c2410"))))
(properties `((upstream-name . "s2")))
(build-system r-build-system)
(propagated-inputs
@@ -16603,14 +16597,14 @@ information about geometries.")
(define-public r-sf
(package
(name "r-sf")
- (version "1.0-2")
+ (version "1.0-3")
(source
(origin
(method url-fetch)
(uri (cran-uri "sf" version))
(sha256
(base32
- "0hh54krf4gjwrzxj2r3p5q7amdf8kblv8nm7hmbwmfv1rs30i1gc"))))
+ "1y1im0wxqx0vqas6ggmi6p1dyp98l895jy3asxky4vq5wpjfrqrf"))))
(build-system r-build-system)
(inputs
`(("gdal" ,gdal)
@@ -16693,14 +16687,14 @@ spanning tree.")
(define-public r-adegenet
(package
(name "r-adegenet")
- (version "2.1.4")
+ (version "2.1.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "adegenet" version))
(sha256
(base32
- "0sxbw5l92xmkazndxbqaa2cxmgk8bqzzbk77q9li850s2i1fdssp"))))
+ "1wjp31634n6z6wglf4z3ydrhhn5jmpwwckmp3n2b0v5f3p2fivp4"))))
(build-system r-build-system)
(propagated-inputs
`(("r-ade4" ,r-ade4)
@@ -16713,7 +16707,6 @@ spanning tree.")
("r-reshape2" ,r-reshape2)
("r-seqinr" ,r-seqinr)
("r-shiny" ,r-shiny)
- ("r-spdep" ,r-spdep)
("r-vegan" ,r-vegan)))
(home-page "https://github.com/thibautjombart/adegenet")
(synopsis "Exploratory analysis of genetic and genomic data")
@@ -17142,14 +17135,14 @@ authoring books and technical documents with R Markdown.")
(define-public r-optparse
(package
(name "r-optparse")
- (version "1.6.6")
+ (version "1.7.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "optparse" version))
(sha256
(base32
- "1l301dy3gc8pn7j00awcjh41wmc1ks9kswak255kbsa6f54rsxsi"))))
+ "1rqz0y4r94y3mwbb9kyz97cjqpnprka96qbncvbnbmgg2d630kij"))))
(build-system r-build-system)
(propagated-inputs
`(("r-getopt" ,r-getopt)))
@@ -17331,14 +17324,14 @@ and accessing fields.")
(define-public r-svmisc
(package
(name "r-svmisc")
- (version "1.1.4")
+ (version "1.2.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "svMisc" version))
(sha256
(base32
- "0y8mhiblyzwads4gf4whmxi7c6wdmqs3ahbj132l79bbdk40p83a"))))
+ "1r3kih5bnr4plnzdn5f2gg3xl3krgyl7gkdlf58a2l8vk13j3m9d"))))
(properties `((upstream-name . "svMisc")))
(build-system r-build-system)
(native-inputs
@@ -17591,14 +17584,14 @@ package.")
(define-public r-yulab-utils
(package
(name "r-yulab-utils")
- (version "0.0.2")
+ (version "0.0.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "yulab.utils" version))
(sha256
(base32
- "1haq6k0r64gs76p2vvrm42m64r8s32kzyz573pw9789y32zn0s5q"))))
+ "1bj93gnj7j4b7dgkbr5v22rsbwfcw5dvipl5irmidaakvrihd19q"))))
(properties `((upstream-name . "yulab.utils")))
(build-system r-build-system)
(home-page "https://cran.r-project.org/package=yulab.utils")
@@ -18416,14 +18409,14 @@ more generic data visualisation.")
(define-public r-pmcmr
(package
(name "r-pmcmr")
- (version "4.3")
+ (version "4.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "PMCMR" version))
(sha256
(base32
- "09bvdj2h1086r2cgy3myrhlylplxxlliv8nwx09c8kb1vn02i2ij"))))
+ "05n13pp5yff6pzk4ry07crddfaj3jlglrd1vkcnacyd8jpaxkd77"))))
(properties `((upstream-name . "PMCMR")))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/PMCMR/")
@@ -18721,14 +18714,14 @@ multicore machines.")
(define-public r-mcmcpack
(package
(name "r-mcmcpack")
- (version "1.5-0")
+ (version "1.6-0")
(source
(origin
(method url-fetch)
(uri (cran-uri "MCMCpack" version))
(sha256
(base32
- "1khavqsimiwbfq7gyw5jyj67jxfd579pnc7mngnd655zc8yzspvr"))))
+ "16zjx8yz29ii75wfxj3p562l657bng8jnwzp2b54s7fiaws4kfdm"))))
(properties `((upstream-name . "MCMCpack")))
(build-system r-build-system)
(propagated-inputs
@@ -19007,14 +19000,14 @@ experiments in a well-organized and reproducible way.")
(define-public r-clue
(package
(name "r-clue")
- (version "0.3-59")
+ (version "0.3-60")
(source
(origin
(method url-fetch)
(uri (cran-uri "clue" version))
(sha256
(base32
- "0ychvjbqkcgqdp5gy4hsi4297phywd7fj89y3yi5ckmnmjb39kjm"))))
+ "0apgpdnn74mqg2bnr8yjyxgyvdl411h0r2b1r2xd67k21pyxs8bd"))))
(build-system r-build-system)
(propagated-inputs `(("r-cluster" ,r-cluster)))
(home-page "https://cran.r-project.org/web/packages/clue/")
@@ -19031,16 +19024,18 @@ consensus and secondary clusterings.")
(define-public r-sitmo
(package
(name "r-sitmo")
- (version "2.0.1")
+ (version "2.0.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "sitmo" version))
(sha256
(base32
- "0apdhwy3kxs39agsbvx5vn3xsgb22bf3jrwmr2cmqk9kmxbx740c"))))
+ "1hm89zi38ldgbskyx1cn7gm87yqy7zrxli8q05a36y1ndvazi3j4"))))
(build-system r-build-system)
(propagated-inputs `(("r-rcpp" ,r-rcpp)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://github.com/coatless/sitmo/")
(synopsis "Parallel pseudo random number generator header files")
(description
@@ -19790,14 +19785,14 @@ both R code and compiled C/C++/FORTRAN code.")
(define-public r-systemfonts
(package
(name "r-systemfonts")
- (version "1.0.2")
+ (version "1.0.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "systemfonts" version))
(sha256
(base32
- "1a9nzd4nqawr6ni3mw7xc2yq77fb2f91aarnc906mq26510rdb11"))))
+ "1fmv1ni77ncz6rrm4iv8a7l6pbqnk2ri0yzad2bs943gxbarjz34"))))
(properties `((upstream-name . "systemfonts")))
(build-system r-build-system)
(propagated-inputs
@@ -19848,14 +19843,14 @@ emphasize hidden group structures in networks or focus on specific nodes.")
(define-public r-terra
(package
(name "r-terra")
- (version "1.3-22")
+ (version "1.4-11")
(source
(origin
(method url-fetch)
(uri (cran-uri "terra" version))
(sha256
(base32
- "1z5zql68q4n81ccpl02hndhbavhhqs65bli1hjxlqdwdq192whkh"))))
+ "08gx28ad00adz4fqch3fx27s6yd0rpjhmdy6b83d1wnlzzgc13qa"))))
(properties `((upstream-name . "terra")))
(build-system r-build-system)
(inputs
@@ -19865,8 +19860,7 @@ emphasize hidden group structures in networks or focus on specific nodes.")
("sqlite" ,sqlite) ; needed for proj
("zlib" ,zlib)))
(propagated-inputs
- `(("r-raster" ,r-raster)
- ("r-rcpp" ,r-rcpp)))
+ `(("r-rcpp" ,r-rcpp)))
(native-inputs
`(("pkg-config" ,pkg-config)))
(home-page "https://rspatial.org/terra")
@@ -19973,18 +19967,19 @@ in pipelines.")
(define-public r-parameters
(package
(name "r-parameters")
- (version "0.14.0")
+ (version "0.15.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "parameters" version))
(sha256
(base32
- "03x2h8izbpz9cq25i0a6dh99m26a9isgpv4kxsfkx97qzlh9cd67"))))
+ "0f06bwlc1g0xdyhdqzx8plfx1jwk8a9j4lcbl91wjsil8wja0bkl"))))
(properties `((upstream-name . "parameters")))
(build-system r-build-system)
(propagated-inputs
`(("r-bayestestr" ,r-bayestestr)
+ ("r-datawizard" ,r-datawizard)
("r-insight" ,r-insight)))
(native-inputs
`(("r-knitr" ,r-knitr)))
@@ -20137,13 +20132,13 @@ programming problems.")
(define-public r-desolve
(package
(name "r-desolve")
- (version "1.29")
+ (version "1.30")
(source
(origin
(method url-fetch)
(uri (cran-uri "deSolve" version))
(sha256
- (base32 "02hrd31ky9id7q2bwkj436j4fj4xbs3j9sfmyi1nl7hml5dy2vr6"))))
+ (base32 "0j7mmg1mimdpql8f4i9dn920ciyyq80a5qnc4fq5xn5lyrx5vxir"))))
(properties `((upstream-name . "deSolve")))
(build-system r-build-system)
(native-inputs
@@ -22327,18 +22322,19 @@ variable observed over time.")
(define-public r-fda
(package
(name "r-fda")
- (version "5.1.9")
+ (version "5.4.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "fda" version))
(sha256
(base32
- "0yjrjsv55bcwqn2yxjgj3hn17wfvjvgngfw9xv3w802i52yz9gf8"))))
+ "000flssclb2c1sfm2czyp1qxrfrl9rp6bd8sw87ign8165maplqf"))))
(properties `((upstream-name . "fda")))
(build-system r-build-system)
(propagated-inputs
- `(("r-fds" ,r-fds)
+ `(("r-desolve" ,r-desolve)
+ ("r-fds" ,r-fds)
("r-matrix" ,r-matrix)))
(home-page "https://www.functionaldata.org")
(synopsis "Functional data analysis")
@@ -22568,14 +22564,14 @@ API; see the package vignette for details.")
(define-public r-actuar
(package
(name "r-actuar")
- (version "3.1-4")
+ (version "3.2-0")
(source
(origin
(method url-fetch)
(uri (cran-uri "actuar" version))
(sha256
(base32
- "0m9b4787a866cddf1skjz6634237dvg1i5qyqss4sgvcrbmx3hw0"))))
+ "015brjjgmkwmjajdjdw8gs02jrd96if425pk9a97d499hzsq3xds"))))
(properties `((upstream-name . "actuar")))
(build-system r-build-system)
(propagated-inputs `(("r-expint" ,r-expint)))
@@ -22711,17 +22707,18 @@ it may be seen by an animal with less acute vision.")
(define-public r-caret
(package
(name "r-caret")
- (version "6.0-88")
+ (version "6.0-90")
(source
(origin
(method url-fetch)
(uri (cran-uri "caret" version))
(sha256
(base32
- "174cyyhsw8s6jp80spmi40qq9sw5ys0r58v4ikp53kiw1dhd247s"))))
+ "1g36m06hp2fxxwv155bwbqlf97xhcia1lmg3axg6d74kgpns8lg8"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-foreach" ,r-foreach)
+ `(("r-e1071" ,r-e1071)
+ ("r-foreach" ,r-foreach)
("r-ggplot2" ,r-ggplot2)
("r-lattice" ,r-lattice)
("r-modelmetrics" ,r-modelmetrics)
@@ -23040,14 +23037,14 @@ Edition), John Wiley and Sons.")
(define-public r-anthropometry
(package
(name "r-anthropometry")
- (version "1.15")
+ (version "1.16")
(source
(origin
(method url-fetch)
(uri (cran-uri "Anthropometry" version))
(sha256
(base32
- "03xw0ggb2qqlldrv0qpjwmncnari742habb46im7y65bhgnr2awx"))))
+ "0iqlmp9vig4qdavs37kislqxwhk0c0pgsn1kwz3mm75nylxmpbp0"))))
(properties `((upstream-name . "Anthropometry")))
(build-system r-build-system)
(propagated-inputs
@@ -23967,14 +23964,14 @@ errors; tetrachoric and biserial correlations are special cases.")
(define-public r-msm
(package
(name "r-msm")
- (version "1.6.8")
+ (version "1.6.9")
(source
(origin
(method url-fetch)
(uri (cran-uri "msm" version))
(sha256
(base32
- "1d32y8f0vb2dfv3999liigpns788j145nrvd1xpxb9i2lsg8mwgk"))))
+ "08vhazswyxr3y1zb9y60mbg3bappzlizxml8s08p65mh82xxkz5f"))))
(properties `((upstream-name . "msm")))
(build-system r-build-system)
(propagated-inputs
@@ -24070,20 +24067,19 @@ actuarial models such as pension mathematics.")
(define-public r-sem
(package
(name "r-sem")
- (version "3.1-11")
+ (version "3.1-13")
(source
(origin
(method url-fetch)
(uri (cran-uri "sem" version))
(sha256
(base32
- "03j3ig6fy34pi6nwfq9w8f5m555lilw5skr1vn6ay4yvjmvavc9k"))))
+ "0r9g4j0w6q4qy9jl9gkjkihml4109ymg3y6zmhyg806q19qryx07"))))
(properties `((upstream-name . "sem")))
(build-system r-build-system)
(propagated-inputs
`(("r-boot" ,r-boot)
("r-mass" ,r-mass)
- ("r-matrixcalc" ,r-matrixcalc)
("r-mi" ,r-mi)))
(home-page "https://cran.r-project.org/package=sem")
(synopsis "Structural equation models")
@@ -24190,14 +24186,14 @@ and analyze Stan models.")
(define-public r-rpf
(package
(name "r-rpf")
- (version "1.0.8")
+ (version "1.0.11")
(source
(origin
(method url-fetch)
(uri (cran-uri "rpf" version))
(sha256
(base32
- "039r6yz2ax7i9sv8vi98yg7llwb966ay6mrifpmp6q3xh1f634kl"))))
+ "1yr1i7kswq57mcxv05lh7bvbicz1djqxcl6f13dlgsf3ww56gzg1"))))
(properties `((upstream-name . "rpf")))
(build-system r-build-system)
(propagated-inputs
@@ -24382,21 +24378,20 @@ network, tree, dendrogram, and Sankey graphs from R using data frames.")
(define-public r-qgraph
(package
(name "r-qgraph")
- (version "1.6.9")
+ (version "1.9")
(source
(origin
(method url-fetch)
(uri (cran-uri "qgraph" version))
(sha256
(base32
- "153bqfmsrghkg7598nfr57r3cxv6dn6ir084njl2sqq5np0sj9di"))))
+ "1ahhzp64jdgki5p2wga5mn8a2n1x2zldgpilrpf7hy5l9nf4imz1"))))
(properties `((upstream-name . "qgraph")))
(build-system r-build-system)
(propagated-inputs
`(("r-abind" ,r-abind)
("r-colorspace" ,r-colorspace)
("r-corpcor" ,r-corpcor)
- ("r-dplyr" ,r-dplyr)
("r-fdrtool" ,r-fdrtool)
("r-ggplot2" ,r-ggplot2)
("r-glasso" ,r-glasso)
@@ -25691,14 +25686,14 @@ Mean Test, Durbin-Watson statistic etc.")
(define-public r-rcdd
(package
(name "r-rcdd")
- (version "1.2-2")
+ (version "1.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "rcdd" version))
(sha256
(base32
- "0pzpbqnlgzr240iici70278py5wnbbxkzlgn112f9wv5ga3riric"))))
+ "02jj1lpk4kvjh5484lbdrdlx2ffk9qdxys7afyakd5kl6swqalz2"))))
(properties
`((upstream-name . "rcdd")))
(build-system r-build-system)
@@ -25818,14 +25813,14 @@ estimation.")
(define-public r-optimx
(package
(name "r-optimx")
- (version "2021-6.12")
+ (version "2021-10.12")
(source
(origin
(method url-fetch)
(uri (cran-uri "optimx" version))
(sha256
(base32
- "059md564p2pk5nis9kbcn1kw2fw130vg53fxlr5xzpv1c9gfhq3k"))))
+ "0hvrpfya767vp3anmb8ih516v4zz1sv4h193rn93kyjydf2lqf1r"))))
(properties `((upstream-name . "optimx")))
(build-system r-build-system)
(propagated-inputs `(("r-numderiv" ,r-numderiv)))
@@ -26260,14 +26255,14 @@ input.")
(define-public r-lightgbm
(package
(name "r-lightgbm")
- (version "3.2.1")
+ (version "3.3.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "lightgbm" version))
(sha256
(base32
- "1136di7k3gs9kk7vd9bc3mdm0qrx3a546ngar8inmgyhi0zk6pkd"))))
+ "1sgimzax84rag02gqv2qag2cg8mmhkv71xydawg7bkxk95dycbc2"))))
(properties `((upstream-name . "lightgbm")))
(build-system r-build-system)
(propagated-inputs
@@ -26541,13 +26536,13 @@ doi.org/10.1007/s10115-013-0679-x} for details.")
(define-public r-memuse
(package
(name "r-memuse")
- (version "4.1-0")
+ (version "4.2-1")
(source (origin
(method url-fetch)
(uri (cran-uri "memuse" version))
(sha256
(base32
- "1bbjp8y0ji71956fbaxiil7ynq2nkmmgz7i9xps83m3bbp5d3mjq"))))
+ "1wvwnjaaiv2647561z2b55dss35033ildx4kk8hzxfzgsjmdpsgm"))))
(properties `((upstream-name . "memuse")))
(build-system r-build-system)
(home-page "https://github.com/shinra-dev/memuse")
@@ -26630,14 +26625,14 @@ and predictions of any machine learning model. Implemented methods are:
(define-public r-goftest
(package
(name "r-goftest")
- (version "1.2-2")
+ (version "1.2-3")
(source
(origin
(method url-fetch)
(uri (cran-uri "goftest" version))
(sha256
(base32
- "0ivnkqhv5xgiv05dm648nngacymd8x8g0fyppv3bc0mhcqk9k5z4"))))
+ "06bz6k7smr4jbvzmb73qc5fkf4my59w5gbl18wlmpkkymsv78prs"))))
(properties `((upstream-name . "goftest")))
(build-system r-build-system)
(home-page "https://github.com/baddstats/goftest")
@@ -26743,14 +26738,14 @@ package.")
(define-public r-spatstat-geom
(package
(name "r-spatstat-geom")
- (version "2.2-2")
+ (version "2.3-0")
(source
(origin
(method url-fetch)
(uri (cran-uri "spatstat.geom" version))
(sha256
(base32
- "0rx28g064641yrk2h23qpyc0bgs20lpsnqmyl1d06530ga6r1qc3"))))
+ "1iz9zi45nli5lf96ng6bqqbl4ix3zxzlfclkg4cdb9h98nj4c5vv"))))
(properties `((upstream-name . "spatstat.geom")))
(build-system r-build-system)
(propagated-inputs
@@ -27323,14 +27318,14 @@ the @code{survival} package.")
(define-public r-exactranktests
(package
(name "r-exactranktests")
- (version "0.8-32")
+ (version "0.8-34")
(source
(origin
(method url-fetch)
(uri (cran-uri "exactRankTests" version))
(sha256
(base32
- "0p7h7w470p5qpsbrhw12zlsshyai56za5dsdva8cf9sikn0955qr"))))
+ "1i4mwz61mjlh1ai3dww2pjkicx9ww8c4mljnr8xlawh91479lva9"))))
(properties
`((upstream-name . "exactRankTests")))
(build-system r-build-system)
@@ -27519,14 +27514,14 @@ model.")
(define-public r-igraph
(package
(name "r-igraph")
- (version "1.2.6")
+ (version "1.2.7")
(source
(origin
(method url-fetch)
(uri (cran-uri "igraph" version))
(sha256
(base32
- "0vf7wrx77cdiav8724cw8gchrn0y9wvywphf5km4pa7xcqhsf3b4"))))
+ "1r8vmqm2rq1jnkh8axr4gw1hbj34ca1dil154qp037imfcra1h95"))))
(build-system r-build-system)
(native-inputs
`(("gfortran" ,gfortran)))
@@ -27551,14 +27546,14 @@ more.")
(define-public r-workflows
(package
(name "r-workflows")
- (version "0.2.3")
+ (version "0.2.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "workflows" version))
(sha256
(base32
- "0bca4s49qabam4ny8vckxcghj3z0xfhwfhs5h1136kihrr5pm6mw"))))
+ "1sxrgza922p137z41jcj2iwk19lxzwh6kp4kz7h9kw0b8rvfqwab"))))
(properties `((upstream-name . "workflows")))
(build-system r-build-system)
(propagated-inputs
@@ -28066,14 +28061,14 @@ vignettes in all common formats.")
(define-public r-tidytext
(package
(name "r-tidytext")
- (version "0.3.1")
+ (version "0.3.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "tidytext" version))
(sha256
(base32
- "182gad5pzz6zvhbla3d496sxwiszc1qz8kzzkksaacwpsrc61f9h"))))
+ "0as7lscjl6ywk85almmb4f71vxmgkfds46g52ryggkg2isksvq3g"))))
(properties `((upstream-name . "tidytext")))
(build-system r-build-system)
(propagated-inputs
@@ -28219,14 +28214,14 @@ use.")
(define-public r-tidymodels
(package
(name "r-tidymodels")
- (version "0.1.3")
+ (version "0.1.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "tidymodels" version))
(sha256
(base32
- "18vz0xsgxrfzcfxpvilhj1w0f4v4lx5ws37nwmy40lhv3v05nxn8"))))
+ "18krycdn0h1i8swrq6bgj8qnb200rr0pqhr6maq3h1jc66x0y7nd"))))
(properties `((upstream-name . "tidymodels")))
(build-system r-build-system)
(propagated-inputs
@@ -28236,6 +28231,7 @@ use.")
("r-dials" ,r-dials)
("r-dplyr" ,r-dplyr)
("r-ggplot2" ,r-ggplot2)
+ ("r-hardhat" ,r-hardhat)
("r-infer" ,r-infer)
("r-modeldata" ,r-modeldata)
("r-parsnip" ,r-parsnip)
@@ -28394,14 +28390,14 @@ including:
(define-public r-perm
(package
(name "r-perm")
- (version "1.0-0.0")
+ (version "1.0-0.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "perm" version))
(sha256
(base32
- "0075awl66ynv10vypg63fcxk33qzvxddrp8mi4w08ysvimcyxijk"))))
+ "182ac1y91yzb34zwdcmx5fdfr5z0cha0gx2bgk36gwxhgfc994kj"))))
(properties `((upstream-name . "perm")))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/perm/")
@@ -28417,14 +28413,14 @@ covariate (usually group indicator) and the scores.")
(define-public r-qtl
(package
(name "r-qtl")
- (version "1.48-1")
+ (version "1.50")
(source
(origin
(method url-fetch)
(uri (cran-uri "qtl" version))
(sha256
(base32
- "098mgmfj8ndi8yipr9b3f6gbbh78cgp9j7y561nlnhrnyc8bsih9"))))
+ "1mcy9wlp5lj5f3z4mf3n5li7x32vj67rmhjnzsp8fhfw0ipnaf1d"))))
(build-system r-build-system)
(home-page "https://rqtl.org/")
(synopsis "R package for analyzing QTL experiments in genetics")
@@ -28440,12 +28436,12 @@ genome scans.")
(define-public r-qtl2
(package
(name "r-qtl2")
- (version "0.24")
+ (version "0.28")
(source (origin
(method url-fetch)
(uri (cran-uri "qtl2" version))
(sha256
- (base32 "1558khh0zkwm0rdk87krv9836krvwv5h7ymlz9bsrgcvypyr9186"))))
+ (base32 "0ppc6dzlq77mppxc6bczai9gi40jrbxd1466y2cn2s8a4ah1jg9y"))))
(build-system r-build-system)
(propagated-inputs
`(("r-data-table" ,r-data-table)
@@ -28567,13 +28563,13 @@ other R users.")
(define-public r-seurat
(package
(name "r-seurat")
- (version "4.0.4")
+ (version "4.0.5")
(source (origin
(method url-fetch)
(uri (cran-uri "Seurat" version))
(sha256
(base32
- "1pa2v29mx39swblzwzqc7rpql2rizhi2nj426r1i63wyla6lcxc0"))))
+ "18svlpfbgs5vdzw2jyg99kj0jacag6dwwhjdg1zpmrh0fm0praxg"))))
(properties `((upstream-name . "Seurat")))
(build-system r-build-system)
(propagated-inputs
@@ -28768,14 +28764,14 @@ parabolic or user defined by custom scale factors.")
(define-public r-decon
(package
(name "r-decon")
- (version "1.2-4")
+ (version "1.3-4")
(source
(origin
(method url-fetch)
(uri (cran-uri "decon" version))
(sha256
(base32
- "1v4l0xq29rm8mks354g40g9jxn0didzlxg3g7z08m0gvj29zdj7s"))))
+ "036cv56wf42q2p3d5h15hbrp5rc29xxy20qwv4k1qzhkq6hmw0qs"))))
(properties `((upstream-name . "decon")))
(build-system r-build-system)
(native-inputs
@@ -29386,14 +29382,14 @@ clusterings as resolution increases.")
(define-public r-textshaping
(package
(name "r-textshaping")
- (version "0.3.5")
+ (version "0.3.6")
(source
(origin
(method url-fetch)
(uri (cran-uri "textshaping" version))
(sha256
(base32
- "06bdc5wxvgv38fnzpyjj9p62ifpfshaangkn96gw05yxn11s46h0"))))
+ "1niaj1dh09rqrg9hrh98ddnc0f2nkyq9iizv24lcwm9gjs3w1ql0"))))
(properties `((upstream-name . "textshaping")))
(build-system r-build-system)
(inputs
@@ -30087,14 +30083,14 @@ and formatted text files with additional meta-data, such including @code{.csv},
(define-public r-lwgeom
(package
(name "r-lwgeom")
- (version "0.2-7")
+ (version "0.2-8")
(source
(origin
(method url-fetch)
(uri (cran-uri "lwgeom" version))
(sha256
(base32
- "1qgszbw03haqfjdc07ivkg8r0yd50ldkiqq27ppkaibw7mgiak5k"))))
+ "0d4b1djwrzla91mmyya2m1250mb44fzmq3d36w5mk81d4bg952pl"))))
(properties `((upstream-name . "lwgeom")))
(build-system r-build-system)
(inputs
@@ -30417,14 +30413,14 @@ quantitative real-time polymerase chain reaction (qPCR).")
(define-public r-textplot
(package
(name "r-textplot")
- (version "0.2.0")
+ (version "0.2.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "textplot" version))
(sha256
(base32
- "1fhnwbcgkliq71lry21762djhlbap1qg4mgil0np46aa6619l21m"))))
+ "10nxh9axhy6kyp6f3rz7smq08yl35ydx9jx47bs7i0bmcl2kwxvl"))))
(properties `((upstream-name . "textplot")))
(build-system r-build-system)
(propagated-inputs
@@ -30800,14 +30796,14 @@ Apache2.")
(define-public r-exactextractr
(package
(name "r-exactextractr")
- (version "0.7.0")
+ (version "0.7.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "exactextractr" version))
(sha256
(base32
- "1fwbl0rn0990cs2rvvwjbflp9mall6hjkindpjmdcy6qafiviid6"))))
+ "1gc1p9pgazhblk8jgykxxjpblylbaq5r9hdlw3ilz5g45yjjwcnc"))))
(properties `((upstream-name . "exactextractr")))
(build-system r-build-system)
(inputs `(("geos" ,geos)))
@@ -30828,14 +30824,14 @@ the @code{raster} package that is suitable for extracting raster values using
(define-public r-stringfish
(package
(name "r-stringfish")
- (version "0.15.2")
+ (version "0.15.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "stringfish" version))
(sha256
(base32
- "0m8485p1gb5z2n2g5nyr38zixw4iv8xxm7bxspxlxvx6alhn03pn"))))
+ "1n67y9vgv8vb8qd091d1wm5sgbalcm2avh2fz0hd3mmglpkr83wf"))))
(properties `((upstream-name . "stringfish")))
(build-system r-build-system)
(propagated-inputs
@@ -31019,14 +31015,14 @@ between them.")
(define-public r-keras
(package
(name "r-keras")
- (version "2.6.0")
+ (version "2.6.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "keras" version))
(sha256
(base32
- "1pgdcypp9x9dw7aa5ka7qqgd24jdcp3ja94jpm7j6l6j4930k5vd"))))
+ "0xg4n9sp1pf2yfbba3lb3fzr5gbdwlhv4j1h5njfqmjy5984b8ij"))))
(properties `((upstream-name . "keras")))
(build-system r-build-system)
(propagated-inputs
@@ -31131,14 +31127,14 @@ Bessel K function.")
(define-public r-ztpln
(package
(name "r-ztpln")
- (version "0.1.1")
+ (version "0.1.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "ztpln" version))
(sha256
(base32
- "18rbfdp22jaxg4nkqzj2393nhjdl1gzv4xhmr6aci76ymdixsfnl"))))
+ "1b22m72a8117yrgq5k1gzsrbx6yrsrj7bpd49lh7x3vbaz56c0wr"))))
(properties `((upstream-name . "ztpln")))
(build-system r-build-system)
(propagated-inputs
@@ -31238,20 +31234,21 @@ to archive and assign DOIs to data, software, figures, and more.")
(define-public r-dismo
(package
(name "r-dismo")
- (version "1.3-3")
+ (version "1.3-5")
(source
(origin
(method url-fetch)
(uri (cran-uri "dismo" version))
(sha256
(base32
- "1jj9d78f251bxgrwbv1ycn677qnhvl40bfan12x8fhlaq4d36rgx"))))
+ "1rqf6h4imbqvs7hjd1k4my6154wg0qnmnp5byan403rcshr1jbl1"))))
(properties `((upstream-name . "dismo")))
(build-system r-build-system)
(propagated-inputs
`(("r-raster" ,r-raster)
("r-rcpp" ,r-rcpp)
- ("r-sp" ,r-sp)))
+ ("r-sp" ,r-sp)
+ ("r-terra" ,r-terra)))
(home-page "https://rspatial.org/raster/sdm/")
(synopsis "Species distribution modeling")
(description
@@ -31298,14 +31295,14 @@ fully reproducible.")
