diff options
34 files changed, 1556 insertions, 981 deletions
diff --git a/gnu/build/shepherd.scm b/gnu/build/shepherd.scm index 14bdf4edb8..fd93e7f3f4 100644 --- a/gnu/build/shepherd.scm +++ b/gnu/build/shepherd.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2017, 2018, 2019 Ludovic Courtès <ludo@gnu.org> +;;; Copyright © 2017, 2018, 2019, 2020 Ludovic Courtès <ludo@gnu.org> ;;; ;;; This file is part of GNU Guix. ;;; @@ -21,6 +21,7 @@ #:use-module (gnu build linux-container) #:use-module (guix build utils) #:use-module (srfi srfi-1) + #:use-module (srfi srfi-26) #:use-module (ice-9 match) #:export (make-forkexec-constructor/container)) @@ -91,7 +92,10 @@ ;; XXX: Lazy-bind the Shepherd to avoid a compile-time dependency. (module-autoload! (current-module) - '(shepherd service) '(read-pid-file exec-command)) + '(shepherd service) + '(read-pid-file exec-command %precious-signals)) +(module-autoload! (current-module) + '(shepherd system) '(unblock-signals)) (define* (read-pid-file/container pid pid-file #:key (max-delay 5)) "Read PID-FILE in the container namespaces of PID, which exists in a @@ -101,7 +105,8 @@ separate mount and PID name space. Return the \"outer\" PID. " (read-pid-file pid-file #:max-delay max-delay))) (#f - (catch-system-error (kill pid SIGTERM)) + ;; Send SIGTERM to the whole process group. + (catch-system-error (kill (- pid) SIGTERM)) #f) ((? integer? container-pid) ;; XXX: When COMMAND is started in a separate PID namespace, its @@ -158,6 +163,14 @@ namespace, in addition to essential bind-mounts such /proc." (let ((pid (run-container container-directory mounts namespaces 1 (lambda () + ;; First restore the default handlers. + (for-each (cut sigaction <> SIG_DFL) + %precious-signals) + + ;; Unblock any signals that have been blocked + ;; by the parent process. + (unblock-signals %precious-signals) + (mkdir-p "/var/run") (clean-up pid-file) diff --git a/gnu/image.scm b/gnu/image.scm index 0a92d168e9..19b466527b 100644 --- a/gnu/image.scm +++ b/gnu/image.scm @@ -33,6 +33,7 @@ image image-name image-format + image-target image-size image-operating-system image-partitions @@ -67,6 +68,8 @@ image make-image image? (format image-format) ;symbol + (target image-target + (default #f)) (size image-size ;size in bytes as integer (default 'guess)) (operating-system image-operating-system ;<operating-system> diff --git a/gnu/installer/final.scm b/gnu/installer/final.scm index e06b104d59..a742c2a0cd 100644 --- a/gnu/installer/final.scm +++ b/gnu/installer/final.scm @@ -155,6 +155,8 @@ be much appreciated." ;; restart it. (restart-service 'guix-daemon) + (syslog "Killing cow users.") + ;; Kill all processes started while the cow-store was active (logins ;; on other TTYs for instance). (kill-cow-users tmp-dir) @@ -162,6 +164,7 @@ be much appreciated." ;; Try to umount the store overlay. Some process such as udevd ;; workers might still be active, so do some retries. (let loop ((try 5)) + (syslog "Umount try ~a~%" (- 5 try)) (sleep 1) (let ((umounted? (false-if-exception (umount tmp-dir)))) (if (and (not umounted?) (> try 0)) diff --git a/gnu/local.mk b/gnu/local.mk index 6738973e49..aa5b67ab5f 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1058,7 +1058,6 @@ dist_patch_DATA = \ %D%/packages/patches/guile-present-coding.patch \ %D%/packages/patches/guile-rsvg-pkgconfig.patch \ %D%/packages/patches/guile-emacs-fix-configure.patch \ - %D%/packages/patches/guile-sqlite3-fix-cross-compilation.patch \ %D%/packages/patches/gtk2-respect-GUIX_GTK2_PATH.patch \ %D%/packages/patches/gtk2-respect-GUIX_GTK2_IM_MODULE_FILE.patch \ %D%/packages/patches/gtk2-theme-paths.patch \ diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b4be8aee15..406ed2fb14 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -745,13 +745,13 @@ annotations.") (define-public r-ideoviz (package (name "r-ideoviz") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IdeoViz" version)) (sha256 (base32 - "0rsz6dawrx5qdrypxs2hgihmx3kbpdg1y73h876yxccgdlabvzil")))) + "1ndj14qhpgidjb4qsga80ghqzz1x8kvy2gy1bvvgwlkfxa62rn50")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -1072,13 +1072,13 @@ package @code{affy}.") (define-public r-coverageview (package (name "r-coverageview") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CoverageView" version)) (sha256 (base32 - "0s47svs7xnr9jkylq0dxidqrigihdddiprcl0951vjr4w7kmb5nf")))) + "1fcz7pkffz5l3jdxb9glji2zdmr6nx67h6vfpr2yi8n3slg2hrrj")))) (build-system r-build-system) (propagated-inputs `(("r-s4vectors" ,r-s4vectors) @@ -1099,13 +1099,13 @@ how the coverage distributed across the genome.") (define-public r-cummerbund (package (name "r-cummerbund") - (version "2.28.0") + (version "2.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cummeRbund" version)) (sha256 (base32 - "1fjc3bcclm4gsvw4nq6cv3a1kbrldvrxbkyfb9306708si1n4dwk")))) + "1av7yfxcq1wwbqfqcz7caiz5kf6kg5wq9qcg5v6yccihclzwvxjc")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -1165,14 +1165,14 @@ across the entire multi-'omics experiment.") (define-public r-biocversion (package (name "r-biocversion") - (version "3.10.1") + (version "3.11.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocVersion" version)) (sha256 (base32 - "0mfqjqfvrwwglldq3g7nbic5hf3nwzv02nbfxnl2cfvf9gznlh5f")))) + "1rrzx3dqds0jlj1bmjc744wiamb2hssbh3jfxz1s9jp4cvnwrpmz")))) (properties `((upstream-name . "BiocVersion"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/BiocVersion/") @@ -1185,13 +1185,13 @@ of Bioconductor.") (define-public r-biocgenerics (package (name "r-biocgenerics") - (version "0.32.0") + (version "0.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocGenerics" version)) (sha256 (base32 - "1np8y442zyakm4axpinbw1qsgc6wd3zjsnirbhc8lcii4ky9j0rn")))) + "15nvqyh2gx5zkn1krbs5c4rhw5642bijdfsf2rgic70gzr05cksk")))) (properties `((upstream-name . "BiocGenerics"))) (build-system r-build-system) @@ -1205,14 +1205,14 @@ packages.") (define-public r-affycomp (package (name "r-affycomp") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affycomp" version)) (sha256 (base32 - "0cl7c3m2lz2w8g2k7z7wjd0dyj0dkssvms99qpg8a1v3hx1xs6js")))) + "0zg8dshas5b2ny4pnxxxqihnr4l20666ivrgglb939a23mplgps0")))) (properties `((upstream-name . "affycomp"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase))) @@ -1226,14 +1226,14 @@ measures for Affymetrix Oligonucleotide Arrays.") (define-public r-affycompatible (package (name "r-affycompatible") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AffyCompatible" version)) (sha256 (base32 - "10ahrdlifp1i7rd58zb10w75y5bnigs7xp5gv4fhb5y7p7dvb0ks")))) + "0394sr4spafhfypjsafwjr0y0zsgv52ajdcyvsmkdk7375898lqd")))) (properties `((upstream-name . "AffyCompatible"))) (build-system r-build-system) @@ -1254,14 +1254,14 @@ Command Console} (AGCC)-compatible sample annotation files.") (define-public r-affycontam (package (name "r-affycontam") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affyContam" version)) (sha256 (base32 - "0yd1prgv5zfkg22ski73mvg96qknwz8v6ji6s4qy8p4wrqyj7b7l")))) + "1dh5c3blk2dl9kg13y6snplnx61x2f9hvp5lc7jmg25xk916517i")))) (properties `((upstream-name . "affyContam"))) (build-system r-build-system) (propagated-inputs @@ -1279,14 +1279,14 @@ problems in CEL-level data to help evaluate performance of quality metrics.") (define-public r-affycoretools (package (name "r-affycoretools") - (version "1.58.4") + (version "1.60.1") (source (origin (method url-fetch) (uri (bioconductor-uri "affycoretools" version)) (sha256 (base32 - "1p283ysib04qzaayxmrpsmk5bq0jdq2rlky180jrlskpyg6risfw")))) + "0cnb54b3kmg9rnycvaz949bdali9n98qzrw7gwka6abmg1lv232s")))) (properties `((upstream-name . "affycoretools"))) (build-system r-build-system) (propagated-inputs @@ -1309,6 +1309,8 @@ problems in CEL-level data to help evaluate performance of quality metrics.") ("r-rsqlite" ,r-rsqlite) ("r-s4vectors" ,r-s4vectors) ("r-xtable" ,r-xtable))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/affycoretools/") (synopsis "Functions for analyses with Affymetrix GeneChips") (description @@ -1319,14 +1321,14 @@ to streamline the more common analyses that a Biostatistician might see.") (define-public r-affxparser (package (name "r-affxparser") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affxparser" version)) (sha256 (base32 - "03h4lxr48p84f6i7zb2rm10ma3k4d1nmvdw5yhxcmzqbmd12lk40")))) + "0d4hq1w0a3dm4bg9qsv7wqrbv2y7b9gllxfmnqs9n2nnwmvgi8yq")))) (properties `((upstream-name . "affxparser"))) (build-system r-build-system) (home-page "https://github.com/HenrikBengtsson/affxparser") @@ -1347,14 +1349,14 @@ structure.") (define-public r-annotate (package (name "r-annotate") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotate" version)) (sha256 (base32 - "0rcmdy6hs6m4d6wxgi52c0bhdsbf2sm9f155qbcb05sn0nh8pxwy")))) + "1ivszqknryq6n5a85z8zj12fvgcs6zz3zlza8q08pl6cs4m5rm4w")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -1374,15 +1376,17 @@ microarrays.") (define-public r-hpar (package (name "r-hpar") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hpar" version)) (sha256 (base32 - "1yhay1ryrgj9cqa1x136cw40ca93afyvg0sarm30jsbj8nc1rm5m")))) + "1jq0qw7wq3426cp004divywjm3ryixkykcmwlhrri13agz6rx3r9")))) (build-system r-build-system) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/hpar/") (synopsis "Human Protein Atlas in R") (description "This package provides a simple interface to and data from @@ -1392,14 +1396,14 @@ the Human Protein Atlas project.") (define-public r-regioner (package (name "r-regioner") - (version "1.18.1") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "regioneR" version)) (sha256 (base32 - "0if7r6njz3ahm545383z5mzmzw8fdvw80a9lfz160j5pcgpx2dq9")))) + "10i21gxv0n7lrflhj5ja672xjizy1i4y4iq3pmjgbf0dpy1lxsih")))) (properties `((upstream-name . "regioneR"))) (build-system r-build-system) (propagated-inputs @@ -1411,6 +1415,8 @@ the Human Protein Atlas project.") ("r-memoise" ,r-memoise) ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/regioneR/") (synopsis "Association analysis of genomic regions") (description "This package offers a statistical framework based on @@ -1421,14 +1427,14 @@ region sets and other genomic features.") (define-public r-reportingtools (package (name "r-reportingtools") - (version "2.26.0") + (version "2.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReportingTools" version)) (sha256 (base32 - "0wmi2219wydyzc07rz3azsrksa7wiacfh9pr5x2fsmj9f0w3n15w")))) + "1ig1h224silbdbdr0j9j9sysp9l9dzpcsjzn8jp57h3gh4pdqbfx")))) (properties `((upstream-name . "ReportingTools"))) (build-system r-build-system) @@ -1452,6 +1458,8 @@ region sets and other genomic features.") ("r-pfam-db" ,r-pfam-db) ("r-r-utils" ,r-r-utils) ("r-xml" ,r-xml))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/ReportingTools/") (synopsis "Tools for making reports in various formats") (description @@ -1469,14 +1477,14 @@ browser.") (define-public r-geneplotter (package (name "r-geneplotter") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "geneplotter" version)) (sha256 (base32 - "1k6780fn1kkghpm1prhhsyw621441a3bmnqfl9ns0zbc1zdq39nx")))) + "1y494da1llmrvn3qm7akwgwjazvpffabi8llw3fbday14cay1br5")))) (build-system r-build-system) (propagated-inputs `(("r-annotate" ,r-annotate) @@ -1494,14 +1502,14 @@ browser.") (define-public r-oligoclasses (package (name "r-oligoclasses") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "oligoClasses" version)) (sha256 (base32 - "02m1m3dkiyywalphw3i5n6y3bs8zp24xh59v9cz6jgjpah811skf")))) + "05jy9qz3ir4maxackr1xqlfi1czhy1qd22wwibjdhfh5dp534cpn")))) (properties `((upstream-name . "oligoClasses"))) (build-system r-build-system) (propagated-inputs @@ -1529,14 +1537,14 @@ packages.") (define-public r-oligo (package (name "r-oligo") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "oligo" version)) (sha256 (base32 - "01icfyy82f9k0m7ngrppz1ckq3wpq7zp6kgf8ppc55j6582c5jh3")))) + "102szyiicws4c6l3k282236ml1m1vl9zmars4q1kdjfnvsyclfc4")))) (properties `((upstream-name . "oligo"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) @@ -1552,6 +1560,8 @@ packages.") ("r-preprocesscore" ,r-preprocesscore) ("r-rsqlite" ,r-rsqlite) ("r-zlibbioc" ,r-zlibbioc))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/oligo/") (synopsis "Preprocessing tools for oligonucleotide arrays") (description @@ -1563,18 +1573,20 @@ Affymetrix (CEL files) and NimbleGen arrays (XYS files).") (define-public r-qvalue (package (name "r-qvalue") - (version "2.18.0") + (version "2.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "qvalue" version)) (sha256 (base32 - "0njnidyncm3g3712mnp77cs4kghn596ss1pz6fhp1cr0wxcayp6j")))) + "1hndmdr9niagbr4ry0vbhffvjzjg9im27kdbn0sa774k6r5b4z3f")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) ("r-reshape2" ,r-reshape2))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "http://github.com/jdstorey/qvalue") (synopsis "Q-value estimation for false discovery rate control") (description @@ -1592,14 +1604,14 @@ problems in genomics, brain imaging, astrophysics, and data mining.") (define-public r-diffbind (package (name "r-diffbind") - (version "2.14.0") + (version "2.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DiffBind" version)) (sha256 (base32 - "1729wyi2l4480yrkp5wg3ryirrmlk0j3njqs1qyckq3c8bjk12h2")))) + "1mwqgljya1c7r2dfrdds3nswn9bn1l3ak1wavbpv4lbv3nkmykn5")))) (properties `((upstream-name . "DiffBind"))) (build-system r-build-system) (inputs @@ -1670,14 +1682,14 @@ processing to visualization and annotation.") (define-public r-multtest (package (name "r-multtest") - (version "2.42.0") + (version "2.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "multtest" version)) (sha256 (base32 - "0qna9lx76ldsfy8qf5xmhl4ymqfkj29m1gdqhph06s470c8mwari")))) + "12li7nzzygm3sjfx472095irqpawixk48d0k591wlnrms6sxchx2")))) (build-system r-build-system) (propagated-inputs `(("r-survival" ,r-survival) @@ -1708,13 +1720,13 @@ expressed genes in DNA microarray experiments.") (define-public r-graph (package (name "r-graph") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "graph" version)) (sha256 (base32 - "1ivf59k7k552m7zd8g3wwazd71dq3xmgmhcq435738i02h0fqnyc")))) + "15v0nx9gzpszmdn5lil1s1y8qfmsirlznh56wcyqq4sxwjbyjn9g")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics))) @@ -1779,14 +1791,14 @@ determining dependencies between variables, code improvement suggestions.") (define-public r-chippeakanno (package (name "r-chippeakanno") - (version "3.20.1") + (version "3.22.2") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPpeakAnno" version)) (sha256 (base32 - "0kmfha4vprbi0z6n7v9w28xfrqcx5qad7yfr0b316j5aj8v9f4hc")))) + "199mlg0gwjy39afyk0ah6lzcm759bzxla4hgcajj0ay9jiibjqpa")))) (properties `((upstream-name . "ChIPpeakAnno"))) (build-system r-build-system) (propagated-inputs @@ -1819,6 +1831,8 @@ determining dependencies between variables, code improvement suggestions.") ("r-seqinr" ,r-seqinr) ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-venndiagram" ,r-venndiagram))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/ChIPpeakAnno") (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments") (description @@ -1835,12 +1849,12 @@ enrichedGO (addGeneIDs).") (define-public r-marray (package (name "r-marray") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "marray" version)) (sha256 - (base32 "1mbs9rk279hnm9yz34za3xz3hb88ll1d0abw4m2pgjgbh4kkhdrl")))) + (base32 "1sym3nis5qzg05b2in83xr019mvz8czy8qvispc0hzsq42yng6kd")))) (build-system r-build-system) (propagated-inputs `(("r-limma" ,r-limma))) @@ -1854,12 +1868,12 @@ normalization and quality checking.") (define-public r-cghbase (package (name "r-cghbase") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CGHbase" version)) (sha256 - (base32 "0136pk6pfwpiiy9vca4pgg4wh74jfb5ssglpdszzhamljpvg765x")))) + (base32 "0gfqqa9rs5hid53ihlky88qndgrwxxz0s6j7s505f660dd5nzlkf")))) (properties `((upstream-name . "CGHbase"))) (build-system r-build-system) (propagated-inputs @@ -1874,12 +1888,12 @@ the @code{arrayCGH} packages.") (define-public r-cghcall (package (name "r-cghcall") - (version "2.48.0") + (version "2.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CGHcall" version)) (sha256 - (base32 "1x8pz7zhw2nabik1vgdhlivndqvil3s7vnl5070k493v6gza0p3s")))) + (base32 "1dz6sag8khl18vkb97b5w6fk6k9s7s9xxnc467dd3bmhmajlmrrg")))) (properties `((upstream-name . "CGHcall"))) (build-system r-build-system) (propagated-inputs @@ -1897,12 +1911,12 @@ the @code{arrayCGH} packages.") (define-public r-qdnaseq (package (name "r-qdnaseq") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "QDNAseq" version)) (sha256 - (base32 "0xcqdpv9a47zpxx0q9sif5y4s1yzx3pig0kywy961kh5xgl5bcrq")))) + (base32 "1ji9pl2r1idyj3qzggj7qd2kqx31i6b3igwk2hqjb8qzkyb37p86")))) (properties `((upstream-name . "QDNAseq"))) (build-system r-build-system) (propagated-inputs @@ -1930,14 +1944,14 @@ respectively.") (define-public r-bayseq (package (name "r-bayseq") - (version "2.20.0") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "baySeq" version)) (sha256 (base32 - "040s1d3756spyzblkyx2vcy7bn3vf87mhsp3is35yxkj55n3myjk")))) + "1x0d34pqv9s15nmmxsfbw0ycxbf5348mi30ahycarjkjsyzycymj")))) (properties `((upstream-name . "baySeq"))) (build-system r-build-system) (propagated-inputs @@ -1956,14 +1970,14 @@ more complex hypotheses) via empirical Bayesian methods.") (define-public r-chipcomp (package (name "r-chipcomp") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPComp" version)) (sha256 (base32 - "0wk0vvg6dk9wk60lzbadrnqar75dppvyr4hiwrhv9rhhah2mg2mg")))) + "0780kj9vbzdhf2jkfb1my8m58pcdwk6jqw6zfng82g46jias98cp")))) (properties `((upstream-name . "ChIPComp"))) (build-system r-build-system) (propagated-inputs @@ -1990,14 +2004,14 @@ datasets.") (define-public r-riboprofiling (package (name "r-riboprofiling") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RiboProfiling" version)) (sha256 (base32 - "0nfzyiq7cd6fs5agzl1zyfg8s631wi7kjngiyvd3vxlhi8wsjicx")))) + "0s30m96dbbrzbywz3wai5ar0nsshb16lq101nyl20w1bk7sk2bha")))) (properties `((upstream-name . "RiboProfiling"))) (build-system r-build-system) (propagated-inputs @@ -2017,6 +2031,8 @@ datasets.") ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors) ("r-sqldf" ,r-sqldf))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/RiboProfiling/") (synopsis "Ribosome profiling data analysis") (description "Starting with a BAM file, this package provides the @@ -2029,14 +2045,14 @@ assessment, principal component analysis on codon coverage.") (define-public r-riboseqr (package (name "r-riboseqr") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "riboSeqR" version)) (sha256 (base32 - "1jr7h64hyhyf9gf15lah6iqwyljfc8mraf9kya4lql6lcjjkjiqm")))) + "04a4dkmacd6xy55m84amxa0fspbc4kgg9r9k7bc3wrxswk77ccxk")))) (properties `((upstream-name . "riboSeqR"))) (build-system r-build-system) (propagated-inputs @@ -2057,14 +2073,14 @@ parsing of genetic sequencing data from ribosome profiling experiments.") (define-public r-interactionset (package (name "r-interactionset") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "InteractionSet" version)) (sha256 (base32 - "0n2l95h56x5g68p10cap8p4x3a6vaph2hjlk09vmi3j48lrzb2kh")))) + "1nsivm9j0mzkfhwqsa2y9gxxdbaplg4z8vn5dfvls3nrihnqpk4v")))) (properties `((upstream-name . "InteractionSet"))) (build-system r-build-system) @@ -2077,6 +2093,8 @@ parsing of genetic sequencing data from ribosome profiling experiments.") ("r-rcpp" ,r-rcpp) ("r-s4vectors" ,r-s4vectors) ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/InteractionSet") (synopsis "Base classes for storing genomic interaction data") (description @@ -2089,14 +2107,14 @@ experiments.") (define-public r-genomicinteractions (package (name "r-genomicinteractions") - (version "1.20.3") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicInteractions" version)) (sha256 (base32 - "01ps97cs29qvzy5piq2l2k0yyr56rmg5cycfiqhbbvqpjrfvy60g")))) + "0fg66v31nfajb40da6gxpigm2z11ywkdijs7npvc1mr62ynx9qmy")))) (properties `((upstream-name . "GenomicInteractions"))) (build-system r-build-system) @@ -2130,14 +2148,14 @@ information and producing various plots and statistics.") (define-public r-ctc (package (name "r-ctc") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ctc" version)) (sha256 (base32 - "0wh27izkyr1j26nznisw654mb5c94xpwjjkx7r6bhwg9ihxxcl6d")))) + "0lv126xj092hps3f3dsv7hasdyy26wcx8npl9idq2l4h9addk6v6")))) (build-system r-build-system) (propagated-inputs `(("r-amap" ,r-amap))) (home-page "https://bioconductor.org/packages/ctc/") @@ -2150,14 +2168,14 @@ trees and clusters to other programs.") (define-public r-goseq (package (name "r-goseq") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "goseq" version)) (sha256 (base32 - "11ypa41qv1nx3cncxlwlbhdxqlwq95rb9byv2z3crrf9nfp24byv")))) + "1iyri4rrchzsn8p6wjxr4k30d3cqx3km5mnd9hkfm5d0s7fjzlym")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -2176,20 +2194,22 @@ defined categories which are over/under represented in RNA-seq data.") (define-public r-glimma (package (name "r-glimma") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Glimma" version)) (sha256 (base32 - "1rjrqgl96iz4b3xqpc174wgz7bqmc8gbm9ljag0y27kz29fwng8r")))) + "1bxfgwjqb9p400a5a5q6p17kcnl3ddz090llihkfih9kyxii9n4y")))) (properties `((upstream-name . "Glimma"))) (build-system r-build-system) (propagated-inputs `(("r-edger" ,r-edger) ("r-jsonlite" ,r-jsonlite) ("r-s4vectors" ,r-s4vectors))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/Shians/Glimma") (synopsis "Interactive HTML graphics") (description @@ -2203,14 +2223,14 @@ information.") (define-public r-rots (package (name "r-rots") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ROTS" version)) (sha256 (base32 - "08mwlb0lpprys2b7vif8aj5bnprmn09mm79zz158gbhrv9j9d1qm")))) + "1mqhi1rfiw7mhiyify7vm3w17p7sc76wjda3ak6690hrc3gsm3cm")))) (properties `((upstream-name . "ROTS"))) (build-system r-build-system) (propagated-inputs @@ -2227,14 +2247,14 @@ in omics data.") (define-public r-plgem (package (name "r-plgem") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "plgem" version)) (sha256 (base32 - "0fkyvcw2qxp4g527s9rzia45yapi0r6gbij7svisil8rbgfdp45v")))) + "1fs5nbjnrm7x23y7d9krq56r1kzxka40ca1rs6sq70mn6syhj90a")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -2252,14 +2272,14 @@ genes or proteins in these datasets.") (define-public r-inspect (package (name "r-inspect") - (version "1.16.3") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "INSPEcT" version)) (sha256 (base32 - "0y4gpvrbmcipdnyz9lz9ywn0317xnpcriiisqvxygin05vgcpilp")))) + "1yyglkdc3ww2jzswhcxk9g1imydfm39krl87as5l9fbm7mv3vd4z")))) (properties `((upstream-name . "INSPEcT"))) (build-system r-build-system) (propagated-inputs @@ -2279,11 +2299,14 @@ genes or proteins in these datasets.") ("r-proc" ,r-proc) ("r-rootsolve" ,r-rootsolve) ("r-rsamtools" ,r-rsamtools) + ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors) ("r-shiny" ,r-shiny) ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-txdb-mmusculus-ucsc-mm9-knowngene" ,r-txdb-mmusculus-ucsc-mm9-knowngene))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/INSPEcT") (synopsis "Analysis of 4sU-seq and RNA-seq time-course data") (description @@ -2296,20 +2319,22 @@ modeling the rates that determines changes in mature mRNA levels.") (define-public r-dnabarcodes (package (name "r-dnabarcodes") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DNABarcodes" version)) (sha256 (base32 - "0r2r9qc2qvf7rfl1h5ynvv3xd7n444zbc697s85qxqdpr4sxqmfd")))) + "03y39hjpkb05fnawy3k797bph1iydi1blmpgyy4244zjgk6rs5x7")))) (properties `((upstream-name . "DNABarcodes"))) (build-system r-build-system) (propagated-inputs `(("r-bh" ,r-bh) ("r-matrix" ,r-matrix) ("r-rcpp" ,r-rcpp))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/DNABarcodes") (synopsis "Create and analyze DNA barcodes") (description @@ -2323,14 +2348,14 @@ demultiplexed, i.e. assigned to their original reference barcode.") (define-public r-ruvseq (package (name "r-ruvseq") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RUVSeq" version)) (sha256 (base32 - "1ipbbzpngx988lsmwqv7vbmqm65m43xvsmipayfppkrr6jipzxrj")))) + "0yqs9xgyzw3cwb4l7zjl1cjgbsjp05qrqnwyvh7q81wdp7x5p55x")))) (properties `((upstream-name . "RUVSeq"))) (build-system r-build-system) (propagated-inputs @@ -2338,6 +2363,8 @@ demultiplexed, i.e. assigned to their original reference barcode.") ("r-edaseq" ,r-edaseq) ("r-edger" ,r-edger) ("r-mass" ,r-mass))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/drisso/RUVSeq") (synopsis "Remove unwanted variation from RNA-Seq data") (description @@ -2349,14 +2376,14 @@ samples.") (define-public r-biocneighbors (package (name "r-biocneighbors") - (version "1.4.2") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocNeighbors" version)) (sha256 (base32 - "1bx7i5pifj8w89fnhfgcfgcar2ik2ad8wqs2rix7yks90vz185i6")))) + "14cyyrwxi82xm5wy6bb1176zg322ll67wjrw9vvi4fhfs1k4wqxy")))) (properties `((upstream-name . "BiocNeighbors"))) (build-system r-build-system) (propagated-inputs @@ -2366,6 +2393,8 @@ samples.") ("r-rcppannoy" ,r-rcppannoy) ("r-rcpphnsw" ,r-rcpphnsw) ("r-s4vectors" ,r-s4vectors))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/BiocNeighbors") (synopsis "Nearest Neighbor Detection for Bioconductor packages") (description @@ -2380,14 +2409,14 @@ achieved for all methods using the BiocParallel framework.") (define-public r-biocsingular (package (name "r-biocsingular") - (version "1.2.2") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocSingular" version)) (sha256 (base32 - "1282fdwxrpga87y8xflr0sl8ajwawgn2i9i65my8mbg5vrixs407")))) + "0368a9xj4cvicqkxmhh12ln46q9gnxla70s1dqrxxfn3b6k525ih")))) (properties `((upstream-name . "BiocSingular"))) (build-system r-build-system) (propagated-inputs @@ -2400,6 +2429,8 @@ achieved for all methods using the BiocParallel framework.") ("r-rcpp" ,r-rcpp) ("r-rsvd" ,r-rsvd) ("r-s4vectors" ,r-s4vectors))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/LTLA/BiocSingular") (synopsis "Singular value decomposition for Bioconductor packages") (description @@ -2412,14 +2443,14 @@ possible, parallelization is achieved using the BiocParallel framework.") (define-public r-destiny (package (name "r-destiny") - (version "3.0.1") + (version "3.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "destiny" version)) (sha256 (base32 - "1hzg53p1cz21bvnfyyz40bpvjhg89zi3rahlqf0c4w85iwc1i4vi")))) + "0ik5vwxz9cci3glwgb5ff03sfyr4sjcp8ckfymlgmlm6fz8cp21n")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -2430,6 +2461,7 @@ possible, parallelization is achieved using the BiocParallel framework.") ("r-irlba" ,r-irlba) ("r-knn-covertree" ,r-knn-covertree) ("r-matrix" ,r-matrix) + ("r-nbconvertr" ,r-nbconvertr) ("r-pcamethods" ,r-pcamethods) ("r-proxy" ,r-proxy) ("r-rcpp" ,r-rcpp) @@ -2456,14 +2488,14 @@ maps.") (define-public r-savr (package (name "r-savr") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "savR" version)) (sha256 (base32 - "1lsnqjl6qxbj0wai05qb2wrxrhxq5iarv2livmvwiwv70iigqygf")))) + "17jdnr47ivblfspr4b32z9fds1fqiiwsi2z6r524g1v4944p8w5a")))) (properties `((upstream-name . "savR"))) (build-system r-build-system) (propagated-inputs @@ -2482,14 +2514,14 @@ Viewer (SAV) files, access data, and generate QC plots.") (define-public r-chipexoqual (package (name "r-chipexoqual") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPexoQual" version)) (sha256 (base32 - "044n6kn16qczpdhp0w0z5x8xpr0rfs9s8q70rafgnvj7a2q1xdd0")))) + "02rsf1rvm0p6dn18zq2a4hpvpd9m2i5rziyi4zm8j43qvs8xhafp")))) (properties `((upstream-name . "ChIPexoQual"))) (build-system r-build-system) (propagated-inputs @@ -2510,6 +2542,8 @@ Viewer (SAV) files, access data, and generate QC plots.") ("r-s4vectors" ,r-s4vectors) ("r-scales" ,r-scales) ("r-viridis" ,r-viridis))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/keleslab/ChIPexoQual") (synopsis "Quality control pipeline for ChIP-exo/nexus data") (description @@ -2520,13 +2554,13 @@ sequencing data.") (define-public r-copynumber (package (name "r-copynumber") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "copynumber" version)) (sha256 (base32 - "0r6r1adj20x3ckm0dlipxlf1rzngr92xsxxpy81mqxf4jpmyr8gj")))) + "1b7v6xijpi2mir49cf83gpadhxm5pnbs6d8q8qga7y06hn9jx6my")))) (build-system r-build-system) (propagated-inputs `(("r-s4vectors" ,r-s4vectors) @@ -2543,14 +2577,14 @@ penalized least squares regression method.") (define-public r-dnacopy (package (name "r-dnacopy") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DNAcopy" version)) (sha256 (base32 - "119z5lqhhw9ppg6s4dvbxk1kxf3wc55ibpm9b88c91s04yd7m9yw")))) + "0jg8lr83drzfs5h73c7mk7x99vj99a2p2s1sqjc4gicn927xvhza")))) (properties `((upstream-name . "DNAcopy"))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -2643,14 +2677,14 @@ and regression inferences from RNA-sequencing data.") (define-public r-ebseq (package (name "r-ebseq") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBSeq" version)) (sha256 (base32 - "0ay1vcccpc29r3vinlnwp9256345bfb346kg2y11kib4bnrabjb6")))) + "0s9r1xxpfm5794ipjm5a5c8gfxicc6arma6f74aaz8zi5y5q9x5f")))) (properties `((upstream-name . "EBSeq"))) (build-system r-build-system) (propagated-inputs @@ -2667,29 +2701,32 @@ gene and isoform level using RNA-seq data") (define-public r-karyoploter (package (name "r-karyoploter") - (version "1.12.4") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "karyoploteR" version)) (sha256 (base32 - "03jmfgmw35hrgn3pc5lq6pblzhfx9fp4l6dx50rp303lr7kjxp9v")))) + "0h0gk4xd95k5phy6qcsv7j931d7gk3p24i2fg4mz5dsk110lpifs")))) (build-system r-build-system) (propagated-inputs - `(("r-regioner" ,r-regioner) + `(("r-annotationdbi" ,r-annotationdbi) + ("r-bamsignals" ,r-bamsignals) + ("r-bezier" ,r-bezier) + ("r-biovizbase" ,r-biovizbase) + ("r-digest" ,r-digest) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) - ("r-rsamtools" ,r-rsamtools) ("r-memoise" ,r-memoise) + ("r-regioner" ,r-regioner) + ("r-rsamtools" ,r-rsamtools) ("r-rtracklayer" ,r-rtracklayer) - ("r-genomeinfodb" ,r-genomeinfodb) ("r-s4vectors" ,r-s4vectors) - ("r-biovizbase" ,r-biovizbase) - ("r-digest" ,r-digest) - ("r-bezier" ,r-bezier) - ("r-bamsignals" ,r-bamsignals) - ("r-annotationdbi" ,r-annotationdbi) ("r-variantannotation" ,r-variantannotation))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/karyoploteR/") (synopsis "Plot customizable linear genomes displaying arbitrary data") (description "This package creates karyotype plots of arbitrary genomes and @@ -2702,20 +2739,20 @@ coordinates.") (define-public r-lpsymphony (package (name "r-lpsymphony") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lpsymphony" version)) (sha256 (base32 - "0j5j9kggh3l61vp6hpnqf45d5kzifksaj0sqhvs1zahmx2c1gfdv")))) + "072ikmd267n18hrj7dip4dp1vb5dinj82p3h95n2jaf04h9hwfn4")))) (build-system r-build-system) (inputs - `(("gfortran" ,gfortran) - ("zlib" ,zlib))) + `(("zlib" ,zlib))) (native-inputs - `(("pkg-config" ,pkg-config))) + `(("pkg-config" ,pkg-config) + ("r-knitr" ,r-knitr))) (home-page "https://r-forge.r-project.org/projects/rsymphony") (synopsis "Symphony integer linear programming solver in R") (description @@ -2732,14 +2769,14 @@ to install interface to SYMPHONY.") (define-public r-ihw (package (name "r-ihw") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IHW" version)) (sha256 (base32 - "0rnw7r9pylpj3a5graavcpiqv2v67rv2a4dlcynkf4ihpxs4bg8x")))) + "169ir0k1gygdh1wybwa0drdxnhrdrlyzzy0rkygi7jsirn69m74j")))) (properties `((upstream-name . "IHW"))) (build-system r-build-system) (propagated-inputs @@ -2747,6 +2784,8 @@ to install interface to SYMPHONY.") ("r-fdrtool" ,r-fdrtool) ("r-lpsymphony" ,r-lpsymphony) ("r-slam" ,r-slam))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/IHW") (synopsis "Independent hypothesis weighting") (description @@ -2762,14 +2801,14 @@ independent of the p-value under the null hypothesis.") (define-public r-icobra (package (name "r-icobra") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "iCOBRA" version)) (sha256 (base32 - "1l0yr2grpwmr3pc5h50p1j4nxyb1ddmc55l7rhxpp4igh4fq1avz")))) + "0cvklagby3i221dlhyb51cciv0b3ch4a8z0wpm67q5n6n3k0cil1")))) (properties `((upstream-name . "iCOBRA"))) (build-system r-build-system) (propagated-inputs @@ -2784,6 +2823,8 @@ independent of the p-value under the null hypothesis.") ("r-shinybs" ,r-shinybs) ("r-shinydashboard" ,r-shinydashboard) ("r-upsetr" ,r-upsetr))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/iCOBRA") (synopsis "Comparison and visualization of ranking and assignment methods") (description @@ -2796,14 +2837,14 @@ interactive exploration of results.") (define-public r-mast (package (name "r-mast") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MAST" version)) (sha256 (base32 - "1l78rrwkzyswpj6pgc9z8290fqrk4akba76invkkazpyh91r8gga")))) + "12d0q2fbq9d5jgyccmfv0cghv282s0j86wjfbnjpdf73fdrp6brr")))) (properties `((upstream-name . "MAST"))) (build-system r-build-system) (propagated-inputs @@ -2831,14 +2872,14 @@ single cell assay data.") (define-public r-monocle (package (name "r-monocle") - (version "2.14.0") + (version "2.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "monocle" version)) (sha256 (base32 - "18b9y592q48mbcp5w095qs1kaklq64v6dcnlpqhv3rwxvywygsz2")))) + "1vziidavlyhixmx6j7lf29qx8xcjwrc9q3x2f63gcff41q3jf9xd")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -2871,6 +2912,8 @@ single cell assay data.") ("r-tibble" ,r-tibble) ("r-vgam" ,r-vgam) ("r-viridis" ,r-viridis))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/monocle") (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq") (description @@ -2948,14 +2991,14 @@ qPCR data, but could be used with other types as well.") (define-public r-noiseq (package (name "r-noiseq") - (version "2.30.0") + (version "2.31.0") (source (origin (method url-fetch) (uri (bioconductor-uri "NOISeq" version)) (sha256 (base32 - "1a8p66hhnwmay0rjabwq7356wr93yn33nqgr9rr7whpp9nls1hg4")))) + "0lg3za0km6v9l6dxigbxx6nsx9y6m3dyzh9srngi53s8387vhj33")))) (properties `((upstream-name . "NOISeq"))) (build-system r-build-system) (propagated-inputs @@ -2975,14 +3018,14 @@ assumptions.") (define-public r-scdd (package (name "r-scdd") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scDD" version)) (sha256 (base32 - "0nk0qq664zs7dnlcamdkrrhvll01p7f96jj3igbxxlzj3dvr58w4")))) + "19q01jksxpv4p26wp2c6faa4fffkjnqlbcds2x955pk35jkqknxx")))) (properties `((upstream-name . "scDD"))) (build-system r-build-system) (propagated-inputs @@ -2997,6 +3040,8 @@ assumptions.") ("r-scran" ,r-scran) ("r-singlecellexperiment" ,r-singlecellexperiment) ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/kdkorthauer/scDD") (synopsis "Mixture modeling of single-cell RNA-seq data") (description @@ -3011,14 +3056,14 @@ distributions.") (define-public r-scone (package (name "r-scone") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scone" version)) (sha256 (base32 - "1hfsbnix0y9ad6bj0d8q2aw13pb3vjcaa0dfwxxapzl90zwbsjhp")))) + "12hcmbpncm0l1yxhm3sgkqqfri7s5qc46ikv5qcj8pw5a42rkx3g")))) (build-system r-build-system) (propagated-inputs `(("r-aroma-light" ,r-aroma-light) @@ -3040,6 +3085,8 @@ distributions.") ("r-rhdf5" ,r-rhdf5) ("r-ruvseq" ,r-ruvseq) ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/scone") (synopsis "Single cell overview of normalized expression data") (description @@ -3051,14 +3098,14 @@ high-throughput analyses.") (define-public r-geoquery (package (name "r-geoquery") - (version "2.54.1") + (version "2.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GEOquery" version)) (sha256 (base32 - "0j8mlldy7dc38fx5zwj6z6l4b9bhvrn8sil3z8asnd4ic7w9ifx5")))) + "0sap1dsa3k3qpv5z5y3cimxyhbm8qai87gqn3g1w3hwlcqsss92m")))) (properties `((upstream-name . "GEOquery"))) (build-system r-build-system) (propagated-inputs @@ -3070,6 +3117,8 @@ high-throughput analyses.") ("r-readr" ,r-readr) ("r-tidyr" ,r-tidyr) ("r-xml2" ,r-xml2))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/seandavi/GEOquery/") (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)") (description @@ -3082,14 +3131,14 @@ the bridge between GEO and BioConductor.") (define-public r-illuminaio (package (name "r-illuminaio") - (version "0.28.0") + (version "0.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "illuminaio" version)) (sha256 (base32 - "1psza8jq6h8fv2rm91ah67dgjlnj1l80yracwgdl1agd0ycv90sh")))) + "0i587r1v5aa25w0jm1zvh7spc1gqmvza49i2kv00g1qzj8whq67c")))) (build-system r-build-system) (propagated-inputs `(("r-base64" ,r-base64))) @@ -3103,14 +3152,14 @@ files, including IDAT.") (define-public r-siggenes (package (name "r-siggenes") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "siggenes" version)) (sha256 (base32 - "03lmq3hqprwps4miynl2vhqi3v4als5vqmz4lb19lk5a4zja72b4")))) + "0i4y1hgq1ljxkf6sypb6c8yp412a8q5v5z68cx1zrgxnccvp0mfy")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -3129,14 +3178,14 @@ Bayes Analyses of Microarrays} (EBAM).") (define-public r-bumphunter (package (name "r-bumphunter") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bumphunter" version)) (sha256 (base32 - "1p3gwb954zns61d1pwgkplxnvgk2lixrl93kkkf439wa3vlgsnjv")))) + "04y6spdx89j3bsq2xniqd3sbfmakwc0klbpzjlp1q2xs9kywr4dq")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -3163,14 +3212,14 @@ studies.") (define-public r-minfi (package (name "r-minfi") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "minfi" version)) (sha256 (base32 - "177isdvcq2476xybvfbh7x11qsj5nzckgh3b6p156wlx9ap9dvl3")))) + "0bl1sk9syy770d5wqa0k1y0wrs5x8sbj13px1v03v3693pdj081w")))) (build-system r-build-system) (propagated-inputs `(("r-beanplot" ,r-beanplot) @@ -3202,6 +3251,8 @@ studies.") ("r-s4vectors" ,r-s4vectors) ("r-siggenes" ,r-siggenes) ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/hansenlab/minfi") (synopsis "Analyze Illumina Infinium DNA methylation arrays") (description @@ -3212,14 +3263,14 @@ methylation arrays.") (define-public r-methylumi (package (name "r-methylumi") - (version "2.32.0") + (version "2.