diff options
Diffstat (limited to 'gnu')
41 files changed, 4136 insertions, 1595 deletions
diff --git a/gnu/home/services/shells.scm b/gnu/home/services/shells.scm index e2730967b2..81d07da86c 100644 --- a/gnu/home/services/shells.scm +++ b/gnu/home/services/shells.scm @@ -305,18 +305,50 @@ source ~/.profile ;;; Bash. ;;; +(define (bash-serialize-aliases field-name val) + #~(string-append + #$@(map + (match-lambda + ((key . #f) + "") + ((key . #t) + #~(string-append "alias " #$key "\n")) + ((key . value) + #~(string-append "alias " #$key "=\"" #$value "\"\n"))) + val))) + (define-configuration home-bash-configuration (package (package bash) "The Bash package to use.") (guix-defaults? (boolean #t) - "Add sane defaults like reading @file{/etc/bashrc}, coloring output -for @code{ls} provided by guix to @file{.bashrc}.") + "Add sane defaults like reading @file{/etc/bashrc} and coloring the output of +@command{ls} to the end of the @file{.bashrc} file.") (environment-variables (alist '()) - "Association list of environment variables to set for the Bash session." + "Association list of environment variables to set for the Bash session. The +rules for the @code{home-environment-variables-service-type} apply +here (@pxref{Essential Home Services}). The contents of this field will be +added after the contents of the @code{bash-profile} field." serialize-posix-env-vars) + (aliases + (alist '()) + "Association list of aliases to set for the Bash session. The aliases will be +defined after the contents of the @code{bashrc} field has been put in the +@file{.bashrc} file. The alias will automatically be quoted, so something line +this: + +@lisp +'((\"ls\" . \"ls -alF\")) +@end lisp + +turns into + +@example +alias ls=\"ls -alF\" +@end example" + bash-serialize-aliases) (bash-profile (text-config '()) "List of file-like objects, which will be added to @file{.bash_profile}. @@ -387,10 +419,10 @@ alias grep='grep --color=auto'\n") (if (or extra-content (not (null? ((configuration-field-getter field-obj) config)))) `(,(object->snake-case-string file-name) - ,(mixed-text-file + ,(apply mixed-text-file (object->snake-case-string file-name) - (if extra-content extra-content "") - (serialize-field field))) + (cons (serialize-field field) + (if extra-content extra-content '())))) '()))) (filter @@ -413,8 +445,8 @@ if [ -f ~/.bashrc ]; then source ~/.bashrc; fi ,@(list (file-if-not-empty 'bashrc (if (home-bash-configuration-guix-defaults? config) - guix-bashrc - #f)) + (list (serialize-field 'aliases) guix-bashrc) + (list (serialize-field 'alises)))) (file-if-not-empty 'bash-logout))))) (define (add-bash-packages config) @@ -423,36 +455,52 @@ if [ -f ~/.bashrc ]; then source ~/.bashrc; fi (define-configuration/no-serialization home-bash-extension (environment-variables (alist '()) - "Association list of environment variables to set.") + "Additional environment variables to set. These will be combined with the +environment variables from other extensions and the base service to form one +coherent block of environment variables.") + (aliases + (alist '()) + "Additional aliases to set. These will be combined with the aliases from +other extensions and the base service.") (bash-profile (text-config '()) - "List of file-like objects.") + "Additional text blocks to add to @file{.bash_profile}, which will be combined +with text blocks from other extensions and the base service.") (bashrc (text-config '()) - "List of file-like objects.") + "Additional text blocks to add to @file{.bashrc}, which will be combined +with text blocks from other extensions and the base service.") (bash-logout (text-config '()) - "List of file-like objects.")) + "Additional text blocks to add to @file{.bash_logout}, which will be combined +with text blocks from other extensions and the base service.")) (define (home-bash-extensions original-config extension-configs) - (home-bash-configuration - (inherit original-config) - (environment-variables - (append (home-bash-configuration-environment-variables original-config) - (append-map - home-bash-extension-environment-variables extension-configs))) - (bash-profile - (append (home-bash-configuration-bash-profile original-config) - (append-map - home-bash-extension-bash-profile extension-configs))) - (bashrc - (append (home-bash-configuration-bashrc original-config) - (append-map - home-bash-extension-bashrc extension-configs))) - (bash-logout - (append (home-bash-configuration-bash-logout original-config) - (append-map - home-bash-extension-bash-logout