(define-public r-paws-common
(package
(name "r-paws-common")
- (version "0.3.12")
+ (version "0.3.13")
(source
(origin
(method url-fetch)
(uri (cran-uri "paws.common" version))
(sha256
(base32
- "1khq1rv0yij4l0vi2x6hslnzpsd6m5n6nipfac7g3na9ah93h8i9"))))
+ "15sj7yw4hj76minr00xhgzkg1rwb7gsr2ib9q4d053i5f3jcy54a"))))
(properties `((upstream-name . "paws.common")))
(build-system r-build-system)
(propagated-inputs
@@ -32128,13 +32125,13 @@ Monte Carlo approach implemented in JAGS.")
(define-public r-logger
(package
(name "r-logger")
- (version "0.2.1")
+ (version "0.2.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "logger" version))
(sha256
- (base32 "0p607da2rdrfj9sbrrq9hpqp26nyj3imd1590c13bxskqfhv0sz8"))))
+ (base32 "08kym5i5fvbf5xhh9qdszp4jdgyc7j7zpnwzy68wabqz73aff6sg"))))
(properties `((upstream-name . "logger")))
(build-system r-build-system)
(native-inputs `(("r-knitr" ,r-knitr)))
diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm
index c896b9e3d6..c96bc65e14 100644
--- a/gnu/packages/crates-io.scm
+++ b/gnu/packages/crates-io.scm
@@ -47,6 +47,7 @@
#:use-module (gnu packages admin)
#:use-module (gnu packages cmake)
#:use-module (gnu packages compression)
+ #:use-module (gnu packages cpp)
#:use-module (gnu packages crates-graphics)
#:use-module (gnu packages crates-gtk)
#:use-module (gnu packages crypto)
@@ -64,6 +65,7 @@
#:use-module (gnu packages nettle)
#:use-module (gnu packages pcre)
#:use-module (gnu packages pkg-config)
+ #:use-module (gnu packages pulseaudio)
#:use-module (gnu packages python)
#:use-module (gnu packages rust)
#:use-module (gnu packages rust-apps)
@@ -1174,8 +1176,34 @@ with Associated Data (AEAD) algorithms.")
(("rust-generic-array" ,rust-generic-array-0.12)
("rust-heapless" ,rust-heapless-0.5))))))
+(define-public rust-aes-0.6
+ (package
+ (name "rust-aes")
+ (version "0.6.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "aes" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "0q85mw70mgr4glza9y9lrs9nxfa1cdcqzfk6wx0smb3623pr2hw8"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:cargo-inputs
+ (("rust-aes-soft" ,rust-aes-soft-0.6)
+ ("rust-aesni" ,rust-aesni-0.10)
+ ("rust-cipher" ,rust-cipher-0.2))
+ #:cargo-development-inputs
+ (("rust-cipher" ,rust-cipher-0.2))))
+ (home-page "https://github.com/RustCrypto/block-ciphers")
+ (synopsis "Facade for AES (Rijndael) block ciphers implementations")
+ (description "This package provides a facade for AES (Rijndael) block
+ciphers implementations.")
+ (license (list license:expat license:asl2.0))))
+
(define-public rust-aes-0.4
(package
+ (inherit rust-aes-0.6)
(name "rust-aes")
(version "0.4.0")
(source
@@ -1186,19 +1214,13 @@ with Associated Data (AEAD) algorithms.")
(sha256
(base32
"1xgsp2bn5llsppald60iw4497gaspslg0a8hknhniiz4zmki607p"))))
- (build-system cargo-build-system)
(arguments
`(#:cargo-inputs
(("rust-aes-soft" ,rust-aes-soft-0.4)
("rust-aesni" ,rust-aesni-0.7)
("rust-block-cipher" ,rust-block-cipher-0.7))
#:cargo-development-inputs
- (("rust-block-cipher" ,rust-block-cipher-0.7))))
- (home-page "https://github.com/RustCrypto/block-ciphers")
- (synopsis "Facade for AES (Rijndael) block ciphers implementations")
- (description "This package provides a facade for AES (Rijndael) block
-ciphers implementations.")
- (license (list license:expat license:asl2.0))))
+ (("rust-block-cipher" ,rust-block-cipher-0.7))))))
(define-public rust-aes-0.3
(package
@@ -1275,21 +1297,21 @@ acceleration.")
("rust-subtle" ,rust-subtle-2)
("rust-zeroize" ,rust-zeroize-1))))))
-(define-public rust-aes-soft-0.4
+(define-public rust-aes-soft-0.6
(package
(name "rust-aes-soft")
- (version "0.4.0")
+ (version "0.6.4")
(source
(origin
(method url-fetch)
(uri (crate-uri "aes-soft" version))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
- (base32
- "19szsg0qqxq42k7bj5p3svb147n8wxy9a20n4g7mcl2fwrz689a9"))))
+ (base32 "0wj0fi2pvmlw09yvb1aqf0mfkzrfxmjsf90finijh255ir4wf55y"))))
(build-system cargo-build-system)
(arguments
- `(#:cargo-inputs
+ `(#:skip-build? #t
+ #:cargo-inputs
(("rust-block-cipher" ,rust-block-cipher-0.7)
("rust-byteorder" ,rust-byteorder-1)
("rust-opaque-debug" ,rust-opaque-debug-0.2))
@@ -1298,9 +1320,32 @@ acceleration.")
(home-page "https://github.com/RustCrypto/block-ciphers")
(synopsis "Bit-sliced implementation of AES (Rijndael) block ciphers")
(description "This package provides a bit-sliced implementation of
-AES (Rijndael) block ciphers.")
+AES (Rijndael) block ciphers.
+
+This package is deprecated and was replaced by the @code{aes} crate.")
(license (list license:expat license:asl2.0))))
+(define-public rust-aes-soft-0.4
+ (package
+ (inherit rust-aes-soft-0.6)
+ (name "rust-aes-soft")
+ (version "0.4.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "aes-soft" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "19szsg0qqxq42k7bj5p3svb147n8wxy9a20n4g7mcl2fwrz689a9"))))
+ (arguments
+ `(#:cargo-inputs
+ (("rust-block-cipher" ,rust-block-cipher-0.7)
+ ("rust-byteorder" ,rust-byteorder-1)
+ ("rust-opaque-debug" ,rust-opaque-debug-0.2))
+ #:cargo-development-inputs
+ (("rust-block-cipher" ,rust-block-cipher-0.7))))))
+
(define-public rust-aes-soft-0.3
(package
(inherit rust-aes-soft-0.4)
@@ -1320,8 +1365,34 @@ AES (Rijndael) block ciphers.")
("rust-byteorder" ,rust-byteorder-1)
("rust-opaque-debug" ,rust-opaque-debug-0.2))))))
+(define-public rust-aesni-0.10
+ (package
+ (name "rust-aesni")
+ (version "0.10.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "aesni" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "1kmh07fp9hbi1aa8dr2rybbgw8vqz6hjmk34c4w7sbscx7si2bpa"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:skip-build? #t
+ #:cargo-inputs
+ (("rust-cipher" ,rust-cipher-0.2)
+ ("rust-opaque-debug" ,rust-opaque-debug-0.3))))
+ (home-page "https://github.com/RustCrypto/block-ciphers")
+ (synopsis "AES (Rijndael) block ciphers implementation using AES-NI")
+ (description "This package provides an implementation of AES (Rijndael)
+block ciphers using AES-NI.
+
+This package is deprecated and was replaced by the @code{aes} crate.")
+ (license (list license:expat license:asl2.0))))
+
(define-public rust-aesni-0.7
(package
+ (inherit rust-aesni-0.10)
(name "rust-aesni")
(version "0.7.0")
(source
@@ -1332,7 +1403,6 @@ AES (Rijndael) block ciphers.")
(sha256
(base32
"0r6j0mjkyqnwvgib01cvrwfw8rlx1biw75234niv723n1fdx6l6h"))))
- (build-system cargo-build-system)
(arguments
`(#:cargo-inputs
(("rust-block-cipher" ,rust-block-cipher-0.7)
@@ -1340,12 +1410,7 @@ AES (Rijndael) block ciphers.")
("rust-stream-cipher" ,rust-stream-cipher-0.4))
#:cargo-development-inputs
(("rust-block-cipher" ,rust-block-cipher-0.7)
- ("rust-stream-cipher" ,rust-stream-cipher-0.4))))
- (home-page "https://github.com/RustCrypto/block-ciphers")
- (synopsis "AES (Rijndael) block ciphers implementation using AES-NI")
- (description "This package provides an implementation of AES (Rijndael)
-block ciphers using AES-NI.")
- (license (list license:expat license:asl2.0))))
+ ("rust-stream-cipher" ,rust-stream-cipher-0.4))))))
(define-public rust-aesni-0.6
(package
@@ -2434,6 +2499,95 @@ format.")
("rust-serde-derive" ,rust-serde-derive-1)
("rust-serde-json" ,rust-serde-json-1))))))
+(define-public rust-arrow2-0.5
+ (package
+ (name "rust-arrow2")
+ (version "0.5.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "arrow2" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "042m859jfffnhi84qc919pkyanlr98wqqf67pcrylk4hhh0v84xx"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:skip-build? #t
+ #:cargo-inputs
+ (("rust-ahash" ,rust-ahash-0.7)
+ ("rust-base64" ,rust-base64-0.13)
+ ("rust-chrono" ,rust-chrono-0.4)
+ ("rust-chrono-tz" ,rust-chrono-tz-0.5)
+ ("rust-comfy-table" ,rust-comfy-table-4)
+ ("rust-csv" ,rust-csv-1)
+ ("rust-flatbuffers" ,rust-flatbuffers-2)
+ ("rust-futures" ,rust-futures-0.3)
+ ("rust-hash-hasher" ,rust-hash-hasher-2)
+ ("rust-hex" ,rust-hex-0.4)
+ ("rust-indexmap" ,rust-indexmap-1)
+ ("rust-itertools" ,rust-itertools-0.10)
+ ("rust-lazy-static" ,rust-lazy-static-1)
+ ("rust-lexical-core" ,rust-lexical-core-0.8)
+ ("rust-lz4" ,rust-lz4-1)
+ ("rust-multiversion" ,rust-multiversion-0.6)
+ ("rust-num-traits" ,rust-num-traits-0.2)
+ ("rust-packed-simd-2" ,rust-packed-simd-2-0.3)
+ ("rust-parquet2" ,rust-parquet2-0.4)
+ ("rust-rand" ,rust-rand-0.8)
+ ("rust-regex" ,rust-regex-1)
+ ("rust-serde" ,rust-serde-1)
+ ("rust-serde-derive" ,rust-serde-derive-1)
+ ("rust-serde-json" ,rust-serde-json-1)
+ ("rust-streaming-iterator" ,rust-streaming-iterator-0.1)
+ ("rust-strength-reduce" ,rust-strength-reduce-0.2)
+ ("rust-zstd" ,rust-zstd-0.9))))
+ (home-page "https://github.com/jorgecarleitao/arrow2")
+ (synopsis "Unofficial implementation of Apache Arrow spec in safe Rust")
+ (description
+ "Arrow2 is a Rust library to work with the Arrow format. It is
+a re-write of the official Arrow crate using transmute-free operations.")
+ (license license:asl2.0)))
+
+(define-public rust-article-scraper-1
+ (package
+ (name "rust-article-scraper")
+ (version "1.1.7")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "article_scraper" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "1l904hn99fgj83f3dhspxgz1j3xzgjbnbfsgvmhd1jg5l4hqfhxp"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:tests? #f ;tests use the network
+ #:cargo-inputs
+ (("rust-base64" ,rust-base64-0.13)
+ ("rust-chrono" ,rust-chrono-0.4)
+ ("rust-encoding-rs" ,rust-encoding-rs-0.8)
+ ("rust-failure" ,rust-failure-0.1)
+ ("rust-image" ,rust-image-0.23)
+ ("rust-libxml" ,rust-libxml-0.2)
+ ("rust-log" ,rust-log-0.4)
+ ("rust-parking-lot" ,rust-parking-lot-0.11)
+ ("rust-regex" ,rust-regex-1)
+ ("rust-reqwest" ,rust-reqwest-0.11)
+ ("rust-tokio" ,rust-tokio-1)
+ ("rust-url" ,rust-url-2))))
+ (native-inputs
+ `(("pkg-config" ,pkg-config)))
+ (inputs
+ `(("libxml2" ,libxml2)
+ ("openssl" ,openssl)))
+ (home-page "https://gitlab.com/news-flash/article_scraper")
+ (synopsis "Scrap article contents from the web")
+ (description "This package provides a crate to scrap article contents from
+the web.")
+ ;; No copyright headers in the source code. LICENSE indicates gpl3.
+ (license license:gpl3)))
+
(define-public rust-askama-escape-0.10
(package
(name "rust-askama-escape")
@@ -3549,23 +3703,25 @@ interfaces you are used to, but in an async version and ready for Rust's
(define-public rust-async-stream-0.3
(package
(name "rust-async-stream")
- (version "0.3.0")
+ (version "0.3.2")
(source
(origin
(method url-fetch)
(uri (crate-uri "async-stream" version))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
- (base32 "0p19qn5igblb86d35lda72q8vimk2iw8hk7r07wjj5y0rdqdyw1n"))))
+ (base32 "0986b72jksg4lndw76py9glry3snc29bbqrna874wl5jwgkp84qp"))))
(build-system cargo-build-system)
(arguments
- `(#:cargo-inputs
+ `(#:cargo-test-flags '("--release" "--"
+ "--skip=test")
+ #:cargo-inputs
(("rust-async-stream-impl" ,rust-async-stream-impl-0.3)
("rust-futures-core" ,rust-futures-core-0.3))
#:cargo-development-inputs
(("rust-futures-util" ,rust-futures-util-0.3)
- ("rust-tokio" ,rust-tokio-0.2)
- ("rust-tokio-test" ,rust-tokio-test-0.2)
+ ("rust-tokio" ,rust-tokio-1)
+ ("rust-tokio-test" ,rust-tokio-test-0.4)
("rust-trybuild" ,rust-trybuild-1))))
(home-page "https://github.com/tokio-rs/async-stream")
(synopsis "Asynchronous streams using async & await notation")
@@ -3577,14 +3733,14 @@ notation.")
(define-public rust-async-stream-impl-0.3
(package
(name "rust-async-stream-impl")
- (version "0.3.0")
+ (version "0.3.2")
(source
(origin
(method url-fetch)
(uri (crate-uri "async-stream-impl" version))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
- (base32 "0w0aif9aw103b5wrm1svkqdh7aaihjywa21819d8m3lzzj78nm53"))))
+ (base32 "024k57iwmmhzvbzacxlkssh45cqlnb8xjlvlsp60jm6fsb4di3k4"))))
(build-system cargo-build-system)
(arguments
`(#:cargo-test-flags '("--release" "--"
@@ -3597,7 +3753,7 @@ notation.")
#:cargo-development-inputs
(("rust-futures-core" ,rust-futures-core-0.3)
("rust-futures-util" ,rust-futures-util-0.3)
- ("rust-tokio" ,rust-tokio-0.2))))
+ ("rust-tokio" ,rust-tokio-1))))
(home-page "https://github.com/tokio-rs/async-stream")
(synopsis "Proc macros for async-stream crate")
(description
@@ -4116,6 +4272,29 @@ trace (backtrace) at runtime in a Rust program.")
(license (list license:asl2.0
license:expat))))
+(define-public rust-barrel-0.6
+ (package
+ (name "rust-barrel")
+ (version "0.6.5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "barrel" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "1qgzrfpp2acb06bbqrf5a8pjjwf3dwinq7sv2hqq0b1jn5wcjrwx"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:cargo-inputs
+ (("rust-diesel" ,rust-diesel-1)
+ ("rust-tempfile" ,rust-tempfile-3))))
+ (home-page "https://rust-db.github.io/barrel/")
+ (synopsis "Powerful schema migration building API for Rust")
+ (description "This package provides a powerful schema migration building
+API for Rust.")
+ (license (list license:expat license:x11 license:asl2.0))))
+
(define-public rust-base32-0.4
(package
(name "rust-base32")
@@ -5329,6 +5508,27 @@ behave like a set of bitflags.")
declaring and working with fixed size bitmaps in Rust.")
(license license:mpl2.0)))
+(define-public rust-bitpacking-0.8
+ (package
+ (name "rust-bitpacking")
+ (version "0.8.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "bitpacking" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "1mw2xbpkw9zhfq5lir6bgkalhhfqb5p7xwx5yimc0ry1ffnd5ix8"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:skip-build? #t #:cargo-inputs (("rust-crunchy" ,rust-crunchy-0.2))))
+ (home-page "https://crates.io/crates/bitpacking")
+ (synopsis "Fast integer compression/decompression via SIMD bit-packing")
+ (description
+ "This crate provides fast integer compression and decompression via SIMD
+bit-packing. It is a port of simdcomp C library to Rust.")
+ (license license:expat)))
+
(define-public rust-bitreader-0.3
(package
(name "rust-bitreader")
@@ -5766,6 +5966,32 @@ algorithms. This package is deprecated. Please use block-cipher instead.")
`(#:cargo-inputs
(("rust-generic-array" ,rust-generic-array-0.8))))))
+(define-public rust-block-modes-0.7
+ (package
+ (name "rust-block-modes")
+ (version "0.7.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "block-modes" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "1w3jc3n7k4xq98b9mfina4wwpg1fq1s3b0mm5whqialb7q3yi82p"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:cargo-inputs
+ (("rust-block-padding" ,rust-block-padding-0.2)
+ ("rust-cipher" ,rust-cipher-0.2))
+ #:cargo-development-inputs
+ (("rust-aes" ,rust-aes-0.6)
+ ("rust-hex-literal" ,rust-hex-literal-0.2))))
+ (home-page "https://github.com/RustCrypto/block-ciphers")
+ (synopsis "Block cipher modes of operation")
+ (description "This package provides a collection of block ciphers
+and block modes.")
+ (license (list license:expat license:asl2.0))))
+
(define-public rust-block-padding-0.2
(package
(name "rust-block-padding")
@@ -9081,6 +9307,30 @@ diagnostics easy and relatively painless for everyone!")
("rust-structopt" ,rust-structopt-0.3)
("rust-unindent" ,rust-unindent-0.1))))))
+(define-public rust-color-backtrace-0.5
+ (package
+ (name "rust-color-backtrace")
+ (version "0.5.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "color-backtrace" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "11fn3snykx90w3nznzrcf4r164zmhk790asx0kzryf4r7i308v6d"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:cargo-inputs
+ (("rust-atty" ,rust-atty-0.2)
+ ("rust-backtrace" ,rust-backtrace-0.3)
+ ("rust-regex" ,rust-regex-1)
+ ("rust-termcolor" ,rust-termcolor-1))))
+ (home-page "https://github.com/athre0z/color-backtrace")
+ (synopsis "Colorful panic backtraces")
+ (description "This package provides colorful panic backtraces.")
+ (license (list license:expat license:asl2.0))))
+
(define-public rust-color-quant-1
(package
(name "rust-color-quant")
@@ -9250,24 +9500,25 @@ combinator.")
and 1.0.")
(license (list license:expat license:asl2.0))))
-(define-public rust-comfy-table-1
+(define-public rust-comfy-table-4
(package
(name "rust-comfy-table")
- (version "1.6.0")
+ (version "4.1.1")
(source
(origin
(method url-fetch)
(uri (crate-uri "comfy-table" version))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
- (base32 "1y6lc8h2lyyrrrdc36fz7brwyjz5l9w4nld4qx9mlacfibm8i92j"))))
+ (base32 "1wzk894p2s725cpdip5968ydb50zczsl34040j6zs8klhqz5ms8i"))))
(build-system cargo-build-system)
(arguments
`(#:skip-build? #t
#:cargo-inputs
- (("rust-crossterm" ,rust-crossterm-0.19)
- ("rust-strum" ,rust-strum-0.20)
- ("rust-strum-macros" ,rust-strum-macros-0.20))))
+ (("rust-crossterm" ,rust-crossterm-0.20)
+ ("rust-strum" ,rust-strum-0.21)
+ ("rust-strum-macros" ,rust-strum-macros-0.21)
+ ("rust-unicode-width" ,rust-unicode-width-0.1))))
(home-page "https://github.com/nukesor/comfy-table")
(synopsis "Library for building tables with automatic content wrapping")
(description
@@ -9275,6 +9526,25 @@ and 1.0.")
wrapping.")
(license license:expat)))
+(define-public rust-comfy-table-1
+ (package
+ (inherit rust-comfy-table-4)
+ (name "rust-comfy-table")
+ (version "1.6.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "comfy-table" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "1y6lc8h2lyyrrrdc36fz7brwyjz5l9w4nld4qx9mlacfibm8i92j"))))
+ (arguments
+ `(#:skip-build? #t
+ #:cargo-inputs
+ (("rust-crossterm" ,rust-crossterm-0.19)
+ ("rust-strum" ,rust-strum-0.20)
+ ("rust-strum-macros" ,rust-strum-macros-0.20))))))
+
(define-public rust-commoncrypto-sys-0.2
(package
(name "rust-commoncrypto-sys")
@@ -10481,6 +10751,32 @@ to the @code{is_x86_feature_detected!} macro.")
to @code{is_x86_feature_detected}.")
(license (list license:expat license:asl2.0))))
+(define-public rust-cpuprofiler-0.0
+ (package
+ (name "rust-cpuprofiler")
+ (version "0.0.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "cpuprofiler" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0az588yyl9r13w4k7xfdh5ckfaq52fwpjry2q2hblazxpjflgy23"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:cargo-inputs
+ (("rust-error-chain" ,rust-error-chain-0.12)
+ ("rust-lazy-static" ,rust-lazy-static-1)
+ ("rust-pkg-config" ,rust-pkg-config-0.3))))
+ (inputs
+ `(("gperftools" ,gperftools)))
+ (home-page "https://github.com/AtheMathmo/cpuprofiler")
+ (synopsis "Bindings to Google's cpu profiler")
+ (description "This package provides bindings to Google's cpu profiler.")
+ (license license:bsd-2)))
+
(define-public rust-crates-index-0.13
(package
(name "rust-crates-index")
@@ -10569,6 +10865,32 @@ to @code{is_x86_feature_detected}.")
64) with support for various standards.")
(license (list license:expat license:asl2.0))))
+(define-public rust-crc-any-2
+ (package
+ (name "rust-crc-any")
+ (version "2.3.12")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "crc-any" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "0fq85y5akcadahnj5nqbs47qhgp5cpfn2z19zc3gp4wpxr3989kr"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:cargo-inputs
+ (("rust-debug-helper" ,rust-debug-helper-0.3)
+ ("rust-heapless" ,rust-heapless-0.5))
+ #:cargo-development-inputs
+ (("rust-bencher" ,rust-bencher-0.1))))
+ (home-page "https://magiclen.org/crc-any")
+ (synopsis "Compute CRC values")
+ (description "This package provides a crate to compute CRC values by
+providing the length of bits, expression, reflection, an initial value and a
+final xor value. It has many built-in CRC functions.")
+ (license license:expat)))
+
(define-public rust-crc32fast-1
(package
(name "rust-crc32fast")
@@ -11221,30 +11543,30 @@ rasterizing glyphs, using native font engines whenever possible.")
("rust-servo-fontconfig" ,rust-servo-fontconfig-0.5)
("rust-winapi" ,rust-winapi-0.3))))))
-(define-public rust-crossterm-0.19
+(define-public rust-crossterm-0.20
(package
(name "rust-crossterm")
- (version "0.19.0")
+ (version "0.20.0")
(source
(origin
(method url-fetch)
(uri (crate-uri "crossterm" version))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
- (base32 "1348lqf8vy3lb2s5icsl3rxs4a4vrpfw5z2j6lplnhnz600w2dkw"))))
+ (base32 "0z8zkk2mfiirbr3slfv564n685yiahr2aj3gdk6k3qymkmmdxsy0"))))
(build-system cargo-build-system)
(arguments
`(#:skip-build? #t
#:cargo-inputs
(("rust-bitflags" ,rust-bitflags-1)
- ("rust-crossterm-winapi" ,rust-crossterm-winapi-0.7)
+ ("rust-crossterm-winapi" ,rust-crossterm-winapi-0.8)
("rust-futures-core" ,rust-futures-core-0.3)
- ("rust-lazy-static" ,rust-lazy-static-1)
("rust-libc" ,rust-libc-0.2)
("rust-mio" ,rust-mio-0.7)
("rust-parking-lot" ,rust-parking-lot-0.11)
("rust-serde" ,rust-serde-1)
- ("rust-signal-hook" ,rust-signal-hook-0.1)
+ ("rust-signal-hook" ,rust-signal-hook-0.3)
+ ("rust-signal-hook-mio" ,rust-signal-hook-mio-0.2)
("rust-winapi" ,rust-winapi-0.3))))
(home-page "https://github.com/crossterm-rs/crossterm")
(synopsis "Crossplatform terminal library for manipulating terminals")
@@ -11253,6 +11575,32 @@ rasterizing glyphs, using native font engines whenever possible.")
terminals.")
(license license:expat)))
+(define-public rust-crossterm-0.19
+ (package
+ (inherit rust-crossterm-0.20)
+ (name "rust-crossterm")
+ (version "0.19.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "crossterm" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "1348lqf8vy3lb2s5icsl3rxs4a4vrpfw5z2j6lplnhnz600w2dkw"))))
+ (arguments
+ `(#:skip-build? #t
+ #:cargo-inputs
+ (("rust-bitflags" ,rust-bitflags-1)
+ ("rust-crossterm-winapi" ,rust-crossterm-winapi-0.7)
+ ("rust-futures-core" ,rust-futures-core-0.3)
+ ("rust-lazy-static" ,rust-lazy-static-1)
+ ("rust-libc" ,rust-libc-0.2)
+ ("rust-mio" ,rust-mio-0.7)
+ ("rust-parking-lot" ,rust-parking-lot-0.11)
+ ("rust-serde" ,rust-serde-1)
+ ("rust-signal-hook" ,rust-signal-hook-0.1)
+ ("rust-winapi" ,rust-winapi-0.3))))))
+
(define-public rust-crossterm-0.18
(package
(inherit rust-crossterm-0.19)
@@ -11300,22 +11648,21 @@ terminals.")
("rust-serde" ,rust-serde-1)
("rust-winapi" ,rust-winapi-0.3))))))
-(define-public rust-crossterm-winapi-0.7
+(define-public rust-crossterm-winapi-0.8
(package
(name "rust-crossterm-winapi")
- (version "0.7.0")
+ (version "0.8.0")
(source
(origin
(method url-fetch)
(uri (crate-uri "crossterm_winapi" version))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
- (base32 "1fa047zz228qyqbcjdss64j0n01p4adr29yh9w24lgjdrr59da0d"))))
+ (base32 "01q57jwnlicqxa2igg5nig3916kf5w6sqgbxk40q6hr2frh6cs9s"))))
(build-system cargo-build-system)
(arguments
`(#:skip-build? #t
- #:cargo-inputs
- (("rust-winapi" ,rust-winapi-0.3))))
+ #:cargo-inputs (("rust-winapi" ,rust-winapi-0.3))))
(home-page "https://github.com/crossterm-rs/crossterm-winapi")
(synopsis "Basic simple abstractions around common WinAPI calls")
(description
@@ -11323,6 +11670,23 @@ terminals.")
abstractions around common WinAPI calls.")
(license license:expat)))
+(define-public rust-crossterm-winapi-0.7
+ (package
+ (inherit rust-crossterm-winapi-0.8)
+ (name "rust-crossterm-winapi")
+ (version "0.7.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "crossterm_winapi" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "1fa047zz228qyqbcjdss64j0n01p4adr29yh9w24lgjdrr59da0d"))))
+ (arguments
+ `(#:skip-build? #t
+ #:cargo-inputs
+ (("rust-winapi" ,rust-winapi-0.3))))))
+
(define-public rust-crossterm-winapi-0.6
(package
(inherit rust-crossterm-winapi-0.7)
@@ -12986,6 +13350,25 @@ sizes. Big-endian order is used. WARNING: Block must be aligned!")
type.")
(license (list license:expat license:asl2.0))))
+(define-public rust-debug-helper-0.3
+ (package
+ (name "rust-debug-helper")
+ (version "0.3.12")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "debug-helper" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "1a73xl73psmzyihd62jy30g1acfmgjmyi2k8khmh170mrq6x3yvn"))))
+ (build-system cargo-build-system)
+ (home-page "https://magiclen.org/debug-helper")
+ (synopsis "Declarative macros to implement the Debug trait manually")
+ (description "This crate provides declarative macros to help you implement
+the Debug trait manually.")
+ (license license:expat)))
+
(define-public rust-decimal-2
(package
(name "rust-decimal")
@@ -13557,6 +13940,32 @@ traits for both structs and enums.")
structs and enums.")
(license license:expat)))
+(define-public rust-des-0.6
+ (package
+ (name "rust-des")
+ (version "0.6.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "des" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "1bigk1x1kxvnfjn1alr8cc383z1flmj8q7g2pjl2zal8i1s7qkmj"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:cargo-inputs
+ (("rust-byteorder" ,rust-byteorder-1)
+ ("rust-cipher" ,rust-cipher-0.2)
+ ("rust-opaque-debug" ,rust-opaque-debug-0.3))
+ #:cargo-development-inputs
+ (("rust-cipher" ,rust-cipher-0.2))))
+ (home-page "https://github.com/RustCrypto/block-ciphers")
+ (synopsis "DES and Triple DES block ciphers implementation")
+ (description "This package provides DES and Triple DES (3DES, TDES) block
+ciphers implementations.")
+ (license (list license:expat license:asl2.0))))
+
(define-public rust-deunicode-0.4
(package
(name "rust-deunicode")
@@ -13808,6 +14217,35 @@ Builder for PostgreSQL, SQLite, and MySQL.")
Diesel.")
(license (list license:expat license:asl2.0))))
+(define-public rust-diesel-migrations-1
+ (package
+ (name "rust-diesel-migrations")
+ (version "1.4.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "diesel_migrations" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "0k4g03ciqwya2xc1xvy5s9cs6q55k45wxa1gszswfg9m2f2dwg5z"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:tests? #f ;doctest_setup.rs: No such file or directory
+ #:cargo-inputs
+ (("rust-migrations-internals"
+ ,rust-migrations-internals-1)
+ ("rust-migrations-macros"
+ ,rust-migrations-macros-1))
+ #:cargo-development-inputs
+ (("rust-cfg-if" ,rust-cfg-if-0.1)
+ ("rust-diesel" ,rust-diesel-1)
+ ("rust-dotenv" ,rust-dotenv-0.10))))
+ (home-page "https://diesel.rs")
+ (synopsis "Migration management for diesel")
+ (description "This package provides migration management for Diesel.")