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "methylumi" version)) (sha256 (base32 - "0zd4h6n37v3z0mas69z2xsf5s0naih828987m8v0g9hhq4f6hf5w")))) + "0phb2dyndnk9rv79nx246cn1sc9wbzdqqbgl6402knc7dgh799wr")))) (build-system r-build-system) (propagated-inputs `(("r-annotate" ,r-annotate) @@ -3240,6 +3291,8 @@ methylation arrays.") ("r-s4vectors" ,r-s4vectors) ("r-scales" ,r-scales) ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/methylumi") (synopsis "Handle Illumina methylation data") (description @@ -3256,14 +3309,14 @@ and Infinium HD arrays are also included.") (define-public r-lumi (package (name "r-lumi") - (version "2.38.0") + (version "2.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lumi" version)) (sha256 (base32 - "0lgrqbdvp7ykcafc0bpnbcsf396na3jj5c35x9ysf5bpcas23nmm")))) + "196izc4mdh8j4f04fsf8cqm99w1inzpwy34kwvhz6zvxj2ywn1i9")))) (build-system r-build-system) (propagated-inputs `(("r-affy" ,r-affy) @@ -3295,14 +3348,14 @@ especially Illumina Infinium methylation microarrays.") (define-public r-linnorm (package (name "r-linnorm") - (version "2.10.0") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Linnorm" version)) (sha256 (base32 - "15mhwiqmp9m65zvrdbr2hhy3x81lf4jbwgjsf75g41if2v2g8x67")))) + "143hdfswp5sda5al1igrm5gyn7a6mp1j7hjm5jsc300335lm3kgp")))) (properties `((upstream-name . "Linnorm"))) (build-system r-build-system) (propagated-inputs @@ -3324,6 +3377,8 @@ especially Illumina Infinium methylation microarrays.") ("r-statmod" ,r-statmod) ("r-vegan" ,r-vegan) ("r-zoo" ,r-zoo))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "http://www.jjwanglab.org/Linnorm/") (synopsis "Linear model and normality based transformation method") (description @@ -3354,14 +3409,14 @@ evaluation of DEG analysis methods.") (define-public r-ioniser (package (name "r-ioniser") - (version "2.10.0") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IONiseR" version)) (sha256 (base32 - "1c265bzh923i9mw83mjpj0bzbkixbs6sg1h1z51y9xjkakdgg90f")))) + "05fndlblczabva60gn6h0dijqxyn0wknrv8a925fgc4bn415g31w")))) (properties `((upstream-name . "IONiseR"))) (build-system r-build-system) (propagated-inputs @@ -3378,6 +3433,8 @@ evaluation of DEG analysis methods.") ("r-tibble" ,r-tibble) ("r-tidyr" ,r-tidyr) ("r-xvector" ,r-xvector))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/IONiseR/") (synopsis "Quality assessment tools for Oxford Nanopore MinION data") (description @@ -3476,14 +3533,14 @@ published results; and a routine for graphical display.") (define-public r-triform (package (name "r-triform") - (version "1.28.0") + (version "1.29.0") (source (origin (method url-fetch) (uri (bioconductor-uri "triform" version)) (sha256 (base32 - "12qdyrcw2mcawqdw65v0hjaghzlwa10xl6j8458izcrm5k6dlvz9")))) + "089b7f6dwpi9abj0ncswbi4s30k45996zb99sh43avw6jcb6qj60")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) @@ -3500,14 +3557,14 @@ peak definition in combination with known profile characteristics.") (define-public r-varianttools (package (name "r-varianttools") - (version "1.28.1") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantTools" version)) (sha256 (base32 - "1x57shc3slcbnc807ra1nwnjr37sqjh04n2xfwd469m4hkjb0jzh")))) + "0g93rljlmhk1d53z0bgi84i2cn5c3r1dpm8id2pv0nk9ncdh3yxx")))) (properties `((upstream-name . "VariantTools"))) (build-system r-build-system) (propagated-inputs @@ -3540,14 +3597,14 @@ gmapR.") (define-public r-heatplus (package (name "r-heatplus") - (version "2.32.1") + (version "2.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Heatplus" version)) (sha256 (base32 - "1ldxj2hasg6ysh70sc73mz2v4h3n8gf3lii09c3sqc4wmz5h7rp1")))) + "12nd0h8svx7qydv1shk0gdpvnbixf7qi6zh06881wsmxf5s970rw")))) (properties `((upstream-name . "Heatplus"))) (build-system r-build-system) (propagated-inputs @@ -3565,14 +3622,14 @@ information about samples and features can be added to the plot.") (define-public r-gosemsim (package (name "r-gosemsim") - (version "2.12.1") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOSemSim" version)) (sha256 (base32 - "1r8yx6qw6d6602cp8aspzl3shi1l1zqcrc8fm9d5wg01sw1whs05")))) + "0mg4d8whq90iyl2jjj5dx3kyar17yqn00jvia3b4a8lhmjw8l1hk")))) (properties `((upstream-name . "GOSemSim"))) (build-system r-build-system) (propagated-inputs @@ -3594,14 +3651,14 @@ sets of GO terms, gene products and gene clusters.") (define-public r-anota (package (name "r-anota") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "anota" version)) (sha256 (base32 - "1bkavzrxy1bjz0bwapwa9i3ysln7gljgziwd8c05fmg2f46j1z6m")))) + "1ind5cyq85l63xpqmg2n9rg805s5amh48iiw05zqr8kih6hlilpm")))) (build-system r-build-system) (propagated-inputs `(("r-multtest" ,r-multtest) @@ -3625,14 +3682,14 @@ the data set is suitable for such analysis.") (define-public r-sigpathway (package (name "r-sigpathway") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sigPathway" version)) (sha256 (base32 - "057qdkbfldpy6hsysk9mrs1vvsqgyl9yx2s6c2f26jz1pardkbqb")))) + "0a79sdvag80p7xcdz8mp8wiby36yxmappzycfd2rp36v9drjk0h5")))) (properties `((upstream-name . "sigPathway"))) (build-system r-build-system) (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102") @@ -3647,14 +3704,14 @@ phenotype of interest.") (define-public r-fgsea (package (name "r-fgsea") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fgsea" version)) (sha256 (base32 - "0pbq3g515kcbi4wvfx8m09p01h2f8vwsi1qqsyahxz4r1fasz4c1")))) + "0zbjj8al1ps7immxixsn5g8lvbmpmxvqwqbpdgsicxp00gb9bybc")))) (build-system r-build-system) (propagated-inputs `(("r-bh" ,r-bh) @@ -3665,6 +3722,8 @@ phenotype of interest.") ("r-gridextra" ,r-gridextra) ("r-matrix" ,r-matrix) ("r-rcpp" ,r-rcpp))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/ctlab/fgsea/") (synopsis "Fast gene set enrichment analysis") (description @@ -3677,14 +3736,14 @@ to multiple hypothesis correction.") (define-public r-dose (package (name "r-dose") - (version "3.12.0") + (version "3.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DOSE" version)) (sha256 (base32 - "0ss8mr28q0vswxjmhcas0aqag5nl099jbyn5w3ypbbxqwfvf9jj5")))) + "1j0wcg7w2ns3ag9d272cqlg3j62ag2xnc5gfsjl6g2ij5xkvylb8")))) (properties `((upstream-name . "DOSE"))) (build-system r-build-system) (propagated-inputs @@ -3695,8 +3754,7 @@ to multiple hypothesis correction.") ("r-ggplot2" ,r-ggplot2) ("r-gosemsim" ,r-gosemsim) ("r-qvalue" ,r-qvalue) - ("r-reshape2" ,r-reshape2) - ("r-s4vectors" ,r-s4vectors))) + ("r-reshape2" ,r-reshape2))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://guangchuangyu.github.io/software/DOSE/") @@ -3713,14 +3771,14 @@ data.") (define-public r-enrichplot (package (name "r-enrichplot") - (version "1.6.1") + (version "1.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "enrichplot" version)) (sha256 (base32 - "0707f5ll58psh7pr001cmmk5di7dprnbry1cy2mw20vn8p24nf3x")))) + "01m3cp717ldfbz5w3yfywvjg6sfjzz7s3vlk7w268lmmcg6g6bz7")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -3734,9 +3792,13 @@ data.") ("r-gosemsim" ,r-gosemsim) ("r-gridextra" ,r-gridextra) ("r-igraph" ,r-igraph) + ("r-plyr" ,r-plyr) ("r-purrr" ,r-purrr) ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-reshape2" ,r-reshape2))) + ("r-reshape2" ,r-reshape2) + ("r-scatterpie" ,r-scatterpie))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/GuangchuangYu/enrichplot") (synopsis "Visualization of functional enrichment result") (description @@ -3748,22 +3810,23 @@ All the visualization methods are developed based on ggplot2 graphics.") (define-public r-clusterprofiler (package (name "r-clusterprofiler") - (version "3.14.3") + (version "3.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterProfiler" version)) (sha256 (base32 - "08pd7bmqmyxncj09ilz8yb9sf1pv9ni98y8b93pz2giy7pl407hg")))) + "0m7919gzrd2fddb4kcznwpshhab1ha2yppnkxg11zmh40wcdawyi")))) (properties `((upstream-name . "clusterProfiler"))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-dose" ,r-dose) + ("r-downloader" ,r-downloader) + ("r-dplyr" ,r-dplyr) ("r-enrichplot" ,r-enrichplot) - ("r-ggplot2" ,r-ggplot2) ("r-go-db" ,r-go-db) ("r-gosemsim" ,r-gosemsim) ("r-magrittr" ,r-magrittr) @@ -3771,6 +3834,8 @@ All the visualization methods are developed based on ggplot2 graphics.") ("r-qvalue" ,r-qvalue) ("r-rvcheck" ,r-rvcheck) ("r-tidyr" ,r-tidyr))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://guangchuangyu.github.io/software/clusterProfiler/") (synopsis "Analysis and visualization of functional profiles for gene clusters") (description @@ -3781,14 +3846,14 @@ profiles (GO and KEGG) of gene and gene clusters.") (define-public r-mlinterfaces (package (name "r-mlinterfaces") - (version "1.66.5") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MLInterfaces" version)) (sha256 (base32 - "05bg7qcrv485m03rkyq3qg5hrr1m3y7zx49bipwaivzqm3s1mbw5")))) + "0x3mnvb5a6kri4q5w0wfmx02v79my08zhmkaik9pqlprd7y5wynq")))) (properties `((upstream-name . "MLInterfaces"))) (build-system r-build-system) (propagated-inputs @@ -3806,6 +3871,7 @@ profiles (GO and KEGG) of gene and gene clusters.") ("r-mlbench" ,r-mlbench) ("r-pls" ,r-pls) ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rcpp" ,r-rcpp) ("r-rpart" ,r-rpart) ("r-sfsmisc" ,r-sfsmisc) ("r-shiny" ,r-shiny) @@ -3821,14 +3887,14 @@ data in R and Bioconductor containers.") (define-public r-annaffy (package (name "r-annaffy") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annaffy" version)) (sha256 (base32 - "1jrf4bq2wky4ay1jrcy60si6hxdcn4j05w5vgs38yfb92gq77i16")))) + "1rc9fb83by9jfgwfj2zhhbj93v296blwd8jl2rh7jj200mrpznn4")))) (build-system r-build-system) (arguments `(#:phases @@ -3857,14 +3923,14 @@ It allows searching of biological metadata using various criteria.") (define-public r-a4core (package (name "r-a4core") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Core" version)) (sha256 (base32 - "0xcs9wl2yrprl4yc0z5s4zrkil3752k9xc1fi8fcx7zab1mm80df")))) + "1hn9lkaib1bx5n52as882f8zwsln8w40sx8hxbrnimjvgfxrbvnp")))) (properties `((upstream-name . "a4Core"))) (build-system r-build-system) (propagated-inputs @@ -3880,14 +3946,14 @@ arrays.") (define-public r-a4classif (package (name "r-a4classif") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Classif" version)) (sha256 (base32 - "0gj3hdflfs1ybc2kshl9w1dzy0rfzppfj08hx3wa2chjsm0m9brn")))) + "0bj8m4nprw3maahd1qx9jjdxfip9ihbbpydbzwjxn6dlgw2i8mcr")))) (properties `((upstream-name . "a4Classif"))) (build-system r-build-system) (propagated-inputs @@ -3908,14 +3974,14 @@ Affymetrix arrays.") (define-public r-a4preproc (package (name "r-a4preproc") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Preproc" version)) (sha256 (base32 - "11j5nc33gd6yis1fyagr0y39g21bzkc59kq8b8sd6b3pfc84zrjd")))) + "1hy3jvhdjyjzzmw5wkil3cs26hvqnb056r09x0p2bjg5sc9hh8b8")))) (properties `((upstream-name . "a4Preproc"))) (build-system r-build-system) (propagated-inputs @@ -3930,14 +3996,14 @@ is used for preprocessing the arrays.") (define-public r-a4reporting (package (name "r-a4reporting") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Reporting" version)) (sha256 (base32 - "15nd4pa5hkdzkhinvqw5ijdqb7k5gk37v2hmk3jsg2d6m0jqphi5")))) + "1jhlxqwfbgflcyzy9gyxznzcadj9zxchl3lfdlc4ffm0hwz5jl2f")))) (properties `((upstream-name . "a4Reporting"))) (build-system r-build-system) (propagated-inputs @@ -3953,14 +4019,14 @@ provides reporting features.") (define-public r-a4base (package (name "r-a4base") - (version "1.34.1") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Base" version)) (sha256 (base32 - "1a0yk05ikk1hr1vpxynydrb5xb1hj4hdqlh9zd13n83ir89dss83")))) + "0b7fy1wcydb9z43wb1663skswvhivn7ji15g00gqcshwkkiq4x02")))) (properties `((upstream-name . "a4Base"))) (build-system r-build-system) (propagated-inputs @@ -3985,14 +4051,14 @@ Affymetrix arrays.") (define-public r-a4 (package (name "r-a4") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4" version)) (sha256 (base32 - "14yipy6s2wqr9q0yp09x1mm17npknrhs6yd34i3wrb5id64ywnq4")))) + "1rzxg1h48jnlwqfjyyqzz6i3zlkfzc0i714rfplry7dyni6asgr7")))) (build-system r-build-system) (propagated-inputs `(("r-a4base" ,r-a4base) @@ -4010,14 +4076,14 @@ Affymetrix arrays.") (define-public r-abseqr (package (name "r-abseqr") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "abseqR" version)) (sha256 (base32 - "1n9h5qkj4njr1f8fvhg9sj9wxcd7hljnnk8m80zwswzs2n9ivppa")))) + "0pzyfn0jv41rja6l4jbgwgsqy0q1d3kz23m9m6pc67p2a231i9c5")))) (properties `((upstream-name . "abseqR"))) (build-system r-build-system) (inputs @@ -4041,6 +4107,8 @@ Affymetrix arrays.") ("r-stringr" ,r-stringr) ("r-vegan" ,r-vegan) ("r-venndiagram" ,r-venndiagram))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/malhamdoosh/abseqR") (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries") (description @@ -4056,14 +4124,14 @@ further downstream analysis on its output.") (define-public r-bacon (package (name "r-bacon") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bacon" version)) (sha256 (base32 - "1q18vm4znl47v56cnvx9y5ygrial2mdjpl8x1043jq00kyygrc86")))) + "066b9vyp8ivnzm9741mb5z763a7z40ar9m8w31yw84fjiv01v3dl")))) (build-system r-build-system) (propagated-inputs `(("r-biocparallel" ,r-biocparallel) @@ -4083,14 +4151,14 @@ fitting a three-component normal mixture on z-scores.") (define-public r-rgadem (package (name "r-rgadem") - (version "2.34.1") + (version "2.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rGADEM" version)) (sha256 (base32 - "12xm4p4qsczf57kip8bvi6pr8sb5gvn11dnbz7lbh6sc03sx3q2h")))) + "14mflbwhhj9f3b05zdlsdjwxmpb120r23fy306qkvxjprdqn4sz8")))) (properties `((upstream-name . "rGADEM"))) (build-system r-build-system) (propagated-inputs @@ -4109,14 +4177,14 @@ genomic sequence data.") (define-public r-motiv (package (name "r-motiv") - (version "1.42.0") + (version "1.43.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MotIV" version)) (sha256 (base32 - "07k4rw4nhcn4sg43psv1h7qr064gws22m2yyr7x8sy3f1i1c954k")))) + "1yqqymcrnwlpv6h3w80yliv19922g32xqlqszaqjk6zp853qilh6")))) (properties `((upstream-name . "MotIV"))) (build-system r-build-system) (inputs @@ -4141,21 +4209,24 @@ distributions, modules and filter motifs.") (define-public r-motifdb (package (name "r-motifdb") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MotifDb" version)) (sha256 - (base32 "0m5apkjlvdq9yhjdyds3hivfnkbm6f059hy2bkjhalrlhd2si2jc")))) + (base32 "0ixmdqp0s0xv9ar85n2wirbbssrzlk8a892wam55jdsf9y8aabkm")))) (properties `((upstream-name . "MotifDb"))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-biostrings" ,r-biostrings) + ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors) ("r-splitstackshape" ,r-splitstackshape))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://www.bioconductor.org/packages/MotifDb/") (synopsis "Annotated collection of protein-DNA binding sequence motifs") (description "This package provides more than 2000 annotated position @@ -4165,32 +4236,35 @@ frequency matrices from nine public sources, for multiple organisms.") (define-public r-motifbreakr (package (name "r-motifbreakr") - (version "2.0.0") + (version "2.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifbreakR" version)) (sha256 - (base32 "190z8gj393qdpq5wz7gph96k0l8c1j9wd0p0llscysvk5kr1hf9n")))) + (base32 "09czgmyjcycsvyvadpjddwwvqvxzd0ba3zhczh4mqc09gwa6vhlm")))) (properties `((upstream-name . "motifbreakR"))) (build-system r-build-system) (propagated-inputs - `(("r-grimport" ,r-grimport) - ("r-stringr" ,r-stringr) - ("r-biocgenerics" ,r-biocgenerics) - ("r-s4vectors" ,r-s4vectors) - ("r-iranges" ,r-iranges) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) ("r-biostrings" ,r-biostrings) ("r-bsgenome" ,r-bsgenome) - ("r-rtracklayer" ,r-rtracklayer) - ("r-variantannotation" ,r-variantannotation) - ("r-biocparallel" ,r-biocparallel) - ("r-motifstack" ,r-motifstack) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-grimport" ,r-grimport) ("r-gviz" ,r-gviz) + ("r-iranges" ,r-iranges) ("r-matrixstats" ,r-matrixstats) + ("r-motifdb" ,r-motifdb) + ("r-motifstack" ,r-motifstack) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-stringr" ,r-stringr) + ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-tfmpvalue" ,r-tfmpvalue) - ("r-motifdb" ,r-motifdb))) + ("r-variantannotation" ,r-variantannotation))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://www.bioconductor.org/packages/motifbreakR/") (synopsis "Predicting disruptiveness of single nucleotide polymorphisms") (description "This package allows biologists to judge in the first place @@ -4213,14 +4287,14 @@ Bioconductor.") (define-public r-motifstack (package (name "r-motifstack") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifStack" version)) (sha256 (base32 - "00rafqs1gqlcxlbsdn9qnq9xb7wjphiksb3hsx76viqjbjzi14wg")))) + "008f2mjcyyiz84ilrsldpqwvxy2lp93hjggrq4nrqwi78nyx3ls5")))) (properties `((upstream-name . "motifStack"))) (build-system r-build-system) (propagated-inputs @@ -4232,6 +4306,8 @@ Bioconductor.") ("r-motiv" ,r-motiv) ("r-scales" ,r-scales) ("r-xml" ,r-xml))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/motifStack/") (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences") (description @@ -4245,14 +4321,14 @@ type and symbol colors.") (define-public r-genomicscores (package (name "r-genomicscores") - (version "1.10.0") + (version "2.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicScores" version)) (sha256 (base32 - "175iaqv7npa11yw48vmqpgx0qqs3g44c3dsya7ccwd1lg97fznkj")))) + "0si2lgc37mkah4w990q1q2bf8xmshxj7cbx92bcrp0zaipjr96bb")))) (properties `((upstream-name . "GenomicScores"))) (build-system r-build-system) (propagated-inputs @@ -4260,12 +4336,16 @@ type and symbol colors.") ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) + ("r-delayedarray" ,r-delayedarray) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicranges" ,r-genomicranges) + ("r-hdf5array" ,r-hdf5array) ("r-iranges" ,r-iranges) + ("r-rhdf5" ,r-rhdf5) ("r-s4vectors" ,r-s4vectors) ("r-xml" ,r-xml))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/rcastelo/GenomicScores/") (synopsis "Work with genome-wide position-specific scores") (description @@ -4276,14 +4356,14 @@ position-specific scores within R and Bioconductor.") (define-public r-atacseqqc (package (name "r-atacseqqc") - (version "1.10.4") + (version "1.12.3") (source (origin (method url-fetch) (uri (bioconductor-uri "ATACseqQC" version)) (sha256 (base32 - "1g07ni134cyl3jd9y19afip39kxddfgpm1jjm0rhrm7jgssp24in")))) + "12710c4024pndwwqiiqr6dhrd360z26fc8r3fxhs739gyd0ddk9r")))) (properties `((upstream-name . "ATACseqQC"))) (build-system r-build-system) (propagated-inputs @@ -4323,14 +4403,14 @@ footprints.") (define-public r-gofuncr (package (name "r-gofuncr") - (version "1.6.1") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOfuncR" version)) (sha256 (base32 - "1wk7ja6f5il8jx8v05ijzcs9pijp3b953h566ya66xp7dz5jg9rb")))) + "1ixjkqb9wpwqfzxsg0h96c6fa63wrk72sfh6x4pq0kpyrcc0ind1")))) (properties `((upstream-name . "GOfuncR"))) (build-system r-build-system) (propagated-inputs @@ -4372,14 +4452,14 @@ annotations and ontologies.") (define-public r-abaenrichment (package (name "r-abaenrichment") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ABAEnrichment" version)) (sha256 (base32 - "128ik28j8kmdkycffhxajv5h174zdq9sfn2gz6ai90wgkdadbzwp")))) + "09ihbgxrhpcz2q7svldhm710a0yrhiqk9p0q0myv11c2w50ymwkw")))) (properties `((upstream-name . "ABAEnrichment"))) (build-system r-build-system) (propagated-inputs @@ -4389,6 +4469,8 @@ annotations and ontologies.") ("r-gplots" ,r-gplots) ("r-gtools" ,r-gtools) ("r-rcpp" ,r-rcpp))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/ABAEnrichment/") (synopsis "Gene expression enrichment in human brain regions") (description @@ -4402,14 +4484,14 @@ the brain using an ontology, both provided by the Allen Brain Atlas project.") (define-public r-annotationfuncs (package (name "r-annotationfuncs") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationFuncs" version)) (sha256 (base32 - "0ws14b1ibqml7w8kj0gi7wdp6wd8dcdpnrmcxldjzsyawf17q0yq")))) + "1yfsxzn7s1nlc3xz2yj39j6hmdfapc9qj9h0cd71gkaxj53ial7d")))) (properties `((upstream-name . "AnnotationFuncs"))) (build-system r-build-system) @@ -4427,14 +4509,14 @@ different identifieres using the Biocore Data Team data-packages (e.g. (define-public r-annotationtools (package (name "r-annotationtools") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotationTools" version)) (sha256 (base32 - "1cq7ayq2swp2ahlphz74nh5mb869rgyyr0kkqy1mxyilk8k2g44i")))) + "1b1yfnknr9vbn4y2mxdfyx57i5jbabhp9pwx8axlg2a7lawkfmdk")))) (properties `((upstream-name . "annotationTools"))) (build-system r-build-system) @@ -4452,14 +4534,14 @@ text files).") (define-public r-allelicimbalance (package (name "r-allelicimbalance") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AllelicImbalance" version)) (sha256 (base32 - "0vy8w7ii2qljsmq8lr21lygkcrsshc7syyqhadlbxyj3scgi7kyc")))) + "0irn4xdlvazdkv0055f45693y6zvqaz7j3vml5xscnh45ls6vmqr")))) (properties `((upstream-name . "AllelicImbalance"))) (build-system r-build-system) @@ -4483,6 +4565,8 @@ text files).") ("r-seqinr" ,r-seqinr) ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-variantannotation" ,r-variantannotation))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/pappewaio/AllelicImbalance") (synopsis "Investigate allele-specific expression") (description @@ -4493,14 +4577,14 @@ investigation using RNA-seq data.") (define-public r-aucell (package (name "r-aucell") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AUCell" version)) (sha256 (base32 - "1g4mdq8z29fjxrfjng0fb3cvbph49mwds4ijsa2bn2k6f75dnzky")))) + "0fgqkgjhf92vkljkwn44lm8cjvzq1lvk80nk6xhsp5q6s5isbmns")))) (properties `((upstream-name . "AUCell"))) (build-system r-build-system) (propagated-inputs @@ -4512,6 +4596,8 @@ investigation using RNA-seq data.") ("r-s4vectors" ,r-s4vectors) ("r-shiny" ,r-shiny) ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/AUCell/") (synopsis "Analysis of gene set activity in single-cell RNA-seq data") (description @@ -4530,14 +4616,14 @@ needed.") (define-public r-ebimage (package (name "r-ebimage") - (version "4.28.1") + (version "4.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBImage" version)) (sha256 (base32 - "0q54q2nw6p1s4nrj1l8qz78m67xcysj2x82zs43my8iv2g9iifgs")))) + "13amrbh545hwk7sygndzyv7wpa0m2y0lzlwj89jm1xm62x577w9v")))) (properties `((upstream-name . "EBImage"))) (build-system r-build-system) (propagated-inputs @@ -4569,14 +4655,14 @@ visualization with image data.") (define-public r-yamss (package (name "r-yamss") - (version "1.12.1") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "yamss" version)) (sha256 (base32 - "12jr7hbrwhb1gfjadj1024hv80ra22miy46dn40nmsrbklkfn3rw")))) + "00x2lnssgzbmhy5bb2m0f8rq2nsz3lb5xlp2vhkcagza39h3xb0c")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) @@ -4589,6 +4675,8 @@ visualization with image data.") ("r-s4vectors" ,r-s4vectors) ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/hansenlab/yamss") (synopsis "Tools for high-throughput metabolomics") (description @@ -4601,20 +4689,22 @@ analysis.") (define-public r-gtrellis (package (name "r-gtrellis") - (version "1.18.0") + (version "1.20.1") (source (origin (method url-fetch) (uri (bioconductor-uri "gtrellis" version)) (sha256 (base32 - "0mgspmv6p1a2k98jyy2dfl0wpa2vh7bhnjfm2xaqmcsxzmbjhh9z")))) + "1v2l7r945xx4cf9s8m19csj7716n2ayxy05adkl8zqgxk0gxzqm1")))) (build-system r-build-system) (propagated-inputs `(("r-circlize" ,r-circlize) ("r-genomicranges" ,r-genomicranges) ("r-getoptlong" ,r-getoptlong) ("r-iranges" ,r-iranges))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/jokergoo/gtrellis") (synopsis "Genome level Trellis layout") (description @@ -4628,14 +4718,14 @@ genomic categories and to add self-defined graphics in the plot.") (define-public r-somaticsignatures (package (name "r-somaticsignatures") - (version "2.22.0") + (version "2.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SomaticSignatures" version)) (sha256 (base32 - "1gvrkahllwz38g3hn9pjlikhfqz19a4qglcqmyrxk7h9ybx5zy5z")))) + "0d34mss73w1jdnmilk060a1fywlfmqbnlir089q9m3q1p3x0j4c1")))) (properties `((upstream-name . "SomaticSignatures"))) (build-system r-build-system) @@ -4653,6 +4743,8 @@ genomic categories and to add self-defined graphics in the plot.") ("r-reshape2" ,r-reshape2) ("r-s4vectors" ,r-s4vectors) ("r-variantannotation" ,r-variantannotation))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/juliangehring/SomaticSignatures") (synopsis "Somatic signatures") (description @@ -4665,33 +4757,42 @@ decomposition algorithms.") (define-public r-yapsa (package (name "r-yapsa") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "YAPSA" version)) (sha256 (base32 - "132x51f8k8zyx6j8jk05x4lr9q1hlblgvr69wkhn0q3f8mhaj926")))) + "06lkf01vl4fyhj82srx8k870fhw76a1han0kp4jglh43b1c19c1k")))) (properties `((upstream-name . "YAPSA"))) (build-system r-build-system) (propagated-inputs - `(("r-circlize" ,r-circlize) + `(("r-biostrings" ,r-biostrings) + ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) + ("r-circlize" ,r-circlize) ("r-complexheatmap" ,r-complexheatmap) ("r-corrplot" ,r-corrplot) ("r-dendextend" ,r-dendextend) + ("r-doparallel" ,r-doparallel) + ("r-dplyr" ,r-dplyr) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicranges" ,r-genomicranges) ("r-getoptlong" ,r-getoptlong) + ("r-ggbeeswarm" ,r-ggbeeswarm) ("r-ggplot2" ,r-ggplot2) ("r-gridextra" ,r-gridextra) ("r-gtrellis" ,r-gtrellis) ("r-keggrest" ,r-keggrest) ("r-lsei" ,r-lsei) + ("r-magrittr" ,r-magrittr) ("r-pmcmr" ,r-pmcmr) + ("r-pracma" ,r-pracma) ("r-reshape2" ,r-reshape2) ("r-somaticsignatures" ,r-somaticsignatures) ("r-variantannotation" ,r-variantannotation))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/YAPSA/") (synopsis "Yet another package for signature analysis") (description @@ -4705,14 +4806,14 @@ provided.") (define-public r-gcrma (package (name "r-gcrma") - (version "2.58.0") + (version "2.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gcrma" version)) (sha256 (base32 - "0c9sa9ldlcpdcjdan8m4ndnyaisr6wbarq486sl44ikh7wf1csfx")))) + "1klbnygc1i5ac1x00bsk0rjw5h5dn6pn65fa3y9r09q47gpy1c5g")))) (build-system r-build-system) (propagated-inputs `(("r-affy" ,r-affy) @@ -4741,14 +4842,14 @@ gene-specific bidning is expected.") (define-public r-simpleaffy (package (name "r-simpleaffy") - (version "2.62.0") + (version "2.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "simpleaffy" version)) (sha256 (base32 - "18bz3pfgp0f7906flrljx97ann8s71pnb8gpw7nah46n8vqc0xcs")))) + "040043spblr8v67lkn3nnxhgfmfh2iwaizph4fnms1ik6qz662x7")))) (build-system r-build-system) (propagated-inputs `(("r-affy" ,r-affy) @@ -4769,14 +4870,14 @@ generating high resolution journal figures.") (define-public r-yaqcaffy (package (name "r-yaqcaffy") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "yaqcaffy" version)) (sha256 (base32 - "0kzzqsf1lfbcmy95w2z0c9qrvp7mbwm50k2l9wvz3xa5wz6xa7gz")))) + "1l0cblh9sfrsil15bjya7d8kkas8bj6klj2w3c4384njdsjsjcf0")))) (build-system r-build-system) (propagated-inputs `(("r-simpleaffy" ,r-simpleaffy))) @@ -4791,14 +4892,14 @@ chips with the MAQC reference datasets.") (define-public r-quantro (package (name "r-quantro") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "quantro" version)) (sha256 (base32 - "09f3x1j50ll5hhn3qwys5x06mii3fqsrk6dkvsxai0kdxv9cjz9m")))) + "0ap9cl5z79wg44mnagjsk8py3kngb4f0ddnx85cbnwqkvb769zbz")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -4808,6 +4909,8 @@ chips with the MAQC reference datasets.") ("r-iterators" ,r-iterators) ("r-minfi" ,r-minfi) ("r-rcolorbrewer" ,r-rcolorbrewer))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/quantro/") (synopsis "Test for when to use quantile normalization") (description @@ -4822,14 +4925,14 @@ groups.") (define-public r-yarn (package (name "r-yarn") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "yarn" version)) (sha256 (base32 - "0891a10adkhm1zpm7fpcxc2xfxjf9yrpckaz87b2wdjdiwivc4cp")))) + "1xdjwy1gkfg8lhgq4iwwmbi01903qljjs7yd96cvacmvgn8z6qvx")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -4843,6 +4946,8 @@ groups.") ("r-quantro" ,r-quantro) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-readr" ,r-readr))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/yarn/") (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization") (description @@ -4857,14 +4962,14 @@ large RNA-seq experiments.") (define-public r-roar (package (name "r-roar") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "roar" version)) (sha256 (base32 - "1nqw0agx9x8ycdf0gw17fdlnmzpw9x3zig1wcy10xpyhyjdbbi06")))) + "069g887migvk70n0377dqr0fk7wjbz3w0asgk42bwhp8xpjfym6f")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) @@ -4886,14 +4991,14 @@ sites and alignments obtained from standard RNA-seq experiments.") (define-public r-xbseq (package (name "r-xbseq") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "XBSeq" version)) (sha256 (base32 - "1qr5gvf8jcx6r0ac7d2wmnikswmp3k71lirnw7dyr6fndzrdz9lp")))) + "13br7x1q6dg8daxahskwq24f09wbxr8kyszl1z7dhc26bid2pvy0")))) (properties `((upstream-name . "XBSeq"))) (build-system r-build-system) (propagated-inputs @@ -4906,6 +5011,8 @@ sites and alignments obtained from standard RNA-seq experiments.") ("r-matrixstats" ,r-matrixstats) ("r-pracma" ,r-pracma) ("r-roar" ,r-roar))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/Liuy12/XBSeq") (synopsis "Test for differential expression for RNA-seq data") (description @@ -4923,14 +5030,14 @@ genes.") (define-public r-massspecwavelet (package (name "r-massspecwavelet") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MassSpecWavelet" version)) (sha256 (base32 - "0xnj3ncrwvr2b8msi3g77mgzj0zaksn3lgqdn1abh0ww5wgk83v7")))) + "0nv1r68g7f1rps6sqaccd4n4x0i19wklvyabhp4b03cdk22gl3nq")))) (properties `((upstream-name . "MassSpecWavelet"))) (build-system r-build-system) @@ -4947,14 +5054,14 @@ based on @dfn{Continuous Wavelet Transform} (CWT).") (define-public r-xcms (package (name "r-xcms") - (version "3.8.2") + (version "3.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "xcms" version)) (sha256 (base32 - "0bfl56v3l6k31i11l09nx1yqfjy6z5yragm6k83z4w0mpgk18y7g")))) + "1aa11gy1v7kkamv3hsnvdx715q8f1saw9p664j6wifyjj0hx13kn")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -4964,14 +5071,16 @@ based on @dfn{Continuous Wavelet Transform} (CWT).") ("r-lattice" ,r-lattice) ("r-massspecwavelet" ,r-massspecwavelet) ("r-msnbase" ,r-msnbase) - ("r-multtest" ,r-multtest) ("r-mzr" ,r-mzr) ("r-plyr" ,r-plyr) ("r-protgenerics" ,r-protgenerics) ("r-rann" ,r-rann) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-robustbase" ,r-robustbase) - ("r-s4vectors" ,r-s4vectors))) + ("r-s4vectors" ,r-s4vectors) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/xcms/") (synopsis "LC/MS and GC/MS mass spectrometry data analysis") (description @@ -4984,20 +5093,22 @@ data for high-throughput, untargeted analyte profiling.") (define-public r-wrench (package (name "r-wrench") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Wrench" version)) (sha256 (base32 - "1s8d7jn0dk5zk2fhvsd4sgicypz4c41nzf19nqzcwb9bd6asgrwm")))) + "05dyk3yvbqrzvinv3ig8ad9wffwr14z715cicsbxwxpv5lq84wx6")))) (properties `((upstream-name . "Wrench"))) (build-system r-build-system) (propagated-inputs `(("r-limma" ,r-limma) ("r-locfit" ,r-locfit) ("r-matrixstats" ,r-matrixstats))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/HCBravoLab/Wrench") (synopsis "Wrench normalization for sparse count data") (description @@ -5008,14 +5119,14 @@ that arising from 16s metagenomic surveys.") (define-public r-wiggleplotr (package (name "r-wiggleplotr") - (version "1.10.1") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wiggleplotr" version)) (sha256 (base32 - "1pj2bsn5azs18mp5hr4g7c6rnds2y2rjjnak2785kaj7xi8jly4m")))) + "15l8f7ls2mwhsw68sr1k4r19hmdzjriibr5hpnfbanzj5x6yhdjq")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) @@ -5028,6 +5139,8 @@ that arising from 16s metagenomic surveys.") ("r-purrr" ,r-purrr) ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/wiggleplotr/") (synopsis "Make read coverage plots from BigWig files") (description @@ -5040,14 +5153,14 @@ visualization of exonic read coverage.") (define-public r-widgettools (package (name "r-widgettools") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "widgetTools" version)) (sha256 (base32 - "1nqy3icayacv5mlv5s5xgfli0dqzancs6zpffrl5p237c994nyr5")))) + "0lrdpsgm9r7yfyyj5crvb7px4hrghxhmiic4iissz40slbfyvilx")))) (properties `((upstream-name . "widgetTools"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/widgetTools/") @@ -5061,14 +5174,14 @@ widgets in R.") (define-public r-webbioc (package (name "r-webbioc") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "webbioc" version)) (sha256 (base32 - "1cwrmvh1l603k6j1r425c4vrqp0zf0x7bgx7y1wnbq4r7yc5sp62")))) + "16376ya5a5x2hwkl1v9y4r7np1drdwm912knnqg2dn90zmrdwr5f")))) (build-system r-build-system) (inputs `(("netpbm" ,netpbm) @@ -5094,14 +5207,14 @@ Currently only Affymetrix oligonucleotide analysis is supported.") (define-public r-zfpkm (package (name "r-zfpkm") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zFPKM" version)) (sha256 (base32 - "1hg0vc0ns8d4jpddn1v5a5m13a033b0wf1al01pb1lvmx5mzzr2n")))) + "0scszhfqrgzhglz1a6kxfydq9dx8fqx28j3dypp91y5ah2w6mdys")))) (properties `((upstream-name . "zFPKM"))) (build-system r-build-system) (propagated-inputs @@ -5110,6 +5223,8 @@ Currently only Affymetrix oligonucleotide analysis is supported.") ("r-ggplot2" ,r-ggplot2) ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-tidyr" ,r-tidyr))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/ronammar/zFPKM/") (synopsis "Functions to facilitate zFPKM transformations") (description @@ -5121,18 +5236,20 @@ This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID (define-public r-rbowtie2 (package (name "r-rbowtie2") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rbowtie2" version)) (sha256 (base32 - "1b7x42n9zisi2w2wwfc0c39j8s9868imyr0ysqgswf6l5mv9ivc5")))) + "1z2dn0q3wcw8b9ibx388kh7p5km16i71sw9miqj3daw7g0v5bxp3")))) (properties `((upstream-name . "Rbowtie2"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/Rbowtie2/") (synopsis "R wrapper for Bowtie2 and AdapterRemoval") (description @@ -5144,16 +5261,24 @@ rapid adapter trimming, identification, and read merging.") (define-public r-progeny (package (name "r-progeny") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "progeny" version)) (sha256 (base32 - "0j3kxjj7xmmwb29p87n3bw7bl38gcb94jrpw32126a578rf1pfrq")))) + "09rq3nf9zm7w9djmx8xc8j3win3597p2v36zqgkhgkjwq5rkjgsh")))) (build-system r-build-system) - (propagated-inputs `(("r-biobase" ,r-biobase))) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-dplyr" ,r-dplyr) + ("r-ggplot2" ,r-ggplot2) + ("r-ggrepel" ,r-ggrepel) + ("r-gridextra" ,r-gridextra) + ("r-tidyr" ,r-tidyr))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/saezlab/progeny") (synopsis "Pathway responsive gene activity inference") (description @@ -5166,14 +5291,14 @@ expression\".") (define-public r-arrmnormalization (package (name "r-arrmnormalization") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ARRmNormalization" version)) (sha256 (base32 - "0jj81q454nyh4hr5c56q1hv7i4ynx3rwnvpv08w34a6m77122bi1")))) + "0zhhvr051fmh6g0bqrl525mkf094j1jnc57j201jlzmvdpkydlpv")))) (properties `((upstream-name . "ARRmNormalization"))) (build-system r-build-system) @@ -5189,14 +5314,14 @@ Infinium HumanMethylation 450k assay.") (define-public r-biocfilecache (package (name "r-biocfilecache") - (version "1.10.2") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocFileCache" version)) (sha256 (base32 - "0jivhn95y6zv5ryamqk6nyd4l8nlskq64j362l9ml9qw746v0ja6")))) + "02chrzwccmazi7rdfpyriizhbgxyxlmprlw32w05wk54as6wrxv8")))) (properties `((upstream-name . "BiocFileCache"))) (build-system r-build-system) (propagated-inputs @@ -5207,6 +5332,8 @@ Infinium HumanMethylation 450k assay.") ("r-httr" ,r-httr) ("r-rappdirs" ,r-rappdirs) ("r-rsqlite" ,r-rsqlite))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/BiocFileCache/") (synopsis "Manage files across sessions") (description @@ -5219,14 +5346,14 @@ and data files used across sessions.") (define-public r-iclusterplus (package (name "r-iclusterplus") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "iClusterPlus" version)) (sha256 (base32 - "1dzgfzf2x8m62hssvsn1zzag7m444kyxj2vpdxl9nk859dr5pf37")))) + "0j987xvxixdz0wnhgp4kgfcgz5jffrcdhmldrgpgv582qmf4r94w")))) (properties `((upstream-name . "iClusterPlus"))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -5249,18 +5376,20 @@ Gaussian distributions.") (define-public r-rbowtie (package (name "r-rbowtie") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rbowtie" version)) (sha256 (base32 - "0yy31xhdmf6xb21wlhmxxwfqpm0nil39pb2cs3pq5ia758lb88z4")))) + "06y1qp915dlwjdi2fs3344sgya55pcv07f3i61y0cxb0bhbcgvrz")))) (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/") (synopsis "R bowtie wrapper") (description @@ -5272,14 +5401,14 @@ alignment tool.") (define-public r-sgseq (package (name "r-sgseq") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SGSeq" version)) (sha256 (base32 - "0950iv08wd0kjaw55rjn7m6syklvrabwr2zqq74wzyc5afyk2mrw")))) + "11rxx7abjyga2sdcp4x4z3n8xjx6973sckyzmh9ax6r46kwhxq8c")))) (properties `((upstream-name . "SGSeq"))) (build-system r-build-system) (propagated-inputs @@ -5297,6 +5426,8 @@ alignment tool.") ("r-runit" ,r-runit) ("r-s4vectors" ,r-s4vectors) ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/SGSeq/") (synopsis "Splice event prediction and quantification from RNA-seq data") (description @@ -5313,14 +5444,14 @@ interpretation.") (define-public r-rhisat2 (package (name "r-rhisat2") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhisat2" version)) (sha256 (base32 - "02fn5cm8sj2s9x00505y3iyipn1r3lpvpwpjy2pdxdbpmhb5hy49")))) + "0hhmcdnixkaqx9x9cl2vjaba3ri8m6wkbnbhxjmy51jwqzy2223a")))) (properties `((upstream-name . "Rhisat2"))) (build-system r-build-system) (arguments @@ -5339,6 +5470,8 @@ interpretation.") `(("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicranges" ,r-genomicranges) ("r-sgseq" ,r-sgseq))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/fmicompbio/Rhisat2") (synopsis "R Wrapper for HISAT2 sequence aligner") (description @@ -5351,14 +5484,14 @@ index.") (define-public r-quasr (package (name "r-quasr") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "QuasR" version)) (sha256 (base32 - "07m5q7wasapj2984kwy897510flbhvz7x0fgs7q2vm5wjhfzdrgv")))) + "0d87ajaaq8a7xgzl820qx5bvxw86ppab8clqk77sj02rfijnvjn8")))) (properties `((upstream-name . "QuasR"))) (build-system r-build-system) (inputs @@ -5384,6 +5517,8 @@ index.") ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors) ("r-shortread" ,r-shortread))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/QuasR/") (synopsis "Quantify and annotate short reads in R") (description @@ -5396,14 +5531,14 @@ quantification of genomic regions of interest.") (define-public r-rqc (package (name "r-rqc") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rqc" version)) (sha256 (base32 - "1nxkrb9kx41g050yz935yrl9pjkakhr8v6whxcvr72gg4r9m2x3m")))) + "1qsm9r6xfsplk8zpf7p0k7fi86l8a74nx963sna8gzig5qgrvnm3")))) (properties `((upstream-name . "Rqc"))) (build-system r-build-system) (propagated-inputs @@ -5425,6 +5560,8 @@ quantification of genomic regions of interest.") ("r-s4vectors" ,r-s4vectors) ("r-shiny" ,r-shiny) ("r-shortread" ,r-shortread))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/labbcb/Rqc") (synopsis "Quality control tool for high-throughput sequencing data") (description @@ -5437,14 +5574,14 @@ graphics.") (define-public r-birewire (package (name "r-birewire") - (version "3.18.0") + (version "3.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiRewire" version)) (sha256 (base32 - "1074cp422ail72yajn8p0bg26h6zzz07nzypnwfyv86qrpvpdw9q")))) + "0y7jb1abnik2y4ivpyqrgfl77rml6fhz88isd54l646ghslwxj0g")))) (properties `((upstream-name . "BiRewire"))) (build-system r-build-system) (propagated-inputs @@ -5466,14 +5603,14 @@ routines to analyse the resulting networks and their natural projections.") (define-public r-birta (package (name "r-birta") - (version "1.30.0") + (version "1.31.0") (source (origin (method url-fetch) (uri (bioconductor-uri "birta" version)) (sha256 (base32 - "1zhlwapdgkz0fpv5bqfxh9aw6ymnmxnnm1r0n0kfzn5izyjavslg")))) + "00a1kcfmcgdbx6wpnhk45wm45bynhry5m93l9hm75j2rwyc4lnca")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -5495,14 +5632,14 @@ Markov-Chain-Monte-Carlo is applied to sample the activity states.") (define-public r-multidataset (package (name "r-multidataset") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MultiDataSet" version)) (sha256 (base32 - "0iw99ymrv3ls023mpmgyagmb5simgsgadpj0k4bnssfaqnklywlj")))) + "0hjnj32m9wwlh2krdpdyl5jk1cakvlgki80z51mabhc62pajzf39")))) (properties `((upstream-name . "MultiDataSet"))) (build-system r-build-system) (propagated-inputs @@ -5516,6 +5653,8 @@ Markov-Chain-Monte-Carlo is applied to sample the activity states.") ("r-qqman" ,r-qqman) ("r-s4vectors" ,r-s4vectors) ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/MultiDataSet/") (synopsis "Implementation of MultiDataSet and ResultSet") (description @@ -5530,14 +5669,14 @@ packages.") (define-public r-ropls (package (name "r-ropls") - (version "1.18.8") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ropls" version)) (sha256 (base32 - "033i39r4037nd54jnp5zdn1vpzh61r671vmq0sf8dqrfblhm4w7a")))) + "1drww1mr0nira3qplyga6s3mljpjxshjgbn524kzxi0nrfbcvmnx")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -5568,14 +5707,14 @@ coefficients).") (define-public r-biosigner (package (name "r-biosigner") - (version "1.14.4") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biosigner" version)) (sha256 (base32 - "0hypk784xcax99mp673md6kvx45chk2nxbqniww7zm9q2hj983hl")))) + "1v760q7hzaybkf2q9230rmr4phi8hglm59qwsjzvncxrhs3dpj06")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -5601,14 +5740,14 @@ datasets.") (define-public r-annotatr (package (name "r-annotatr") - (version "1.12.1") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotatr" version)) (sha256 (base32 - "1bibk3p1q4cavqy11xs6rqqhqdjsq2dd7lf7blwcr27s5ajcd6dj")))) + "0z3ydcybd81w543fw8fiblghndx5m28w8qsphh5vqj726i0nj8cl")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -5624,6 +5763,8 @@ datasets.") ("r-reshape2" ,r-reshape2) ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/annotatr/") (synopsis "Annotation of genomic regions to genomic annotations") (description @@ -5640,17 +5781,19 @@ annotations.") (define-public r-rsubread (package (name "r-rsubread") - (version "2.0.1") + (version "2.2.2") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsubread" version)) (sha256 (base32 - "0pdkx9mhvzw3a4ff725qvda9bxvs9vh2ppb29cc5jrivgjndv5cy")))) + "1wgilpaw70dwg0zilx5i1pmi4j8wri6wi2ha1d3bapfhlwc6igml")))) (properties `((upstream-name . "Rsubread"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) + (propagated-inputs + `(("r-matrix" ,r-matrix))) (home-page "https://bioconductor.org/packages/Rsubread/") (synopsis "Subread sequence alignment and counting for R") (description @@ -5664,14 +5807,14 @@ and to both short and long sequence reads.") (define-public r-flowutils (package (name "r-flowutils") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowUtils" version)) (sha256 (base32 - "1xcs19j9p3izvksyy5wzsbicwby0dsa9g2w7gjzwynzgj5dpfr81")))) + "03jj4zyffm9kwzrg4vbsk6clc2v2m95wgalgqwzi31n9a2zyaza4")))) (properties `((upstream-name . "flowUtils"))) (build-system r-build-system) (propagated-inputs @@ -5690,14 +5833,14 @@ and to both short and long sequence reads.") (define-public r-consensusclusterplus (package (name "r-consensusclusterplus") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ConsensusClusterPlus" version)) (sha256 (base32 - "0pnh5zy6d3c364xxjdn5zp3kf5afhsxv6yzkdn1qspny0pmqlrp4")))) + "06gq3a95h0km1hzbx1za8q0l7kla3jdzvn6cnfz43ijx4n3dzzcq")))) (properties `((upstream-name . "ConsensusClusterPlus"))) (build-system r-build-system) @@ -5715,16 +5858,27 @@ cluster count and membership by stability evidence in unsupervised analysis.") (define-public r-cytolib (package (name "r-cytolib") - (version "1.8.0") + (version "2.0.3") (source (origin (method url-fetch) (uri (bioconductor-uri "cytolib" version)) (sha256 (base32 - "1zk5i09k782lw6297gl3rh0g4fxswr2ang8dgqj7p0814l7h15k9")))) + "123d1wlymq8r8d83as380h1dgw6v4s317acyvp1lsg2cpfp3gslj")))) (properties `((upstream-name . "cytolib"))) (build-system r-build-system) + (inputs + `(("zlib" ,zlib))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (propagated-inputs + `(("r-bh" ,r-bh) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) + ("r-rcppparallel" ,r-rcppparallel) + ("r-rhdf5lib" ,r-rhdf5lib) + ("r-rprotobuflib" ,r-rprotobuflib))) (home-page "https://bioconductor.org/packages/cytolib/") (synopsis "C++ infrastructure for working with gated cytometry") (description @@ -5735,14 +5889,14 @@ interact with gated cytometry data.") (define-public r-flowcore (package (name "r-flowcore") - (version "1.52.1") + (version "2.0.1") (source (origin (method url-fetch) (uri (bioconductor-uri "flowCore" version)) (sha256 (base32 - "08kvxc187iwlixibx1860jcp5g9bsw8abkv06x2qv1w83fas4pp2")))) + "1xalndmfidfzqwlppdanx7cnm4ysznq21ingmykhxni86s42kd8p")))) (properties `((upstream-name . "flowCore"))) (build-system r-build-system) (propagated-inputs @@ -5751,7 +5905,11 @@ interact with gated cytometry data.") ("r-biocgenerics" ,r-biocgenerics) ("r-cytolib" ,r-cytolib) ("r-matrixstats" ,r-matrixstats) - ("r-rcpp" ,r-rcpp))) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) + ("r-rprotobuflib" ,r-rprotobuflib))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/flowCore") (synopsis "Basic structures for flow cytometry data") (description @@ -5762,14 +5920,14 @@ with flow cytometry data.") (define-public r-flowmeans (package (name "r-flowmeans") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowMeans" version)) (sha256 (base32 - "1yisrikaafmpb4sig2c5l0wcz4idrs4as7i9x90v6z2v94iq0m8h")))) + "1sv5vpwm3qdhkn1gdrk3n674harjcni91g63sqzfmybiwq8dlym7")))) (properties `((upstream-name . "flowMeans"))) (build-system r-build-system) (propagated-inputs @@ -5788,14 +5946,14 @@ change point detection.") (define-public r-ncdfflow (package (name "r-ncdfflow") - (version "2.32.0") + (version "2.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ncdfFlow" version)) (sha256 (base32 - "06lscx6h4rg80ifi90rj7z2497b8w1fjipm3l8s3230rkizhh02i")))) + "0avxn2abh4fk1gkncrxz7jwzgvd90m3m0ly318q0z38cjhsw3j9f")))) (properties `((upstream-name . "ncdfFlow"))) (build-system r-build-system) (inputs @@ -5809,6 +5967,8 @@ change point detection.") ("r-rcpparmadillo" ,r-rcpparmadillo) ("r-rhdf5lib" ,r-rhdf5lib) ("r-zlibbioc" ,r-zlibbioc))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/ncdfFlow/") (synopsis "HDF5 based storage for flow cytometry data") (description @@ -5819,14 +5979,14 @@ manipulation of flow cytometry data.") (define-public r-ggcyto (package (name "r-ggcyto") - (version "1.14.1") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ggcyto" version)) (sha256 (base32 - "16jwdslhmj1nsa28wmaircy15cq7qn8nsyiawinjv711qiqhgw50")))) + "1ih6ggay7jjxnx8blc2sk95g8d40gkim145jllkk8sqwl02g44p0")))) (properties `((upstream-name . "ggcyto"))) (build-system r-build-system) (propagated-inputs @@ -5835,6 +5995,7 @@ manipulation of flow cytometry data.") ("r-flowworkspace" ,r-flowworkspace) ("r-ggplot2" ,r-ggplot2) ("r-gridextra" ,r-gridextra) + ("r-hexbin" ,r-hexbin) ("r-ncdfflow" ,r-ncdfflow) ("r-plyr" ,r-plyr) ("r-rcolorbrewer" ,r-rcolorbrewer) @@ -5855,14 +6016,14 @@ statistics to the plot.") (define-public r-flowviz (package (name "r-flowviz") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowViz" version)) (sha256 (base32 - "0ik16bxcfcg3q26ra3055718kskid64aaazcbqsxalca9ppdm4k7")))) + "0f3jfwdmaq9wrgl737blk5gmpc29l9kb6nadqhxpvbjwqsnzx0yq")))) (properties `((upstream-name . "flowViz"))) (build-system r-build-system) (propagated-inputs @@ -5875,6 +6036,8 @@ statistics to the plot.") ("r-latticeextra" ,r-latticeextra) ("r-mass" ,r-mass) ("r-rcolorbrewer" ,r-rcolorbrewer))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/flowViz/") (synopsis "Visualization for flow cytometry") (description @@ -5884,14 +6047,14 @@ statistics to the plot.") (define-public r-flowclust (package (name "r-flowclust") - (version "3.24.0") + (version "3.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowClust" version)) (sha256 (base32 - "0k4bgc4mf512njfdfg5ld9l7slgfxyfh766jab87j96zrrgcnj8s")))) + "06mkq9y41jax07x4knhvhzgrkgqdvpvcw604bxdk6bv9wx3ipq5b")))) (properties `((upstream-name . "flowClust"))) (build-system r-build-system) (arguments @@ -5910,7 +6073,8 @@ statistics to the plot.") (inputs `(("gsl" ,gsl))) (native-inputs - `(("pkg-config" ,pkg-config))) + `(("pkg-config" ,pkg-config) + ("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/flowClust") (synopsis "Clustering for flow cytometry") (description @@ -5923,14 +6087,14 @@ model with Box-Cox transformation.") (define-public r-rprotobuflib (package (name "r-rprotobuflib") - (version "1.8.0") + (version "2.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RProtoBufLib" version)) (sha256 (base32 - "0dlgki21a37bxqh3cf83vl5zqxm86472g8a9plvhrjzzsn3mwnrm")))) + "0kfinf9vzc1i5qxmaw832id557gr1vqdi1m8yiaxz83g37wh8vps")))) (properties `((upstream-name . "RProtoBufLib"))) (build-system r-build-system) (arguments @@ -5939,8 +6103,10 @@ model with Box-Cox transformation.") (add-after 'unpack 'unpack-bundled-sources (lambda _ (with-directory-excursion "src" - (invoke "tar" "xf" "protobuf-2.6.0.tgz")) + (invoke "tar" "xf" "protobuf-3.10.0.tar.gz")) #t))))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/RProtoBufLib/") (synopsis "C++ headers and static libraries of Protocol buffers") (description @@ -5951,14 +6117,14 @@ for other R packages to compile and link against.") (define-public r-flowworkspace (package (name "r-flowworkspace") - (version "3.34.1") + (version "4.0.3") (source (origin (method url-fetch) (uri (bioconductor-uri "flowWorkspace" version)) (sha256 (base32 - "1ijbc6z9ljhrw3cqr02smgplhrfg44gzrb1dq4gbrpq3nj4khhpn")))) + "1fi76m6r5x4w390996989rignffdzl11k3prpimpwjd3566c276w")))) (properties `((upstream-name . "flowWorkspace"))) (build-system r-build-system) (propagated-inputs @@ -5970,21 +6136,24 @@ for other R packages to compile and link against.") ("r-digest" ,r-digest) ("r-dplyr" ,r-dplyr) ("r-flowcore" ,r-flowcore) - ("r-flowviz" ,r-flowviz) + ("r-ggplot2" ,r-ggplot2) ("r-graph" ,r-graph) - ("r-gridextra" ,r-gridextra) ("r-lattice" ,r-lattice) ("r-latticeextra" ,r-latticeextra) ("r-matrixstats" ,r-matrixstats) ("r-ncdfflow" ,r-ncdfflow) ("r-rbgl" ,r-rbgl) - ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) ("r-rcppparallel" ,r-rcppparallel) ("r-rgraphviz" ,r-rgraphviz) + ("r-rhdf5lib" ,r-rhdf5lib) ("r-rprotobuflib" ,r-rprotobuflib) ("r-scales" ,r-scales) - ("r-stringr" ,r-stringr))) + ("r-stringr" ,r-stringr) + ("r-xml" ,r-xml))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/flowWorkspace/") (synopsis "Infrastructure for working with cytometry data") (description @@ -5999,14 +6168,14 @@ matches the flowJo analysis.") (define-public r-flowstats (package (name "r-flowstats") - (version "3.44.0") + (version "4.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowStats" version)) (sha256 (base32 - "0pql0lpf90nra7w6z6nd8l9cgjlsg2pxysfravnbzfhl3pjvd96w")))) + "1ygvxvd7y6jp907y0h3hycdwvw1fch16w84g06nk4f4g4kvrzdir")))) (properties `((upstream-name . "flowStats"))) (build-system r-build-system) (propagated-inputs @@ -6035,14 +6204,14 @@ package.") (define-public r-opencyto (package (name "r-opencyto") - (version "1.24.0") + (version "2.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "openCyto" version)) (sha256 (base32 - "0h25nhvq1zq624wsgb55wjcgri9rcd2fnqkb31h9jdakr01dw2sb")))) + "10dyd6dddskv70vhpwfbsqdb8pb9i3ka0fgvl1h51wqlckbsj89m")))) (properties `((upstream-name . "openCyto"))) (build-system r-build-system) (propagated-inputs @@ -6067,6 +6236,8 @@ package.") ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-rcpp" ,r-rcpp) ("r-rrcov" ,r-rrcov))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/openCyto") (synopsis "Hierarchical gating pipeline for flow cytometry data") (description @@ -6077,14 +6248,14 @@ sequential way to mimic the manual gating strategy.") (define-public r-cytoml (package (name "r-cytoml") - (version "1.12.1") + (version "2.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CytoML" version)) (sha256 (base32 - "0wgi8rwb4spxzd5xvs5amfr5g82ny2nad57j3nmhnhnj1cpirjxz")))) + "0zpq2j4y9i5lls1kj2w4spl8qjp3076idsr2a2rjvy1fykzlp01q")))) (properties `((upstream-name . "CytoML"))) (build-system r-build-system) (inputs @@ -6103,15 +6274,17 @@ sequential way to mimic the manual gating strategy.") ("r-graph" ,r-graph) ("r-jsonlite" ,r-jsonlite) ("r-lattice" ,r-lattice) - ("r-ncdfflow" ,r-ncdfflow) ("r-opencyto" ,r-opencyto) ("r-plyr" ,r-plyr) ("r-rbgl" ,r-rbgl) ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) ("r-rcppparallel" ,r-rcppparallel) ("r-rgraphviz" ,r-rgraphviz) + ("r-rhdf5lib" ,r-rhdf5lib) ("r-rprotobuflib" ,r-rprotobuflib) ("r-runit" ,r-runit) + ("r-tibble" ,r-tibble) ("r-xml" ,r-xml) ("r-yaml" ,r-yaml))) (native-inputs @@ -6126,14 +6299,14 @@ standard to exchange gated cytometry data with other software platforms.") (define-public r-flowsom (package (name "r-flowsom") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FlowSOM" version)) (sha256 (base32 - "0265sq4zvj6d6h5ghqj9xzm4b0z9v65kgyl88cgdcpdkzfnfcvd5")))) + "1p17jv4q1dbcc47jpjy9hbcvzpwrx8waq7qpcj778jsyz6z6jh78")))) (properties `((upstream-name . "FlowSOM"))) (build-system r-build-system) (propagated-inputs @@ -6156,14 +6329,14 @@ self-organizing map clustering and minimal spanning trees.") (define-public r-mixomics (package (name "r-mixomics") - (version "6.10.9") + (version "6.