extension-configs))))) + (match original-config + (($ <home-bash-configuration> _ _ _ environment-variables aliases + bash-profile bashrc bash-logout) + (home-bash-configuration + (inherit original-config) + (environment-variables + (append environment-variables + (append-map + home-bash-extension-environment-variables extension-configs))) + (aliases + (append aliases + (append-map + home-bash-extension-aliases extension-configs))) + (bash-profile + (append bash-profile + (append-map + home-bash-extension-bash-profile extension-configs))) + (bashrc + (append bashrc + (append-map + home-bash-extension-bashrc extension-configs))) + (bash-logout + (append bash-logout + (append-map + home-bash-extension-bash-logout extension-configs))))))) (define home-bash-service-type (service-type (name 'home-bash) @@ -609,10 +657,16 @@ Install and configure Fish, the friendly interactive shell."))) 'home-shell-profile-configuration)) (define (generate-home-bash-documentation) - (generate-documentation - `((home-bash-configuration - ,home-bash-configuration-fields)) - 'home-bash-configuration)) + (string-append + (generate-documentation + `((home-bash-configuration + ,home-bash-configuration-fields)) + 'home-bash-configuration) + "\n\n" + (generate-documentation + `((home-bash-extension + ,home-bash-extension-fields)) + 'home-bash-extension))) (define (generate-home-zsh-documentation) (generate-documentation diff --git a/gnu/local.mk b/gnu/local.mk index 26197c40b9..872fb0128a 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1323,7 +1323,6 @@ dist_patch_DATA = \ %D%/packages/patches/julia-SOURCE_DATE_EPOCH-mtime.patch \ %D%/packages/patches/julia-tracker-16-compat.patch \ %D%/packages/patches/kdbusaddons-kinit-file-name.patch \ - %D%/packages/patches/libblockdev-glib-compat.patch \ %D%/packages/patches/libffi-3.3-powerpc-fixes.patch \ %D%/packages/patches/libffi-float128-powerpc64le.patch \ %D%/packages/patches/librime-fix-build-with-gcc10.patch \ 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. diff --git a/gnu/system/file-systems.scm b/gnu/system/file-systems.scm index e69cfd06e6..c6c1b96d16 100644 --- a/gnu/system/file-systems.scm +++ b/gnu/system/file-systems.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020 Ludovic Courtès <ludo@gnu.org> +;;; Copyright © 2013-2021 Ludovic Courtès <ludo@gnu.org> ;;; Copyright © 2020 Google LLC ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net> ;;; Copyright © 2020, 2021 Maxim Cournoyer <maxim.cournoyer@gmail.com> @@ -30,7 +30,8 @@ #:use-module (srfi srfi-35) #:use-module (srfi srfi-9 gnu) #:use-module (guix records) - #:use-module ((guix diagnostics) #:select (&fix-hint)) + #:use-module ((guix diagnostics) + #:select (source-properties->location leave &fix-hint)) #:use-module (guix i18n) #:use-module (gnu system uuid) #:re-export (uuid ;backward compatibility @@ -107,6 +108,45 @@ ;;; ;;; Code: +(eval-when (expand load eval) + (define invalid-file-system-flags + ;; Note: Keep in sync with 'mount-flags->bit-mask'. + (let ((known-flags '(read-only + bind-mount no-suid no-dev no-exec + no-atime strict-atime lazy-time))) + (lambda (flags) + "Return the subset of FLAGS that is invalid." + (remove (cut memq <> known-flags) flags)))) + + (define (%validate-file-system-flags flags location) + "Raise an error if FLAGS contains invalid mount flags; otherwise return +FLAGS." + (match (invalid-file-system-flags flags) + (() flags) + (invalid + (leave (source-properties->location location) + (N_ "invalid file system mount flag:~{ ~s~}~%" + "invalid file system mount flags:~{ ~s~}~%" + (length invalid)) + invalid))))) + +(define-syntax validate-file-system-flags + (lambda (s) + "Validate the given file system mount flags, raising an error if invalid +flags are found." + (syntax-case s (quote) + ((_ (quote (symbols ...))) ;validate at expansion time + (begin + (%validate-file-system-flags (syntax->datum #'(symbols ...)) + (syntax-source s)) + #'(quote (symbols ...)))) + ((_ flags) + #`(%validate-file-system-flags flags + '#,(datum->syntax s (syntax-source s)))) + (id + (identifier? #'id) + #'%validate-file-system-flags)))) + ;; File system declaration. (define-record-type* <file-system> %file-system make-file-system @@ -115,7 +155,8 @@ (mount-point file-system-mount-point) ; string (type file-system-type) ; string (flags file-system-flags ; list of symbols - (default '())) + (default '()) + (sanitize validate-file-system-flags)) (options file-system-options ; string or #f (default #f)) (mount? file-system-mount? ; Boolean |