+ (license (list license:expat license:asl2.0))))
+
(define-public rust-diff-0.1
(package
(name "rust-diff")
@@ -13921,6 +14359,59 @@ common subsequence. The diff algorithms include Myer's diff and Patience
diff.")
(license (list license:asl2.0 license:expat))))
+(define-public rust-diffus-0.10
+ (package
+ (name "rust-diffus")
+ (version "0.10.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "diffus" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "0lsn5h1mfa8x7bfg9yqgr52p7drigpwgm5q8qh4r07dmfd5g43rw"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:rust ,rust-1.52 ; fix for E0658
+ #:cargo-inputs
+ (("rust-diffus-derive" ,rust-diffus-derive-0.10)
+ ("rust-indexmap" ,rust-indexmap-1)
+ ("rust-itertools" ,rust-itertools-0.10)
+ ("rust-serde" ,rust-serde-1)
+ ("rust-snake-case" ,rust-snake-case-0.3)
+ ("rust-uuid" ,rust-uuid-0.8))))
+ (home-page "https://github.com/distil/diffus")
+ (synopsis "Diff two instances of any data structure")
+ (description "This package finds the difference between two instances of
+any data structure. It supports: collections, Strings, Maps etc. Uses LC
+where applicable. Also supports derive via `diffus-derive`.")
+ (license license:asl2.0)))
+
+(define-public rust-diffus-derive-0.10
+ (package
+ (name "rust-diffus-derive")
+ (version "0.10.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "diffus-derive" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "1a7sgbzhqa7gk3xhvkci91myc86gkwxs04vfxbl8f64y7l1jsfmr"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:cargo-inputs
+ (("rust-proc-macro2" ,rust-proc-macro2-1)
+ ("rust-quote" ,rust-quote-1)
+ ("rust-syn" ,rust-syn-1))))
+ (home-page "https://github.com/distil/diffus")
+ (synopsis "Diff two instances of any data structure")
+ (description "This package finds the difference between two instances of
+any data structure. Supports derive on structs and enums.")
+ (license license:asl2.0)))
+
(define-public rust-digest-0.9
(package
(name "rust-digest")
@@ -15091,6 +15582,24 @@ signing, and verification in pure Rust.")
"Levenshtein edit distance between strings, a measure for similarity.")
(license license:asl2.0)))
+(define-public rust-ego-tree-0.6
+ (package
+ (name "rust-ego-tree")
+ (version "0.6.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "ego-tree" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "149mkc6j7bx653s39rpnsnpl5dvd1rj18czcil57w54k868a8s1s"))))
+ (build-system cargo-build-system)
+ (arguments `(#:skip-build? #t))
+ (home-page "https://github.com/programble/ego-tree")
+ (synopsis "Vec-backed ID-tree")
+ (description "Ego Tree provides a vec-backed ID-tree.")
+ (license license:isc)))
+
(define-public rust-either-1
(package
(name "rust-either")
@@ -15618,6 +16127,25 @@ Standard.")
order.")
(license license:expat)))
+(define-public rust-entities-1
+ (package
+ (name "rust-entities")
+ (version "1.0.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "entities" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "1jnpr0zvj97wm9pnh7fnl74rzaar39hhg65p03cm08bqqgj0lcmm"))))
+ (build-system cargo-build-system)
+ (home-page "https://github.com/p-jackson/entities")
+ (synopsis "Raw data needed to convert to and from HTML entities")
+ (description "This package provides the raw data needed to convert to and
+from HTML entities.")
+ (license license:expat)))
+
(define-public rust-enum-as-inner-0.3
(package
(name "rust-enum-as-inner")
@@ -16177,6 +16705,31 @@ deserialized from environment variables.")
@code{no_std} environment.")
(license license:boost1.0)))
+(define-public rust-escaper-0.1
+ (package
+ (name "rust-escaper")
+ (version "0.1.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "escaper" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "0rhn3ipb5c3zns4wakclilfqzbmax6pwx7l367dipfj9fdxvjgm5"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:cargo-inputs
+ (("rust-entities" ,rust-entities-1))
+ #:cargo-development-inputs
+ (("rust-num" ,rust-num-0.4)
+ ("rust-rand" ,rust-rand-0.8))))
+ (home-page "https://github.com/dignifiedquire/rust-escaper")
+ (synopsis "Library for HTML entity encoding and decoding")
+ (description "This package provides a library for HTML entity encoding and
+decoding.")
+ (license (list license:asl2.0 license:expat license:mpl2.0))))
+
(define-public rust-escargot-0.5
(package
(name "rust-escargot")
@@ -16716,6 +17269,114 @@ it.")
descriptors limit.")
(license license:asl2.0)))
+(define-public rust-feed-rs-0.6
+ (package
+ (name "rust-feed-rs")
+ (version "0.6.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "feed-rs" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "1a1ain6r9k8bx7cz9pxqh3hdqbn8cqdkrbx78c8rxb7vqngyg53z"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:cargo-inputs
+ (("rust-chrono" ,rust-chrono-0.4)
+ ("rust-lazy-static" ,rust-lazy-static-1)
+ ("rust-mime" ,rust-mime-0.3)
+ ("rust-quick-xml" ,rust-quick-xml-0.20)
+ ("rust-regex" ,rust-regex-1)
+ ("rust-serde" ,rust-serde-1)
+ ("rust-serde-json" ,rust-serde-json-1)
+ ("rust-siphasher" ,rust-siphasher-0.3)
+ ("rust-url" ,rust-url-2)
+ ("rust-uuid" ,rust-uuid-0.8))))
+ (home-page "https://github.com/feed-rs/feed-rs")
+ (synopsis "Unified feed parser")
+ (description "This package provides a unified feed parser that handles
+Atom, RSS 2.0, RSS 1.0, RSS 0.x and JSON Feed")
+ (license license:expat)))
+
+(define-public rust-feedbin-api-0.1
+ (package
+ (name "rust-feedbin-api")
+ (version "0.1.6")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "feedbin-api" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "170xf3cgsqgqpnafpdmzzw9yvzc51r22lgr4f4hcrmidxlxpmlkp"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:tests? #f ;tests use the network
+ #:cargo-inputs
+ (("rust-chrono" ,rust-chrono-0.4)
+ ("rust-failure" ,rust-failure-0.1)
+ ("rust-reqwest" ,rust-reqwest-0.11)
+ ("rust-serde" ,rust-serde-1)
+ ("rust-serde-derive" ,rust-serde-derive-1)
+ ("rust-serde-json" ,rust-serde-json-1)
+ ("rust-url" ,rust-url-2))
+ #:cargo-development-inputs
+ (("rust-dotenv" ,rust-dotenv-0.15)
+ ("rust-rand" ,rust-rand-0.8)
+ ("rust-tokio" ,rust-tokio-1))))
+ (native-inputs
+ `(("pkg-config" ,pkg-config)))
+ (inputs
+ `(("openssl" ,openssl)))
+ (home-page "https://gitlab.com/news-flash/feedbin_api")
+ (synopsis "Rust implementation of the Feedbin REST API")
+ (description
+ "This package provides a Rust implementation of the Feedbin REST API.")
+ (license license:unlicense)))
+
+(define-public rust-feedly-api-0.4
+ (package
+ (name "rust-feedly-api")
+ (version "0.4.7")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "feedly-api" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "1knad1bghc8hhfcyl35fcnhrk01vklamq07630rdk0pg6ax04swi"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:tests? #f ;tests open external connections
+ #:cargo-inputs
+ (("rust-chrono" ,rust-chrono-0.4)
+ ("rust-failure" ,rust-failure-0.1)
+ ("rust-log" ,rust-log-0.4)
+ ("rust-percent-encoding"
+ ,rust-percent-encoding-2)
+ ("rust-reqwest" ,rust-reqwest-0.11)
+ ("rust-serde" ,rust-serde-1)
+ ("rust-serde-derive" ,rust-serde-derive-1)
+ ("rust-serde-json" ,rust-serde-json-1)
+ ("rust-url" ,rust-url-2))
+ #:cargo-development-inputs
+ (("rust-dotenv" ,rust-dotenv-0.15)
+ ("rust-tokio" ,rust-tokio-1))))
+ (native-inputs
+ `(("pkg-config" ,pkg-config)))
+ (inputs
+ `(("openssl" ,openssl)))
+ (home-page "https://gitlab.com/news-flash/feedly_api")
+ (synopsis "Rust implementation of the feedly REST API")
+ (description
+ "This package provides a Rust implementation of the feedly REST API.")
+ ;; No copyright headers in the source code. LICENSE indicates gpl3.
+ (license license:gpl3)))
+
(define-public rust-femme-2
(package
(name "rust-femme")
@@ -16833,6 +17494,43 @@ descriptors limit.")
(("rust-clap" ,rust-clap-2)
("rust-tempdir" ,rust-tempdir-0.3))))))
+(define-public rust-fever-api-0.2
+ (package
+ (name "rust-fever-api")
+ (version "0.2.11")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "fever-api" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "0pv4g241pc0bfwy9gjwsmrdv7mplzbifxr5mxf0k82yxawg55anc"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:tests? #f ;tests use the network
+ #:cargo-inputs
+ (("rust-failure" ,rust-failure-0.1)
+ ("rust-log" ,rust-log-0.4)
+ ("rust-md5" ,rust-md5-0.7)
+ ("rust-reqwest" ,rust-reqwest-0.11)
+ ("rust-serde" ,rust-serde-1)
+ ("rust-serde-json" ,rust-serde-json-1)
+ ("rust-url" ,rust-url-2))
+ #:cargo-development-inputs
+ (("rust-dotenv" ,rust-dotenv-0.15)
+ ("rust-tokio" ,rust-tokio-1))))
+ (native-inputs
+ `(("pkg-config" ,pkg-config)))
+ (inputs
+ `(("openssl" ,openssl)))
+ (home-page "https://gitlab.com/news-flash/fever_api")
+ (synopsis "Rust implementation of the Fever API")
+ (description
+ "This packages provides a Rust implementation of the Fever API.")
+ ;; No copyright headers in the source code. LICENSE indicates gpl3.
+ (license license:gpl3)))
+
(define-public rust-filesize-0.2
(package
(name "rust-filesize")
@@ -20661,6 +21359,26 @@ the template engine that renders the official Rust website")
"This package provides a Rust implementation of VG handle graph.")
(license license:expat)))
+(define-public rust-hash-hasher-2
+ (package
+ (name "rust-hash-hasher")
+ (version "2.0.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "hash_hasher" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "034cd4m3znwff3cd1i54c40944y999jz086d70rwpl0jfl01swkl"))))
+ (build-system cargo-build-system)
+ (arguments `(#:skip-build? #t))
+ (home-page "https://github.com/Fraser999/Hash-Hasher.git")
+ (synopsis "Hasher designed to work with already-hashed or hash-like data")
+ (description
+ "This package provides a hasher which is designed to work with
+already-hashed or hash-like data.")
+ (license (list license:asl2.0 license:expat))))
+
(define-public rust-hash32-0.1
(package
(name "rust-hash32")
@@ -23173,24 +23891,24 @@ data efficiently.")
that works on WASM too.")
(license license:bsd-3)))
-(define-public rust-integer-encoding-1
+(define-public rust-integer-encoding-3
(package
(name "rust-integer-encoding")
- (version "1.2.2")
+ (version "3.0.2")
(source
(origin
(method url-fetch)
(uri (crate-uri "integer-encoding" version))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
- (base32 "1c032xhif5d6a8nc4cak60g5ylwd6p9569122m5hm67brx2l5yhb"))))
+ (base32 "1f0mk7d694g2sz4my5zh7i5w4kijx5y16x6dip7fv0pazx013hch"))))
(build-system cargo-build-system)
(arguments
`(#:skip-build? #t
#:cargo-inputs
(("rust-async-trait" ,rust-async-trait-0.1)
("rust-futures-util" ,rust-futures-util-0.3)
- ("rust-tokio" ,rust-tokio-0.2))))
+ ("rust-tokio" ,rust-tokio-1))))
(home-page "https://github.com/dermesser/integer-encoding-rs")
(synopsis "Encoding and decoding integers to and from bytestrings")
(description
@@ -23198,6 +23916,25 @@ that works on WASM too.")
bytestring representations.")
(license license:expat)))
+(define-public rust-integer-encoding-1
+ (package
+ (inherit rust-integer-encoding-3)
+ (name "rust-integer-encoding")
+ (version "1.2.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "integer-encoding" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "1c032xhif5d6a8nc4cak60g5ylwd6p9569122m5hm67brx2l5yhb"))))
+ (arguments
+ `(#:skip-build? #t
+ #:cargo-inputs
+ (("rust-async-trait" ,rust-async-trait-0.1)
+ ("rust-futures-util" ,rust-futures-util-0.3)
+ ("rust-tokio" ,rust-tokio-0.2))))))
+
(define-public rust-interpolate-name-0.2
(package
(name "rust-interpolate-name")
@@ -23906,27 +24643,46 @@ primitives to an @code{io::Write}.")
(native-inputs
`(("jemalloc" ,jemalloc)))))
-(define-public rust-jetscii-0.3
+(define-public rust-jetscii-0.5
(package
(name "rust-jetscii")
- (version "0.3.1")
+ (version "0.5.0")
(source
(origin
(method url-fetch)
(uri (crate-uri "jetscii" version))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
- (base32 "1sq6d6c9vi44gkr566w2f1d4n6mmrjx8gjdwgnhkgcsg051j391j"))))
+ (base32 "1x4z5ixlxv1wa70d3d6ad3n8qxz6z00i13zwnv219v45qcwybbnb"))))
(build-system cargo-build-system)
- (arguments `(#:skip-build? #t))
+ (arguments
+ `(#:rust ,rust-1.52 ; fix for E0658
+ #:cargo-development-inputs
+ (("rust-lazy-static" ,rust-lazy-static-1)
+ ("rust-memmap" ,rust-memmap-0.7)
+ ("rust-proptest" ,rust-proptest-1)
+ ("rust-region" ,rust-region-2))))
(home-page "https://github.com/shepmaster/jetscii")
(synopsis
"Search strings and byte slices for sets of ASCII characters or bytes")
- (description
- "This package provides a tiny library to efficiently search strings and
-byte slices for sets of ASCII characters or bytes.")
+ (description "This package provides a tiny library to efficiently search
+strings and byte slices for sets of ASCII characters or bytes.")
(license license:expat)))
+(define-public rust-jetscii-0.3
+ (package
+ (inherit rust-jetscii-0.5)
+ (name "rust-jetscii")
+ (version "0.3.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "jetscii" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "1sq6d6c9vi44gkr566w2f1d4n6mmrjx8gjdwgnhkgcsg051j391j"))))
+ (arguments `(#:skip-build? #t))))
+
(define-public rust-jni-0.18
(package
(name "rust-jni")
@@ -24706,8 +25462,36 @@ requires non-const function calls to be computed.")
sending emails from Rust applications.")
(license license:expat)))
+(define-public rust-lexical-core-0.8
+ (package
+ (name "rust-lexical-core")
+ (version "0.8.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "lexical-core" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "1152ll9xa7v4jz2mjvz0048gy32yg39mzgjaps89h0any7c2cfba"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:skip-build? #t
+ #:cargo-inputs
+ (("rust-lexical-parse-float" ,rust-lexical-parse-float-0.8)
+ ("rust-lexical-parse-integer" ,rust-lexical-parse-integer-0.8)
+ ("rust-lexical-util" ,rust-lexical-util-0.8)
+ ("rust-lexical-write-float" ,rust-lexical-write-float-0.8)
+ ("rust-lexical-write-integer" ,rust-lexical-write-integer-0.8))))
+ (home-page
+ "https://github.com/Alexhuszagh/rust-lexical/tree/master/lexical-core")
+ (synopsis "Lexical, to- and from-string conversion routines")
+ (description
+ "This crate provides lexical, to- and from-string conversion routines.")
+ (license (list license:expat license:asl2.0))))
+
(define-public rust-lexical-core-0.7
(package
+ (inherit rust-lexical-core-0.8)
(name "rust-lexical-core")
(version "0.7.6")
(source
@@ -24718,7 +25502,6 @@ sending emails from Rust applications.")
(string-append name "-" version ".tar.gz"))
(sha256
(base32 "1zjzab1fnaw4kj6ixyrskp4dyz761gdcab07m4bkvlk1l4mcc1v6"))))
- (build-system cargo-build-system)
(arguments
`(#:cargo-inputs
(("rust-arrayvec" ,rust-arrayvec-0.5)
@@ -24731,14 +25514,7 @@ sending emails from Rust applications.")
#:cargo-development-inputs
(("rust-approx" ,rust-approx-0.4)
("rust-proptest" ,rust-proptest-0.10)
- ("rust-quickcheck" ,rust-quickcheck-1))))
- (home-page
- "https://github.com/Alexhuszagh/rust-lexical/tree/master/lexical-core")
- (synopsis
- "Lexical, to- and from-string conversion routines")
- (description
- "Lexical, to- and from-string conversion routines.")
- (license (list license:expat license:asl2.0))))
+ ("rust-quickcheck" ,rust-quickcheck-1))))))
(define-public rust-lexical-core-0.4
(package
@@ -24768,8 +25544,148 @@ sending emails from Rust applications.")
("rust-quickcheck" ,rust-quickcheck-0.8)
("rust-rustc-version" ,rust-rustc-version-0.2))))))
+(define-public rust-lexical-parse-float-0.8
+ (package
+ (name "rust-lexical-parse-float")
+ (version "0.8.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "lexical-parse-float" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "03mzjx8k2jzv2vbl1xb589p9zfs5i2m23vcmm6fjsxps0k86dl5l"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:skip-build? #t
+ #:cargo-inputs
+ (("rust-lexical-parse-integer" ,rust-lexical-parse-integer-0.8)
+ ("rust-lexical-util" ,rust-lexical-util-0.8)
+ ("rust-static-assertions" ,rust-static-assertions-1))))
+ (home-page "https://github.com/Alexhuszagh/rust-lexical")
+ (synopsis "Efficient parsing of floats from strings")
+ (description
+ "This crate provides efficient parsing of floats from strings.")
+ (license (list license:expat license:asl2.0))))
+
+(define-public rust-lexical-parse-integer-0.8
+ (package
+ (name "rust-lexical-parse-integer")
+ (version "0.8.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "lexical-parse-integer" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "1b2kxprq3636x3j1qy68202q7yzsmq5c7h9w7m7zrh4cvanjpjgj"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:skip-build? #t
+ #:cargo-inputs
+ (("rust-lexical-util" ,rust-lexical-util-0.8)
+ ("rust-static-assertions" ,rust-static-assertions-1))))
+ (home-page "https://github.com/Alexhuszagh/rust-lexical")
+ (synopsis "Efficient parsing of integers from strings")
+ (description
+ "This crate provides efficient parsing of integers from strings.")
+ (license (list license:expat license:asl2.0))))
+
+(define-public rust-lexical-util-0.8
+ (package
+ (name "rust-lexical-util")
+ (version "0.8.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "lexical-util" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "14g224mm2li0q6jnnqh92dzx3zjyflji3i8dz4xf6vp1mb66kxkg"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:skip-build? #t
+ #:cargo-inputs
+ (("rust-static-assertions" ,rust-static-assertions-1))))
+ (home-page "https://github.com/Alexhuszagh/rust-lexical")
+ (synopsis "Shared utilities for lexical crate")
+ (description "This package provides shared utilities for lexical crate.")
+ (license (list license:expat license:asl2.0))))
+
+(define-public rust-lexical-write-float-0.8
+ (package
+ (name "rust-lexical-write-float")
+ (version "0.8.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "lexical-write-float" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "0xn5dpdmld2nvj7jvz3xrvjjbrnsh4jhymjimax7labvija8clcb"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:skip-build? #t
+ #:cargo-inputs
+ (("rust-lexical-util" ,rust-lexical-util-0.8)
+ ("rust-lexical-write-integer" ,rust-lexical-write-integer-0.8)
+ ("rust-static-assertions" ,rust-static-assertions-1))))
+ (home-page "https://github.com/Alexhuszagh/rust-lexical")
+ (synopsis "Efficient formatting of floats to strings")
+ (description
+ "This crate provides efficient formatting of floats to strings.")
+ (license (list license:expat license:asl2.0))))
+
+(define-public rust-lexical-write-integer-0.8
+ (package
+ (name "rust-lexical-write-integer")
+ (version "0.8.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "lexical-write-integer" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "1vsn3zg2hyqnyapwmzb2aw0w5f53ad6s6n46xyazsh0f5r4mdsgc"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:skip-build? #t
+ #:cargo-inputs
+ (("rust-lexical-util" ,rust-lexical-util-0.8)
+ ("rust-static-assertions" ,rust-static-assertions-1))))
+ (home-page "https://github.com/Alexhuszagh/rust-lexical")
+ (synopsis "Efficient formatting of integers to strings")
+ (description
+ "This crate provides efficient formatting of integers to strings.")
+ (license (list license:expat license:asl2.0))))
+
+(define-public rust-lexical-6
+ (package
+ (name "rust-lexical")
+ (version "6.0.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "lexical" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "1y8v2s8g2hjinwf5hbm1ncbazw9q4qbp111q2mwacq6hi0grhkn3"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:skip-build? #t
+ #:cargo-inputs
+ (("rust-lexical-core" ,rust-lexical-core-0.8))))
+ (home-page "https://github.com/Alexhuszagh/rust-lexical")
+ (synopsis "Lexical, to- and from-string conversion routines")
+ (description
+ "Lexical is high-performance numeric conversion routines for use in
+a no_std environment. This does not depend on any standard library features,
+nor a system allocator.")
+ (license (list license:expat license:asl2.0))))
+
(define-public rust-lexical-5
(package
+ (inherit rust-lexical-6)
(name "rust-lexical")
(version "5.2.2")
(source
@@ -24779,7 +25695,6 @@ sending emails from Rust applications.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32 "1r8lsi523h53kbb99xgv31jabwhcp4rzqd4hfazfhcjffh5aj17l"))))
- (build-system cargo-build-system)
(arguments
`(#:skip-build? #t
#:cargo-inputs
@@ -24788,13 +25703,7 @@ sending emails from Rust applications.")
("rust-rand" ,rust-rand-0.4)
("rust-serde" ,rust-serde-1)
("rust-serde-derive" ,rust-serde-derive-1)
- ("rust-toml" ,rust-toml-0.5))))
- (home-page "https://github.com/Alexhuszagh/rust-lexical")
- (synopsis "Lexical, to- and from-string conversion routines")
- (description
- "Lexical provides routines to convert numbers to and from decimal
-strings.")
- (license (list license:expat license:asl2.0))))
+ ("rust-toml" ,rust-toml-0.5))))))
(define-public rust-libc-0.2
(package
@@ -25316,6 +26225,77 @@ file.
@end itemize")
(license license:gpl2+)))
+;; https://github.com/jnqnfe/pulse-binding-rust/blob/c788a8069f455f864d2ba5f0aa5f62e6648dfd26/pulse-sys/build.rs
+;; fix location of pulseaudio
+(define-public rust-libpulse-binding-2
+ (package
+ (name "rust-libpulse-binding")
+ (version "2.23.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "libpulse-binding" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1qx85j489mmad9cvw5k71271l3qy4s8a5qq8a9wac6cfi4viz5fv"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:cargo-inputs
+ (("rust-bitflags" ,rust-bitflags-1)
+ ("rust-libc" ,rust-libc-0.2)
+ ("rust-libpulse-sys" ,rust-libpulse-sys-1)
+ ("rust-num-derive" ,rust-num-derive-0.3)
+ ("rust-num-traits" ,rust-num-traits-0.2)
+ ("rust-winapi" ,rust-winapi-0.3))
+ #:phases
+ (modify-phases %standard-phases
+ (add-before 'check 'set-HOME
+ (lambda _ (setenv "HOME" "/tmp") #t)))))
+ (native-inputs
+ `(("pkg-config" ,pkg-config)))
+ (inputs
+ `(("pulseaudio" ,pulseaudio)))
+ (home-page "https://github.com/jnqnfe/pulse-binding-rust")
+ (synopsis "Binding for the PulseAudio libpulse library")
+ (description
+ "This package provides a Rust language binding for the PulseAudio libpulse
+library.")
+ (license (list license:expat license:asl2.0))))
+
+(define-public rust-libpulse-sys-1
+ (package
+ (name "rust-libpulse-sys")
+ (version "1.18.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "libpulse-sys" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "10msfr8f951v86ag0fl2bsm4a3siq2r7hz9bqhhg7i234s1yj5yg"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:cargo-inputs
+ (("rust-libc" ,rust-libc-0.2)
+ ("rust-num-derive" ,rust-num-derive-0.3)
+ ("rust-num-traits" ,rust-num-traits-0.2)
+ ("rust-pkg-config" ,rust-pkg-config-0.3)
+ ("rust-winapi" ,rust-winapi-0.3))))
+ (native-inputs
+ `(("pkg-config" ,pkg-config)))
+ (inputs
+ `(("pulseaudio" ,pulseaudio)))
+ (home-page "https://github.com/jnqnfe/pulse-binding-rust")
+ (synopsis "FFI bindings for the PulseAudio")
+ (description
+ "This package provides FFI bindings for the PulseAudio libpulse system
+library.")
+ (license (list license:expat license:asl2.0))))
+
(define-public rust-libsqlite3-sys-0.22
(package
(name "rust-libsqlite3-sys")
@@ -25425,6 +26405,51 @@ file.
("rust-pkg-config" ,rust-pkg-config-0.3)
("rust-vcpkg" ,rust-vcpkg-0.2))))))
+(define-public rust-libxml-0.3
+ (package
+ (name "rust-libxml")
+ (version "0.3.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "libxml" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "1f42qrc1mim85ivh2d4bn2wbqrn7dfg1i3l1q32yajcr835pxh02"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:cargo-inputs
+ (("rust-libc" ,rust-libc-0.2)
+ ("rust-pkg-config" ,rust-pkg-config-0.3)
+ ("rust-vcpkg" ,rust-vcpkg-0.2))
+ #:cargo-development-inputs
+ (("rust-criterion" ,rust-criterion-0.3)
+ ("rust-rayon" ,rust-rayon-1))))
+ (native-inputs
+ `(("pkg-config" ,pkg-config)))
+ (inputs
+ `(("libxml2" ,libxml2)))
+ (home-page "https://github.com/KWARC/rust-libxml")
+ (synopsis "Rust wrapper for libxml2")
+ (description "This package provides a Rust wrapper for libxml2, the XML
+C parser and toolkit developed for the GNOME project.")
+ (license license:expat)))
+
+(define-public rust-libxml-0.2
+ (package
+ (inherit rust-libxml-0.3)
+ (name "rust-libxml")
+ (version "0.2.17")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "libxml" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "1z567rqb55hxn0g7hpvcsh3nfvz9mdzlwk4mk179z9bkf7v10r29"))))))
+
(define-public rust-libz-sys-1
(package
(name "rust-libz-sys")
@@ -25932,6 +26957,74 @@ by inspecting the system for user preference.")
`(#:cargo-inputs
(("rust-log" ,rust-log-0.4))))))
+(define-public rust-log-mdc-0.1
+ (package
+ (name "rust-log-mdc")
+ (version "0.1.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "log-mdc" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "1iw1x3qhjvrac35spikn5h06a1rxd9vw216jk8h52jhz9i0j2kd9"))))
+ (build-system cargo-build-system)
+ (home-page "https://github.com/sfackler/rust-log-mdc")
+ (synopsis "Mapped diagnostic context (MDC) for use with the `log` crate")
+ (description "This package provides a mapped diagnostic context (MDC) for
+use with the `log` crate.")
+ (license (list license:expat license:asl2.0))))
+
+(define-public rust-log4rs-1
+ (package
+ (name "rust-log4rs")
+ (version "1.0.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "log4rs" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "04d21kkb6if7hly0syp64m15a9695fpfgvlnff3gy58i1n42lmyi"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:tests? #f ; 37 passed, 1 failed
+ #:cargo-inputs
+ (("rust-anyhow" ,rust-anyhow-1)
+ ("rust-arc-swap" ,rust-arc-swap-0.4)
+ ("rust-chrono" ,rust-chrono-0.4)
+ ("rust-derivative" ,rust-derivative-2)
+ ("rust-flate2" ,rust-flate2-1)
+ ("rust-fnv" ,rust-fnv-1)
+ ("rust-humantime" ,rust-humantime-2)
+ ("rust-libc" ,rust-libc-0.2)
+ ("rust-log" ,rust-log-0.4)
+ ("rust-log-mdc" ,rust-log-mdc-0.1)
+ ("rust-parking-lot" ,rust-parking-lot-0.11)
+ ("rust-regex" ,rust-regex-1)
+ ("rust-serde" ,rust-serde-1)
+ ("rust-serde-value" ,rust-serde-value-0.7)
+ ("rust-serde-json" ,rust-serde-json-1)
+ ("rust-serde-yaml" ,rust-serde-yaml-0.8)
+ ("rust-thiserror" ,rust-thiserror-1)
+ ("rust-thread-id" ,rust-thread-id-3)
+ ("rust-toml" ,rust-toml-0.5)
+ ("rust-typemap" ,rust-typemap-0.3)
+ ("rust-winapi" ,rust-winapi-0.3))
+ #:cargo-development-inputs
+ (("rust-humantime" ,rust-humantime-2)
+ ("rust-lazy-static" ,rust-lazy-static-1)
+ ("rust-streaming-stats"
+ ,rust-streaming-stats-0.2)
+ ("rust-tempfile" ,rust-tempfile-3))))
+ (home-page "https://github.com/estk/log4rs")
+ (synopsis "Highly configurable logging implementation")
+ (description "This package provides a highly configurable multi-output
+logging implementation for the `log` facade.")
+ (license (list license:expat license:asl2.0))))
+
(define-public rust-logtest-2
(package
(name "rust-logtest")
@@ -26479,6 +27572,39 @@ Mach 3.0 kernel that underlies OSX.")
library")
(license (list license:asl2.0 license:expat))))
+(define-public rust-magic-crypt-3
+ (package
+ (name "rust-magic-crypt")
+ (version "3.1.8")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "magic-crypt" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "1jb4m8wqxm2qkg9gcflxa0sg1d33a1a0r876h47njg43h494zjfk"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:cargo-inputs
+ (("rust-aes-soft" ,rust-aes-soft-0.6)
+ ("rust-base64" ,rust-base64-0.13)
+ ("rust-block-modes" ,rust-block-modes-0.7)
+ ("rust-crc-any" ,rust-crc-any-2)
+ ("rust-des" ,rust-des-0.6)
+ ("rust-digest" ,rust-digest-0.9)
+ ("rust-md-5" ,rust-md-5-0.9)
+ ("rust-sha2" ,rust-sha2-0.9)
+ ("rust-tiger" ,rust-tiger-0.1))))
+ (home-page "https://magiclen.org/aes")
+ (synopsis "Library for DES or AES encryption")
+ (description
+ "MagicCrypt is a library to encrypt/decrypt strings, files, or data,
+using Data Encryption Standard(DES) or Advanced Encryption Standard(AES)
+algorithms. It supports CBC block cipher mode, PKCS5 padding and 64, 128,
+192 or 256-bits key length.")