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "mixOmics" version)) (sha256 (base32 - "0b457yg8mwqlrn5l344w8qcj8v2ghlj1wdx1ysxbncqvqx7nvgig")))) + "13kq9l5xwhwp30y5gfqfh5f11n63vn8rk195mb2y2mww4cwi6lv4")))) (properties `((upstream-name . "mixOmics"))) (build-system r-build-system) (propagated-inputs @@ -6200,14 +6373,14 @@ delete entire rows with missing data.") (define-public r-depecher (package (name "r-depecher") - (version "1.2.2") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DepecheR" version)) (sha256 (base32 - "199j2kw0xnw7y4v1gakm2jgyc7zzlj8xh0570f2yjq55gp1kggbm")))) + "0nmx04qybzf6nhfngmdxwpbbz9x32v34mbnpg8jq7a2cgchzsj9s")))) (properties `((upstream-name . "DepecheR"))) (build-system r-build-system) (propagated-inputs @@ -6245,14 +6418,14 @@ data, to only emphasize the data that actually matters.") (define-public r-rcistarget (package (name "r-rcistarget") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RcisTarget" version)) (sha256 (base32 - "1nnah7s0jd24fpfyxsf76jas8dm23c3266aps124wdlqsp9q5qjw")))) + "1lvi873dv0vhw53s1pmcilw8qwlywm9p2ybphcl168nzh6w31r4i")))) (properties `((upstream-name . "RcisTarget"))) (build-system r-build-system) (propagated-inputs @@ -6263,6 +6436,8 @@ data, to only emphasize the data that actually matters.") ("r-gseabase" ,r-gseabase) ("r-r-utils" ,r-r-utils) ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://aertslab.org/#scenic") (synopsis "Identify transcription factor binding motifs enriched on a gene list") (description @@ -6280,14 +6455,14 @@ genes in the gene-set that are ranked above the leading edge).") (define-public r-cicero (package (name "r-cicero") - (version "1.4.4") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cicero" version)) (sha256 (base32 - "1ay1g2r0la4grcp1y8vcp211lfwzjf7j819ajzdirsh5dab8whld")))) + "0n78lf5hz6zzl550dbf4imis43pv91zicfff8y4lspckljhz9z75")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) @@ -6390,17 +6565,19 @@ cisTopics and explore the nature and regulatory proteins driving them.") (define-public r-genie3 (package (name "r-genie3") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GENIE3" version)) (sha256 (base32 - "0p67lhgy3lb4nc958s51hx7rvgwhzwfic9xhpsrask40k43spv7l")))) + "1bsm0gxracsyg1wnaw3whvskghfpbgbm9navr8wdmxj2hjp3dqs7")))) (properties `((upstream-name . "GENIE3"))) (build-system r-build-system) (propagated-inputs `(("r-reshape2" ,r-reshape2))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/GENIE3") (synopsis "Gene network inference with ensemble of trees") (description @@ -6411,14 +6588,14 @@ regulatory networks from expression data.") (define-public r-roc (package (name "r-roc") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ROC" version)) (sha256 (base32 - "1aqpyc28czagg3nbybh55vf152nbar61jjw79w04326d97mc3j3y")))) + "0gmx3r77yl5fqrj5j2hamwynbis75qd62q28964kx16z33xfgx89")))) (properties `((upstream-name . "ROC"))) (build-system r-build-system) (propagated-inputs @@ -6459,14 +6636,14 @@ data.") (define-public r-watermelon (package (name "r-watermelon") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wateRmelon" version)) (sha256 (base32 - "0a66fq04yph9dis91lzjk9kh134zy6fj98yklrwf24r1080qngx0")))) + "1c3a6bq3ggmv8kmdfrgiar6nwgircgzjrbgd9z9dqiin7j13gxwn")))) (properties `((upstream-name . "wateRmelon"))) (build-system r-build-system) (propagated-inputs @@ -6496,14 +6673,14 @@ metrics, with methods for objects produced by the @code{methylumi} and (define-public r-gdsfmt (package (name "r-gdsfmt") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gdsfmt" version)) (sha256 (base32 - "0zc9v62imd0ykz4h30pxa64q0y45qijmkwdk2pd4ncsg8fc2jlz9")) + "00hggma0i15w03xi9jr02v2593jbqkcxyfcvpp7mdzrshn99m9p6")) (modules '((guix build utils))) ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build ;; them and link with system libraries instead. @@ -6533,6 +6710,8 @@ metrics, with methods for objects produced by the @code{methylumi} and `(("lz4" ,lz4) ("xz" ,xz) ("zlib" ,zlib))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "http://corearray.sourceforge.net/") (synopsis "R Interface to CoreArray Genomic Data Structure (GDS) Files") @@ -6553,14 +6732,14 @@ with multiple R processes supported by the package @code{parallel}.") (define-public r-bigmelon (package (name "r-bigmelon") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bigmelon" version)) (sha256 (base32 - "0sw7rp4p03m1s72b4j06jfb7as3v1n2w2z4ppk8s4f80fb05bcls")))) + "1cryjhbiacm45g097rpqgbva49hs5vdx4y4h5h2v1gw4k78hwb4y")))) (properties `((upstream-name . "bigmelon"))) (build-system r-build-system) (propagated-inputs @@ -6581,14 +6760,14 @@ with multiple R processes supported by the package @code{parallel}.") (define-public r-seqbias (package (name "r-seqbias") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqbias" version)) (sha256 (base32 - "19vbdyjblij2533ibmrw1n0rkqfrbflma6cg5b79ghks0mg7z8hq")))) + "0sy2fv98x4qfz9llns28jh1n4bi991jj856y8a5fbzpx7y990lai")))) (properties `((upstream-name . "seqbias"))) (build-system r-build-system) (propagated-inputs @@ -6647,14 +6826,14 @@ injected in that sequence).") (define-public r-reqon (package (name "r-reqon") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReQON" version)) (sha256 (base32 - "10p6l2zxijqyypdm970jyfqyrnfhaq3nf7cg2q6mgd1srggfa0cx")))) + "06m0hd4aqsxjyzhs8b1zys7lz8289qgwn7jp2dpln1j7cf02q4bz")))) (properties `((upstream-name . "ReQON"))) (build-system r-build-system) (propagated-inputs @@ -6672,14 +6851,14 @@ format.") (define-public r-wavcluster (package (name "r-wavcluster") - (version "2.20.0") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wavClusteR" version)) (sha256 (base32 - "0vq3xxsvwq86rlya7xc92sc4i6b48sib0pcina3xivg3ky2j3z7y")))) + "0204czqjmkwhd6gznwxzb0vj3dg3aif628g8c30085aa2jljn9bk")))) (properties `((upstream-name . "wavClusteR"))) (build-system r-build-system) (propagated-inputs @@ -6698,6 +6877,8 @@ format.") ("r-seqinr" ,r-seqinr) ("r-stringr" ,r-stringr) ("r-wmtsa" ,r-wmtsa))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/wavClusteR/") (synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data") (description @@ -6718,14 +6899,14 @@ procedures that induce nucleotide substitutions (e.g. BisSeq).") (define-public r-timeseriesexperiment (package (name "r-timeseriesexperiment") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TimeSeriesExperiment" version)) (sha256 (base32 - "0xqa6hzknnci20zx2f6mw5cpqx8pq0v6fzf053hh51p1l2ikvgqm")))) + "1k0djvcsyjj1ayncvmi8nlqi3jdn5qp41y3fwsqg1cp0qsvx7zv3")))) (properties `((upstream-name . "TimeSeriesExperiment"))) (build-system r-build-system) @@ -6745,6 +6926,8 @@ procedures that induce nucleotide substitutions (e.g. BisSeq).") ("r-tidyr" ,r-tidyr) ("r-vegan" ,r-vegan) ("r-viridis" ,r-viridis))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/nlhuong/TimeSeriesExperiment/") (synopsis "Analysis for short time-series data") (description @@ -6757,14 +6940,14 @@ provides methods for retrieving enriched pathways.") (define-public r-variantfiltering (package (name "r-variantfiltering") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantFiltering" version)) (sha256 (base32 - "13pgfk2mbffd9smmxnwz7g0jrwng78711053wfzadr107zbyn4r8")))) + "0lsrnybsbm9siyjv4nal6bmprj8ynwgk4n1145f4h52g78wq3br4")))) (properties `((upstream-name . "VariantFiltering"))) (build-system r-build-system) @@ -6863,14 +7046,14 @@ arrays based on fast wavelet-based functional models.") (define-public r-variancepartition (package (name "r-variancepartition") - (version "1.16.1") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "variancePartition" version)) (sha256 (base32 - "02pzsff14j4am2d949mh8xgi0c7k44g09q4lr6nqm08vf92brb6g")))) + "1rn655qq7dshbk1dd41n7y2hfz8498jxd2j4rk7p8hrikd3s32dm")))) (properties `((upstream-name . "variancePartition"))) (build-system r-build-system) @@ -6891,6 +7074,8 @@ arrays based on fast wavelet-based functional models.") ("r-progress" ,r-progress) ("r-reshape2" ,r-reshape2) ("r-scales" ,r-scales))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/variancePartition/") (synopsis "Analyze variation in gene expression experiments") (description @@ -6905,14 +7090,14 @@ measures.") (define-public r-htqpcr (package (name "r-htqpcr") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HTqPCR" version)) (sha256 (base32 - "008iczqaa0wn5nw144vfg3qylg7qa1q963nq9mqhgj3sxlg4rmjx")))) + "08bd5zkjdnz726s03bvvzv03va0xbrr818ipp6737z9g3nk9m81j")))) (properties `((upstream-name . "HTqPCR"))) (build-system r-build-system) (propagated-inputs @@ -6939,14 +7124,14 @@ features (e.g. genes, microRNAs).") (define-public r-unifiedwmwqpcr (package (name "r-unifiedwmwqpcr") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "unifiedWMWqPCR" version)) (sha256 (base32 - "1l6rf7scxxyz4x0m4li54y6905sqj4jrx481zb9h3vqhcfcmn8lj")))) + "1l9gxq3askr3cz2a4bqsw7vjr1agivzvx651cblkygv57x08zf81")))) (properties `((upstream-name . "unifiedWMWqPCR"))) (build-system r-build-system) @@ -7030,14 +7215,14 @@ cellular organization in health and disease.") (define-public r-bgmix (package (name "r-bgmix") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BGmix" version)) (sha256 (base32 - "1bwqqhkh4m3hhpd71grwjrg7n07lzvys4y7aghmw2gw5ibnk5683")))) + "1pfi3hinjn6ymikadgj8dqm59h7mapf01wj86dbbvf8y1xqp8y8n")))) (properties `((upstream-name . "BGmix"))) (build-system r-build-system) (propagated-inputs @@ -7052,14 +7237,14 @@ gene expression.") (define-public r-bgx (package (name "r-bgx") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bgx" version)) (sha256 (base32 - "0fiqqv6pin0zhxaw67hzfjccq2qkl9qfqjf10nx2zmpxm2licavm")))) + "0r67a6m5hrnsxgk0f57hl5yaagi2wai2kpfyjjlhrck4rlm1sjcx")))) (properties `((upstream-name . "bgx"))) (build-system r-build-system) (propagated-inputs @@ -7077,14 +7262,14 @@ Affymetrix GeneChips.") (define-public r-bhc (package (name "r-bhc") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BHC" version)) (sha256 (base32 - "1bxx3jak8mgvay3j1xd59bb9j86pzl6hh5abxww9x1b7rswmy1jh")))) + "06milqjg2nl3ra47sxi7a2p2d3mbrx3wk168pqgimvs8snldd2xr")))) (properties `((upstream-name . "BHC"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/BHC/") @@ -7103,14 +7288,14 @@ algorithm which is more efficient for larger data sets.") (define-public r-bicare (package (name "r-bicare") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BicARE" version)) (sha256 (base32 - "1gia5vzmvbk4k1vx3bh9nld1ws9s3c0y11qfbzqhfnfjbd7n8qcs")))) + "0llckbl3l26lf6wgjg7rxs8k1yrk043vvdhnkc6ncg33sydj383y")))) (properties `((upstream-name . "BicARE"))) (build-system r-build-system) (propagated-inputs @@ -7127,19 +7312,21 @@ results.") (define-public r-bifet (package (name "r-bifet") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiFET" version)) (sha256 (base32 - "0ck1d6hxd4f40hfz8p2z5xmjbz79yhrf6fisjka2xzk5v9fm4p4k")))) + "1v2dshs09iy2glzq0vwxmr83x867j844i1ixsfcamvfq33fwbbr5")))) (properties `((upstream-name . "BiFET"))) (build-system r-build-system) (propagated-inputs `(("r-genomicranges" ,r-genomicranges) ("r-poibin" ,r-poibin))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/BiFET") (synopsis "Bias-free footprint enrichment test") (description @@ -7155,14 +7342,14 @@ the read count and GC content bias.") (define-public r-rsbml (package (name "r-rsbml") - (version "2.44.0") + (version "2.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rsbml" version)) (sha256 (base32 - "1dbp0aaijxn3na26b68ws0v9qzvml61ifb9z4i8pz7q6h48n7lxa")))) + "1i1izznnwzrc6m7s3hblfff466icfvxl2gjdqaln8qfg9v87rslx")))) (properties `((upstream-name . "rsbml"))) (build-system r-build-system) (inputs @@ -7183,14 +7370,14 @@ validating output, provides an S4 SBML DOM, converts SBML to R graph objects.") (define-public r-hypergraph (package (name "r-hypergraph") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hypergraph" version)) (sha256 (base32 - "1bixmslxy7r987zw1vf4dg72hfi04lf4vj03n7ygym2g8nfhbh7m")))) + "1iq9b9rzy3ikx8xszsjiv3p8l702n2h2s9w33797wcmkg4apslb7")))) (properties `((upstream-name . "hypergraph"))) (build-system r-build-system) (propagated-inputs @@ -7205,14 +7392,14 @@ manipulating hypergraphs.") (define-public r-hyperdraw (package (name "r-hyperdraw") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hyperdraw" version)) (sha256 (base32 - "0a8h3pb7196qi49ady8ni92m5wqb1hvxw6khk9j63mwj3h7jinbj")))) + "1qzx5sqp7rpspk8g1j34p03ds1vmw0h7hpzb2ijpbvmsja5drzvf")))) (properties `((upstream-name . "hyperdraw"))) (build-system r-build-system) (inputs `(("graphviz" ,graphviz))) @@ -7229,14 +7416,14 @@ manipulating hypergraphs.") (define-public r-biggr (package (name "r-biggr") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiGGR" version)) (sha256 (base32 - "1n2ypc84abmhn6br0yi87k7lvjc11k7abzhgvzdabc2ai1qgcqif")))) + "05afi6hsh1dv6lc6l0dfhvvi8k34wyzf1k1jimam7a6pbrhyy5dk")))) (properties `((upstream-name . "BiGGR"))) (build-system r-build-system) (propagated-inputs @@ -7259,19 +7446,21 @@ networks and estimated fluxes can be visualized with hypergraphs.") (define-public r-bigmemoryextras (package (name "r-bigmemoryextras") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bigmemoryExtras" version)) (sha256 (base32 - "17dk7c44ikphcrpi8hnxyvlmj30qmj098kc0ihfi69bp9rw1cibq")))) + "053bqcd3p4i7agj43ccjxfz40a1sxrymd49vdpfq8ypslkwk7g0g")))) (properties `((upstream-name . "bigmemoryExtras"))) (build-system r-build-system) (propagated-inputs `(("r-bigmemory" ,r-bigmemory))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/phaverty/bigmemoryExtras") (synopsis "Extension of the bigmemory package") (description @@ -7291,18 +7480,19 @@ a file-backed matrix with factor properties.") (define-public r-bigpint (package (name "r-bigpint") - (version "1.2.2") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bigPint" version)) (sha256 (base32 - "1zkakxi1iqavzmjxnkkd02qm5jk28ldcvcdcxaafz748dz6s67fs")))) + "1m92ngkzimcc37byf0ziphrby8wmjd5hfa53gvfphgaakyj9bjg8")))) (properties `((upstream-name . "bigPint"))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) + `(("r-delayedarray" ,r-delayedarray) + ("r-dplyr" ,r-dplyr) ("r-ggally" ,r-ggally) ("r-ggplot2" ,r-ggplot2) ("r-gridextra" ,r-gridextra) @@ -7317,6 +7507,7 @@ a file-backed matrix with factor properties.") ("r-shinycssloaders" ,r-shinycssloaders) ("r-shinydashboard" ,r-shinydashboard) ("r-stringr" ,r-stringr) + ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-tidyr" ,r-tidyr))) (native-inputs `(("r-knitr" ,r-knitr))) @@ -7332,14 +7523,14 @@ visualizing RNA-sequencing datasets and differentially expressed genes.") (define-public r-chemminer (package (name "r-chemminer") - (version "3.38.0") + (version "3.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChemmineR" version)) (sha256 (base32 - "1j6vmkhc03dmmkm5wgbcv62pw5dclp49f906xkx1pwg27bdldbga")))) + "0cna5xsqflvhlp2k47asxyv3w4ympmz2wy2cwjyzlal6936fjikf")))) (properties `((upstream-name . "ChemmineR"))) (build-system r-build-system) (propagated-inputs @@ -7356,6 +7547,8 @@ visualizing RNA-sequencing datasets and differentially expressed genes.") ("r-rcurl" ,r-rcurl) ("r-rjson" ,r-rjson) ("r-rsvg" ,r-rsvg))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/girke-lab/ChemmineR") (synopsis "Cheminformatics toolkit for R") (description @@ -7371,14 +7564,14 @@ structures.") (define-public r-bioassayr (package (name "r-bioassayr") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bioassayR" version)) (sha256 (base32 - "08vxkvxhqnryfbj4dwk3ifb9pn544www9zk2pj9fjbh5xfpwi7zw")))) + "1n0gsnxcl0lplqk8rs5ygxrxpx389ddl6wv3ciyz9g2xry5biyfy")))) (properties `((upstream-name . "bioassayR"))) (build-system r-build-system) (propagated-inputs @@ -7406,14 +7599,14 @@ available bioactivity data.") (define-public r-biobroom (package (name "r-biobroom") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biobroom" version)) (sha256 (base32 - "1480ycdsh9xdhbpr47vdw5g6m8arqsnp8hc19wwhzm8npxh4qqlb")))) + "06qcrprn58kbrr5kyw1jl6z88b9w9g8xs6rkhrbnz8k7rv373fhf")))) (properties `((upstream-name . "biobroom"))) (build-system r-build-system) (propagated-inputs @@ -7421,6 +7614,8 @@ available bioactivity data.") ("r-broom" ,r-broom) ("r-dplyr" ,r-dplyr) ("r-tidyr" ,r-tidyr))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/StoreyLab/biobroom") (synopsis "Turn Bioconductor objects into tidy data frames") (description @@ -7436,14 +7631,14 @@ visualize bioinformatics analyses.") (define-public r-graphite (package (name "r-graphite") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "graphite" version)) (sha256 (base32 - "1r9fk0cpdwm7012pa85dkjcpkml2j89zcznpf4hfdz66anfyyycd")))) + "0rc9cw3picz1y0lwhbzpk03ciij8kij74m15qgzh2ykla7zprb2p")))) (properties `((upstream-name . "graphite"))) (build-system r-build-system) (propagated-inputs @@ -7463,14 +7658,14 @@ symbols).") (define-public r-reactomepa (package (name "r-reactomepa") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReactomePA" version)) (sha256 (base32 - "1vwc9kj1l4yi7c4f4lnq0i3wl2nrmmhcxyakz8qak122fi92z3j1")))) + "1ngilyn1mihwxs4sh5gk9y829xghdmh277cfw3vfgflz9sgwy21x")))) (properties `((upstream-name . "ReactomePA"))) (build-system r-build-system) (propagated-inputs @@ -7482,6 +7677,8 @@ symbols).") ("r-graphite" ,r-graphite) ("r-igraph" ,r-igraph) ("r-reactome-db" ,r-reactome-db))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://guangchuangyu.github.io/software/ReactomePA") (synopsis "Reactome pathway analysis") (description @@ -7493,14 +7690,14 @@ enrichment analysis and several functions for visualization.") (define-public r-ebarrays (package (name "r-ebarrays") - (version "2.50.0") + (version "2.