+ (license license:asl2.0)))
+
(define-public rust-maildir-0.5
(package
(name "rust-maildir")
@@ -27608,6 +28734,63 @@ quality, high performance hash algorithm.")
"This package provides a simple math expression parser and evaluator.")
(license (list license:unlicense license:expat))))
+(define-public rust-migrations-internals-1
+ (package
+ (name "rust-migrations-internals")
+ (version "1.4.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "migrations_internals" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "0q2qk4jpa16mcfcmhjz6hdg2s73az1k7j0cy08vvh87h997chkrb"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:cargo-inputs
+ (("rust-barrel" ,rust-barrel-0.6)
+ ("rust-diesel" ,rust-diesel-1))
+ #:cargo-development-inputs
+ (("rust-tempdir" ,rust-tempdir-0.3))))
+ (home-page "https://diesel.rs")
+ (synopsis "Internal implementation of Diesel's migration mechanism")
+ (description "This package provides an internal implementation of Diesel's
+migration mechanism.")
+ (license (list license:expat license:asl2.0))))
+
+(define-public rust-migrations-macros-1
+ (package
+ (name "rust-migrations-macros")
+ (version "1.4.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "migrations_macros" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "173qgwans6n2jf6b7qajq273rvg1r9c34p5fflzr53gx14lz2lwp"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:cargo-inputs
+ (("rust-migrations-internals"
+ ,rust-migrations-internals-1)
+ ("rust-proc-macro2" ,rust-proc-macro2-1)
+ ("rust-quote" ,rust-quote-1)
+ ("rust-syn" ,rust-syn-1))
+ #:cargo-development-inputs
+ (("rust-tempdir" ,rust-tempdir-0.3))))
+ (native-inputs
+ `(("pkg-config" ,pkg-config)))
+ (inputs
+ `(("sqlite" ,sqlite)))
+ (home-page "https://diesel.rs")
+ (synopsis "Code generation macros for Diesel's embedded migrations")
+ (description "This package provides code generation macros for Diesel's
+embedded migrations.")
+ (license (list license:expat license:asl2.0))))
+
(define-public rust-mimalloc-0.1
(package
(name "rust-mimalloc")
@@ -27716,6 +28899,44 @@ file's MIME type by its extension.")
("rust-phf-codegen" ,rust-phf-codegen-0.7)
("rust-unicase" ,rust-unicase-1))))))
+(define-public rust-miniflux-api-0.3
+ (package
+ (name "rust-miniflux-api")
+ (version "0.3.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "miniflux-api" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "0r0bd907v2abv40i0c0xaj87ik4w9d3syn1f4byy0ssv55dw7mdq"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:tests? #f ;tests use the network
+ #:cargo-inputs
+ (("rust-base64" ,rust-base64-0.13)
+ ("rust-failure" ,rust-failure-0.1)
+ ("rust-log" ,rust-log-0.4)
+ ("rust-reqwest" ,rust-reqwest-0.11)
+ ("rust-serde" ,rust-serde-1)
+ ("rust-serde-derive" ,rust-serde-derive-1)
+ ("rust-serde-json" ,rust-serde-json-1)
+ ("rust-url" ,rust-url-2))
+ #:cargo-development-inputs
+ (("rust-dotenv" ,rust-dotenv-0.15)
+ ("rust-tokio" ,rust-tokio-1))))
+ (native-inputs
+ `(("pkg-config" ,pkg-config)))
+ (inputs
+ `(("openssl" ,openssl)))
+ (home-page "https://gitlab.com/news-flash/miniflux_api")
+ (synopsis "Rust implementation of the Miniflux REST API")
+ (description
+ "This package provides a Rust implementation of the Miniflux REST API.")
+ ;; No copyright headers in the source code. LICENSE indicates gpl3.
+ (license license:gpl3)))
+
(define-public rust-minimal-lexical-0.1
(package
(name "rust-minimal-lexical")
@@ -29410,6 +30631,113 @@ cryptographic library.")
release (fork of debug_unreachable)")
(license license:expat)))
+(define-public rust-news-flash-1
+ (package
+ (name "rust-news-flash")
+ (version "1.2.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "news-flash" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "0r3hz725kblxr6mhl8rkf2bffzmyya0ib3xr3jk5zm8x2jlpvlq6"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:rust ,rust-1.52 ; some inputs fail with E0658
+ #:tests? #f ; FIXME: "error reading DNS system conf" from reqwest
+ #:cargo-inputs
+ (("rust-article-scraper" ,rust-article-scraper-1)
+ ("rust-async-trait" ,rust-async-trait-0.1)
+ ("rust-base64" ,rust-base64-0.13)
+ ("rust-bitflags" ,rust-bitflags-1)
+ ("rust-bytes" ,rust-bytes-1)
+ ("rust-chrono" ,rust-chrono-0.4)
+ ("rust-diesel" ,rust-diesel-1)
+ ("rust-diesel-migrations"
+ ,rust-diesel-migrations-1)
+ ("rust-escaper" ,rust-escaper-0.1)
+ ("rust-failure" ,rust-failure-0.1)
+ ("rust-feed-rs" ,rust-feed-rs-0.6)
+ ("rust-feedbin-api" ,rust-feedbin-api-0.1)
+ ("rust-feedly-api" ,rust-feedly-api-0.4)
+ ("rust-fever-api" ,rust-fever-api-0.2)
+ ("rust-futures" ,rust-futures-0.3)
+ ("rust-hmac" ,rust-hmac-0.11)
+ ("rust-image" ,rust-image-0.23)
+ ("rust-itertools" ,rust-itertools-0.10)
+ ("rust-lazy-static" ,rust-lazy-static-1)
+ ("rust-libxml" ,rust-libxml-0.3)
+ ("rust-log" ,rust-log-0.4)
+ ("rust-magic-crypt" ,rust-magic-crypt-3)
+ ("rust-mime" ,rust-mime-0.3)
+ ("rust-mime-guess" ,rust-mime-guess-2)
+ ("rust-miniflux-api" ,rust-miniflux-api-0.3)
+ ("rust-newsblur-api" ,rust-newsblur-api-0.1)
+ ("rust-obfstr" ,rust-obfstr-0.3)
+ ("rust-opml" ,rust-opml-1)
+ ("rust-parking-lot" ,rust-parking-lot-0.11)
+ ("rust-rayon" ,rust-rayon-1)
+ ("rust-regex" ,rust-regex-1)
+ ("rust-reqwest" ,rust-reqwest-0.11)
+ ("rust-rust-embed" ,rust-rust-embed-5)
+ ("rust-serde" ,rust-serde-1)
+ ("rust-serde-derive" ,rust-serde-derive-1)
+ ("rust-serde-json" ,rust-serde-json-1)
+ ("rust-sha-1" ,rust-sha-1-0.9)
+ ("rust-url" ,rust-url-2))
+ #:cargo-development-inputs
+ (("rust-tempfile" ,rust-tempfile-3)
+ ("rust-tokio" ,rust-tokio-1))))
+ (native-inputs
+ `(("pkg-config" ,pkg-config)))
+ (inputs
+ `(("libxml2" ,libxml2)
+ ("openssl" ,openssl)
+ ("sqlite" ,sqlite)))
+ (home-page "https://gitlab.com/news-flash/news_flash")
+ (synopsis "Base library for NewsFlash")
+ (description "This package provides the base library for the NewsFlash
+feed reader.")
+ ;; No copyright headers in the source code. LICENSE indicates gpl3.
+ (license license:gpl3)))
+
+(define-public rust-newsblur-api-0.1
+ (package
+ (name "rust-newsblur-api")
+ (version "0.1.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "newsblur_api" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "1lh5njrrk4fjc168npk1q3962dzsgmvz4fzvha46g9b83cf3jxzx"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:tests? #f ;tests use the network
+ #:cargo-inputs
+ (("rust-failure" ,rust-failure-0.1)
+ ("rust-reqwest" ,rust-reqwest-0.11)
+ ("rust-serde" ,rust-serde-1)
+ ("rust-serde-json" ,rust-serde-json-1)
+ ("rust-url" ,rust-url-2))
+ #:cargo-development-inputs
+ (("rust-dotenv" ,rust-dotenv-0.15)
+ ("rust-tokio" ,rust-tokio-1))))
+ (native-inputs
+ `(("pkg-config" ,pkg-config)))
+ (inputs
+ `(("openssl" ,openssl)))
+ (home-page "https://gitlab.com/news-flash/newsblur_api/")
+ (synopsis "Rust implementation of the NewsBlur API")
+ (description
+ "This package provides a Rust implementation of the NewsBlur API.")
+ ;; No copyright headers in the source code. LICENSE indicates gpl3.
+ (license license:gpl3)))
+
(define-public rust-nibble-vec-0.1
(package
(name "rust-nibble-vec")
@@ -31147,6 +32475,28 @@ giga, kibi.")
"This package can convert numbers into stack-allocated byte arrays.")
(license (list license:expat license:asl2.0))))
+(define-public rust-obfstr-0.3
+ (package
+ (name "rust-obfstr")
+ (version "0.3.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "obfstr" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "0y5azgk8ds43m1sd5pc4hhakxzxkfcfscl24y8gsbvwdznxjqavv"))))
+ (arguments
+ `(#:rust ,rust-1.52)) ; fix for E0658
+ (build-system cargo-build-system)
+ (home-page "https://github.com/CasualX/obfstr")
+ (synopsis "Compile time string constant obfuscation for Rust")
+ (description "This package provides a compile time string constant
+obfuscation for Rust. The string constant itself is embedded in obfuscated
+form and deobfuscated locally.")
+ (license license:expat)))
+
(define-public rust-obj-0.9
(package
(name "rust-obj")
@@ -31936,6 +33286,31 @@ system for OpenSSL.")
"Extra FFI bindings to OpenSSL that require a C shim.")
(license license:expat)))
+(define-public rust-opml-1
+ (package
+ (name "rust-opml")
+ (version "1.1.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "opml" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "0zr7f101inkz3rknl0r3q0qkklfxhqrji7yxmqixajfn3m5mbjfa"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:rust ,rust-1.52 ; fix for E0658
+ #:cargo-inputs
+ (("rust-regex" ,rust-regex-1)
+ ("rust-serde" ,rust-serde-1)
+ ("rust-strong-xml" ,rust-strong-xml-0.6)
+ ("rust-thiserror" ,rust-thiserror-1))))
+ (home-page "https://github.com/Holllo/opml")
+ (synopsis "OPML parser for Rust")
+ (description "This package provides an OPML parser for Rust.")
+ (license (list license:expat license:asl2.0))))
+
(define-public rust-ord-subset-3
(package
(name "rust-ord-subset")
@@ -32900,6 +34275,65 @@ synchronization primitives.")
file and the generated @file{.rs} file.")
(license license:asl2.0)))
+(define-public rust-parquet-format-async-temp-0.2
+ (package
+ (name "rust-parquet-format-async-temp")
+ (version "0.2.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "parquet-format-async-temp" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "0i7mn4x64d8g6d046y9kpb55dz8v0z67cz7lhgncxs9zr3ww5aq3"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:skip-build? #t
+ #:cargo-inputs
+ (("rust-async-trait" ,rust-async-trait-0.1)
+ ("rust-byteorder" ,rust-byteorder-1)
+ ("rust-futures" ,rust-futures-0.3)
+ ("rust-integer-encoding" ,rust-integer-encoding-3)
+ ("rust-ordered-float" ,rust-ordered-float-1))))
+ (home-page "https://github.com/sunchao/parquet-format-rs")
+ (synopsis "Temporary crate containing thrift library + parquet definitions")
+ (description
+ "This is a temporary crate containing thrift library and parquet
+definitions compiled to support read+write async.")
+ (license license:asl2.0)))
+
+(define-public rust-parquet2-0.4
+ (package
+ (name "rust-parquet2")
+ (version "0.4.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "parquet2" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "1rsmrjy0r8q56gygycc5j0kgdbvrazh6xg6z8vcdyhn8r1v8yxbk"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:skip-build? #t
+ #:cargo-inputs
+ (("rust-async-stream" ,rust-async-stream-0.3)
+ ("rust-bitpacking" ,rust-bitpacking-0.8)
+ ("rust-brotli" ,rust-brotli-3)
+ ("rust-flate2" ,rust-flate2-1)
+ ("rust-futures" ,rust-futures-0.3)
+ ("rust-lz4" ,rust-lz4-1)
+ ("rust-parquet-format-async-temp" ,rust-parquet-format-async-temp-0.2)
+ ("rust-snap" ,rust-snap-1)
+ ("rust-streaming-iterator" ,rust-streaming-iterator-0.1)
+ ("rust-zstd" ,rust-zstd-0.9))))
+ (home-page "https://crates.io/crates/parquet2")
+ (synopsis "Safe implementation of Parquet IO")
+ (description
+ "Parquet2 is a re-write of the official Parquet crate with performance,
+parallelism and safety in mind.")
+ (license license:asl2.0)))
+
(define-public rust-parse-zoneinfo-0.3
(package
(name "rust-parse-zoneinfo")
@@ -34502,30 +35936,49 @@ applications.")
"Additional trait for Read and Write to read and write Plain Old Data.")
(license (list license:expat license:asl2.0))))
-(define-public rust-polars-0.15
+(define-public rust-polars-0.16
(package
(name "rust-polars")
- (version "0.15.1")
+ (version "0.16.0")
(source
(origin
(method url-fetch)
(uri (crate-uri "polars" version))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
- (base32 "1sl7vs6ck05f8w8jp7v75431b4v5j2rvvvw53jqgxc5226i7a2h8"))))
+ (base32 "1s4fqc3vlpz73dbagfsj3hx7y7xmpqnp7nj0cn9srijxgxq5nm73"))))
(build-system cargo-build-system)
(arguments
`(#:skip-build? #t
#:cargo-inputs
- (("rust-polars-core" ,rust-polars-core-0.15)
- ("rust-polars-io" ,rust-polars-io-0.15)
- ("rust-polars-lazy" ,rust-polars-lazy-0.15))))
+ (("rust-polars-core" ,rust-polars-core-0.16)
+ ("rust-polars-io" ,rust-polars-io-0.16)
+ ("rust-polars-lazy" ,rust-polars-lazy-0.16))))
(home-page "https://github.com/ritchie46/polars")
(synopsis "DataFrame Library based on Apache Arrow")
(description
"Polars is a dataframe Library based on Apache Arrow.")
(license license:expat)))
+(define-public rust-polars-0.15
+ (package
+ (inherit rust-polars-0.16)
+ (name "rust-polars")
+ (version "0.15.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "polars" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "1sl7vs6ck05f8w8jp7v75431b4v5j2rvvvw53jqgxc5226i7a2h8"))))
+ (arguments
+ `(#:skip-build? #t
+ #:cargo-inputs
+ (("rust-polars-core" ,rust-polars-core-0.15)
+ ("rust-polars-io" ,rust-polars-io-0.15)
+ ("rust-polars-lazy" ,rust-polars-lazy-0.15))))))
+
(define-public rust-polars-0.14
(package
(inherit rust-polars-0.15)
@@ -34566,22 +36019,22 @@ applications.")
("rust-polars-io" ,rust-polars-io-0.13)
("rust-polars-lazy" ,rust-polars-lazy-0.13))))))
-(define-public rust-polars-arrow-0.15
+(define-public rust-polars-arrow-0.16
(package
(name "rust-polars-arrow")
- (version "0.15.1")
+ (version "0.16.0")
(source
(origin
(method url-fetch)
(uri (crate-uri "polars-arrow" version))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
- (base32 "0d8ir9dajywfqg6ck557vbvzsdmndc1ipn9mgrqi15yini1qmw2z"))))
+ (base32 "0pwx7nsayn526r9gw16yzqq3r6mn6ivcdxzsj8737whk04qy3ssb"))))
(build-system cargo-build-system)
(arguments
`(#:skip-build? #t
#:cargo-inputs
- (("rust-arrow" ,rust-arrow-5)
+ (("rust-arrow2" ,rust-arrow2-0.5)
("rust-num" ,rust-num-0.4)
("rust-thiserror" ,rust-thiserror-1))))
(home-page "https://github.com/ritchie46/polars")
@@ -34590,6 +36043,25 @@ applications.")
"This crate provides Arrow interfaces for Polars DataFrame library.")
(license license:expat)))
+(define-public rust-polars-arrow-0.15
+ (package
+ (inherit rust-polars-arrow-0.16)
+ (name "rust-polars-arrow")
+ (version "0.15.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "polars-arrow" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "0d8ir9dajywfqg6ck557vbvzsdmndc1ipn9mgrqi15yini1qmw2z"))))
+ (arguments
+ `(#:skip-build? #t
+ #:cargo-inputs
+ (("rust-arrow" ,rust-arrow-5)
+ ("rust-num" ,rust-num-0.4)
+ ("rust-thiserror" ,rust-thiserror-1))))))
+
(define-public rust-polars-arrow-0.14
(package
(inherit rust-polars-arrow-0.15)
@@ -34629,24 +36101,24 @@ applications.")
("rust-num" ,rust-num-0.4)
("rust-thiserror" ,rust-thiserror-1))))))
-(define-public rust-polars-core-0.15
+(define-public rust-polars-core-0.16
(package
(name "rust-polars-core")
- (version "0.15.1")
+ (version "0.16.0")
(source
(origin
(method url-fetch)
(uri (crate-uri "polars-core" version))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
- (base32 "0vzyyqg0s6h3k77z7nkmqrrgnp7nbi7sh5nmlw1ggrlml9ps0aa9"))))
+ (base32 "0knhxc2b0k5jpvm7fxm64b5hjdyqgxjjyi6cnsiy5sya3mj3v9cd"))))
(build-system cargo-build-system)
(arguments
`(#:skip-build? #t
#:cargo-inputs
(("rust-ahash" ,rust-ahash-0.7)
("rust-anyhow" ,rust-anyhow-1)
- ("rust-arrow" ,rust-arrow-5)
+ ("rust-arrow2" ,rust-arrow2-0.5)
("rust-chrono" ,rust-chrono-0.4)
("rust-comfy-table" ,rust-comfy-table-1)
("rust-hashbrown" ,rust-hashbrown-0.11)
@@ -34656,8 +36128,7 @@ applications.")
("rust-ndarray" ,rust-ndarray-0.15)
("rust-num" ,rust-num-0.4)
("rust-num-cpus" ,rust-num-cpus-1)
- ("rust-parquet" ,rust-parquet-5)
- ("rust-polars-arrow" ,rust-polars-arrow-0.15)
+ ("rust-polars-arrow" ,rust-polars-arrow-0.16)
("rust-prettytable-rs" ,rust-prettytable-rs-0.8)
("rust-rand" ,rust-rand-0.7)
("rust-rand-distr" ,rust-rand-distr-0.3)
@@ -34673,6 +36144,45 @@ applications.")
"This crate provides the core of the Polars DataFrame library.")
(license license:expat)))
+(define-public rust-polars-core-0.15
+ (package
+ (inherit rust-polars-core-0.16)
+ (name "rust-polars-core")
+ (version "0.15.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "polars-core" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "0vzyyqg0s6h3k77z7nkmqrrgnp7nbi7sh5nmlw1ggrlml9ps0aa9"))))
+ (arguments
+ `(#:skip-build? #t
+ #:cargo-inputs
+ (("rust-ahash" ,rust-ahash-0.7)
+ ("rust-anyhow" ,rust-anyhow-1)
+ ("rust-arrow" ,rust-arrow-5)
+ ("rust-chrono" ,rust-chrono-0.4)
+ ("rust-comfy-table" ,rust-comfy-table-1)
+ ("rust-hashbrown" ,rust-hashbrown-0.11)
+ ("rust-itertools" ,rust-itertools-0.10)
+ ("rust-jsonpath-lib" ,rust-jsonpath-lib-0.3)
+ ("rust-lazy-static" ,rust-lazy-static-1)
+ ("rust-ndarray" ,rust-ndarray-0.15)
+ ("rust-num" ,rust-num-0.4)
+ ("rust-num-cpus" ,rust-num-cpus-1)
+ ("rust-parquet" ,rust-parquet-5)
+ ("rust-polars-arrow" ,rust-polars-arrow-0.15)
+ ("rust-prettytable-rs" ,rust-prettytable-rs-0.8)
+ ("rust-rand" ,rust-rand-0.7)
+ ("rust-rand-distr" ,rust-rand-distr-0.3)
+ ("rust-rayon" ,rust-rayon-1)
+ ("rust-regex" ,rust-regex-1)
+ ("rust-serde" ,rust-serde-1)
+ ("rust-serde-json" ,rust-serde-json-1)
+ ("rust-thiserror" ,rust-thiserror-1)
+ ("rust-unsafe-unwrap" ,rust-unsafe-unwrap-0.1))))))
+
(define-public rust-polars-core-0.14
(package
(inherit rust-polars-core-0.15)
@@ -34748,8 +36258,46 @@ applications.")
("rust-thiserror" ,rust-thiserror-1)
("rust-unsafe-unwrap" ,rust-unsafe-unwrap-0.1))))))
+(define-public rust-polars-io-0.16
+ (package
+ (name "rust-polars-io")
+ (version "0.16.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "polars-io" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "0yqpjk0ymqpjq6f0mnm9hhw9xmjradx6vqzg5n54qvl6v3s3p3kh"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:skip-build? #t
+ #:cargo-inputs
+ (("rust-ahash" ,rust-ahash-0.7)
+ ("rust-anyhow" ,rust-anyhow-1)
+ ("rust-arrow2" ,rust-arrow2-0.5)
+ ("rust-csv-core" ,rust-csv-core-0.1)
+ ("rust-dirs" ,rust-dirs-3)
+ ("rust-flate2" ,rust-flate2-1)
+ ("rust-lazy-static" ,rust-lazy-static-1)
+ ("rust-lexical" ,rust-lexical-6)
+ ("rust-memmap2" ,rust-memmap2-0.2)
+ ("rust-num" ,rust-num-0.4)
+ ("rust-num-cpus" ,rust-num-cpus-1)
+ ("rust-polars-arrow" ,rust-polars-arrow-0.16)
+ ("rust-polars-core" ,rust-polars-core-0.16)
+ ("rust-rayon" ,rust-rayon-1)
+ ("rust-regex" ,rust-regex-1)
+ ("rust-simdutf8" ,rust-simdutf8-0.1))))
+ (home-page "https://github.com/ritchie46/polars")
+ (synopsis "IO related logic for the Polars DataFrame library")
+ (description
+ "This crate provides IO related logic for the Polars DataFrame library.")
+ (license license:expat)))
+
(define-public rust-polars-io-0.15
(package
+ (inherit rust-polars-io-0.16)
(name "rust-polars-io")
(version "0.15.1")
(source
@@ -34759,7 +36307,6 @@ applications.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32 "19r2l3rxjdk25ir93l85ap4q0w5p7apjw3g57pszxph9nh2j8ba2"))))
- (build-system cargo-build-system)
(arguments
`(#:skip-build? #t
#:cargo-inputs
@@ -34780,12 +36327,7 @@ applications.")
("rust-polars-core" ,rust-polars-core-0.15)
("rust-rayon" ,rust-rayon-1)
("rust-regex" ,rust-regex-1)
- ("rust-simdutf8" ,rust-simdutf8-0.1))))
- (home-page "https://github.com/ritchie46/polars")
- (synopsis "IO related logic for the Polars DataFrame library")
- (description
- "This crate provides IO related logic for the Polars DataFrame library.")
- (license license:expat)))
+ ("rust-simdutf8" ,rust-simdutf8-0.1))))))
(define-public rust-polars-io-0.14
(package
@@ -34854,26 +36396,26 @@ applications.")
("rust-rayon" ,rust-rayon-1)
("rust-regex" ,rust-regex-1))))))
-(define-public rust-polars-lazy-0.15
+(define-public rust-polars-lazy-0.16
(package
(name "rust-polars-lazy")
- (version "0.15.1")
+ (version "0.16.0")
(source
(origin
(method url-fetch)
(uri (crate-uri "polars-lazy" version))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
- (base32 "0xh3a0gjsisx62zwjmawxg9giin7bwmh7z7y4cc2d3ygy8nk19jh"))))
+ (base32 "01bjsk880dvigyqx7aj3f8zvxpk9gl14k3s40w3dv3aanhdzq7wx"))))
(build-system cargo-build-system)
(arguments
`(#:skip-build? #t
#:cargo-inputs
(("rust-ahash" ,rust-ahash-0.7)
("rust-itertools" ,rust-itertools-0.10)
- ("rust-polars-arrow" ,rust-polars-arrow-0.15)
- ("rust-polars-core" ,rust-polars-core-0.15)
- ("rust-polars-io" ,rust-polars-io-0.15)
+ ("rust-polars-arrow" ,rust-polars-arrow-0.16)
+ ("rust-polars-core" ,rust-polars-core-0.16)
+ ("rust-polars-io" ,rust-polars-io-0.16)
("rust-rayon" ,rust-rayon-1)
("rust-regex" ,rust-regex-1))))
(home-page "https://github.com/ritchie46/polars")
@@ -34883,6 +36425,29 @@ applications.")
library.")
(license license:expat)))
+(define-public rust-polars-lazy-0.15
+ (package
+ (inherit rust-polars-lazy-0.16)
+ (name "rust-polars-lazy")
+ (version "0.15.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "polars-lazy" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "0xh3a0gjsisx62zwjmawxg9giin7bwmh7z7y4cc2d3ygy8nk19jh"))))
+ (arguments
+ `(#:skip-build? #t
+ #:cargo-inputs
+ (("rust-ahash" ,rust-ahash-0.7)
+ ("rust-itertools" ,rust-itertools-0.10)
+ ("rust-polars-arrow" ,rust-polars-arrow-0.15)
+ ("rust-polars-core" ,rust-polars-core-0.15)
+ ("rust-polars-io" ,rust-polars-io-0.15)
+ ("rust-rayon" ,rust-rayon-1)
+ ("rust-regex" ,rust-regex-1))))))
+
(define-public rust-polars-lazy-0.14
(package
(inherit rust-polars-lazy-0.15)
@@ -38263,14 +39828,14 @@ accessors.")
(define-public rust-rayon-1
(package
(name "rust-rayon")
- (version "1.5.0")
+ (version "1.5.1")
(source
(origin
(method url-fetch)
(uri (crate-uri "rayon" version))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
- (base32 "0x2n4zkrm6z3avdfh7zgcwx0wq6hx8332dx89v3j1p7s3448w3cb"))))
+ (base32 "143dl2453bazgk7rwjrickmyqd0ks3q69nfz8axcins19n0clsn0"))))
(build-system cargo-build-system)
(arguments
`(#:cargo-inputs
@@ -38342,14 +39907,14 @@ Rust.")
(define-public rust-rayon-core-1
(package
(name "rust-rayon-core")
- (version "1.9.0")
+ (version "1.9.1")
(source
(origin
(method url-fetch)
(uri (crate-uri "rayon-core" version))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
- (base32 "0jpsi8zf66xyx4m5f329lpgiql8775vpm6zqm7zn5p11b6n4dcws"))))
+ (base32 "13kdcnqp2p1a5a3amamfjpnm7ay463vq4dfxy4rrh9shr3i210fp"))))
(build-system cargo-build-system)
(arguments
;; One of the tests attempts to overflow the stack, but the compiler has
@@ -38899,6 +40464,33 @@ uses finite automata and guarantees linear time matching on all inputs.")
(("rust-quickcheck" ,rust-quickcheck-0.2)
("rust-rand" ,rust-rand-0.3))))))
+(define-public rust-region-2
+ (package
+ (name "rust-region")
+ (version "2.2.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "region" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "1q4szar3ms76552iygmhsvzhvvwkgz4l94qpx600vmyw5bm58zl7"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:cargo-inputs
+ (("rust-bitflags" ,rust-bitflags-1)
+ ("rust-libc" ,rust-libc-0.2)
+ ("rust-mach" ,rust-mach-0.3)
+ ("rust-winapi" ,rust-winapi-0.3))
+ #:cargo-development-inputs
+ (("rust-memmap" ,rust-memmap-0.7))))
+ (home-page "https://github.com/darfink/region-rs")
+ (synopsis "Library for manipulating memory regions")
+ (description
+ "This package provides a library for manipulating memory regions.")
+ (license license:expat)))
+
(define-public rust-relative-path-1
(package
(name "rust-relative-path")
@@ -42557,6 +44149,36 @@ with one of the implemented strategies.")
(base32
"09sy9wbqp409pkwmqni40qmwa99ldqpl48pp95m1xw8sc19qy9cl"))))))
+(define-public rust-scraper-0.12
+ (package
+ (name "rust-scraper")
+ (version "0.12.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "scraper" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "04icx88wdrlz1qv0dz1zc0inlfq34ajwdpih854jw368j2kjmq28"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:skip-build? #t
+ #:cargo-inputs
+ (("rust-cssparser" ,rust-cssparser-0.27)
+ ("rust-ego-tree" ,rust-ego-tree-0.6)
+ ("rust-getopts" ,rust-getopts-0.2)
+ ("rust-html5ever" ,rust-html5ever-0.25)
+ ("rust-matches" ,rust-matches-0.1)
+ ("rust-selectors" ,rust-selectors-0.22)
+ ("rust-smallvec" ,rust-smallvec-1)
+ ("rust-tendril" ,rust-tendril-0.4))))
+ (home-page "https://github.com/programble/scraper")
+ (synopsis "HTML parsing and querying with CSS selectors")
+ (description
+ "Scraper provides an interface to Servo's html5ever and selectors crates,
+for browser-grade parsing and querying.")
+ (license license:isc)))
+
(define-public rust-scratch-1
(package
(name "rust-scratch")
@@ -45272,14 +46894,14 @@ words, like Python's shlex.")