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBarrays" version)) (sha256 (base32 - "063rhsdp8x0f881kslq06zxfp6b2qabrz4vmfrn8a4v3pd3n7s13")))) + "00ld26bld8xgin9zqwxybahvhmqbrvr09jfphg0yr4j4zck6sqgf")))) (properties `((upstream-name . "EBarrays"))) (build-system r-build-system) (propagated-inputs @@ -7517,14 +7714,14 @@ microarray data.") (define-public r-bioccasestudies (package (name "r-bioccasestudies") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocCaseStudies" version)) (sha256 (base32 - "1sg9vxs24zfz3dg9y0qlrdsq43y0pbahbvcfxzlxjzjw80xzxpbd")))) + "0fadck1dk1zavpn9yrcwx6zgfi18fw5xfs8svgzipns6bq41j8ix")))) (properties `((upstream-name . "BiocCaseStudies"))) (build-system r-build-system) @@ -7539,14 +7736,14 @@ monograph.") (define-public r-biocgraph (package (name "r-biocgraph") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biocGraph" version)) (sha256 (base32 - "1rv2lwiqwg7h7za23n896fs4dpla3xhw6kzwghb6iw5nlm2m61yw")))) + "1372bm4y3czqhpki10pnprxfkfncfcsy59zzvf8wj6q03acaavrj")))) (properties `((upstream-name . "biocGraph"))) (build-system r-build-system) (propagated-inputs @@ -7564,14 +7761,14 @@ different graph related packages produced by Bioconductor.") (define-public r-experimenthub (package (name "r-experimenthub") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ExperimentHub" version)) (sha256 (base32 - "054w2lkyirbmhgia0rp4nk9zzw3zphz6jxg6fc9zlarp90g64z24")))) + "18d6kjfavy5b769gpkblihdkz2nz2hsgyjki8mp1sywi0ik08ncd")))) (properties `((upstream-name . "ExperimentHub"))) (build-system r-build-system) (propagated-inputs @@ -7582,6 +7779,8 @@ different graph related packages produced by Bioconductor.") ("r-curl" ,r-curl) ("r-rappdirs" ,r-rappdirs) ("r-s4vectors" ,r-s4vectors))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/ExperimentHub/") (synopsis "Client to access ExperimentHub resources") (description @@ -7596,14 +7795,14 @@ access.") (define-public r-multiassayexperiment (package (name "r-multiassayexperiment") - (version "1.12.6") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MultiAssayExperiment" version)) (sha256 (base32 - "174vzlxsyayb5il77cb3zzgszxl3l0wkprc9w6pgz4yv5ix13adi")))) + "0qlfnd86999jqv2nd0ikixi2sfd449dyg3ml4nbs8ycs57c2irgh")))) (properties `((upstream-name . "MultiAssayExperiment"))) (build-system r-build-system) @@ -7631,14 +7830,14 @@ rownames.") (define-public r-bioconcotk (package (name "r-bioconcotk") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocOncoTK" version)) (sha256 (base32 - "0rnah6c01a33yb9663jim9iclan61rpcwprb56mykgn1pf5hywbj")))) + "021qzygfwdnd3naz1iqq01zr3zxv3k7wm1lklik24vc7axshxbmk")))) (properties `((upstream-name . "BiocOncoTK"))) (build-system r-build-system) (propagated-inputs @@ -7664,6 +7863,8 @@ rownames.") ("r-scales" ,r-scales) ("r-shiny" ,r-shiny) ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/BiocOncoTK") (synopsis "Bioconductor components for general cancer genomics") (description @@ -7674,20 +7875,22 @@ tools for genome-scale analysis of cancer studies.") (define-public r-biocor (package (name "r-biocor") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioCor" version)) (sha256 (base32 - "1bjw02rwmz2d715sgpfp08njb15200ch7cmipsf9hd5835ppg1jl")))) + "1xghclfqv8d23g72g8914br5zjx4sz9zihzczwwmpl15lghpnqwy")))) (properties `((upstream-name . "BioCor"))) (build-system r-build-system) (propagated-inputs `(("r-biocparallel" ,r-biocparallel) ("r-gseabase" ,r-gseabase) ("r-matrix" ,r-matrix))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://llrs.github.io/BioCor/") (synopsis "Functional similarities") (description @@ -7701,14 +7904,14 @@ gene selection, testing relationships, and so on.") (define-public r-biocpkgtools (package (name "r-biocpkgtools") - (version "1.4.6") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocPkgTools" version)) (sha256 (base32 - "0grwnmncmpqcplbfw3j210m1a8f7mmdizklh4zksg4ic21dpjj1a")))) + "0l5fvi1m4834n4h0iswbap135s9mpaiabw9czzn1r72ssz86vrcr")))) (properties `((upstream-name . "BiocPkgTools"))) (build-system r-build-system) (propagated-inputs @@ -7751,14 +7954,14 @@ analytics on packages.") (define-public r-biocset (package (name "r-biocset") - (version "1.0.1") + (version "1.2.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocSet" version)) (sha256 (base32 - "1xcksnvjflrdarn8xqmgf0n6wbsjkq9jazqwp35i52vqcq4ic1j9")))) + "14dmkc878lskbm001kgjyqmrwnn6s032z4h64f617f1xd9zx9wrj")))) (properties `((upstream-name . "BiocSet"))) (build-system r-build-system) (propagated-inputs @@ -7769,6 +7972,8 @@ analytics on packages.") ("r-rlang" ,r-rlang) ("r-rtracklayer" ,r-rtracklayer) ("r-tibble" ,r-tibble))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/BiocSet") (synopsis @@ -7784,14 +7989,14 @@ accessing web references for elements/sets are also available in BiocSet.") (define-public r-biocworkflowtools (package (name "r-biocworkflowtools") - (version "1.12.1") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocWorkflowTools" version)) (sha256 (base32 - "0z28s572wg9qxv52dmixxz1xf1z3fyp2j7kzk0k32fp628918wr6")))) + "0p9r71ql67sdlgd5pv118lhz8b85pr5y4ijfwzcy8wrr8jwlbddy")))) (properties `((upstream-name . "BiocWorkflowTools"))) (build-system r-build-system) @@ -7817,14 +8022,14 @@ Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.") (define-public r-biodist (package (name "r-biodist") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bioDist" version)) (sha256 (base32 - "0iabw07px3ybdgbbab0vv350051cm4aq8w47rz9dnmzx4kil9h5q")))) + "17bvxk0anvsp29j5nbblvaymf8qgbj3sz4ir2l7wj8kb8jfi19cp")))) (properties `((upstream-name . "bioDist"))) (build-system r-build-system) (propagated-inputs @@ -7836,3 +8041,49 @@ Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.") "This package provides a collection of software tools for calculating distance measures.") (license license:artistic2.0))) + +(define-public r-pcatools + (package + (name "r-pcatools") + (version "2.0.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "PCAtools" version)) + (sha256 + (base32 + "0mnwqrhm1hmhzwrpidf6z207w1ycpm572snvpp5swlg6hnxq6bnc")))) + (properties `((upstream-name . "PCAtools"))) + (build-system r-build-system) + (propagated-inputs + `(("r-beachmat" ,r-beachmat) + ("r-bh" ,r-bh) + ("r-biocparallel" ,r-biocparallel) + ("r-biocsingular" ,r-biocsingular) + ("r-cowplot" ,r-cowplot) + ("r-delayedarray" ,r-delayedarray) + ("r-delayedmatrixstats" ,r-delayedmatrixstats) + ("r-dqrng" ,r-dqrng) + ("r-ggplot2" ,r-ggplot2) + ("r-ggrepel" ,r-ggrepel) + ("r-lattice" ,r-lattice) + ("r-matrix" ,r-matrix) + ("r-rcpp" ,r-rcpp) + ("r-reshape2" ,r-reshape2))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/kevinblighe/PCAtools") + (synopsis "PCAtools: everything Principal Components Analysis") + (description + "@dfn{Principal Component Analysis} (PCA) extracts the fundamental +structure of the data without the need to build any model to represent it. +This \"summary\" of the data is arrived at through a process of reduction that +can transform the large number of variables into a lesser number that are +uncorrelated (i.e. the 'principal components'), while at the same time being +capable of easy interpretation on the original data. PCAtools provides +functions for data exploration via PCA, and allows the user to generate +publication-ready figures. PCA is performed via @code{BiocSingular}; users +can also identify an optimal number of principal components via different +metrics, such as the elbow method and Horn's parallel analysis, which has +relevance for data reduction in single-cell RNA-seq (scRNA-seq) and high +dimensional mass cytometry data.") + (license license:gpl3))) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 550c0387e9..f60a918d75 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6947,17 +6947,18 @@ information as possible.") (define-public r-genefilter (package (name "r-genefilter") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "genefilter" version)) (sha256 (base32 - "1xjr02qhldspjwd6y374wgik18fgywb6408wsz471i8b4ik98ckc")))) + "1sbbrnq6p90fri0ik6aq2zw26kasw63nyiy7xkzrj6vgyq7x258g")))) (build-system r-build-system) (native-inputs - `(("gfortran" ,gfortran))) + `(("gfortran" ,gfortran) + ("r-knitr" ,r-knitr))) (propagated-inputs `(("r-annotate" ,r-annotate) ("r-annotationdbi" ,r-annotationdbi) @@ -6974,14 +6975,14 @@ high-throughput sequencing experiments.") (define-public r-deseq2 (package (name "r-deseq2") - (version "1.26.0") + (version "1.28.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DESeq2" version)) (sha256 (base32 - "1lmbhznfs8dz9ipd53z4ccwvwxqwzx1ayw56jlrvlsambaj8fash")))) + "0xh12c2skr0bbv893p05gvbismkcnqw8zwh7yz4wmycgajfzg2pp")))) (properties `((upstream-name . "DESeq2"))) (build-system r-build-system) (propagated-inputs @@ -6992,13 +6993,14 @@ high-throughput sequencing experiments.") ("r-geneplotter" ,r-geneplotter) ("r-genomicranges" ,r-genomicranges) ("r-ggplot2" ,r-ggplot2) - ("r-hmisc" ,r-hmisc) ("r-iranges" ,r-iranges) ("r-locfit" ,r-locfit) ("r-rcpp" ,r-rcpp) ("r-rcpparmadillo" ,r-rcpparmadillo) ("r-s4vectors" ,r-s4vectors) ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/DESeq2") (synopsis "Differential gene expression analysis") (description @@ -7011,14 +7013,14 @@ distribution.") (define-public r-dexseq (package (name "r-dexseq") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DEXSeq" version)) (sha256 (base32 - "0sqqb65ckliif2nmvlvc7w49id59z0nvqcdz5gry8l2mn6azrf6a")))) + "1inyxb89hd5bn0sl7a9qbv9d1g40z4v1s9qwxkcsx5c79fl04n1h")))) (properties `((upstream-name . "DEXSeq"))) (build-system r-build-system) (propagated-inputs @@ -7039,6 +7041,8 @@ distribution.") ("r-statmod" ,r-statmod) ("r-stringr" ,r-stringr) ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/DEXSeq") (synopsis "Inference of differential exon usage in RNA-Seq") (description @@ -7054,14 +7058,14 @@ exploration of the results.") (define-public r-annotationforge (package (name "r-annotationforge") - (version "1.28.0") + (version "1.30.1") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationForge" version)) (sha256 (base32 - "0h2r60v339ajk5r6xq4iwwcpihdvf12fi8255byr2dhglzrd8xl7")))) + "1a2155jxbwc6qr3dcyvp850grhdr7czc7bs3s87ff4sgdl0jp3jw")))) (properties `((upstream-name . "AnnotationForge"))) (build-system r-build-system) @@ -7074,6 +7078,8 @@ exploration of the results.") ("r-rsqlite" ,r-rsqlite) ("r-s4vectors" ,r-s4vectors) ("r-xml" ,r-xml))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/AnnotationForge") (synopsis "Code for building annotation database packages") (description @@ -7084,14 +7090,14 @@ databases. Packages produced are intended to be used with AnnotationDbi.") (define-public r-rbgl (package (name "r-rbgl") - (version "1.62.1") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RBGL" version)) (sha256 (base32 - "0ixbkdirf08i400db587r262j52sdwdgk3884nxk5xkbhx2m6vg0")))) + "079599a6xn2i7snfn2vgshkw0c00rrfhj44pvi03ap8id29bkayy")))) (properties `((upstream-name . "RBGL"))) (build-system r-build-system) (propagated-inputs @@ -7107,14 +7113,14 @@ the graph algorithms contained in the Boost library.") (define-public r-gseabase (package (name "r-gseabase") - (version "1.48.0") + (version "1.50.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GSEABase" version)) (sha256 (base32 - "0kcb90sxlf19d5dxhdbqk9x62svky4262cccl0wxarbq6gf3bd57")))) + "1k4faj53cwvqijad8cf7fcghzxcv9shlbpl8n73bsncc8k192y2j")))) (properties `((upstream-name . "GSEABase"))) (build-system r-build-system) (propagated-inputs @@ -7124,6 +7130,8 @@ the graph algorithms contained in the Boost library.") ("r-biocgenerics" ,r-biocgenerics) ("r-graph" ,r-graph) ("r-xml" ,r-xml))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/GSEABase") (synopsis "Gene set enrichment data structures and methods") (description @@ -7134,14 +7142,14 @@ Enrichment Analysis} (GSEA).") (define-public r-category (package (name "r-category") - (version "2.52.1") + (version "2.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Category" version)) (sha256 (base32 - "0ga0ij9hyzsxa5pavwmv35i8xggia2wygrk4m4z8an0qcvgy3v5g")))) + "1grspdzk5a4vidnxwcd1jmy1vcn494aydsp3vydx235yv7iqac1b")))) (properties `((upstream-name . "Category"))) (build-system r-build-system) (propagated-inputs @@ -7165,14 +7173,14 @@ analysis.") (define-public r-gostats (package (name "r-gostats") - (version "2.52.0") + (version "2.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOstats" version)) (sha256 (base32 - "19f4gxm3sbprqrnwzvskvywv6j4ibm8xkrbgg4h0fvh2b5331nwc")))) + "00q39cyv4l28r6s9gjnd0qhl7h80vmwp4lpmchisqzj44xzyics9")))) (properties `((upstream-name . "GOstats"))) (build-system r-build-system) (propagated-inputs @@ -7196,14 +7204,14 @@ testing and other simple calculations.") (define-public r-shortread (package (name "r-shortread") - (version "1.44.3") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ShortRead" version)) (sha256 (base32 - "0ykyrj4g6vc67d5s46sp4659qvar2iavflzhggm79w4p50hxia4s")))) + "0l4kdln69y6yhln0xiv2jmpxg05fjcglln406p43a2bqvk2lr03d")))) (properties `((upstream-name . "ShortRead"))) (build-system r-build-system) (inputs @@ -7238,22 +7246,23 @@ ungapped alignment formats.") (define-public r-systempiper (package (name "r-systempiper") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "systemPipeR" version)) (sha256 (base32 - "17r25v9wcglyma2v1c8fka80dm7fx86saxlsb2aprmwi4h3dhb0j")))) + "01ilhlrvy28jfdyxjria4024yryj5zgympgqznw17g3y3az78kk2")))) (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-deseq2" ,r-deseq2) + ("r-dot" ,r-dot) ("r-edger" ,r-edger) ("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicranges" ,r-genomicranges) @@ -7261,13 +7270,18 @@ ungapped alignment formats.") ("r-go-db" ,r-go-db) ("r-gostats" ,r-gostats) ("r-limma" ,r-limma) + ("r-magrittr" ,r-magrittr) ("r-pheatmap" ,r-pheatmap) ("r-rjson" ,r-rjson) ("r-rsamtools" ,r-rsamtools) + ("r-rsvg" ,r-rsvg) ("r-shortread" ,r-shortread) + ("r-stringr" ,r-stringr) ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-yaml" ,r-yaml) ("r-variantannotation" ,r-variantannotation))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/tgirke/systemPipeR") (synopsis "Next generation sequencing workflow and reporting environment") (description @@ -7285,14 +7299,14 @@ annotation infrastructure.") (define-public r-grohmm (package (name "r-grohmm") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "groHMM" version)) (sha256 (base32 - "0ywr8f6bfhg2ia3n4rmsxr4v1xqmlyhkwh0rvkgh3yqgnbvihndg")))) + "04z9qq1xwdsaxbqhyld37w0ybvzly9pc1hcyrnwdbyjwd7n1fncb")))) (properties `((upstream-name . "groHMM"))) (build-system r-build-system) (propagated-inputs @@ -7518,13 +7532,13 @@ BLAST, KEGG, GenBank, MEDLINE and GO.") (define-public r-biocviews (package (name "r-biocviews") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biocViews" version)) (sha256 (base32 - "0yn8jys1900d31haayz0ppqk5y79mwjajwp4alz6pln3dbs70f3g")))) + "1h4cmfbff79v9xrh271dp3rv0877ris06lmkvc39kqzj7yjsh7c2")))) (properties `((upstream-name . "biocViews"))) (build-system r-build-system) @@ -7546,13 +7560,13 @@ also known as views, in a controlled vocabulary.") (define-public r-biocstyle (package (name "r-biocstyle") - (version "2.14.4") + (version "2.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocStyle" version)) (sha256 (base32 - "1x71in059zql40f4c87bd1gf96r945kdvwbq61jmch9d3d8nwxbb")))) + "07rjl2n4sazdg581zh7w3yykzphgr2gpz41ba4ryqs7347vh9nbf")))) (properties `((upstream-name . "BiocStyle"))) (build-system r-build-system) @@ -7562,6 +7576,8 @@ also known as views, in a controlled vocabulary.") ("r-knitr" ,r-knitr) ("r-rmarkdown" ,r-rmarkdown) ("r-yaml" ,r-yaml))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/BiocStyle") (synopsis "Bioconductor formatting styles") (description "This package provides standard formatting styles for @@ -7572,13 +7588,13 @@ functionality.") (define-public r-bioccheck (package (name "r-bioccheck") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocCheck" version)) (sha256 (base32 - "1qnvl5yajgh67ijkq6gdsafri1k5hyw5gzn2ccqk9ymx6i2xd80g")))) + "1p9ys18sn1crxw1iac2jdgqvwpb5hjd9nfxx0qn0ncrv0b550mny")))) (properties `((upstream-name . "BiocCheck"))) (build-system r-build-system) @@ -7610,6 +7626,8 @@ functionality.") ("r-biocmanager" ,r-biocmanager) ("r-biocviews" ,r-biocviews) ("r-stringdist" ,r-stringdist))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/BiocCheck") (synopsis "Executes Bioconductor-specific package checks") (description "This package contains tools to perform additional quality @@ -7619,13 +7637,13 @@ checks on R packages that are to be submitted to the Bioconductor repository.") (define-public r-s4vectors (package (name "r-s4vectors") - (version "0.24.4") + (version "0.26.1") (source (origin (method url-fetch) (uri (bioconductor-uri "S4Vectors" version)) (sha256 (base32 - "1fzs8j2d3wwfzm2fq63ywf68a4dbggyl5l098f148yn4jw7jd3bc")))) + "1ddr3ngyczx332zw9ai1a6h7442lgrbfcj8vrhvbkdkzqwj14xmb")))) (properties `((upstream-name . "S4Vectors"))) (build-system r-build-system) @@ -7646,13 +7664,13 @@ S4Vectors package itself.") (define-public r-iranges (package (name "r-iranges") - (version "2.20.2") + (version "2.22.2") (source (origin (method url-fetch) (uri (bioconductor-uri "IRanges" version)) (sha256 (base32 - "1jhnxb9yacmj2z82b6992gihjvj1a0gnjwbjiagyyx03fqnv23kg")))) + "1y24jw62806wp2afiyj1x6n00gj7d3323klqdypra9q43pg1w49d")))) (properties `((upstream-name . "IRanges"))) (build-system r-build-system) @@ -7698,13 +7716,13 @@ ID and species. It is used by functions in the GenomeInfoDb package.") (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.22.1") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "0phadr67yb4l25x41a9wg4pjy1wbxlk14jhidhz6g5n4z6x45qbm")))) + "0ab92nq7lvhvhgp512qhiiphpby0b17c666qska6p8a636zzmqiv")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) @@ -7728,13 +7746,13 @@ names in their natural, rather than lexicographic, order.") (define-public r-edger (package (name "r-edger") - (version "3.28.1") + (version "3.30.3") (source (origin (method url-fetch) (uri (bioconductor-uri "edgeR" version)) (sha256 (base32 - "07dv99kl7jfa62nzcq705r56gcpb1hq7p4px48j71y2ddi1rqmr6")))) + "1z9bkg08rgqn3jm2s4ndbj641w33wl8jd3j6m5if6h2nnw6011ic")))) (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs @@ -7756,13 +7774,13 @@ CAGE.") (define-public r-variantannotation (package (name "r-variantannotation") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantAnnotation" version)) (sha256 (base32 - "009s7rzp78s2w6iybizina42qx2w8qv3xwjbkpqphmm451maykgs")))) + "09y6ymwky839nb0y7y93w810hk9mvwqn7595q1276c28dkddiqvw")))) (properties `((upstream-name . "VariantAnnotation"))) (inputs @@ -7795,13 +7813,13 @@ coding changes and predict coding outcomes.") (define-public r-limma (package (name "r-limma") - (version "3.42.2") + (version "3.44.1") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "1nd01r7rd7jb5qz84vbgfnyrmgm9wiq7fsdji68537kjgvrzmm9z")))) + "0l6f6lz1rghj8c5s14ljbnmsrwz27fi6a7g42n15n3d3msvflw36")))) (build-system r-build-system) (home-page "http://bioinf.wehi.edu.au/limma") (synopsis "Package for linear models for microarray and RNA-seq data") @@ -7814,13 +7832,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") (define-public r-xvector (package (name "r-xvector") - (version "0.26.0") + (version "0.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "XVector" version)) (sha256 (base32 - "0s2gg84yzl5ffkzp6n7kh0jjk1vd90z189f5hkfn18rn67cy2nv7")))) + "11h1hszv4798q1gbx8r6zf8vlaqx4v9ql0lbh2xaxybp66a03pvc")))) (properties `((upstream-name . "XVector"))) (build-system r-build-system) @@ -7850,13 +7868,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") (define-public r-genomicranges (package (name "r-genomicranges") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicRanges" version)) (sha256 (base32 - "0xdds6ws7jjdfy4x3mb0qhy43kpxdmifmpw0jdk4wgw999zabb50")))) + "0wn1zr2qq0rpv9z2wialgizn6xzdlcjg1w2kif67n53svz6vk2x1")))) (properties `((upstream-name . "GenomicRanges"))) (build-system r-build-system) @@ -7866,6 +7884,8 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") ("r-iranges" ,r-iranges) ("r-s4vectors" ,r-s4vectors) ("r-xvector" ,r-xvector))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/GenomicRanges") (synopsis "Representation and manipulation of genomic intervals") (description @@ -7879,13 +7899,13 @@ manipulating genomic intervals and variables defined along a genome.") (define-public r-biobase (package (name "r-biobase") - (version "2.46.0") + (version "2.