(define-public rust-signal-hook-0.3
(package
(name "rust-signal-hook")
- (version "0.3.4")
+ (version "0.3.10")
(source
(origin
(method url-fetch)
(uri (crate-uri "signal-hook" version))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
- (base32 "0h628smm9y22qi3szpkg3xpj31hyvs4ps29nf8cnfvy6w0zmw3vq"))))
+ (base32 "1lgg8rwyz97pqkpg4ii7iswvs5mx8sgg2pl2ahlil9vyfcfqk64w"))))
(build-system cargo-build-system)
(arguments
`(#:skip-build? #t
@@ -45318,19 +46940,42 @@ words, like Python's shlex.")
(("rust-tokio" ,rust-tokio-0.1)
("rust-version-sync" ,rust-version-sync-0.8))))))
+(define-public rust-signal-hook-mio-0.2
+ (package
+ (name "rust-signal-hook-mio")
+ (version "0.2.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "signal-hook-mio" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "1m3yc37dxdq4ym0x7i2b9aqfnlhivwm7mvls0yzcbwn4y5kmiz99"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:skip-build? #t
+ #:cargo-inputs
+ (("rust-libc" ,rust-libc-0.2)
+ ("rust-mio" ,rust-mio-0.7)
+ ("rust-mio" ,rust-mio-0.6)
+ ("rust-mio-uds" ,rust-mio-uds-0.6)
+ ("rust-signal-hook" ,rust-signal-hook-0.3))))
+ (home-page "https://github.com/vorner/signal-hook")
+ (synopsis "MIO support for signal-hook")
+ (description "This crate provides MIO support for signal-hook.")
+ (license (list license:asl2.0 license:expat))))
+
(define-public rust-signal-hook-registry-1
(package
(name "rust-signal-hook-registry")
- (version "1.3.0")
+ (version "1.4.0")
(source
(origin
(method url-fetch)
(uri (crate-uri "signal-hook-registry" version))
- (file-name
- (string-append name "-" version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
(sha256
- (base32
- "19hirq0h33jjyh505s8hf9q5dq0ky80ygivkl3vshjv0y7zd1w8n"))))
+ (base32 "1c2mhijg54y6c1zi4630yki1vpq3z96ljfnsrdy0rb64ilr767p5"))))
(build-system cargo-build-system)
(arguments
`(#:skip-build? #t
@@ -46315,6 +47960,29 @@ More importantly, this library also provides the ability to un-escape a given
escaped text to recover the original string.")
(license license:gpl3)))
+(define-public rust-snake-case-0.3
+ (package
+ (name "rust-snake-case")
+ (version "0.3.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "snake-case" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "1v4f132rk9wxiw8hb3kgnixirzr8kbfhg2lgsf4b85vbg02a0jfn"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:rust ,rust-1.52 ; fix for E0658
+ #:cargo-inputs (("rust-serde" ,rust-serde-1))))
+ (home-page "https://github.com/emilk/snake_case")
+ (synopsis "String-like type that only contains non-empty snake_case")
+ (description
+ "This package provides a String-like type that can only contain valid
+non-empty snake_case.")
+ (license license:expat)))
+
(define-public rust-snap-1
(package
(name "rust-snap")
@@ -47176,6 +48844,29 @@ UTF-8.")
(("rust-blobby" ,rust-blobby-0.1)
("rust-generic-array" ,rust-generic-array-0.13))))))
+(define-public rust-streaming-iterator-0.1
+ (package
+ (name "rust-streaming-iterator")
+ (version "0.1.5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "streaming-iterator" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "1xc1gyq137b020m29g85zdhbbdrksdmhf3dq4ri4fjlrfz0kacih"))))
+ (build-system cargo-build-system)
+ (arguments `(#:skip-build? #t))
+ (home-page "https://github.com/sfackler/streaming-iterator")
+ (synopsis "Streaming iterators")
+ (description "The iterator APIs in the Rust standard library do not allow
+elements to be yielded which borrow from the iterator itself. That means, for
+example, that the @code{std::io::Lines} iterator must allocate a new
+@code{String} for each line rather than reusing an internal buffer. The
+@code{StreamingIterator} trait instead provides access to elements being
+iterated over only by reference rather than by value.")
+ (license (list license:expat license:asl2.0))))
+
(define-public rust-streaming-stats-0.2
(package
(name "rust-streaming-stats")
@@ -47227,6 +48918,30 @@ UTF-8.")
"This package provides a streebog (GOST R 34.11-2012) hash function.")
(license (list license:expat license:asl2.0))))
+(define-public rust-strength-reduce-0.2
+ (package
+ (name "rust-strength-reduce")
+ (version "0.2.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "strength_reduce" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "0m12phq654mfxpmh2h5akqkag5ha6nlhjc2bp9jwarr5r1qjzzx3"))))
+ (build-system cargo-build-system)
+ (arguments `(#:skip-build? #t))
+ (home-page "http://github.com/ejmahler/strength_reduce")
+ (synopsis "Faster integer division and modulus operations")
+ (description "Strength_reduce implements integer division and modulo via
+@dfn{arithmetic strength reduction}. Modern processors can do multiplication
+and shifts much faster than division, and arithmetic strength reduction is an
+algorithm to transform divisions into multiplications and shifts. Compilers
+already perform this optimization for divisors that are known at compile time;
+this library enables this optimization for divisors that are only known at
+runtime.")
+ (license (list license:expat license:asl2.0))))
+
(define-public rust-string-0.2
(package
(name "rust-string")
@@ -47398,19 +49113,19 @@ as defined in RFC 3454.")
(define-public rust-strip-ansi-escapes-0.1
(package
(name "rust-strip-ansi-escapes")
- (version "0.1.0")
+ (version "0.1.1")
(source
(origin
(method url-fetch)
(uri (crate-uri "strip-ansi-escapes" version))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
- (base32 "1vmc6cwxsvp02b17b6x42mnnnn5vlc1dqbcqc2a71yms59p6fqwx"))))
+ (base32 "1n36ly9vxb1wr5q76i7995xr7c0pb1pc8g7a3a3n47vwrwwvn701"))))
(build-system cargo-build-system)
(arguments
`(#:skip-build? #t
#:cargo-inputs
- (("rust-vte" ,rust-vte-0.3))))
+ (("rust-vte" ,rust-vte-0.10))))
(home-page "https://github.com/luser/strip-ansi-escapes")
(synopsis "Strip ANSI escape sequences from byte streams")
(description
@@ -47421,6 +49136,61 @@ and write it somewhere that does not easily support them, such as a log
file.")
(license (list license:asl2.0 license:expat))))
+(define-public rust-strong-xml-0.6
+ (package
+ (name "rust-strong-xml")
+ (version "0.6.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "strong-xml" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "1gxy34j42x5a572cfkkhmxamrm764pswj5r3wcwi0bwfc4xgn68x"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:rust ,rust-1.52 ; fix for E0658
+ #:cargo-inputs
+ (("rust-jetscii" ,rust-jetscii-0.5)
+ ("rust-lazy-static" ,rust-lazy-static-1)
+ ("rust-log" ,rust-log-0.4)
+ ("rust-memchr" ,rust-memchr-2)
+ ("rust-strong-xml-derive"
+ ,rust-strong-xml-derive-0.6)
+ ("rust-xmlparser" ,rust-xmlparser-0.13))
+ #:cargo-development-inputs
+ (("rust-env-logger" ,rust-env-logger-0.8))))
+ (home-page "https://github.com/PoiScript/strong-xml")
+ (synopsis "Strong typed xml")
+ (description
+ "This package provides a strong typed XML parser, based on xmlparser.")
+ (license license:expat)))
+
+(define-public rust-strong-xml-derive-0.6
+ (package
+ (name "rust-strong-xml-derive")
+ (version "0.6.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "strong-xml-derive" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "1qf7smxaaglj7p9fs0csd0cyvwcy30w96pdy2aqi65ijk7s83iwj"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:cargo-inputs
+ (("rust-proc-macro2" ,rust-proc-macro2-1)
+ ("rust-quote" ,rust-quote-1)
+ ("rust-syn" ,rust-syn-1))))
+ (home-page "https://github.com/PoiScript/strong-xml")
+ (synopsis "Strong typed XML")
+ (description
+ "This package provides a strong typed XML parser, based on xmlparser.")
+ (license license:expat)))
+
(define-public rust-strsim-0.10
(package
(name "rust-strsim")
@@ -47619,22 +49389,22 @@ struct.")
"Parse command line argument by defining a struct, derive crate.")
(license (list license:asl2.0 license:expat))))
-(define-public rust-strum-0.20
+(define-public rust-strum-0.21
(package
(name "rust-strum")
- (version "0.20.0")
+ (version "0.21.0")
(source
(origin
(method url-fetch)
(uri (crate-uri "strum" version))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
- (base32 "0p5cslmdnz261kiwmm4h7qsmv9bh83r0f9lq6f2z2mxsnl4wa63k"))))
+ (base32 "1qnd2by1zrwgx7li0hmwy7jbzjwz1ky697qjg85nga8zzny6py5a"))))
(build-system cargo-build-system)
(arguments
`(#:skip-build? #t
#:cargo-inputs
- (("rust-strum-macros" ,rust-strum-macros-0.20))))
+ (("rust-strum-macros" ,rust-strum-macros-0.21))))
(home-page "https://github.com/Peternator7/strum")
(synopsis "Set of traits for working with enums and strings")
(description
@@ -47642,6 +49412,23 @@ struct.")
easier in Rust.")
(license license:expat)))
+(define-public rust-strum-0.20
+ (package
+ (inherit rust-strum-0.21)
+ (name "rust-strum")
+ (version "0.20.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "strum" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "0p5cslmdnz261kiwmm4h7qsmv9bh83r0f9lq6f2z2mxsnl4wa63k"))))
+ (arguments
+ `(#:skip-build? #t
+ #:cargo-inputs
+ (("rust-strum-macros" ,rust-strum-macros-0.20))))))
+
(define-public rust-strum-0.19
(package
(inherit rust-strum-0.20)
@@ -47676,17 +49463,17 @@ easier in Rust.")
`(#:cargo-inputs
(("rust-strum-macros" ,rust-strum-macros-0.18))))))
-(define-public rust-strum-macros-0.20
+(define-public rust-strum-macros-0.21
(package
(name "rust-strum-macros")
- (version "0.20.1")
+ (version "0.21.1")
(source
(origin
(method url-fetch)
(uri (crate-uri "strum_macros" version))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
- (base32 "0j9ikvxlqzr667ghc045qkpwprjgcfmzgagln7maw4jigawcd2zf"))))
+ (base32 "1v55b1in7dn07s6vxr8dajqpvxkxjbfq6qamnjgcbnq9x3pawsnh"))))
(build-system cargo-build-system)
(arguments
`(#:skip-build? #t
@@ -47701,6 +49488,26 @@ easier in Rust.")
"This crate provides helpful macros for working with enums and strings.")
(license license:expat)))
+(define-public rust-strum-macros-0.20
+ (package
+ (inherit rust-strum-macros-0.21)
+ (name "rust-strum-macros")
+ (version "0.20.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "strum_macros" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "0j9ikvxlqzr667ghc045qkpwprjgcfmzgagln7maw4jigawcd2zf"))))
+ (arguments
+ `(#:skip-build? #t
+ #:cargo-inputs
+ (("rust-heck" ,rust-heck-0.3)
+ ("rust-proc-macro2" ,rust-proc-macro2-1)
+ ("rust-quote" ,rust-quote-1)
+ ("rust-syn" ,rust-syn-1))))))
+
(define-public rust-strum-macros-0.19
(package
(inherit rust-strum-macros-0.20)
@@ -50689,6 +52496,33 @@ fixed set of worker threads.")
"You can bind to libsodium from Rust with this crate.")
(license (list license:asl2.0 license:expat))))
+(define-public rust-tiger-0.1
+ (package
+ (name "rust-tiger")
+ (version "0.1.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "tiger" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "01bhc7h8kxc5kjqx9sqrb3g8h4f9av6hpxzyihjq7pprphf56gj4"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:cargo-inputs
+ (("rust-block-buffer" ,rust-block-buffer-0.9)
+ ("rust-byteorder" ,rust-byteorder-1)
+ ("rust-digest" ,rust-digest-0.9))
+ #:cargo-development-inputs
+ (("rust-digest" ,rust-digest-0.9)
+ ("rust-hex-literal" ,rust-hex-literal-0.2))))
+ (home-page "https://github.com/RustCrypto/hashes")
+ (synopsis "Tiger hash function")
+ (description
+ "This package provides the Tiger cryptographic hash function.")
+ (license (list license:expat license:asl2.0))))
+
(define-public rust-tikv-jemalloc-sys-0.4
(package
(name "rust-tikv-jemalloc-sys")
@@ -58958,31 +60792,47 @@ formatters with per-field documentation generated for each structure.
configuration file and/or environment variables.")
(license (list license:expat license:asl2.0))))
-(define-public rust-xmltree-0.8
+(define-public rust-xmltree-0.10
(package
(name "rust-xmltree")
- (version "0.8.0")
+ (version "0.10.3")
(source
- (origin
- (method url-fetch)
- (uri (crate-uri "xmltree" version))
- (file-name
- (string-append name "-" version ".tar.gz"))
- (sha256
- (base32
- "0w0y0jz7lhxg05ca6ngfj0lj8sbrjh4vaqv13q7qaqkhs7lsx3pz"))))
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "xmltree" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "1jqzwhr1a5cknflsshhhjlllmd1xi04qdkjsls2bnmv5mxgagn6p"))))
(build-system cargo-build-system)
(arguments
- `(#:cargo-inputs
- (("rust-indexmap" ,rust-indexmap-1)
- ("rust-xml-rs" ,rust-xml-rs-0.7))))
- (home-page #f)
- (synopsis
- "Parse an XML file into a simple tree-like structure")
- (description
- "Parse an XML file into a simple tree-like structure")
+ `(#:cargo-inputs
+ (("rust-indexmap" ,rust-indexmap-1)
+ ("rust-xml-rs" ,rust-xml-rs-0.8))))
+ (home-page "https://github.com/eminence/xmltree-rs")
+ (synopsis "Parse an XML file into a simple tree-like structure")
+ (description "This package provides a small library for parsing an XML
+file into an in-memory tree structure.")
(license license:expat)))
+(define-public rust-xmltree-0.8
+ (package
+ (inherit rust-xmltree-0.10)
+ (name "rust-xmltree")
+ (version "0.8.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (crate-uri "xmltree" version))
+ (file-name
+ (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "0w0y0jz7lhxg05ca6ngfj0lj8sbrjh4vaqv13q7qaqkhs7lsx3pz"))))
+ (arguments
+ `(#:cargo-inputs
+ (("rust-indexmap" ,rust-indexmap-1)
+ ("rust-xml-rs" ,rust-xml-rs-0.7))))))
+
(define-public rust-svd-parser-0.9
(package
(name "rust-svd-parser")
diff --git a/gnu/packages/cups.scm b/gnu/packages/cups.scm
index cb9a36b962..bf92905f9c 100644
--- a/gnu/packages/cups.scm
+++ b/gnu/packages/cups.scm
@@ -502,14 +502,14 @@ should only be used as part of the Guix cups-pk-helper service.")
(define-public hplip
(package
(name "hplip")
- (version "3.21.8")
+ (version "3.21.10")
(source (origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/hplip/hplip/" version
"/hplip-" version ".tar.gz"))
(sha256
(base32
- "076fjzgw86q817c660h1vzwdp00cyjr49b9bfi7qkhphq6am4gpi"))
+ "0q3adcp8iygravp4bq4gw14jk20c5rhnawj1333qyw8yvlghw8yy"))
(modules '((guix build utils)))
(snippet
'(begin
@@ -524,9 +524,13 @@ should only be used as part of the Guix cups-pk-helper service.")
(delete-file "prnt/hpcups/ImageProcessor.h")
(substitute* "Makefile.in"
((" -lImageProcessor ") " ")
- (("(\\@HPLIP_BUILD_TRUE\\@[[:blank:]]*).*libImageProcessor.*"
+ ;; Turn shell commands inside an if…fi into harmless no-ops.
+ (("^(\\@HPLIP_BUILD_TRUE\\@[[:blank:]]*).*libImageProcessor.*"
_ prefix)
- (string-append prefix ":; \\\n")))
+ (string-append prefix ": ; \\\n"))
+ ;; Remove the lines adding file targets altogether.
+ (("^\\@FULL_BUILD_TRUE\\@.*libImageProcessor.*")
+ ""))
;; Install binaries under libexec/hplip instead of
;; share/hplip; that'll at least ensure they get stripped.
diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 56dbf6440f..505d5c2753 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -2198,7 +2198,7 @@ easy, requiring concise and simple code.")
"UnQLite is an in-process software library which implements a
self-contained, serverless, zero-configuration, transactional NoSQL
database engine. UnQLite is a document store database similar to
-MongoDB, Redis, CouchDB, etc. as well as a standard Key/Value store
+Redis, CouchDB, etc., as well as a standard key/value store
similar to BerkeleyDB, LevelDB, etc.")
(license license:bsd-2)))
@@ -2961,13 +2961,13 @@ Database API 2.0T.")
(define-public python-sqlalchemy
(package
(name "python-sqlalchemy")
- (version "1.4.23")
+ (version "1.4.26")
(source
(origin
(method url-fetch)
(uri (pypi-uri "SQLAlchemy" version))
(sha256
- (base32 "10vm8hm8w4yfsab076ak8r4vp5v1jqdi71cky6dhha7mh5l29zvn"))))
+ (base32 "06imr96jirwmkc8mkxrl9bi413yd3638lc5idn65xx8fv7bzkivb"))))
(build-system python-build-system)
(native-inputs
`(("python-cython" ,python-cython) ; for C extensions
@@ -2979,7 +2979,9 @@ Database API 2.0T.")
`(#:phases
(modify-phases %standard-phases
(replace 'check
- (lambda _ (invoke "py.test"))))))
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (invoke "py.test")))))))
(home-page "https://www.sqlalchemy.org")
(synopsis "Database abstraction library")
(description
@@ -2990,6 +2992,18 @@ designed for efficient and high-performing database access, adapted into a
simple and Pythonic domain language.")
(license license:x11)))
+(define-public python-sqlalchemy-1.3
+ (package
+ (inherit python-sqlalchemy)
+ (version "1.3.20")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "SQLAlchemy" version))
+ (sha256
+ (base32 "18b9am7bsqc4nj3d2h5r93i002apczxfvpfpcqbd6f0385zmrwnj"))))
+ (propagated-inputs '())))
+
(define-public python2-sqlalchemy
(package-with-python2 python-sqlalchemy))
diff --git a/gnu/packages/diffoscope.scm b/gnu/packages/diffoscope.scm
index 728aa6b8b4..26ae8edcd1 100644
--- a/gnu/packages/diffoscope.scm
+++ b/gnu/packages/diffoscope.scm
@@ -73,7 +73,7 @@
(define-public diffoscope
(package
(name "diffoscope")
- (version "189")
+ (version "190")
(source
(origin
(method git-fetch)
@@ -82,7 +82,7 @@
(commit version)))
(file-name (git-file-name name version))
(sha256
- (base32 "0dai9gwsr9xnficjy8myq6xr301y4iy82aidm936qsqjwrp8q1sm"))
+ (base32 "10q93qybwqf2nzj3iakw1pxhccq10ixm9fn7xgdr4p88qb0wchb5"))
(patches
(search-patches "diffoscope-fix-llvm-test.patch"))))
(build-system python-build-system)
diff --git a/gnu/packages/disk.scm b/gnu/packages/disk.scm
index 0ed740202c..e5355f9de8 100644
--- a/gnu/packages/disk.scm
+++ b/gnu/packages/disk.scm
@@ -923,16 +923,15 @@ to create devices with respective mappings for the ATARAID sets discovered.")
(define-public libblockdev
(package
(name "libblockdev")
- (version "2.25")
+ (version "2.26")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/storaged-project/"
"libblockdev/releases/download/"
version "-1/libblockdev-" version ".tar.gz"))
- (patches (search-patches "libblockdev-glib-compat.patch"))
(sha256
(base32
- "0s0nazkpzpn4an00qghjkk9n7gdm5a8dqfr5hfnlk5mk5lma8njm"))))
+ "0sg068jb87ljhn8yazrqxi6ri10ic2sh1lp6ikd2nqxc6l5y3h64"))))
(build-system gnu-build-system)
(arguments
`(#:phases
diff --git a/gnu/packages/dns.scm b/gnu/packages/dns.scm
index 89ebe588fd..b289aa999e 100644
--- a/gnu/packages/dns.scm
+++ b/gnu/packages/dns.scm
@@ -592,14 +592,14 @@ asynchronous fashion.")
(define-public nsd
(package
(name "nsd")
- (version "4.3.7")
+ (version "4.3.8")
(source
(origin
(method url-fetch)
(uri (string-append "https://www.nlnetlabs.nl/downloads/nsd/nsd-"
version ".tar.gz"))
(sha256
- (base32 "1bg87g0i66hw16fm7gbqmzyi2rcn1hadzz0bg9b8s5mx7g2rwfzx"))))
+ (base32 "1qcrrglm3r486r6n26h5fr1xb1k8jf63gm9b43wrhnigywjpx28i"))))
(build-system gnu-build-system)
(arguments
`(#:configure-flags
@@ -635,8 +635,7 @@ asynchronous fashion.")
((".*INSTALL.*\\$\\((config|pid|xfr|db)dir" command)
(string-append "#" command))
(("\\$\\(nsdconfigfile\\)\\.sample" file-name)
- (string-append doc "/examples/" file-name)))
- #t))))
+ (string-append doc "/examples/" file-name)))))))
#:tests? #f)) ; no tests
(inputs
`(("libevent" ,libevent)
@@ -924,7 +923,7 @@ Extensions} (DNSSEC).")
(define-public knot
(package
(name "knot")
- (version "3.1.2")
+ (version "3.1.4")
(source
(origin
(method git-fetch)
@@ -933,7 +932,7 @@ Extensions} (DNSSEC).")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "1kyjf6d1jx8q0zjzwy06f4d3ar5cbbqxka8cc7ckwmbpf1n6cij5"))
+ (base32 "0wx8ad95adryzp527m4k0lja8y39qqd65f5z9immhfpb9cyax6i7"))
(modules '((guix build utils)))
(snippet
'(begin
diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm
index 935a1f62ca..096ba06edc 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -47,6 +47,7 @@
;;; Copyright © 2019 mikadoZero <mikadozero@yandex.com>
;;; Copyright © 2019 Gabriel Hondet <gabrielhondet@gmail.com>
;;; Copyright © 2019, 2020, 2021 Joseph LaFreniere <joseph@lafreniere.xyz>
+;;; Copyright © 2019 Todor Kondić <tk.code@protonmail.com>15669
;;; Copyright © 2019 Amar Singh <nly@disroot.org>
;;; Copyright © 2019 Baptiste Strazzulla <bstrazzull@hotmail.fr>
;;; Copyright © 2019 Giacomo Leidi <goodoldpaul@autistici.org>
@@ -280,7 +281,7 @@ e.g. emacs-geiser-guile for Guile.")
(define-public emacs-geiser-guile
(package
(name "emacs-geiser-guile")
- (version "0.17")
+ (version "0.18")
(source
(origin
(method git-fetch)
@@ -289,7 +290,7 @@ e.g. emacs-geiser-guile for Guile.")
(commit version)))
(file-name (git-file-name name version))
(sha256
- (base32 "0iw23nlgqppf6f00ly50m8lq85n9mv244pw3whxv0hynfjxr2ic0"))))
+ (base32 "0gndf0w8dbv54bzc04svp2ck8wypa7i3b8kpixf6rkg91l79xpci"))))
(build-system emacs-build-system)
(arguments
'(#:include (cons "^src/" %default-include)
@@ -304,8 +305,7 @@ e.g. emacs-geiser-guile for Guile.")
;; loaded, so let's defer that until it is.
(("\\(geiser-activate-implementation .*\\)" all)
(string-append
- "(eval-after-load 'geiser-impl '" all ")")))
- #t)))))
+ "(eval-after-load 'geiser-impl '" all ")"))))))))
(inputs
`(("guile" ,guile-3.0)))
(propagated-inputs
@@ -650,22 +650,23 @@ some utility functions, and commands using that infrastructure.")
(define-public git-modes
(package
(name "emacs-git-modes")
- (version "1.3.0")
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/magit/git-modes")
- (commit version)))
- (file-name (git-file-name name version))
- (sha256
- (base32
- "0m8qfjj5hzxwyyi34sbk11qz5fix6z80hiki0v0a838sq4f586b6"))))
+ (version "1.4.0")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/magit/git-modes")
+ (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0aqz65pcqc35h5z4s606f48iqn87h5v9nj3cp6n9yjxa2v7w5hfk"))))
(build-system emacs-build-system)
(home-page "https://github.com/magit/git-modes")
(synopsis "Emacs major modes for Git configuration files")
(description
"This package provides Emacs major modes for editing various Git
-configuration files, such as .gitattributes, .gitignore, and .git/config.")
+configuration files, such as @file{.gitattributes}, @file{.gitignore}, and
+@file{.git/config}.")
(license license:gpl3+)))
(define-public emacs-with-editor
@@ -1646,6 +1647,19 @@ boilerplate code from defining new Flymake backend functions.")
(sha256
(base32 "04yfb4sy41spjzk9mhm4gy0h8vnjx09p2g6nm1yzgd9a5ph9sqgl"))))
(build-system emacs-build-system)
+ (arguments
+ '(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'substitute-shellcheck-path
+ (lambda* (#:key inputs #:allow-other-keys)
+ (make-file-writable "flymake-shellcheck.el")
+ (emacs-substitute-sexps "flymake-shellcheck.el"
+ ("defcustom flymake-shellcheck-path"
+ `(or (executable-find "shellcheck")
+ ,(string-append (assoc-ref inputs "shellcheck")
+ "/bin/shellcheck")))))))))
+ (inputs
+ `(("shellcheck" ,shellcheck)))
(home-page "https://github.com/federicotdn/flymake-shellcheck")
(synopsis "Flymake backend for Bash/Sh powered by ShellCheck")
(description
@@ -12645,7 +12659,6 @@ editing nginx config files.")
(method url-fetch)
(uri (string-append "https://elpa.gnu.org/packages/"
"stream-" version ".tar"))
- (file-name (git-file-name name version))
(sha256
(base32 "00c3n4gyxzv7vczqms0d62kl8zsmjfyxa92mwxn2snyx857a9jfw"))))
(build-system emacs-build-system)
@@ -13922,14 +13935,14 @@ methods from a given list.")
(define-public emacs-posframe
(package
(name "emacs-posframe")
- (version "1.0.4")
+ (version "1.1.0")
(source
(origin
(method url-fetch)
(uri (string-append "https://elpa.gnu.org/packages/"
"posframe-" version ".tar"))
(sha256
- (base32 "0i2pw90gw9zb22gj8yyvcp3b2k1bxxhbjj0idvr5iz1vd9023bc6"))))
+ (base32 "0ddm149dz71nksbpz7rwa8cax1nisf6wklv5iq4zrcbf5ghpagkg"))))
(build-system emacs-build-system)
;; emacs-minimal does not include the function font-info.
(arguments
@@ -17677,7 +17690,7 @@ files to be expanded upon opening them.")
(define-public emacs-ebib
(package
(name "emacs-ebib")
- (version "2.32.2")
+ (version "2.33")
(source
(origin
(method git-fetch)
@@ -17686,10 +17699,11 @@ files to be expanded upon opening them.")
(commit version)))
(file-name (git-file-name name version))
(sha256
- (base32 "04kw0akp35r2ibrcav4kaf34d1xs8pckjiygv7h1nqpv6dmrgfq7"))))
+ (base32 "18gvmymkpzws8s4zjcm1kijyr55dgfcq201z3w1jzhkhcs01bfsc"))))
(build-system emacs-build-system)
(propagated-inputs
`(("emacs-biblio" ,emacs-biblio)
+ ("emacs-ivy" ,emacs-ivy)
("emacs-parsebib" ,emacs-parsebib)))
(home-page "https://joostkremers.github.io/ebib/")
(synopsis "BibTeX database manager for Emacs")
@@ -17732,13 +17746,48 @@ and publications from various sources, by keywords or by DOI. References are
automatically fetched from well-curated sources, and formatted as BibTeX.")
(license license:gpl3+)))
+(define-public emacs-citar
+ (package
+ (name "emacs-citar")
+ (version "0.8")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/bdarcus/citar")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1jrfcfr976c9nb2vpfrh6yhck5gm34wcjzbk0m6gq2xg3qfv2g6p"))))
+ (build-system emacs-build-system)
+ (propagated-inputs
+ `(("emacs-auctex" ,emacs-auctex)
+ ("emacs-helm-bibtex" ,emacs-helm-bibtex)
+ ("emacs-org" ,emacs-org)
+ ("emacs-parsebib" ,emacs-parsebib)
+ ("emacs-s" ,emacs-s)))
+ (home-page "https://github.com/bdarcus/citar")
+ (synopsis "Emacs package to quickly find and act on bibliographic entries")
+ (description
+ "This package provides a completing-read front-end to browse and
+act on BibTeX, BibLaTeX, and CSL JSON bibliographic data, and LaTeX,
+markdown, and Org cite editing support.
+
+When used with Vertico (or Selectrum), Embark, and Marginalia, it
+provides similar functionality to helm-bibtex and ivy-bibtex: quick
+filtering and selecting of bibliographic entries from the minibuffer,
+and the option to run different commands against them.
+
+With Embark, it also makes available at-point actions in Org
+citations.")
+ (license license:gpl3+)))
+
(define-public emacs-helm-bibtex
- (let ((commit "d4471232be26793fbf56c0ac3690b5f537c378b9")
- (revision "2"))
+ (let ((commit "aa775340ba691d2322948bfdc6a88158568a1399")
+ (revision "3"))
(package
(name "emacs-helm-bibtex")
- (version (string-append "2.0.0" "-" revision "."
- (string-take commit 7)))
+ (version (git-version "2.0.0" revision commit))
(source
(origin
(method git-fetch)
@@ -17747,8 +17796,7 @@ automatically fetched from well-curated sources, and formatted as BibTeX.")
(commit commit)))
(file-name (git-file-name name version))
(sha256
- (base32
- "1bkzhic6qckb267025il1r3xcpz99kisphxiafni1pxvf9jafr0j"))))
+ (base32 "1d3mc17ga09m41i06khghlvixr6gsiacifnhdbrfnp0w5592aprk"))))
(build-system emacs-build-system)
(propagated-inputs
`(("emacs-helm" ,emacs-helm)
@@ -25160,6 +25208,27 @@ Dash docsets.")
through Dash docsets.")
(license license:expat))))
+(define-public emacs-devdocs
+ (package
+ (name "emacs-devdocs")
+ (version "0.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://elpa.gnu.org/packages/"
+ "devdocs-" version ".tar"))
+ (sha256
+ (base32 "1npc7yra7pvf86ahmz1h7hnjxrz15ar1vjcalg4ilizypycpgrwj"))))
+ (build-system emacs-build-system)
+ (home-page "https://github.com/astoff/devdocs.el")
+ (synopsis "Emacs viewer for DevDocs")
+ (description
+ "This package provides a documentation viewer similar to Emacs's
+built-in Info browser, but geared towards documentation obtained from
+@url{https://devdocs.io}.")
+ (license license:gpl3+)))
+
(define-public emacs-cascading-dir-locals
(let ((release "0.1")
(revision "0")
@@ -25636,6 +25705,120 @@ provided. Those alternative commands are and bound by default to their
corresponding Evil keys.")
(license license:expat))))
+(define-public emacs-ntlm
+ (package
+ (name "emacs-ntlm")
+ (version "2.1.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://elpa.gnu.org/packages/ntlm-" version ".el"))
+ (sha256
+ (base32 "01d0bcmh8a36qf871w6bc05kjk9bmnh843m9869xw06zyvqwg9mv"))))
+ (build-system emacs-build-system)
+ (home-page "https://elpa.gnu.org/packages/ntlm.html")
+ (synopsis "NTLM (NT LanManager) authentication support")
+ (description
+ "This library is a direct translation of the Samba release 2.2.0
+implementation of Windows NT and LanManager compatible password encryption.")
+ (license license:gpl3+)))
+
+(define-public emacs-nadvice
+ (package
+ (name "emacs-nadvice")
+ (version "0.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://elpa.gnu.org/packages/"
+ "nadvice-" version ".el"))
+ (sha256
+ (base32 "0gi3csnxbs8h7iy0scsl35sic3gv90swa89hhdjwb7qvpirfdcgw"))))
+ (build-system emacs-build-system)
+ (home-page "https://elpa.gnu.org/packages/nadvice.html")
+ (synopsis "Forward compatibility for Emacs-24.4's nadvice")
+ (description
+ "This package tries to re-implement some of nadvice.el's functionality on
+top of the old defadvice system, to help users of defadvice move to the new
+advice system without dropping support for Emacs<24.4.")
+ (license license:gpl3+)))
+
+(define-public emacs-url-http-ntlm
+ (package
+ (name "emacs-url-http-ntlm")
+ (version "2.0.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://elpa.gnu.org/packages/"
+ "url-http-ntlm-" version ".el"))
+ (sha256
+ (base32 "1cakq2ykraci7d1gl8rnpv4f2f5ffyaidhqb1282g7i72adwmb98"))))
+ (build-system emacs-build-system)
+ (propagated-inputs `(("emacs-ntlm" ,emacs-ntlm)))
+ (home-page "https://elpa.gnu.org/packages/url-http-ntlm.html")
+ (synopsis "NTLM authentication for the url library")
+ (description "This package provides a NTLM handler for the URL package.")
+ (license license:gpl3+)))
+
+(define-public emacs-soap-client
+ (package
+ (name "emacs-soap-client")
+ (version "3.2.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://elpa.gnu.org/packages/"
+ "soap-client-" version ".tar"))
+ (sha256
+ (base32 "1s0bwnip22nj6kgjadd4zlj9j729hiyyjb66sr51i2mddnf9i95s"))))
+ (build-system emacs-build-system)
+ (home-page "httpa://elpa.gnu.org/packages/soap-client.html")
+ (synopsis "Access SOAP web services")
+ (description
+ "This package provides a SOAP client to access web services.")
+ (license license:gpl3+)))
+
+(define-public emacs-fsm
+ (package
+ (name "emacs-fsm")
+ (version "0.2.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://elpa.gnu.org/packages/fsm-" version ".el"))
+ (sha256
+ (base32 "1jyxyqdbfl8nv7c50q0sg3w5p7whp1sqgi7w921k5hfar4d11qqp"))))
+ (build-system emacs-build-system)
+ (home-page "https://elpa.gnu.org/packages/fsm.html")
+ (synopsis "Finite State Machine library")
+ (description
+ "This package provides Finite State Machine library to make asynchronous
+programming in Emacs Lisp easy and fun.")
+ (license license:gpl3+)))
+
+(define-public emacs-excorporate
+ (package
+ (name "emacs-excorporate")
+ (version "1.0.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://elpa.gnu.org/packages/"
+ "excorporate-" version ".tar"))
+ (sha256
+ (base32 "1g0wc2kp15ra323b4rxvdh58q9c4h7m20grw6a0cs53m7l9xi62f"))))
+ (build-system emacs-build-system)
+ (propagated-inputs
+ `(("emacs-fsm" ,emacs-fsm)
+ ("emacs-nadvice" ,emacs-nadvice)
+ ("emacs-soap-client" ,emacs-soap-client)
+ ("emacs-url-http-ntlm" ,emacs-url-http-ntlm)))
+ (home-page "https://elpa.gnu.org/packages/excorporate.html")
+ (synopsis "Exchange integration")
+ (description "This package provides Exchange integration for Emacs.")
+ (license license:gpl3+)))
+
(define-public emacs-evil-traces
(let ((commit "1931e3ea2c64b4aec393a9c25063c330deff55e3")
(revision "2"))
@@ -26618,19 +26801,18 @@ available.")
(define-public emacs-eshell-did-you-mean
(package
(name "emacs-eshell-did-you-mean")
- (version "0.1")
- (home-page "https://github.com/xuchunyang/eshell-did-you-mean")
+ (version "0.2")
(source
(origin
(method git-fetch)
(uri (git-reference
- (url home-page)
+ (url "https://github.com/xuchunyang/eshell-did-you-mean")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32
- "0v0wshck5n4hspcv1zk1g2nm6xiigcjp16lx0dc8wzkl6ymljvbg"))))
+ (base32 "158g8b4crm0gf5pilfxf89hdsb22gr1wbrjyx9gf45bmcll3i9vf"))))
(build-system emacs-build-system)
+ (home-page "https://github.com/xuchunyang/eshell-did-you-mean")
(synopsis "Display suggestions on 'command not found' in Eshell")
(description "This library adds a list of 'Did you mean...' suggestions
when the command was not found in Eshell. The suggestions are found after the
@@ -27225,14 +27407,14 @@ interface.")
(define-public emacs-ivy-posframe
(package
(name "emacs-ivy-posframe")
- (version "0.6.2")
+ (version "0.6.3")
(source
(origin
(method url-fetch)
(uri (string-append "https://elpa.gnu.org/packages/"
"ivy-posframe-" version ".tar"))
(sha256
- (base32 "1x6pm0pry2j7yazhxvq1gydbymwll9yg85m8qi4sh8s0pnm0vjzk"))))
+ (base32 "0b498qzaydjrhplx4d7zcrs883dlrhfiz812sv4m3pmhfwifcchh"))))
(build-system emacs-build-system)
(propagated-inputs
`(("emacs-ivy" ,emacs-ivy)
diff --git a/gnu/packages/file-systems.scm b/gnu/packages/file-systems.scm
index 7f88c34671..e6716e55bc 100644
--- a/gnu/packages/file-systems.scm
+++ b/gnu/packages/file-systems.scm
@@ -1029,8 +1029,8 @@ APFS.")
(define-public xfstests
;; The last release (1.1.0) is from 2011.
- (let ((revision "0")
- (commit "1c18b9ec2fcc94bd05ecdd136aa51c97bf3fa70d"))
+ (let ((revision "1")
+ (commit "bae1d15f6421cbe99b3e2e134c39d50248e7c261"))
(package
(name "xfstests")
(version (git-version "1.1.0" revision commit))
@@ -1042,7 +1042,7 @@ APFS.")
(commit commit)))
(file-name (git-file-name name version))
(sha256
- (base32 "0rrv0rs9nhaza0jk5k0bj27w4lcd1s4a1ls8nr679qi02bgx630x"))))
+ (base32 "01y7dx5sx1xg3dycqlp2b6azclz3xcnx7vdy2rr6zmf210501xd9"))))
(build-system gnu-build-system)
(arguments
`(#:phases
diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm
index 521bfcca2c..dd2444e3c9 100644
--- a/gnu/packages/games.scm
+++ b/gnu/packages/games.scm
@@ -65,6 +65,8 @@
;;; Copyright © 2021 Solene Rapenne <solene@perso.pw>
;;; Copyright © 2021 Noisytoot <noisytoot@disroot.org>
;;; Copyright © 2021 Petr Hodina <phodina@protonmail.com>
+;;; Copyright © 2021 Brendan Tildesley <mail@brendan.scot>
+;;; Copyright © 2021 Christopher Baines <mail@cbaines.net>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -151,6 +153,7 @@
#:use-module (gnu packages less)
#:use-module (gnu packages libcanberra)
#:use-module (gnu packages libedit)
+ #:use-module (gnu packages libidn)
#:use-module (gnu packages libunwind)
#:use-module (gnu packages linux)
#:use-module (gnu packages llvm)
@@ -171,6 +174,7 @@
#:use-module (gnu packages perl-check)
#:use-module (gnu packages perl-compression)
#:use-module (gnu packages pkg-config)
+ #:use-module (gnu packages pretty-print)
#:use-module (gnu packages protobuf)
#:use-module (gnu packages pulseaudio)
#:use-module (gnu packages python)
@@ -4276,14 +4280,14 @@ world}, @uref{http://evolonline.org, Evol Online} and
(define openttd-engine
(package
(name "openttd-engine")
- (version "1.11.2")
+ (version "12.0")
(source
(origin (method url-fetch)
(uri (string-append "https://cdn.openttd.org/openttd-releases/"
version "/openttd-" version "-source.tar.xz"))
(sha256
(base32
- "0v9f93lsdcv3ia28y8iihx9nj9zp6fpf5hkdrpl4ypw159d97fhg"))))
+ "1p1j5cf4ry57dcgm7qx2g2s00z1c6qgjabb4kqjp00yz00wgv85v"))))
(build-system cmake-build-system)
(inputs
`(("allegro" ,allegro)
@@ -4313,7 +4317,7 @@ engine. When you start it you will be prompted to download a graphics set.")
(define openttd-opengfx
(package
(name "openttd-opengfx")
- (version "0.6.1")
+ (version "7.1")
(source
(origin
(method url-fetch)
@@ -4321,10 +4325,10 @@ engine. When you start it you will be prompted to download a graphics set.")
version "/opengfx-" version "-source.tar.xz"))
(sha256
(base32
- "0jgy8xv7r72m127qn09vr3rxhnbakl2990f7lldsk0d5d8n993vd"))))
+ "0nhzlk6s73qvznm5fdwcs1b42g2plf26s5ag39fvck45zm7m48jk"))))
(build-system gnu-build-system)
(arguments
- '(#:make-flags (list "CC=gcc"
+ `(#:make-flags (list (string-append "CC=" ,(cc-for-target))
(string-append "INSTALL_DIR="
(assoc-ref %outputs "out")
"/share/games/openttd/baseset/opengfx"))
@@ -4352,7 +4356,7 @@ engine. When you start it you will be prompted to download a graphics set.")
("grfcodec" ,grfcodec)
("nml" ,nml)
("which" ,which)
- ("python" ,python-2)))
+ ("python" ,python)))
(home-page "http://dev.openttdcoop.org/projects/opengfx")
(synopsis "Base graphics set for OpenTTD")
(description
@@ -4372,7 +4376,7 @@ OpenGFX provides you with...
(define openttd-opensfx
(package
(name "openttd-opensfx")
- (version "1.0.1")
+ (version "1.0.2")
(source
(origin
(method url-fetch)
@@ -4381,11 +4385,11 @@ OpenGFX provides you with...
version "/opensfx-" version "-source.tar.xz"))
(sha256
(base32
- "06vycppqcxbfdqlxzna5xr303zgcmpcvj6ylw5b2ws0ssph2f1s0"))))
+ "0aym026lg0r7dp3jxxs9c0rj8lwy1fz3v9hmk3mml6sycsg3fv42"))))
(build-system gnu-build-system)
(native-inputs
`(("catcodec" ,catcodec)
- ("python" ,python-2)
+ ("python" ,python)
("tar" ,tar)))
(arguments
`(#:make-flags
@@ -4422,7 +4426,7 @@ the original Transport Tycoon Deluxe.")
(define openttd-openmsx
(package
(name "openttd-openmsx")
- (version "0.4.0")
+ (version "0.4.2")
(source
(origin
(method url-fetch)
@@ -4431,11 +4435,13 @@ the original Transport Tycoon Deluxe.")
version "/openmsx-" version "-source.tar.xz"))
(sha256
(base32
- "0prjljsdgdxqdhhcriqskqha004ybs575xcjq80zha3pqnmrdk0k"))))
+ "0h583d8fxy78kc3jvpp78r76a48qhxrhm4q7jbnj74aw0kwrcl8g"))))
(build-system gnu-build-system)
(native-inputs
`(("grfcodec" ,grfcodec)
- ("python" ,python-2)
+ ; Scripts are Python3 compatible, but call the interpreter as
+ ; python instead of python3.
+ ("python" ,python-wrapper)
("tar" ,tar)))
(arguments
`(#:make-flags
@@ -4484,6 +4490,7 @@ Transport Tycoon Deluxe.")
`(("opengfx" ,openttd-opengfx)
("openmsx" ,openttd-openmsx)
("opensfx" ,openttd-opensfx)
+ ("gcc" ,gcc-9) ; for #include <charconv>
,@(package-native-inputs openttd-engine)))))
(define openrct2-title-sequences
@@ -6647,7 +6654,7 @@ fight against their plot and save his fellow rabbits from slavery.")
(define-public 0ad-data
(package
(name "0ad-data")
- (version "0.0.23b-alpha")
+ (version "0.0.25b-alpha")
(source
(origin
(method url-fetch)
@@ -6655,21 +6662,10 @@ fight against their plot and save his fellow rabbits from slavery.")
version "-unix-data.tar.xz"))
(file-name (string-append name "-" version ".tar.xz"))
(sha256
- (base32
- "04x7729hk6zw1xj3n4s4lvaviijsnbjf5rhzvjxlr5fygvg4l6z1"))
- (modules '((guix build utils)))
- (snippet
- #~(begin
- (for-each (lambda (name)
- (let* ((dir (string-append "binaries/data/mods/" name))
- (file (string-append dir "/" name ".zip"))
- (unzip #$(file-append unzip "/bin/unzip")))
- (invoke unzip "-d" dir file)
- (delete-file file)))
- '("mod" "public"))
- #t))))
+ (base32 "1c9zrddmjxvvacismld6fbwbw9vrdbq6g6d3424p8w5p6xg5wlwy"))))
(build-system trivial-build-system)
(native-inputs `(("tar" ,tar)
+ ("unzip" ,unzip)
("xz" ,xz)))
(arguments
`(#:modules ((guix build utils))
@@ -6679,10 +6675,17 @@ fight against their plot and save his fellow rabbits from slavery.")
(let ((out (assoc-ref %outputs "out"))
(source (assoc-ref %build-inputs "source"))
(tar (search-input-file %build-inputs "/bin/tar"))
+ (unzip (search-input-file %build-inputs "/bin/unzip"))
(xz-path (string-append (assoc-ref %build-inputs "xz") "/bin")))
(setenv "PATH" xz-path)
(mkdir out)
- (invoke tar "xvf" source "-C" out "--strip=3")))))
+ (invoke tar "xvf" source "-C" out "--strip=3")
+ (for-each (lambda (name)
+ (let* ((dir (string-append out "/mods/" name))
+ (file (string-append dir "/" name ".zip")))
+ (invoke unzip "-o" "-d" dir file)
+ (delete-file file)))
+ '("mod" "public"))))))
(synopsis "Data files for 0ad")
(description "0ad-data provides the data files required by the game 0ad.")
(home-page "https://play0ad.com")
@@ -6700,7 +6703,7 @@ fight against their plot and save his fellow rabbits from slavery.")
(define-public 0ad
(package
(name "0ad")
- (version "0.0.23b-alpha")
+ (version "0.0.25b-alpha")
(source
(origin
(method url-fetch)
@@ -6708,23 +6711,24 @@ fight against their plot and save his fellow rabbits from slavery.")
version "-unix-build.tar.xz"))
(file-name (string-append name "-" version ".tar.xz"))
(sha256
- (base32
- "0draa53xg69i5qhqym85658m45xhwkbiimaldj4sr3703rjgggq1"))))
- ;; A snippet here would cause a build failure because of timestamps
- ;; reset. See https://bugs.gnu.org/26734.
+ (base32 "1p9fa8f7sjb9c5wl3mawzyfqvgr614kdkhrj2k4db9vkyisws3fp"))))
+ ;; A snippet here would cause a build failure because of timestamps
+ ;; reset. See https://bugs.gnu.org/26734.
(inputs
`(("0ad-data" ,0ad-data)
("curl" ,curl)
("enet" ,enet)
+ ("fmt" ,fmt)
("gloox" ,gloox)
- ("icu4c" ,icu4c)
+ ("icu4c" ,icu4c-68)
+ ("libidn" ,libidn)
("libpng" ,libpng)
("libsodium" ,libsodium)
("libvorbis" ,libvorbis)
("libxcursor" ,libxcursor)
("libxml2" ,libxml2)
("miniupnpc" ,miniupnpc)
- ("mozjs-38" ,mozjs-38)
+ ("mozjs" ,mozjs-78)
("openal" ,openal)
("sdl2" ,sdl2)
("wxwidgets" ,wxwidgets)
@@ -6732,29 +6736,27 @@ fight against their plot and save his fellow rabbits from slavery.")
(native-inputs
`(("boost" ,boost)
("cmake" ,cmake-minimal)
+ ("cxxtest" ,cxxtest)
("mesa" ,mesa)
("pkg-config" ,pkg-config)
("python-2" ,python-2)))
(build-system gnu-build-system)
(arguments
`(#:make-flags '("config=release" "verbose=1" "-C" "build/workspaces/gcc")
+ #:tests? #f ;tests fail currently
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'delete-bundles
- (lambda _
+ (lambda* (#:key inputs #:allow-other-keys)
(delete-file-recursively "libraries/source/spidermonkey")
- #t))
- (add-after 'unpack 'fix-x11-includes
- (lambda _
- (substitute* "source/lib/sysdep/os/unix/x/x.cpp"
- (("<Xlib.h>") "<X11/Xlib.h>"))
- (substitute* "source/lib/sysdep/os/unix/x/x.cpp"
- (("<Xatom.h>") "<X11/Xatom.h>"))
- (substitute* "source/lib/sysdep/os/unix/x/x.cpp"
- (("<Xcursor/Xcursor.h>") "<X11/Xcursor/Xcursor.h>"))
- #t))
+ (delete-file-recursively "libraries/source/cxxtest-4.4")
+ (substitute* "build/premake/premake5.lua"
+ (("rootdir\\.\\.\"\\/libraries\\/source\\/cxxtest-4.4\\/bin\\/cxxtestgen\"")
+ (string-append "\"" (assoc-ref inputs "cxxtest")
+ "/bin/cxxtestgen"
+ "\"")))))
(replace 'configure
- (lambda* (#:key inputs outputs #:allow-other-keys)
+ (lambda* (#:key inputs outputs tests? #:allow-other-keys)
(let* ((jobs (number->string (parallel-job-count)))
(out (assoc-ref outputs "out"))
(lib (string-append out "/lib"))
@@ -6762,11 +6764,13 @@ fight against their plot and save his fellow rabbits from slavery.")
(setenv "JOBS" (string-append "-j" jobs))
(setenv "CC" "gcc")
(with-directory-excursion "build/workspaces"
- (invoke "./update-workspaces.sh"
- (string-append "--libdir=" lib)
- (string-append "--datadir=" data)
- ;; TODO: "--with-system-nvtt"
- "--with-system-mozjs38")))))
+ (apply invoke
+ `("./update-workspaces.sh"
+ ,(string-append "--libdir=" lib)
+ ,(string-append "--datadir=" data)
+ ;; TODO: "--with-system-nvtt"
+ "--with-system-mozjs"
+ ,@(if tests? '() '("--without-tests"))))))))
(delete 'check)
(replace 'install
(lambda* (#:key inputs outputs #:allow-other-keys)
@@ -6776,7 +6780,9 @@ fight against their plot and save his fellow rabbits from slavery.")
(lib (string-append out "/lib"))
(data (string-append out "/share/0ad"))
(applications (string-append out "/share/applications"))
- (pixmaps (string-append out "/share/pixmaps"))
+ (hicolor (string-append out "/share/icons/hicolor/128x128/apps"))
+ (metainfo (string-append out "/share/metainfo"))
+ (mime (string-append out "/share/mime/application"))
(0ad-data (assoc-ref inputs "0ad-data")))
;; data
(copy-recursively "data" data)
@@ -6795,12 +6801,14 @@ fight against their plot and save his fellow rabbits from slavery.")
;; resources
(with-directory-excursion "../build/resources"
(install-file "0ad.desktop" applications)
- (install-file "0ad.png" pixmaps))
- #t)))
+ (install-file "0ad.png" hicolor)
+ (install-file "0ad.appdata.xml" metainfo)
+ (install-file "pyrogenesis.xml" mime)))))
(add-after 'install 'check
- (lambda _
- (with-directory-excursion "system"
- (invoke "./test")))))))
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (with-directory-excursion "system"
+ (invoke "./test"))))))))
(home-page "https://play0ad.com")
(synopsis "3D real-time strategy game of ancient warfare")
(description "0 A.D. is a real-time strategy (RTS) game of ancient
@@ -9242,7 +9250,7 @@ levels to unlock.")
(define simgear
(package
(name "simgear")
- (version "2018.3.5")
+ (version "2020.3.11")
(source
(origin
(method url-fetch)
@@ -9250,22 +9258,31 @@ levels to unlock.")
(version-major+minor version) "/"
"simgear-" version ".tar.bz2"))
(sha256
- (base32 "1vkqm66r1205k3hdjmx5wmx5kvmsb0dgfzrs8n5gqnxj8szs42dl"))))
+ (base32 "0g2g3n3sb6kdimvcrn9kvlhyyrp5c6lx20fgzz8l609v5aygr3dv"))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ ;; There are some bundled libraries.
+ (for-each delete-file-recursively
+ '("3rdparty/expat/"))
+ #t))))
(build-system cmake-build-system)
(arguments
- `(#:phases
+ `(#:configure-flags (list "-DSYSTEM_EXPAT=ON")
+ #:phases
(modify-phases %standard-phases
(replace 'check
- (lambda _
- ;; Skip tests that require internet access.
- (invoke "ctest" "-E" "(http|dns)"))))))
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ ;; Skip tests that require internet access.
+ (invoke "ctest" "-E" "(http|dns)")))))))
(inputs
- `(("boost" ,boost-for-mysql) ; fails with 1.69
+ `(("boost" ,boost)
("curl" ,curl)
("expat" ,expat)
("mesa" ,mesa)
("openal" ,openal)
- ("openscenegraph" ,openscenegraph-3.4)
+ ("openscenegraph" ,openscenegraph)
("zlib" ,zlib)))
(home-page "https://home.flightgear.org/")
(synopsis "Libraries for 3D simulations and games")
@@ -9286,41 +9303,42 @@ and also provides the base for the FlightGear Flight Simulator.")
(version-major+minor version) "/"
"flightgear-" version ".tar.bz2"))
(sha256
- (base32 "0ya3vb539kwi1qrifqhsj5j3k4w6s06hrllp2vdzxf6id7cgf0hc"))
+ (base32 "15sar94x13j2y1m6adgmz2q1m1i9bzj3sxqla6y3m9vyf33hc9zy"))
(modules '((guix build utils)))
(snippet
'(begin
;; There are some bundled libraries.
(for-each delete-file-recursively
- '("3rdparty/sqlite3/"))
+ '("3rdparty/sqlite3/"
+ "3rdparty/cppunit/"))
#t))))
- (build-system cmake-build-system)
+ (build-system qt-build-system)
(arguments
`(#:configure-flags
(list "-DSYSTEM_SQLITE=ON"
+ "-DSYSTEM_CPPUNIT=ON"
(string-append "-DFG_DATA_DIR="
(assoc-ref %outputs "out")
"/share/flightgear"))
- ;; TODO: test cannot be run because the "run_test_suite" executable
- ;; does not seem to be built.
+ ;; TODO: test suite segfaults.
#:tests? #f
#:phases
(modify-phases %standard-phases
- (add-after 'install 'wrap-executable
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (let ((out (assoc-ref outputs "out")))
- (wrap-program (string-append out "/bin/fgfs")
- `("QT_PLUGIN_PATH" ":" prefix
- ,(map (lambda (label)
- (string-append (assoc-ref inputs label)
- "/lib/qt5/plugins"))
- '("qtbase" "qtdeclarative" "qtsvg")))
- `("QML2_IMPORT_PATH" ":" prefix
- ,(map (lambda (label)
- (string-append (assoc-ref inputs label)
- "/lib/qt5/qml"))
- '("qtdeclarative" "qtsvg"))))
- #t)))
+ (add-after 'unpack 'skip-some-tests
+ (lambda _
+ (substitute* "test_suite/unit_tests/Instrumentation/test_gps.hxx"
+ (("CPPUNIT_TEST\\(testLongLegWestbound\\);" all)
+ (string-append "// " all))
+ (("CPPUNIT_TEST\\(testFinalLegCourse\\);" all)
+ (string-append "// " all)))))
+ (add-after 'build 'build-test-suite
+ (lambda* args
+ ((assoc-ref %standard-phases 'build)
+ #:make-flags (list "fgfs_test_suite"))))
+ ;; Test suite needs access to FGData so run it after 'install.
+ (delete 'check)
+ (add-after 'install-data 'check
+ (assoc-ref %standard-phases 'check))
(add-after 'install 'install-data
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((share (string-append (assoc-ref outputs "out") "/share/flightgear")))
@@ -9330,7 +9348,7 @@ and also provides the base for the FlightGear Flight Simulator.")
"--strip-components=1")))
#t)))))
(inputs
- `(("boost" ,boost-for-mysql) ; same as simgear
+ `(("boost" ,boost)
("dbus" ,dbus)
("eudev" ,eudev)
("freeglut" ,freeglut)
@@ -9338,7 +9356,7 @@ and also provides the base for the FlightGear Flight Simulator.")
("glew" ,glew)
("libpng" ,libpng)
("openal" ,openal)
- ("openscenegraph" ,openscenegraph-3.4)
+ ("openscenegraph" ,openscenegraph)
("plib" ,plib)
("qtbase" ,qtbase-5)
("qtdeclarative" ,qtdeclarative)
@@ -9356,11 +9374,11 @@ and also provides the base for the FlightGear Flight Simulator.")
(method url-fetch)
(uri (string-append "mirror://sourceforge/flightgear/release-"
(version-major+minor version) "/"
- "FlightGear-" version "-data.tar.bz2"))
+ "FlightGear-" version "-data.txz"))
(sha256
(base32
- "04fv9za5zlyxlyfh6jx78y42l3jazvzl9dq2y6rzxqlcc9g5swhk"))))))
- (home-page "https://home.flightgear.org/")
+ "0n5mw9vw1snab16c1y3i9ylkiv54az57bs2mvpq20hhg5hdiagqj"))))))
+ (home-page "https://www.flightgear.org/")
(synopsis "Flight simulator")
(description "The goal of the FlightGear project is to create a
sophisticated flight simulator framework for use in research or academic
@@ -12656,7 +12674,7 @@ disassembly of the DOS version, extended with new features.")
(define-public fheroes2
(package
(name "fheroes2")
- (version "0.9.8")
+ (version "0.9.9")
(build-system cmake-build-system)
(arguments
`(#:tests? #f ; no tests
@@ -12676,7 +12694,7 @@ disassembly of the DOS version, extended with new features.")
(commit version)))
(file-name (git-file-name name version))
(sha256
- (base32 "1sc7rmyiciahxh5f6rarhil2hrw8q8sjdssh063grji50mlnrf6a"))))
+ (base32 "030kfaagxy3i7bjvbx2nf05jmbbh5g2r52l17y9bl6vbfj67yvxy"))))
(home-page "https://ihhub.github.io/fheroes2/")
(synopsis "Turn-based strategy game engine")
(description "@code{fheroes2} is an implementation of Heroes of Might and
diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index 938720f928..7532943839 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -1181,7 +1181,7 @@ to create databases that are optimized for rendering/tile/map-services.")
(define-public libosmium
(package
(name "libosmium")
- (version "2.15.6")
+ (version "2.17.1")
(source
(origin
(method git-fetch)
@@ -1190,7 +1190,7 @@ to create databases that are optimized for rendering/tile/map-services.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "0rqy18bbakp41f44y5id9ixh0ar2dby46z17p4115z8k1vv9znq2"))))
+ (base32 "0xw71lrw4q4sdm51rl0zg87ywxfkxbw9h52zqim0z0xl5qh5q8xf"))))
(build-system cmake-build-system)
(propagated-inputs
`(("boost" ,boost)
@@ -1214,7 +1214,7 @@ OpenStreetMap data.")
(define-public osm2pgsql
(package
(name "osm2pgsql")
- (version "1.2.2")
+ (version "1.5.1")
(source
(origin
(method git-fetch)
@@ -1223,7 +1223,7 @@ OpenStreetMap data.")
(commit version)))
(file-name (git-file-name name version))
(sha256
- (base32 "1j35aa8qinhavliqi5pdm0viyi7lm5xyk402rliaxxs1r2hbsafn"))
+ (base32 "0i18mskcs087dn3f3h9n7j0wafn8502m0h13mrjwin38xsz0crfj"))
(modules '((guix build utils)))
(snippet
'(begin
diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm
index 36ffd3f4a7..f027e287cd 100644
--- a/gnu/packages/gnome.scm
+++ b/gnu/packages/gnome.scm
@@ -48,7 +48,7 @@
;;; Copyright © 2020 Oleg Pykhalov <go.wigust@gmail.com>
;;; Copyright © 2020 Pierre Neidhardt <mail@ambrevar.xyz>
;;; Copyright © 2020 raingloom <raingloom@riseup.net>
-;;; Copyright © 2020 Nicolas Goaziou <mail@nicolasgoaziou.fr>
+;;; Copyright © 2020, 2021 Nicolas Goaziou <mail@nicolasgoaziou.fr>
;;; Copyright © 2020 Naga Malleswari <nagamalli@riseup.net>
;;; Copyright © 2020 Ryan Prior <rprior@protonmail.com>
;;; Copyright © 2020, 2021 Vinicius Monego <monego@posteo.net>
@@ -12003,7 +12003,7 @@ provided there is a DBus service present:
(define-public parlatype
(package
(name "parlatype")
- (version "2.1")
+ (version "3.0")
(source
(origin
(method git-fetch)
@@ -12012,13 +12012,17 @@ provided there is a DBus service present:
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "1c15ja0rwz3jj8bnqdq0nmqka39iwrhy8krdv2a2x8nl4shfpmv0"))))
+ (base32 "0mvzagkg9kq2ji6mffi37mdjxmlj3wa65d4lcayij9hsmjlklnzs"))))
(build-system meson-build-system)
(arguments
`(#:glib-or-gtk? #t
#:tests? #f ;require internet access
#:phases
(modify-phases %standard-phases
+ (add-after 'unpack 'skip-gtk-update-icon-cache
+ (lambda _
+ (substitute* "data/meson_post_install.py"
+ (("gtk-update-icon-cache") "true"))))
(add-after 'install 'wrap-parlatype
;; Add gstreamer plugin provided in this package to system's
;; plugins.
@@ -12029,8 +12033,7 @@ provided there is a DBus service present:
":"
(getenv "GST_PLUGIN_SYSTEM_PATH"))))
(wrap-program (string-append out "/bin/parlatype")
- `("GST_PLUGIN_SYSTEM_PATH" ":" = (,gst-plugin-path))))
- #t)))))
+ `("GST_PLUGIN_SYSTEM_PATH" ":" = (,gst-plugin-path)))))))))
(native-inputs
`(("appstream-glib" ,appstream-glib)
("desktop-file-utils" ,desktop-file-utils) ;for desktop-file-validate
@@ -12043,10 +12046,11 @@ provided there is a DBus service present:
("gst-plugins-good" ,gst-plugins-good)
("gstreamer" ,gstreamer)
("gtk+" ,gtk+)
+ ("iso-codes" ,iso-codes)
("pocketsphinx" ,pocketsphinx)
("pulseaudio" ,pulseaudio)
("sphinxbase" ,sphinxbase)))
- (home-page "http://gkarsay.github.io/parlatype/")
+ (home-page "https://www.parlatype.org")
(synopsis "GNOME audio player for transcription")
(description "Parlatype is an audio player for the GNOME desktop
environment. Its main purpose is the manual transcription of spoken
diff --git a/gnu/packages/graphics.scm b/gnu/packages/graphics.scm
index c3b55f695a..dbb489452e 100644
--- a/gnu/packages/graphics.scm
+++ b/gnu/packages/graphics.scm
@@ -1289,32 +1289,6 @@ virtual reality, scientific visualization and modeling.")
;; LGPL 2.1, but with 4 exceptions. This version is called OSGPL.
(license license:lgpl2.1)))
-;; We need this for simgear
-(define-public openscenegraph-3.4
- (package (inherit openscenegraph)
- (name "openscenegraph")
- (version "3.4.1")
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/openscenegraph/OpenSceneGraph")
- (commit (string-append "OpenSceneGraph-" version))))
- (file-name (git-file-name name version))
- (sha256
- (base32
- "1fbzg1ihjpxk6smlq80p3h3ggllbr16ihd2fxpfwzam8yr8yxip9"))))
- (arguments
- (substitute-keyword-arguments (package-arguments openscenegraph)
- ((#:configure-flags flags)
- `(cons
- ;; The jpeg plugin requires conversion between integers and booleans
- "-DCMAKE_CXX_FLAGS=-fpermissive"
- ,flags))))
- (inputs
- `(("libjpeg" ,libjpeg-turbo)
- ,@(package-inputs openscenegraph)))))
-
(define-public gr-framework
(package
(name "gr-framework")
diff --git a/gnu/packages/haskell-apps.scm b/gnu/packages/haskell-apps.scm
index 994214e900..faa3b52c5c 100644
--- a/gnu/packages/haskell-apps.scm
+++ b/gnu/packages/haskell-apps.scm
@@ -316,14 +316,14 @@ to @code{cabal repl}).")
(define-public git-annex
(package
(name "git-annex")
- (version "8.20211011")
+ (version "8.20211028")
(source
(origin
(method url-fetch)
(uri (string-append "https://hackage.haskell.org/package/"
"git-annex/git-annex-" version ".tar.gz"))
(sha256
- (base32 "02s7921ihmbndp7lk1nhhiljky02ikq4qax4mhg609qjhbl6piwd"))))
+ (base32 "0bff1bchp60hbslb9yaagvd7hym26w0c3gkkssm7sildwqazwpng"))))
(build-system haskell-build-system)
(arguments
`(#:configure-flags
diff --git a/gnu/packages/haskell-xyz.scm b/gnu/packages/haskell-xyz.scm
index 45bf97febd..8373d93c76 100644
--- a/gnu/packages/haskell-xyz.scm
+++ b/gnu/packages/haskell-xyz.scm
@@ -9873,8 +9873,7 @@ syntax and semantics as Perl 5.")
(home-page "https://www.yesodweb.com/book/persistent")
(synopsis "Type-safe, multi-backend data serialization for Haskell")
(description "This Haskell package allows Haskell programs to access data
-storage systems like PostgreSQL, SQLite, MySQL and MongoDB in a type-safe
-way.")
+storage systems like PostgreSQL, SQLite, and MariaDB in a type-safe way.")
(license license:expat)))
(define-public ghc-persistent-sqlite
diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index bcdadfbe80..b8997dd42b 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -352,7 +352,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
;; The current "stable" kernels. That is, the most recently released major
;; versions that are still supported upstream.
-(define-public linux-libre-5.14-version "5.14.15")
+(define-public linux-libre-5.14-version "5.14.16")
(define-public linux-libre-5.14-gnu-revision "gnu")
(define deblob-scripts-5.14
(linux-libre-deblob-scripts
@@ -362,7 +362,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
(base32 "024rz0bp3n3r5nkwbib7byx10d72c2fh5cw9iv00diyzgnp819g7")))
(define-public linux-libre-5.14-pristine-source
(let ((version linux-libre-5.14-version)
- (hash (base32 "01m4qw1z7xn3ngsbm1bvcvikqpkjjr9n8585556wkmz9d469mwvl")))
+ (hash (base32 "005wis2y5dhksb6n0r4p3xjldppmdnd360dhxa04rfc4z2qwn3f3")))
(make-linux-libre-source version
(%upstream-linux-source version hash)
deblob-scripts-5.14)))
@@ -370,7 +370,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
;; The "longterm" kernels — the older releases with long-term upstream support.
;; Here are the support timelines:
;; <https://www.kernel.org/category/releases.html>
-(define-public linux-libre-5.10-version "5.10.76")
+(define-public linux-libre-5.10-version "5.10.77")
(define-public linux-libre-5.10-gnu-revision "gnu1")
(define deblob-scripts-5.10
(linux-libre-deblob-scripts
@@ -380,12 +380,12 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
(base32 "024rz0bp3n3r5nkwbib7byx10d72c2fh5cw9iv00diyzgnp819g7")))
(define-public linux-libre-5.10-pristine-source
(let ((version linux-libre-5.10-version)
- (hash (base32 "140qkvs88b5zh6mxxzpf36z1r8bbvyh3yigripqjz1k236x0j2j8")))
+ (hash (base32 "1hwgbcfv9wfx9ka25lsqjrnzskynfgmswcyp5vk14wnxq7glxdnk")))
(make-linux-libre-source version
(%upstream-linux-source version hash)
deblob-scripts-5.10)))
-(define-public linux-libre-5.4-version "5.4.156")
+(define-public linux-libre-5.4-version "5.4.157")
(define-public linux-libre-5.4-gnu-revision "gnu1")
(define deblob-scripts-5.4
(linux-libre-deblob-scripts
@@ -395,12 +395,12 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
(base32 "1a0k9i8gnzkyvfr80f8xw2fnxfwddhz1pzicz9fh0y3jzzkzk45p")))
(define-public linux-libre-5.4-pristine-source
(let ((version linux-libre-5.4-version)
- (hash (base32 "1zkpqfhrc5n0yiij3jzvzywgabva53c8668f1ly1pkrzcbj77zh6")))
+ (hash (base32 "0jl62j22vs59bc90mvzavv0ii9hvk436pbnrpqf3x9f8nfybngwz")))
(make-linux-libre-source version
(%upstream-linux-source version hash)
deblob-scripts-5.4)))
-(define-public linux-libre-4.19-version "4.19.214")
+(define-public linux-libre-4.19-version "4.19.215")
(define-public linux-libre-4.19-gnu-revision "gnu1")
(define deblob-scripts-4.19
(linux-libre-deblob-scripts
@@ -410,12 +410,12 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
(base32 "1a0k9i8gnzkyvfr80f8xw2fnxfwddhz1pzicz9fh0y3jzzkzk45p")))
(define-public linux-libre-4.19-pristine-source
(let ((version linux-libre-4.19-version)
- (hash (base32 "0i08np4gxiks7chp6j328pdqb02apbba53mj4zvxb9v37qpxzqgz")))
+ (hash (base32 "1czjqa5wbsmzgl7wwqlp9qbdig45ibq11m9pcykrjaclrgwn884y")))
(make-linux-libre-source version
(%upstream-linux-source version hash)
deblob-scripts-4.19)))
-(define-public linux-libre-4.14-version "4.14.253")
+(define-public linux-libre-4.14-version "4.14.254")
(define-public linux-libre-4.14-gnu-revision "gnu1")
(define deblob-scripts-4.14
(linux-libre-deblob-scripts
@@ -425,12 +425,12 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
(base32 "1a0k9i8gnzkyvfr80f8xw2fnxfwddhz1pzicz9fh0y3jzzkzk45p")))
(define-public linux-libre-4.14-pristine-source
(let ((version linux-libre-4.14-version)
- (hash (base32 "1mgl55c8fa2ry4qp0phkdkzjhwfnkbhvi266n348kyjyqnjl234f")))
+ (hash (base32 "0ihdlsg4jg9wwhhcbjjmrcchnl9pc0szh21nwmbhwnxgqcdmrnfz")))
(make-linux-libre-source version
(%upstream-linux-source version hash)
deblob-scripts-4.14)))
-(define-public linux-libre-4.9-version "4.9.288")
+(define-public linux-libre-4.9-version "4.9.289")
(define-public linux-libre-4.9-gnu-revision "gnu1")
(define deblob-scripts-4.9
(linux-libre-deblob-scripts
@@ -440,12 +440,12 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
(base32 "1a0k9i8gnzkyvfr80f8xw2fnxfwddhz1pzicz9fh0y3jzzkzk45p")))
(define-public linux-libre-4.9-pristine-source
(let ((version linux-libre-4.9-version)
- (hash (base32 "0v5592v565bl924c23m1n7p5zddr0w7zn8m97pmikk6p7cyhjq9n")))
+ (hash (base32 "19kz74qgw5yzfinnsvljmn2zm855lr4cxgfpn8gwljmkspyx1hm5")))
(make-linux-libre-source version
(%upstream-linux-source version hash)
deblob-scripts-4.9)))
-(define-public linux-libre-4.4-version "4.4.290")
+(define-public linux-libre-4.4-version "4.4.291")
(define-public linux-libre-4.4-gnu-revision "gnu1")
(define deblob-scripts-4.4
(linux-libre-deblob-scripts
@@ -455,7 +455,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
(base32 "1a0k9i8gnzkyvfr80f8xw2fnxfwddhz1pzicz9fh0y3jzzkzk45p")))
(define-public linux-libre-4.4-pristine-source
(let ((version linux-libre-4.4-version)
- (hash (base32 "1dcx58nmzkcc5nz2b5b7mgw4w7y28v3s9wd8h78czdqfa0kxrl20")))
+ (hash (base32 "0lbbvv3ha4d8nwzjh8bdk0aqyd12w6gw0nsxsdnp8pbmnndgb9vh")))
(make-linux-libre-source version
(%upstream-linux-source version hash)
deblob-scripts-4.4)))
diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm
index e88df7d3f4..b9e68231ef 100644
--- a/gnu/packages/mail.scm
+++ b/gnu/packages/mail.scm
@@ -1734,14 +1734,14 @@ addons which can add many functionalities to the base client.")
(define-public msmtp
(package
(name "msmtp")
- (version "1.8.18")
+ (version "1.8.19")
(source
(origin
(method url-fetch)
(uri (string-append "https://marlam.de/msmtp/releases/"
"/msmtp-" version ".tar.xz"))
(sha256
- (base32 "19b0anfrkg4lqp4h13qi2rqgwvipp1ga0id237nwbp7b6ypn5z0l"))))
+ (base32 "0ssj8izcw1fywihlip6wljd9i41w23cy0vp69sz4v1vn26cf389l"))))
(build-system gnu-build-system)
(inputs
`(("libsecret" ,libsecret)
@@ -1772,6 +1772,8 @@ addons which can add many functionalities to the base client.")
;; connection, instead look up and ping debian.org.
(substitute* (string-append bin "/msmtpq")
(("EMAIL_CONN_TEST=n") "EMAIL_CONN_TEST=p"))))))))
+ (properties
+ '((release-monitoring-url . "https://marlam.de/msmtp/download/")))
(synopsis
"Simple and easy to use SMTP client with decent sendmail compatibility")
(description
diff --git a/gnu/packages/markup.scm b/gnu/packages/markup.scm
index 359b8c47e8..d0b987159f 100644
--- a/gnu/packages/markup.scm
+++ b/gnu/packages/markup.scm
@@ -7,6 +7,8 @@
;;; Copyright © 2020 Marius Bakke <mbakke@fastmail.com>
;;; Copyright © 2020 EuAndreh <eu@euandre.org>
;;; Copyright © 2021 Noisytoot <noisytoot@disroot.org>
+;;; Copyright © 2021 Zhu Zihao <all_but_last@163.com>
+;;; Copyright © 2021 Petr Hodina <phodina@protonmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -24,7 +26,7 @@
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
(define-module (gnu packages markup)
- #:use-module (guix licenses)
+ #:use-module ((guix licenses) #:prefix license:)
#:use-module (guix download)
#:use-module (guix git-download)
#:use-module (guix packages)
@@ -34,6 +36,7 @@
#:use-module (guix build-system perl)
#:use-module (guix build-system python)
#:use-module (guix utils)
+ #:use-module (gnu packages base)
#:use-module (gnu packages compression)
#:use-module (gnu packages)
#:use-module (gnu packages perl)
@@ -67,7 +70,7 @@
(description "Hoedown is a standards compliant, fast, secure markdown
processing library written in C.")
(home-page "https://github.com/hoedown/hoedown")
- (license expat)))
+ (license license:expat)))
(define-public markdown
(package
@@ -110,8 +113,38 @@ processing library written in C.")
"Markdown is a text-to-HTML conversion tool for web writers. It allows
you to write using an easy-to-read, easy-to-write plain text format, then
convert it to structurally valid XHTML (or HTML).")
- (license (non-copyleft "file://License.text"
- "See License.text in the distribution."))))
+ (license (license:non-copyleft "file://License.text"
+ "See License.text in the distribution."))))
+
+(define-public lowdown
+ (package
+ (name "lowdown")
+ (version "0.10.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://kristaps.bsd.lv/lowdown/snapshots/lowdown-"
+ version ".tar.gz"))
+ (sha256
+ (base32 "15v2kk4ffqw3n6y6n9plch4qcib3ynnhw0ih8wn2v9qgn4jssp5p"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:test-target "regress"
+ #:phases
+ (modify-phases %standard-phases
+ (replace 'configure
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "out")))
+ (invoke "./configure"
+ (string-append "PREFIX=" out)
+ (string-append "MANDIR=" out "/share/man"))))))))
+ (native-inputs
+ `(("which" ,which)))
+ (home-page "https://kristaps.bsd.lv/lowdown/")
+ (synopsis "Simple Markdown translator")
+ (description "Lowdown is a Markdown translator producing HTML5,
+roff documents in the ms and man formats, LaTeX, gemini, and terminal output.")
+ (license license:isc)))
(define-public discount
(package
@@ -157,7 +190,7 @@ convert it to structurally valid XHTML (or HTML).")
"Discount is a markdown implementation, written in C. It provides a
@command{markdown} command, and a library.")
(home-page "https://www.pell.portland.or.us/~orc/Code/discount/")
- (license bsd-3)))
+ (license license:bsd-3)))
(define-public perl-text-markdown-discount
(package
@@ -202,7 +235,7 @@ implementation.
use Text::Markdown::Discount;
my $html = markdown($text)
@end example")
- (license perl-license)))
+ (license license:perl-license)))
(define-public cmark
(package
@@ -242,7 +275,7 @@ for parsing and rendering CommonMark.")
;; cmark is distributed with a BSD-2 license, but some components are Expat
;; licensed. The CommonMark specification is Creative Commons CC-BY-SA 4.0
;; licensed. See 'COPYING' in the source distribution for more information.
- (license (list bsd-2 expat cc-by-sa4.0))))
+ (license (list license:bsd-2 license:expat license:cc-by-sa4.0))))
(define-public smu
(package
@@ -278,7 +311,7 @@ amount of indents it scales just great.
Smu was started as a rewrite of Markdown but became something more
lightweight and consistent. The biggest difference between Markdown
and smu is that smu doesn't support reference style links.")
- (license x11)))
+ (license license:x11)))
(define-public md4c
(package
@@ -300,7 +333,7 @@ and smu is that smu doesn't support reference style links.")
(description "MD4C is a C Markdown parser with a
SAX-like interface. It is compliant to the CommonMark specification,
with a few extensions.")
- (license expat)))
+ (license license:expat)))
(define-public python-mistletoe
(package
@@ -322,4 +355,4 @@ parser that supports definitions of custom tokens.
Parsing Markdown into an abstract syntax tree also allows @code{mistletoe} to
swap out renderers for different output formats, without touching any of the
core components.")
- (license expat)))
+ (license license:expat)))
diff --git a/gnu/packages/messaging.scm b/gnu/packages/messaging.scm
index 9a3cfc9308..479ed00c94 100644
--- a/gnu/packages/messaging.scm
+++ b/gnu/packages/messaging.scm
@@ -9,7 +9,7 @@
;;; Copyright © 2016 Andy Patterson <ajpatter@uwaterloo.ca>
;;; Copyright © 2016, 2017, 2018, 2019 Clément Lassieur <clement@lassieur.org>
;;; Copyright © 2017 Mekeor Melire <mekeor.melire@gmail.com>
-;;; Copyright © 2017, 2018, 2020 Arun Isaac <arunisaac@systemreboot.net>
+;;; Copyright © 2017, 2018, 2020, 2021 Arun Isaac <arunisaac@systemreboot.net>
;;; Copyright © 2017–2021 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2017 Theodoros Foradis <theodoros@foradis.org>
;;; Copyright © 2017, 2018, 2019 Rutger Helling <rhelling@mykolab.com>
@@ -2986,4 +2986,121 @@ API. Mattermost is not required.")
(home-page "https://github.com/42wim/matterbridge")
(license license:asl2.0)))
+(define-public weechat-matrix
+ (package
+ (name "weechat-matrix")
+ (version "0.3.0")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/poljar/weechat-matrix")
+ (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1iv55n4k05139f7jzkhczgw4qp6qwilrvfsy3c6v2m1kxffj12d3"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (delete 'build)
+ (replace 'install
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let* ((weechat-python (string-append (assoc-ref outputs "out")
+ "/share/weechat/python")))
+ ;; Avoid circular import by renaming the matrix module to
+ ;; weechat_matrix.
+ (substitute* (cons "main.py"
+ (append (find-files "matrix")
+ (find-files "tests")))
+ (("from matrix") "from weechat_matrix")
+ (("import matrix") "import weechat_matrix"))
+ ;; Install python modules.
+ (invoke "make" "install-lib"
+ (string-append "INSTALLDIR="
+ (site-packages inputs outputs)
+ "/weechat_matrix"))
+ ;; Extend PYTHONPATH to find installed python modules.
+ (add-installed-pythonpath inputs outputs)
+ ;; Augment sys.path so that dependencies are found.
+ (substitute* "main.py"
+ (("import os\n" all)
+ (apply string-append
+ all
+ "import sys\n"
+ (map (lambda (path)
+ (string-append "sys.path.append('" path "')\n"))
+ (string-split (getenv "PYTHONPATH") #\:)))))
+ ;; Install script.
+ (mkdir-p weechat-python)
+ (copy-file "main.py"
+ (string-append weechat-python "/matrix.py")))))
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (invoke "pytest")))))))
+ (inputs
+ `(("python-matrix-nio" ,python-matrix-nio)
+ ("python-pygments" ,python-pygments)
+ ("python-pyopenssl" ,python-pyopenssl)
+ ("python-webcolors" ,python-webcolors)))
+ (native-inputs
+ `(("python-pytest" ,python-pytest)))
+ (home-page "https://github.com/poljar/weechat-matrix")
+ (synopsis "Weechat Matrix protocol script")
+ (description "@code{weechat-matrix} is a Python plugin for Weechat that lets
+Weechat communicate over the Matrix protocol.")
+ (license license:isc)))
+
+(define-public weechat-wee-slack
+ (package
+ (name "weechat-wee-slack")
+ (version "2.8.0")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/wee-slack/wee-slack")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0xfklr0gsc9jgxfyrrb2j756lclz9g8imcb0pk0xgyj8mhsw23zk"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (delete 'build)
+ (replace 'install
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ ;; Augment sys.path so that dependencies are found.
+ (substitute* "wee_slack.py"
+ (("import sys\n" all)
+ (apply string-append
+ all
+ (map (lambda (path)
+ (string-append "sys.path.append('" path "')\n"))
+ (string-split (getenv "PYTHONPATH") #\:)))))
+ ;; Install script.
+ (install-file "wee_slack.py"
+ (string-append (assoc-ref outputs "out")
+ "/share/weechat/python"))))
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (invoke "pytest")))))))
+ (inputs
+ `(("python-websocket-client" ,python-websocket-client)))
+ (native-inputs
+ `(("python-pytest" ,python-pytest)))
+ (home-page "https://github.com/wee-slack/wee-slack")
+ (synopsis "Weechat Slack script")
+ (description "@code{weechat-wee-slack} is a WeeChat native client for
+Slack. It provides supplemental features only available in the web/mobile
+clients such as synchronizing read markers, typing notification, threads (and
+more)! It connects via the Slack API, and maintains a persistent websocket
+for notification of events.")
+ (license license:expat)))
+
;;; messaging.scm ends here
diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index 8ed245474f..8d1836c44e 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -6079,7 +6079,7 @@ short-time Fourier transform, available as LV2 audio plugin and JACK client.")
(define-public x42-plugins
(package
(name "x42-plugins")
- (version "20200714")
+ (version "20211016")
(source
(origin
(method url-fetch)
@@ -6087,7 +6087,7 @@ short-time Fourier transform, available as LV2 audio plugin and JACK client.")
(string-append "https://gareus.org/misc/x42-plugins/x42-plugins-"
version ".tar.xz"))
(sha256
- (base32 "1av05ykph8x67018hm9zfgh1vk0zi39mvrsxkj6bm4hkarxf0vvl"))))
+ (base32 "11bf6q42ihyk4qxwf83y0847zzyl65kwpbk3hmyz0f0ykil5fsb7"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; no "check" target
@@ -6096,13 +6096,10 @@ short-time Fourier transform, available as LV2 audio plugin and JACK client.")
"LIBZITACONVOLVER=-lzita-convolver"
(string-append "FONTFILE="
(assoc-ref %build-inputs "font-dejavu")
- "/share/fonts/truetype/DejaVuSans-Bold.ttf"))
+ "/share/fonts/truetype/DejaVuSans-Bold.ttf")
+ (string-append "CC=" ,(cc-for-target)))
#:phases
(modify-phases %standard-phases
- (add-before 'build 'set-CC-variable
- (lambda _
- (setenv "CC" "gcc")
- #t))
(delete 'configure))))
(inputs
`(("cairo" ,cairo)
diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm
index 7b1363a5c3..2f8b9da32a 100644
--- a/gnu/packages/ocaml.scm
+++ b/gnu/packages/ocaml.scm
@@ -778,7 +778,7 @@ the opam file format.")
(define-public opam
(package
(name "opam")
- (version "2.1.0")
+ (version "2.1.1")
(source (origin
(method git-fetch)
(uri (git-reference
@@ -787,7 +787,7 @@ the opam file format.")
(file-name (git-file-name name version))
(sha256
(base32
- "12l7l4pbzy71k1yc7ym5aczajszvc9bqkdnfg8xhqc8ch8j1h1lj"))))
+ "12cxpnkv8n90g66b31c7hsxl2yy537fgf19xhr6zn4n024bh6dh3"))))
(build-system dune-build-system)
(arguments
`(#:test-target "."
diff --git a/gnu/packages/patches/i3status-rust-enable-unstable-features.patch b/gnu/packages/patches/i3status-rust-enable-unstable-features.patch
new file mode 100644
index 0000000000..535b45d865
--- /dev/null
+++ b/gnu/packages/patches/i3status-rust-enable-unstable-features.patch
@@ -0,0 +1,20 @@
+From 3006390c0058f06c255d9850327163aebcdc3b40 Mon Sep 17 00:00:00 2001
+From: Petr Hodina <phodina@protonmail.com>
+Date: Mon, 11 Oct 2021 22:35:39 +0200
+Subject: [PATCH] Enable unstable features.
+
+
+diff --git a/src/main.rs b/src/main.rs
+index d9e964b..820e22e 100644
+--- a/src/main.rs
++++ b/src/main.rs
+@@ -1,3 +1,6 @@
++#![feature(bool_to_option)]
++#![feature(clamp)]
++
+ #[macro_use]
+ mod de;
+ #[macro_use]
+--
+2.33.0
+
diff --git a/gnu/packages/patches/libblockdev-glib-compat.patch b/gnu/packages/patches/libblockdev-glib-compat.patch
deleted file mode 100644
index bb25d5d963..0000000000
--- a/gnu/packages/patches/libblockdev-glib-compat.patch
+++ /dev/null
@@ -1,61 +0,0 @@
-Don't use g_memdup() which is removed in newer versions of GLib.
-
-See <https://github.com/storaged-project/libblockdev/pull/623>.
-
-Taken from upstream:
-https://github.com/storaged-project/libblockdev/commit/5528baef6ccc835a06c45f9db34a2c9c3f2dd940
-
-diff --git a/src/lib/plugin_apis/vdo.api b/src/lib/plugin_apis/vdo.api
---- a/src/lib/plugin_apis/vdo.api
-+++ b/src/lib/plugin_apis/vdo.api
-@@ -170,7 +170,22 @@ void bd_vdo_stats_free (BDVDOStats *stats) {
- * Deprecated: 2.24: Use LVM-VDO integration instead.
- */
- BDVDOStats* bd_vdo_stats_copy (BDVDOStats *stats) {
-- return g_memdup (stats, sizeof (BDVDOStats));
-+ if (stats == NULL)
-+ return NULL;
-+
-+ BDVDOStats *new_stats = g_new0 (BDVDOStats, 1);
-+
-+ new_stats->block_size = stats->block_size;
-+ new_stats->logical_block_size = stats->logical_block_size;
-+ new_stats->physical_blocks = stats->physical_blocks;
-+ new_stats->data_blocks_used = stats->data_blocks_used;
-+ new_stats->overhead_blocks_used = stats->overhead_blocks_used;
-+ new_stats->logical_blocks_used = stats->logical_blocks_used;
-+ new_stats->used_percent = stats->used_percent;
-+ new_stats->saving_percent = stats->saving_percent;
-+ new_stats->write_amplification_ratio = stats->write_amplification_ratio;
-+
-+ return new_stats;
- }
-
- GType bd_vdo_stats_get_type () {
-diff --git a/src/plugins/vdo.c b/src/plugins/vdo.c
---- a/src/plugins/vdo.c
-+++ b/src/plugins/vdo.c
-@@ -81,7 +81,22 @@ void bd_vdo_stats_free (BDVDOStats *stats) {
- }
-
- BDVDOStats* bd_vdo_stats_copy (BDVDOStats *stats) {
-- return g_memdup (stats, sizeof (BDVDOStats));
-+ if (stats == NULL)
-+ return NULL;
-+
-+ BDVDOStats *new_stats = g_new0 (BDVDOStats, 1);
-+
-+ new_stats->block_size = stats->block_size;
-+ new_stats->logical_block_size = stats->logical_block_size;
-+ new_stats->physical_blocks = stats->physical_blocks;
-+ new_stats->data_blocks_used = stats->data_blocks_used;
-+ new_stats->overhead_blocks_used = stats->overhead_blocks_used;
-+ new_stats->logical_blocks_used = stats->logical_blocks_used;
-+ new_stats->used_percent = stats->used_percent;
-+ new_stats->saving_percent = stats->saving_percent;
-+ new_stats->write_amplification_ratio = stats->write_amplification_ratio;
-+
-+ return new_stats;
- }
-
-
diff --git a/gnu/packages/protobuf.scm b/gnu/packages/protobuf.scm
index f8dff1f229..59b0d4a3c8 100644
--- a/gnu/packages/protobuf.scm
+++ b/gnu/packages/protobuf.scm
@@ -7,6 +7,7 @@
;;; Copyright © 2020, 2021 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;; Copyright © 2020 Vinicius Monego <monego@posteo.net>
;;; Copyright © 2020 Brett Gilio <brettg@gnu.org>
+;;; Copyright © 2021 Felix Gruber <felgru@posteo.net>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -209,7 +210,7 @@ code.")
(define-public protozero
(package
(name "protozero")
- (version "1.6.8")
+ (version "1.7.0")
(source
(origin
(method git-fetch)
@@ -218,7 +219,7 @@ code.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "1hfijpfylf1c71wa3mk70gjc88b6k1q7cxb87cwqdflw5q2x8ma6"))))
+ (base32 "0fdihfl5j68wayjjxvpvhvnjq1anzcfnfl09f68wpzbkg3zmhblz"))))
(build-system cmake-build-system)
(home-page "https://github.com/mapbox/protozero")
(synopsis "Minimalistic protocol buffer decoder and encoder in C++")
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 6439b7a611..49d9410c59 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -44,6 +44,7 @@
;;; Copyright © 2021 Greg Hogan <code@greghogan.com>
;;; Copyright © 2021 Maxime Devos <maximedevos@telenet.be>
;;; Copyright © 2021 Pradana Aumars <paumars@courrier.dev>
+;;; Copyright © 2021 Arun Isaac <arunisaac@systemreboot.net>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -6242,3 +6243,79 @@ communicate with Microsoft Azure Storage services.")
comments, or tags from HTML snippets, extract base url from HTML snippets,
translate entities on HTML strings, among other things.")
(license license:bsd-3)))
+
+(define-public python-webcolors
+ (package
+ (name "python-webcolors")
+ (version "1.11.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "webcolors" version))
+ (sha256
+ (base32 "1rkda75h2p65zx6r84c9mjavn4xpviqvqrklvdvcklapd5in1wvn"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (replace 'check
+ (lambda* (#:key tests? inputs outputs #:allow-other-keys)
+ (when tests?
+ (add-installed-pythonpath inputs outputs)
+ (invoke "pytest")))))))
+ (native-inputs
+ `(("python-pytest" ,python-pytest)))
+ (home-page "https://github.com/ubernostrum/webcolors")
+ (synopsis "HTML/CSS color definitions library")
+ (description "@code{python-webcolors} is a module for working with
+HTML/CSS color definitions. Normalizing and converting between the following
+formats is supported.
+@itemize
+@item Specification-defined color names
+@item Six-digit hexadecimal
+@item Three-digit hexadecimal
+@item Integer rgb() triplet
+@item Percentage rgb() triplet
+@end itemize
+Only the RGB colorspace is supported. Conversion to/from the HSL colorspace
+can be handled by the @code{colorsys} module in the Python standard library.")
+ (license license:bsd-3)))
+
+(define-public python-flask-combo-jsonapi
+ (package
+ (name "python-flask-combo-jsonapi")
+ (version "1.1.0")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/AdCombo/flask-combo-jsonapi")
+ (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "07fhcjiyif80z1vyh35za29sqx1mmqh568jrbrrs675j4a797sj1"))))
+ (build-system python-build-system)
+ (propagated-inputs
+ `(("python-flask" ,python-flask)
+ ("python-marshmallow" ,python-marshmallow-3.2)
+ ("python-marshmallow-jsonapi" ,python-marshmallow-jsonapi)
+ ("python-simplejson" ,python-simplejson)
+ ("python-sqlalchemy" ,python-sqlalchemy-1.3)
+ ("python-apispec" ,python-apispec)
+ ("python-simplejson" ,python-simplejson)
+ ("python-six" ,python-six)))
+ (native-inputs
+ `(("python-coverage" ,python-coverage)
+ ("python-coveralls" ,python-coveralls)
+ ("python-pytest" ,python-pytest)
+ ("python-pytest-runner" ,python-pytest-runner)))
+ (home-page "https://github.com/AdCombo/flask-combo-jsonapi")
+ (synopsis "Flask extension to quickly create JSON:API 1.0 REST Web APIs")
+ (description
+ "Flask-COMBO-JSONAPI is a Python Flask extension for building REST Web APIs
+compliant with the @uref{https://jsonapi.org, JSON:API 1.0} specification.
+
+It tries to combine the power of Flask-Restless with the flexibility of
+Flask-RESTful to quickly build APIs that fit the complexity of existing
+real-life projects with legacy data and diverse storage providers.")
+ (license license:expat)))
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index ee37c05dac..60531288a1 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -19203,11 +19203,52 @@ address is valid and really exists.")
("python-pytz" ,python-pytz)))
(home-page "https://github.com/marshmallow-code/marshmallow")
(synopsis "Convert complex datatypes to and from native
-Python datatypes.")
+Python datatypes")
(description "@code{marshmallow} provides a library for converting
complex datatypes to and from native Python datatypes.")
(license license:expat)))
+(define-public python-marshmallow-3.2
+ (package
+ (inherit python-marshmallow)
+ (version "3.2.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "marshmallow" version))
+ (sha256
+ (base32 "1w18klwj0z9bqxj252qpj1hz8l46nl27sbc89rkajc7mln73wbws"))))))
+
+(define-public python-marshmallow-jsonapi
+ (package
+ (name "python-marshmallow-jsonapi")
+ (version "0.24.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "marshmallow-jsonapi" version))
+ (sha256
+ (base32 "1d9pxcgmln4gls99vwj1h24qv0lz7fb2jqmqrsiv1pid1snc125x"))))
+ (build-system python-build-system)
+ (propagated-inputs
+ `(("python-marshmallow" ,python-marshmallow-3.2)))
+ (native-inputs
+ `(("python-faker" ,python-faker)
+ ("python-flake8" ,python-flake8)
+ ("python-flake8-bugbear" ,python-flake8-bugbear)
+ ("python-flask" ,python-flask)
+ ("python-mock" ,python-mock)
+ ("python-pre-commit" ,python-pre-commit)
+ ("python-pytest" ,python-pytest)
+ ("python-tox" ,python-tox)))
+ (home-page "https://github.com/marshmallow-code/marshmallow-jsonapi")
+ (synopsis "JSON:API 1.0 formatting with Marshmallow")
+ (description
+ "The marshmallow-jsonapi package provides a simple way to produce
+@uref{https://jsonapi.org, JSON:API}-compliant data in any Python Web framework.
+It includes optional utilities to integrate with Flask.")
+ (license license:expat)))
+
(define-public python-apispec
(package
(name "python-apispec")
diff --git a/gnu/packages/rust-apps.scm b/gnu/packages/rust-apps.scm
index 94667c79d5..6d95b496c3 100644
--- a/gnu/packages/rust-apps.scm
+++ b/gnu/packages/rust-apps.scm
@@ -12,6 +12,7 @@
;;; Copyright © 2021 Zheng Junjie <873216071@qq.com>
;;; Copyright © 2021 Alexandru-Sergiu Marton <brown121407@posteo.ro>
;;; Copyright © 2021 Maxim Cournoyer <maxim.cournoyer@gmail.com>
+;;; Copyright © 2021 Petr Hodina <phodina@protonmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -34,6 +35,8 @@
#:use-module (guix download)
#:use-module (guix git-download)
#:use-module (guix packages)
+ #:use-module (guix utils)
+ #:use-module (gnu packages)
#:use-module (gnu packages admin)
#:use-module (gnu packages compression)
#:use-module (gnu packages crates-io)
@@ -41,12 +44,14 @@
#:use-module (gnu packages curl)
#:use-module (gnu packages documentation)
#:use-module (gnu packages fontutils)
+ #:use-module (gnu packages glib)
#:use-module (gnu packages gtk)
#:use-module (gnu packages jemalloc)
#:use-module (gnu packages linux)
#:use-module (gnu packages ssh)
#:use-module (gnu packages pcre)
#:use-module (gnu packages pkg-config)
+ #:use-module (gnu packages pulseaudio)
#:use-module (gnu packages python-xyz)
#:use-module (gnu packages rust)
#:use-module (gnu packages tls)
@@ -439,6 +444,78 @@ characters, ASCII whitespace characters, other ASCII characters and non-ASCII.")
"This package provides a command-line benchmarking tool.")
(license (list license:expat license:asl2.0))))
+(define-public i3status-rust
+ (package
+ (name "i3status-rust")
+ (version "0.20.1")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/greshake/i3status-rust")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (patches (search-patches "i3status-rust-enable-unstable-features.patch"))
+ (sha256
+ (base32 "00gzm3g297s9bfp13vnb623p7dfac3g6cdhz2b3lc6l0kmnnqs1s"))))
+ (build-system cargo-build-system)
+ (native-inputs
+ `(("pkg-config" ,pkg-config)))
+ (inputs
+ `(("curl" ,curl)
+ ("dbus" ,dbus)
+ ("pulseaudio" ,pulseaudio)
+ ("openssl" ,openssl)
+ ("zlib" ,zlib)))
+ (arguments
+ `(#:features '("pulseaudio" "libpulse-binding")
+ #:install-source? #f
+ #:cargo-inputs
+ (("rust-chrono" ,rust-chrono-0.4)
+ ("rust-chrono-tz" ,rust-chrono-tz-0.5)
+ ("rust-crossbeam-channel" ,rust-crossbeam-channel-0.5)
+ ("rust-curl" ,rust-curl-0.4)
+ ("rust-dbus" ,rust-dbus-0.9)
+ ("rust-dbus-tree" ,rust-dbus-tree-0.9)
+ ("rust-lazy-static" ,rust-lazy-static-1)
+ ("rust-nix" ,rust-nix-0.20)
+ ("rust-nl80211" ,rust-nl80211-0.0.2)
+ ("rust-serde" ,rust-serde-1)
+ ("rust-serde-derive" ,rust-serde-derive-1)
+ ("rust-serde-json" ,rust-serde-json-1)
+ ("rust-signal-hook" ,rust-signal-hook-0.3)
+ ("rust-swayipc" ,rust-swayipc-2)
+ ("rust-toml" ,rust-toml-0.5)
+ ("rust-cpuprofiler" ,rust-cpuprofiler-0.0)
+ ("rust-inotify" ,rust-inotify-0.9)
+ ("rust-libpulse-binding" ,rust-libpulse-binding-2)
+ ("rust-maildir" ,rust-maildir-0.5)
+ ("rust-notmuch" ,rust-notmuch-0.6)
+ ("rust-progress" ,rust-progress-0.2))
+ #:cargo-development-inputs
+ (("rust-assert-fs" ,rust-assert-fs-1))
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'fix-resources-path
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((resources (string-append %output "/share")))
+ (substitute* "src/util.rs"
+ (("/usr/share/i3status-rust") resources)))))
+ (add-after 'install 'install-resources
+ (lambda* (#:key outputs #:allow-other-keys)
+ (copy-recursively "files" (string-append %output "/share"))))
+ (add-after 'unpack 'enable-unstable-features
+ (lambda _
+ (setenv "RUSTC_BOOTSTRAP" "1")
+ #t)))))
+ (home-page "https://github.com/greshake/i3status-rust")
+ (synopsis "i3status, written in pure Rust")
+ (description "@code{i3status-rs} is a feature-rich and resource-friendly
+replacement for i3status, written in pure Rust. It provides a way to display
+@code{blocks} of system information (time, battery status, volume, etc) on the i3
+bar. It is also compatible with sway.")
+ (license license:gpl3)))
+
(define-public ripgrep
(package
(name "ripgrep")
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 87cb7def34..9a4cdd219d 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -191,7 +191,7 @@ This package also provides @command{xls2csv} to export Excel files to CSV.")
(define r-with-tests
(package
(name "r-with-tests")
- (version "4.1.1")
+ (version "4.1.2")
(source (origin
(method url-fetch)
(uri (string-append "mirror://cran/src/base/R-"
@@ -199,7 +199,7 @@ This package also provides @command{xls2csv} to export Excel files to CSV.")
version ".tar.gz"))
(sha256
(base32
- "0r6kpnxjbvb7gdfg4m1z8zc6xd225vw81wrnf05ps9ajawk06pji"))))
+ "1brqmc7mmb0z94kcs4crgl6v9a6sxhm9fm3y177d81vjkxg24di0"))))
(build-system gnu-build-system)
(arguments
`(#:disallowed-references (,tzdata-for-tests)
@@ -216,8 +216,7 @@ This package also provides @command{xls2csv} to export Excel files to CSV.")
;; This ensures that Guix can detect embedded store references;
;; see bug #28157 for details.
(substitute* "src/library/base/makebasedb.R"
- (("compress = TRUE") "compress = FALSE"))
- #t))
+ (("compress = TRUE") "compress = FALSE"))))
(add-before 'configure 'patch-coreutils-paths
(lambda* (#:key inputs #:allow-other-keys)
(let ((uname-bin (search-input-file inputs "/bin/uname"))
@@ -225,8 +224,7 @@ This package also provides @command{xls2csv} to export Excel files to CSV.")
(substitute* "src/scripts/R.sh.in"
(("uname") uname-bin))
(substitute* "src/unix/sys-std.c"
- (("rm -Rf ") (string-append rm-bin " -Rf "))))
- #t))
+ (("rm -Rf ") (string-append rm-bin " -Rf "))))))
(add-after 'unpack 'build-reproducibly
(lambda _
;; The documentation contains time stamps to demonstrate
@@ -285,17 +283,17 @@ as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\
;; that is suspected to be the culprit.
(substitute* "src/library/methods/DESCRIPTION.in"
(("\\(2008\\)\n") "(2008) ")
- ((" ``Software") "``Software"))
- #t))
+ ((" ``Software") "``Software")
+ (("Data Analysis:.") "Data Analysis:\n")
+ (("Programming with R") " Programming with R"))))
(add-before 'build 'set-locales
(lambda _
(setlocale LC_ALL "C")
- (setenv "LC_ALL" "C")
- #t))
+ (setenv "LC_ALL" "C")))
(add-before 'configure 'set-default-pager
;; Set default pager to "cat", because otherwise it is "false",
;; making "help()" print nothing at all.
- (lambda _ (setenv "PAGER" "cat") #t))
+ (lambda _ (setenv "PAGER" "cat")))
(add-before 'check 'set-timezone
;; Some tests require the timezone to be set. However, the
;; timezone may not just be "UTC", or else a brittle regression
@@ -638,13 +636,13 @@ nonlinear mixed-effects models.")
(define-public r-mgcv
(package
(name "r-mgcv")
- (version "1.8-37")
+ (version "1.8-38")
(source
(origin
(method url-fetch)
(uri (cran-uri "mgcv" version))
(sha256
- (base32 "14gw714xcyvgrbajijmyd4v8zs84i701g7gyld6z8p7677dgc8w8"))))
+ (base32 "1fyx8b0xjyx75mp90v314gayzydkca5y90p76jnwxzfnhxbys4nd"))))
(build-system r-build-system)
(propagated-inputs
`(("r-matrix" ,r-matrix)
@@ -1047,14 +1045,14 @@ solution for sending email, including attachments, from within R.")
(define-public r-stringi
(package
(name "r-stringi")
- (version "1.7.4")
+ (version "1.7.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "stringi" version))
(sha256
(base32
- "1mda4612sc573zabsvygnla3vpnf3mql58fc9j450540h6hlwfv2"))))
+ "0r959gzyqkq9683qdfy95g9plwpj3c73n9lhf0a6byybw4scq519"))))
(build-system r-build-system)
(inputs `(("icu4c" ,icu4c)))
(native-inputs `(("pkg-config" ,pkg-config)))
@@ -1386,13 +1384,13 @@ supported via Andre Simon's highlight package.")
(define-public r-mime
(package
(name "r-mime")
- (version "0.11")
+ (version "0.12")
(source (origin
(method url-fetch)
(uri (cran-uri "mime" version))
(sha256
(base32
- "1h7fz0rqnp970r9q0d95qcxpxm9mb98rqhcdncx0w2qdkyj2fm11"))))
+ "0j9qbq9jfsp61h2d0xmb87pa2wi8nhb1h2wih7l5drf1sr8i0059"))))
(build-system r-build-system)
(home-page "https://github.com/yihui/mime")
(synopsis "R package to map filenames to MIME types")
@@ -1449,13 +1447,13 @@ emitter (http://pyyaml.org/wiki/LibYAML) for R.")
(define-public r-knitr
(package
(name "r-knitr")
- (version "1.34")
+ (version "1.36")
(source (origin
(method url-fetch)
(uri (cran-uri "knitr" version))
(sha256
(base32
- "0p6jdicyqknrqilcjm2h4r6vza5lpzccnsdirj92jb3ljg10b0by"))))
+ "0hcf5gii0qlvv15f86y6h08qp0hd9lcrykzj0mdfjdfi52sgbkkf"))))
(build-system r-build-system)
(propagated-inputs
`(("r-evaluate" ,r-evaluate)
@@ -1602,13 +1600,13 @@ R packages that praise their users.")
(define-public r-testthat
(package
(name "r-testthat")
- (version "3.0.4")
+ (version "3.1.0")
(source (origin
(method url-fetch)
(uri (cran-uri "testthat" version))
(sha256
(base32
- "0iqizv2gpv9fg766qv8hbkmc6c5i9xcfrmq9k5m2550p28zff2w3"))))
+ "11s98q0gm37z1cqzwvdm9pq26v0zbdq9vc5ssl1nsxhsi42v2577"))))
(build-system r-build-system)
(propagated-inputs
`(("r-brio" ,r-brio)
@@ -1664,13 +1662,13 @@ defined in different packages.")
(define-public r-rlang
(package
(name "r-rlang")
- (version "0.4.11")
+ (version "0.4.12")
(source (origin
(method url-fetch)
(uri (cran-uri "rlang" version))
(sha256
(base32
- "1pfm24jjkxzdb5qcbc05dcjxyk69zpfr5jv4xakqh1xh41mr43kl"))))
+ "05cr08smr8dlk10m810rw4qi1yhgnny83rwkxib0l4my71br29ia"))))
(build-system r-build-system)
(home-page "http://rlang.tidyverse.org")
(synopsis "Functions for base types, core R and Tidyverse features")
@@ -1682,14 +1680,14 @@ like tidy evaluation.")
(define-public r-tibble
(package
(name "r-tibble")
- (version "3.1.4")
+ (version "3.1.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "tibble" version))
(sha256
(base32
- "0zqpg2haph0qi1x5r6wr083xckab9gw21jbr9spcr8xdf43hx1vk"))))
+ "1ryv1r3cah1s8dyqdhcb0yl81r384jvgc4d1q9zwsrrsd2x8fqys"))))
(build-system r-build-system)
(propagated-inputs
`(("r-ellipsis" ,r-ellipsis)
@@ -1870,13 +1868,13 @@ times.")
(define-public r-data-table
(package
(name "r-data-table")
- (version "1.14.0")
+ (version "1.14.2")
(source (origin
(method url-fetch)
(uri (cran-uri "data.table" version))
(sha256
(base32
- "0kgbvap5v2spnkz3dwfm4jh4qcpvbzdn9s8bzfnhzabz9qjdxw8k"))))
+ "0arx5wna0sh0vf5q8rjhh8nqdmnvg2pdpbhljl9l0x4kwm8vjhgp"))))
(build-system r-build-system)
(inputs
`(("zlib" ,zlib)))
@@ -2284,14 +2282,14 @@ module, Java Server Pages, and Python's psp module.")
(define-public r-desc
(package
(name "r-desc")
- (version "1.3.0")
+ (version "1.4.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "desc" version))
(sha256
(base32
- "1sw4vya3l971gpccq4gnjywgbl73bgx8la18l0wy617qv94f905y"))))
+ "0jfnwn1kpiill8v4hmzdk90yz4gk2ha0prr2p0hq36s40v3y8842"))))
(build-system r-build-system)
(propagated-inputs
`(("r-crayon" ,r-crayon)
@@ -2557,13 +2555,13 @@ time-of-day values, based on the @code{difftime} class.")
(define-public r-readr
(package
(name "r-readr")
- (version "2.0.1")
+ (version "2.0.2")
(source (origin
(method url-fetch)
(uri (cran-uri "readr" version))
(sha256
(base32
- "0cj5k3ykkhixgdsqm1gnmpc0d8z04l3fhvm2dr5xp7cpmhgsrpfr"))))
+ "05bnvcc55i0xjilfrqx3700mwiz8sgihq1wxlbvvr8nxa7bmxc4q"))))
(build-system r-build-system)
(propagated-inputs
`(("r-cli" ,r-cli)
@@ -2650,13 +2648,13 @@ well as additional utilities such as panel and axis annotation functions.")
(define-public r-rcpparmadillo
(package
(name "r-rcpparmadillo")
- (version "0.10.6.0.0")
+ (version "0.10.7.0.0")
(source (origin
(method url-fetch)
(uri (cran-uri "RcppArmadillo" version))
(sha256
(base32
- "1bcx8fk5l5mmwb6cw36ndvld9v3amkz6vyc19059dw0xp7mxx04v"))))
+ "1x35xb5yfslsdpaz9msl5p9f7gilnbkhwvq7pbycwasvkp2fma01"))))
(properties `((upstream-name . "RcppArmadillo")))
(build-system r-build-system)
(propagated-inputs
@@ -4002,13 +4000,13 @@ vignettes.")
(define-public r-mvtnorm
(package
(name "r-mvtnorm")
- (version "1.1-2")
+ (version "1.1-3")
(source (origin
(method url-fetch)
(uri (cran-uri "mvtnorm" version))
(sha256
(base32
- "05wh7mprf2sim2kxh3d72pdcmml6vbikzxavws1dq6mxwlsy2p7j"))))
+ "0j14q2bkc14v35s5k03sw44zsssrd2qjljlwzj014qxs74hk0kpz"))))
(build-system r-build-system)
(native-inputs
`(("gfortran" ,gfortran)))
@@ -4050,13 +4048,13 @@ memory usage.")
(define-public r-viridis
(package
(name "r-viridis")
- (version "0.6.1")
+ (version "0.6.2")
(source (origin
(method url-fetch)
(uri (cran-uri "viridis" version))
(sha256
(base32
- "1fyax36ycjiypcnxhrv58pq67qv03vfg4lx822d38jpjly54q128"))))
+ "048kwhbhd49g86cq11fl7vm0whwhjl5gs9xjn040lwcjv78qrdb9"))))
(build-system r-build-system)
(propagated-inputs
`(("r-ggplot2" ,r-ggplot2)
@@ -4134,14 +4132,14 @@ selection.")
(define-public r-tidyr
(package
(name "r-tidyr")
- (version "1.1.3")
+ (version "1.1.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "tidyr" version))
(sha256
(base32
- "0cpbrvr759z8p7r9lpkjhj2dcdymsbnaib0rma9b4jb7i3qzmh2a"))))
+ "0h8jfsmn4r7zgfyjmg2qkjd54n0sncq07xjh4mdf2cx4k2z9h30b"))))
(build-system r-build-system)
(propagated-inputs
`(("r-cpp11" ,r-cpp11)
@@ -4219,13 +4217,13 @@ features present in other programming languages.")
(define-public r-plotly
(package
(name "r-plotly")
- (version "4.9.4.1")
+ (version "4.10.0")
(source (origin
(method url-fetch)
(uri (cran-uri "plotly" version))
(sha256
(base32
- "1q711c0lg0jmzrmcc2fhjy70ms49as7cakdbgbh2ij9s149fa7iq"))))
+ "16iqj7sv49mva6siibsci7iijsbnk7pqvfns9al0k35w9mjmr6dx"))))
(build-system r-build-system)
(propagated-inputs
`(("r-base64enc" ,r-base64enc)
@@ -4422,13 +4420,13 @@ package instead.")
(define-public r-hmisc
(package
(name "r-hmisc")
- (version "4.5-0")
+ (version "4.6-0")
(source
(origin
(method url-fetch)
(uri (cran-uri "Hmisc" version))
(sha256
- (base32 "11qj73zj16p113jpwn2vv06l99kqlcxcmrldbpyi5s7pwing9jnx"))))
+ (base32 "1bd1c8sichyijprfpnqj5g72nmgs9jvi0zyw8v4nsg1kn83fj71c"))))
(properties `((upstream-name . "Hmisc")))
(build-system r-build-system)
(native-inputs
@@ -4683,13 +4681,13 @@ mechanism.")
(define-public r-ztable
(package
(name "r-ztable")
- (version "0.2.2")
+ (version "0.2.3")
(source (origin
(method url-fetch)
(uri (cran-uri "ztable" version))
(sha256
(base32
- "0wxcdb7yp2r6w5iznz1k49npp5sn4jiybfcj30s3198hkcnv0r8y"))))
+ "1ps7ix0hc84s0p0ra6bkjxky3cffs1rvdcagqzj78lbdq22dk5j8"))))
(build-system r-build-system)
(propagated-inputs
`(("r-flextable" ,r-flextable)
@@ -5173,14 +5171,14 @@ can be efficiently implemented directly in the R language.")
(define-public r-robustbase
(package
(name "r-robustbase")
- (version "0.93-8")
+ (version "0.93-9")
(source
(origin
(method url-fetch)
(uri (cran-uri "robustbase" version))
(sha256
(base32
- "16fmnk3p32mi70rkx89l1v4pry3gnrpy9jicnlfnk6lg1pwz5j8w"))))
+ "0i9wf4aq8zpn2np6z2rjja21ks9n740dgkiv0qfwdzk3ah3vapyp"))))
(build-system r-build-system)
(native-inputs
`(("gfortran" ,gfortran)))
@@ -5886,18 +5884,18 @@ is supported.")
(define-public r-lubridate
(package
(name "r-lubridate")
- (version "1.7.10")
+ (version "1.8.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "lubridate" version))
(sha256
(base32
- "1s653d6rnpf9bkynxmbq4fdjdcz7r9ma19aph8f5y9ck70his4hm"))))
+ "199b00cql07gf3rf4hh5ba34amnk0ai40zhx73dq1mpkn7ynxml7"))))
(build-system r-build-system)
(propagated-inputs
`(("r-generics" ,r-generics)
- ("r-rcpp" ,r-rcpp)))
+ ("r-cpp11" ,r-cpp11)))
(native-inputs
`(("r-knitr" ,r-knitr)))
(home-page "https://cran.r-project.org/web/packages/lubridate/")
diff --git a/gnu/packages/vim.scm b/gnu/packages/vim.scm
index 358e14b3b5..2537f8e305 100644
--- a/gnu/packages/vim.scm
+++ b/gnu/packages/vim.scm
@@ -1294,3 +1294,32 @@ a sidebar that displays the ctags-generated tags of the current file, ordered
by their scope. This means that for example methods in C++ are displayed under
the class they are defined in.")
(license license:vim)))
+
+(define-public vim-nerdcommenter
+ (let ((commit "a65465d321f2f8a74b2ffa540b9b87563f7e12e8")
+ (revision "1"))
+ (package
+ (name "vim-nerdcommenter")
+ (version (git-version "2.5.2" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/preservim/nerdcommenter")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "00ir65iv8jfbgzjmj7332fmydh0qhabbhx8zbvd3j6pgfxqpaafw"))))
+ (build-system copy-build-system)
+ (arguments
+ '(#:install-plan
+ '(("autoload" "share/vim/vimfiles/")
+ ("doc" "share/vim/vimfiles/")
+ ("plugin" "share/vim/vimfiles/"))))
+ (home-page "https://github.com/preservim/nerdcommenter")
+ (synopsis "Vim plugin for easy commenting of code")
+ (description
+ "NERD commenter is a Vim plugin that provides many different commenting
+operations and styles which are invoked via key mappings and a menu. These
+operations are available for most filetypes.")
+ (license license:cc0))))
diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index 38be76d582..03b3b09acd 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -370,18 +370,18 @@ the same, being completely separated from the Internet.")
(define-public nginx
(package
(name "nginx")
+ ;; Please update the nginx-documentation package together with this one!
;; Track the ‘mainline’ branch. Upstream considers it more reliable than
;; ’stable’ and recommends that “in general you deploy the NGINX mainline
;; branch at all times” (https://www.nginx.com/blog/nginx-1-6-1-7-released/)
- ;; Please update the nginx-documentation package together with this one!
- (version "1.21.3")
+ (version "1.21.4")
(source (origin
(method url-fetch)
(uri (string-append "https://nginx.org/download/nginx-"
version ".tar.gz"))
(sha256
(base32
- "0nhps7igdqcpcy1r8677ar807rfclpylmz3y858a678m1np4lxql"))))
+ "1ziv3xargxhxycd5hp6r3r5mww54nvvydiywcpsamg3i9r3jzxyi"))))
(build-system gnu-build-system)
(inputs `(("libxml2" ,libxml2)
("libxslt" ,libxslt)
@@ -476,9 +476,9 @@ and as a proxy to reduce the load on back-end HTTP or mail servers.")
(define-public nginx-documentation
;; This documentation should be relevant for the current nginx package.
- (let ((version "1.21.3")
- (revision 2769)
- (changeset "16f6fa718be2"))
+ (let ((version "1.21.4")
+ (revision 2791)
+ (changeset "9385526a9b2d"))
(package
(name "nginx-documentation")
(version (simple-format #f "~A-~A-~A" version revision changeset))
@@ -490,7 +490,7 @@ and as a proxy to reduce the load on back-end HTTP or mail servers.")
(file-name (string-append name "-" version))
(sha256
(base32
- "1rjq5xqzx843yk9nblz8lq14r4kmlrahap7m0lkvx5mky80vqp79"))))
+ "07v5vpwg2k4y1asbygmrvsk61l1vbdb2pyllc5k4hcjykg9avfza"))))
(build-system gnu-build-system)
(arguments
'(#:tests? #f ; no test suite
diff --git a/gnu/packages/webkit.scm b/gnu/packages/webkit.scm
index e54b680855..688e745d95 100644
--- a/gnu/packages/webkit.scm
+++ b/gnu/packages/webkit.scm
@@ -241,7 +241,7 @@ acceleration in mind, leveraging common 3D graphics APIs for best performance.")
(build-system cmake-build-system)
(outputs '("out" "doc"))
(arguments
- '(#:tests? #f ; no tests
+ `(#:tests? #f ; no tests
#:build-type "Release" ; turn off debugging symbols to save space
#:configure-flags (list
"-DPORT=GTK"
@@ -295,10 +295,24 @@ acceleration in mind, leveraging common 3D graphics APIs for best performance.")
(("libWPEBackend-fdo-([\\.0-9]+)\\.so" all version)
(string-append wpebackend-fdo "/lib/" all)))
#t)))
+ ,@(if (string-prefix? "x86_64" (or (%current-target-system)
+ (%current-system)))
+ '()
+ '((add-after 'unpack 'disable-sse2
+ (lambda _
+ (substitute* "Source/cmake/DetectSSE2.cmake"
+ (("CHECK_FOR_SSE2\\(\\)") ""))))))
(add-before 'configure 'prepare-build-environment
(lambda* (#:key inputs #:allow-other-keys)
(setenv "CC" "clang")
(setenv "CXX" "clang++")
+ ;; XXX Until we switch back to using GCC,
+ ;; work around <https://bugs.gnu.org/51591>.
+ ,@(if (target-x86-32?)
+ '((substitute* "Source/WTF/wtf/CheckedArithmetic.h"
+ (("#define USE_MUL_OVERFLOW 1")
+ "#define USE_MUL_OVERFLOW 0")))
+ '())
#t))
(add-after 'install 'move-doc-files
(lambda* (#:key outputs #:allow-other-keys)
diff --git a/gnu/packages/zig.scm b/gnu/packages/zig.scm
index ab62f554f4..a7966736e8 100644
--- a/gnu/packages/zig.scm
+++ b/gnu/packages/zig.scm
@@ -1,5 +1,5 @@
;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2021 Liliana Prikler <liliana.prikler@gmail.com>
+;;; Copyright © 2021 Liliana Marie Prikler <liliana.prikler@gmail.com>
;;; Copyright © 2021 Sarah Morgensen <iskarian@mgsn.dev>
;;;
;;; This file is part of GNU Guix.