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Biobase" version)) (sha256 (base32 - "1gx41083dqlm59vwqdxvc4ny31x91j48mda9n3scg0f2zwasvqgl")))) + "13p3kgnxm7hbn8cy289kbhaiyfa6rxx7l1pbvajwqzbay3cxznqp")))) (properties `((upstream-name . "Biobase"))) (build-system r-build-system) @@ -7901,13 +7921,13 @@ on Bioconductor or which replace R functions.") (define-public r-annotationdbi (package (name "r-annotationdbi") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationDbi" version)) (sha256 (base32 - "09piz1f0xpbb4amskx4ilby6lfrn27hhwk75il2c4lq6m3hr4w8s")))) + "10gplxal0qphcn29azv0i6hiim9q45lmhzvhhhsnwfhwpgja7p05")))) (properties `((upstream-name . "AnnotationDbi"))) (build-system r-build-system) @@ -7918,6 +7938,8 @@ on Bioconductor or which replace R functions.") ("r-iranges" ,r-iranges) ("r-rsqlite" ,r-rsqlite) ("r-s4vectors" ,r-s4vectors))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/AnnotationDbi") (synopsis "Annotation database interface") (description @@ -7928,13 +7950,13 @@ annotation data packages using SQLite data storage.") (define-public r-biomart (package (name "r-biomart") - (version "2.42.1") + (version "2.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biomaRt" version)) (sha256 (base32 - "0676s8aq9xj2pdrfk28kf5j69fmssn900k4vxrp11ghwjr8z24h7")))) + "0ag26q9283p9mfz4zx8qnx1w7b7ilmsb8wyx737z9cqy9a0i57wj")))) (properties `((upstream-name . "biomaRt"))) (build-system r-build-system) @@ -7965,13 +7987,13 @@ powerful online queries from gene annotation to database mining.") (define-public r-biocparallel (package (name "r-biocparallel") - (version "1.20.1") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocParallel" version)) (sha256 (base32 - "0g0znb4whsvb9hpwx9xaasdi5n4vjqw8cpdyqgrdrjm91rls1h21")))) + "1lsg5xm5j3ly5k60fidzhkgqc9jgscyfkqngjvd9qp6yfzvsb82g")))) (properties `((upstream-name . "BiocParallel"))) (build-system r-build-system) @@ -7979,6 +8001,8 @@ powerful online queries from gene annotation to database mining.") `(("r-futile-logger" ,r-futile-logger) ("r-snow" ,r-snow) ("r-bh" ,r-bh))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/BiocParallel") (synopsis "Bioconductor facilities for parallel evaluation") (description @@ -7990,18 +8014,19 @@ objects.") (define-public r-biostrings (package (name "r-biostrings") - (version "2.54.0") + (version "2.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Biostrings" version)) (sha256 (base32 - "0pq7g2hflx2cjlpwdj6mscw9hnxvlf5y50dxf48lbrf9r3q9kmyp")))) + "0imhfz7dg8b3l5qzipjranqqshdsg2x6zc49drlhn8sc7j40cvi8")))) (properties `((upstream-name . "Biostrings"))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) + ("r-crayon" ,r-crayon) ("r-iranges" ,r-iranges) ("r-s4vectors" ,r-s4vectors) ("r-xvector" ,r-xvector))) @@ -8016,13 +8041,13 @@ biological sequences or sets of sequences.") (define-public r-rsamtools (package (name "r-rsamtools") - (version "2.2.3") + (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsamtools" version)) (sha256 (base32 - "1vj43acawqqkf9yval9fzxarpsf04fmn78m2hq4f083w1k0myhyr")))) + "0z01z0s71f941k7sns46nyabps28c69d6jxx6sppjpc6h4vrw0vq")))) (properties `((upstream-name . "Rsamtools"))) (build-system r-build-system) @@ -8061,19 +8086,18 @@ tab-delimited (tabix) files.") (define-public r-delayedarray (package (name "r-delayedarray") - (version "0.12.3") + (version "0.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedArray" version)) (sha256 (base32 - "02i88ll2d7r83nk0wdj28akvsz3jq19g6ixpaahfy3jy5av4byv6")))) + "1lz7a0rrlfv3w44n073mk8pw39z7lfs0njdxp5vpp0rdsmvdf1qk")))) (properties `((upstream-name . "DelayedArray"))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) ("r-s4vectors" ,r-s4vectors) ("r-iranges" ,r-iranges) ("r-matrix" ,r-matrix) @@ -8095,13 +8119,13 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns), (define-public r-summarizedexperiment (package (name "r-summarizedexperiment") - (version "1.16.1") + (version "1.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "SummarizedExperiment" version)) (sha256 (base32 - "1z9bdk49dajafkfvv99nv6zyn6v70iyyy2jgdp5w5z8174a2bnn1")))) + "07rc79k5dp0dnf4dvsxif995aa9cgfkf13yf84qnwl64k9pf3c2c")))) (properties `((upstream-name . "SummarizedExperiment"))) (build-system r-build-system) @@ -8114,6 +8138,8 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns), ("r-iranges" ,r-iranges) ("r-matrix" ,r-matrix) ("r-s4vectors" ,r-s4vectors))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/SummarizedExperiment") (synopsis "Container for representing genomic ranges by sample") (description @@ -8126,13 +8152,13 @@ samples.") (define-public r-genomicalignments (package (name "r-genomicalignments") - (version "1.22.1") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicAlignments" version)) (sha256 (base32 - "065xvy4pkda0ajvl1b75iski95k1pnbhxwdq7vkfl8v55915vqh6")))) + "0v8k6d7frm5p48cmk4zik78cw9abz4inx0zhl4zrmmx31ifyvk8d")))) (properties `((upstream-name . "GenomicAlignments"))) (build-system r-build-system) @@ -8159,13 +8185,13 @@ alignments.") (define-public r-rtracklayer (package (name "r-rtracklayer") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rtracklayer" version)) (sha256 (base32 - "0lp9xsm8kqrgpwgwj7qaqcv1z6qynbz084grlpwp94zsp2ppf0n6")))) + "1zcgk92sidhy4y7ws9ms4nkkh2hnccfhfh53qgna0kma9jy4v5xf")))) (build-system r-build-system) (arguments `(#:phases @@ -8206,13 +8232,13 @@ as well as query and modify the browser state, such as the current viewport.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.38.2") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "0dd226kgks50jdx5w35f3wmg95hy8aibi4kcn8p5kmqp5i8j580b")))) + "09ffsflk2yhhj9ivm028y3qdkvv8idgxpm4il3y9rym7shc8b3f8")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) @@ -8231,6 +8257,8 @@ as well as query and modify the browser state, such as the current viewport.") ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors) ("r-xvector" ,r-xvector))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/GenomicFeatures") (synopsis "Tools for working with transcript centric annotations") (description @@ -8271,13 +8299,13 @@ information about the latest version of the Gene Ontologies.") (define-public r-topgo (package (name "r-topgo") - (version "2.38.1") + (version "2.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "topGO" version)) (sha256 (base32 - "1kw9m2j67895k58lx9msc248pjwblp8clxwgsl01cql7sgi1xzlf")))) + "13rhbvn27sj75fklf1cnjaazacx8yyjlhqlnbp5zk157q6y5cwdr")))) (properties `((upstream-name . "topGO"))) (build-system r-build-system) @@ -8304,13 +8332,13 @@ dependencies between GO terms can be implemented and applied.") (define-public r-bsgenome (package (name "r-bsgenome") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BSgenome" version)) (sha256 (base32 - "0nn1b3h4hmnx5whf2cmzmyxdrcf4myj8c38rwr0sw4rc07xfzndy")))) + "1jw8r1qm9fpg2s1cw2y4np243jjxm65j2xdy2785h8fc1b02msf6")))) (properties `((upstream-name . "BSgenome"))) (build-system r-build-system) @@ -8320,6 +8348,7 @@ dependencies between GO terms can be implemented and applied.") ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) + ("r-matrixstats" ,r-matrixstats) ("r-rsamtools" ,r-rsamtools) ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors) @@ -8334,13 +8363,13 @@ genome data packages and support for efficient SNP representation.") (define-public r-impute (package (name "r-impute") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "impute" version)) (sha256 (base32 - "0igz1phjd1j9bg9z4kyy7j8v9bxi9sdwz4df26r51i2vavlbrf4q")))) + "161p6l1cp3wwdynkxwvg0yhrh6yv20brdlplw5w5mavn4hf1nm0h")))) (native-inputs `(("gfortran" ,gfortran))) (build-system r-build-system) @@ -8354,13 +8383,13 @@ microarray data, using nearest neighbor averaging.") (define-public r-seqpattern (package (name "r-seqpattern") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqPattern" version)) (sha256 (base32 - "1gxrq6s2hiyac69idh5r1nbr1s69n0hg4ap2skm4g6857av9pwqf")))) + "0f1yvx2ri1557rzjx08q5bgml1cvkm8hjl8xn1qi4rjs64sy6mci")))) (properties `((upstream-name . "seqPattern"))) (build-system r-build-system) @@ -8381,13 +8410,13 @@ reference point and sorted by a user defined feature.") (define-public r-genomation (package (name "r-genomation") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "genomation" version)) (sha256 (base32 - "1sba928h23b67gr3i4yj1bg655g24l3bcgsf5gvymzrv5idrss1l")))) + "1cy8kqwddiha5jy6nda1al956i4wncbgjkrxwijdb08cmka2sfwh")))) (build-system r-build-system) (propagated-inputs `(("r-biostrings" ,r-biostrings) @@ -8411,6 +8440,8 @@ reference point and sorted by a user defined feature.") ("r-runit" ,r-runit) ("r-s4vectors" ,r-s4vectors) ("r-seqpattern" ,r-seqpattern))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "http://bioinformatics.mdc-berlin.de/genomation/") (synopsis "Summary, annotation and visualization of genomic data") (description @@ -8455,14 +8486,14 @@ downloaded from Encode.") (define-public r-seqlogo (package (name "r-seqlogo") - (version "1.52.0") + (version "1.54.3") (source (origin (method url-fetch) (uri (bioconductor-uri "seqLogo" version)) (sha256 (base32 - "0s94aahp8ma1crmp83dz65ifjwrx6wqi3q6005lmbp8yk2x1rkj4")))) + "09kkxir305fv8z2yyihvspkrzclxbw1cx5mvhfkrhl10rap6662j")))) (properties `((upstream-name . "seqLogo"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/seqLogo") @@ -8476,14 +8507,14 @@ Stephens (1990).") (define-public r-motifrg (package (name "r-motifrg") - (version "1.30.0") + (version "1.31.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifRG" version)) (sha256 (base32 - "0s6wdr036lra9x93r9k8wvicbkgzypjh3jp46h92yacw8d829k0d")))) + "1ml6zyzlk8yjbnfhga2qnw8nl43rankvka0kc1yljxr2b66aqbhn")))) (properties `((upstream-name . "motifRG"))) (build-system r-build-system) (propagated-inputs @@ -8557,13 +8588,13 @@ R/qtl, to better handle high-dimensional data and complex cross designs.") (define-public r-zlibbioc (package (name "r-zlibbioc") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zlibbioc" version)) (sha256 (base32 - "1xh7qan0w62mzsmanbx9vcj6ygdfhzw1abaxijkq7f4nh5w87idj")))) + "0j1l052jb2cwc1nifxzwknc9csagf4f2d092zs0i95dz0rma89l0")))) (properties `((upstream-name . "zlibbioc"))) (build-system r-build-system) @@ -8599,14 +8630,14 @@ secondary structure and comparative analysis in R.") (define-public r-rhtslib (package (name "r-rhtslib") - (version "1.18.1") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhtslib" version)) (sha256 (base32 - "0gkbrmrcg55c9s5166ifljlx0v25rv4ijdyp4wf4c292xd6chy2l")))) + "186r7icrkzrni1c4n33ip7dlsfgys7hnqf0simvxrpl3yhh3ygdi")))) (properties `((upstream-name . "Rhtslib"))) (build-system r-build-system) ;; Without this a temporary directory ends up in the Rhtslib.so binary, @@ -8618,7 +8649,8 @@ secondary structure and comparative analysis in R.") (inputs `(("zlib" ,zlib))) (native-inputs - `(("pkg-config" ,pkg-config))) + `(("pkg-config" ,pkg-config) + ("r-knitr" ,r-knitr))) (home-page "https://github.com/nhayden/Rhtslib") (synopsis "High-throughput sequencing library as an R package") (description @@ -8630,14 +8662,14 @@ of other R packages who wish to make use of HTSlib.") (define-public r-bamsignals (package (name "r-bamsignals") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bamsignals" version)) (sha256 (base32 - "0699b0pqbs0dvs91yjibcjc90lxj9mg8rcml4a6wchfr9md7n74w")))) + "0p858xxfv79yc8b3lq58zl9f00irvbn3czsd8wdi5040xg42m402")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) @@ -8648,6 +8680,8 @@ of other R packages who wish to make use of HTSlib.") ("r-zlibbioc" ,r-zlibbioc))) (inputs `(("zlib" ,zlib))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/bamsignals") (synopsis "Extract read count signals from bam files") (description @@ -8660,24 +8694,22 @@ paired-end data.") (define-public r-rcas (package (name "r-rcas") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RCAS" version)) (sha256 (base32 - "1s3gvvxi1029d1vfwnjh21nnw3mlx08kcwz63891hml9y850cvsn")))) + "0f812pgv3ys1zv4n9sqkgm01hj4cdd0i0h85dqbhkwd94zl6cavl")))) (properties `((upstream-name . "RCAS"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biomart" ,r-biomart) + `(("r-biocgenerics" ,r-biocgenerics) ("r-biostrings" ,r-biostrings) + ("r-bsgenome" ,r-bsgenome) ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) ("r-cowplot" ,r-cowplot) ("r-data-table" ,r-data-table) - ("r-dbi" ,r-dbi) ("r-dt" ,r-dt) ("r-genomation" ,r-genomation) ("r-genomeinfodb" ,r-genomeinfodb) @@ -8685,20 +8717,21 @@ paired-end data.") ("r-genomicranges" ,r-genomicranges) ("r-ggplot2" ,r-ggplot2) ("r-ggseqlogo" ,r-ggseqlogo) - ("r-knitr" ,r-knitr) - ("r-motifrg" ,r-motifrg) - ("r-org-hs-eg-db" ,r-org-hs-eg-db) + ("r-gprofiler2" ,r-gprofiler2) + ("r-iranges" ,r-iranges) ("r-pbapply" ,r-pbapply) ("r-pheatmap" ,r-pheatmap) ("r-plotly" ,r-plotly) ("r-plotrix" ,r-plotrix) ("r-proxy" ,r-proxy) + ("r-ranger" ,r-ranger) ("r-rsqlite" ,r-rsqlite) ("r-rtracklayer" ,r-rtracklayer) ("r-rmarkdown" ,r-rmarkdown) ("r-s4vectors" ,r-s4vectors) - ("r-topgo" ,r-topgo) ("pandoc" ,ghc-pandoc))) + (native-inputs + `(("r-knitr" ,r-knitr))) (synopsis "RNA-centric annotation system") (description "RCAS aims to be a standalone RNA-centric annotation system that provides @@ -8761,14 +8794,14 @@ library implementing most of the pipeline's features.") (define-public r-mutationalpatterns (package (name "r-mutationalpatterns") - (version "1.12.0") + (version "2.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MutationalPatterns" version)) (sha256 (base32 - "08715l6swrlccviw7932v5hyrd2x4c6049vy9qnxk0lw3sp1zvsf")))) + "02lyjiabyhmifycksvpcx29a0pb7z9xjw0hgg8n0sd0dy3afqhcm")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) @@ -8866,13 +8899,13 @@ factors bound at the specific regions.") (define-public r-tximport (package (name "r-tximport") - (version "1.14.2") + (version "1.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "tximport" version)) (sha256 (base32 - "1avy0zhgnszmg0dr9w74yq9ml10kwdrrgcni2wysrd48zzskc1n0")))) + "1x9959lkjl2h869rgd1b30q1idxzjkr1fyqbpndqk3kbi4q2gr40")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) @@ -8890,18 +8923,20 @@ of gene-level counts.") (define-public r-rhdf5 (package (name "r-rhdf5") - (version "2.30.1") + (version "2.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rhdf5" version)) (sha256 (base32 - "18pv74jj4wr1981r92ss10qkgf5g1b09dsbz3im3j70a4l5l0df0")))) + "097znwl95y2vd6asyqxs62m7binwxqmna7ss0302yl3b0s72skcy")))) (build-system r-build-system) (propagated-inputs `(("r-rhdf5lib" ,r-rhdf5lib))) (inputs `(("zlib" ,zlib))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/rhdf5") (synopsis "HDF5 interface to R") (description @@ -8917,19 +8952,21 @@ the available RAM.") (define-public r-annotationfilter (package (name "r-annotationfilter") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationFilter" version)) (sha256 (base32 - "1l9sxhlvnwn6327vgg02h11ppmqr2zr07ff8wmcng0i1jbqwa8q5")))) + "18kh1xrhpwb48s1qj4f1v8af3jmw49pnbp5afi2myn9894hxg0cs")))) (properties `((upstream-name . "AnnotationFilter"))) (build-system r-build-system) (propagated-inputs `(("r-genomicranges" ,r-genomicranges) ("r-lazyeval" ,r-lazyeval))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/Bioconductor/AnnotationFilter") (synopsis "Facilities for filtering Bioconductor annotation resources") (description @@ -9262,14 +9299,14 @@ manipulate and analyze genetic variants.") (define-public r-chipseq (package (name "r-chipseq") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "chipseq" version)) (sha256 (base32 - "1ln6bn08xig3j6ryak1xfkjhvpnlm2vf1czz9hlj6f02299nbs6l")))) + "0lh859s0aq73vac1phcgagf6n000qgq2xsk0bmfr61n5swifml2a")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) @@ -9314,14 +9351,14 @@ GenomicRanges Bioconductor package.") (define-public r-copywriter (package (name "r-copywriter") - (version "2.18.0") + (version "2.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CopywriteR" version)) (sha256 (base32 - "0llg1zpxg7qnvja5f5w1z1xic0jdg6zc4mfn97h2sm44skxxcyl1")))) + "0c36wpv0rygkbqpf3dwh5xmc3lr7p8lrdzsq2fbbpw04skl6i7m2")))) (properties `((upstream-name . "CopywriteR"))) (build-system r-build-system) (propagated-inputs @@ -9354,13 +9391,13 @@ number detection tools.") (define-public r-methylkit (package (name "r-methylkit") - (version "1.12.0") + (version "1.14.2") (source (origin (method url-fetch) (uri (bioconductor-uri "methylKit" version)) (sha256 (base32 - "0klwc0sbmrxj1lxbz16pl39rxjm0pi57gjw547hlgnac1p9fspzy")))) + "1qr13d2712ypbn96ijic2z5adr5dsd61kzscx7shw6vyj360rlm5")))) (properties `((upstream-name . "methylKit"))) (build-system r-build-system) (propagated-inputs @@ -9403,17 +9440,18 @@ TAB-Seq.") (define-public r-sva (package (name "r-sva") - (version "3.34.0") + (version "3.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sva" version)) (sha256 (base32 - "1bzms6idx30s4nxl610zwa8rjxsyxb5pf3vxsdfmxg8j4pab9gh1")))) + "0xa1lm0k1a6nig90mab6xh4gln88rbs5l1cdr6ik6agg7jhs7ji4")))) (build-system r-build-system) (propagated-inputs - `(("r-genefilter" ,r-genefilter) + `(("r-edger" ,r-edger) + ("r-genefilter" ,r-genefilter) ("r-mgcv" ,r-mgcv) ("r-biocparallel" ,r-biocparallel) ("r-matrixstats" ,r-matrixstats) @@ -9513,14 +9551,14 @@ as allowing spectra with different resolutions.") (define-public r-protgenerics (package (name "r-protgenerics") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ProtGenerics" version)) (sha256 (base32 - "1k1ggjgx2la8b21841a4ngkp6xfxwz0czv7x960r7i1jqif8y48z")))) + "14xzdh7vxss8vmrw91hcwrszdn3ikm71mah8875b2lkrkrfzbl73")))) (properties `((upstream-name . "ProtGenerics"))) (build-system r-build-system) (home-page "https://github.com/lgatto/ProtGenerics") @@ -9533,14 +9571,14 @@ proteomics packages.") (define-public r-mzr (package (name "r-mzr") - (version "2.20.0") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mzR" version)) (sha256 (base32 - "1cwd7phlc5jbx6r6cznyfbdpvcin5fvsaasbbi65zn0s92a80r13")) + "1r8j8yiz5lcan7j4h37sza2kwczl48dxvld3da3ghjjq67cdc2cm")) (modules '((guix build utils))) (snippet '(begin @@ -9562,7 +9600,7 @@ proteomics packages.") #t))))) (inputs `(;; Our default boost package won't work here, unfortunately, even with - ;; mzR version 2.20.0. + ;; mzR version 2.22.0. ("boost" ,boost-for-mysql) ; use this instead of the bundled boost sources ("zlib" ,zlib))) (propagated-inputs @@ -9573,6 +9611,8 @@ proteomics packages.") ("r-rcpp" ,r-rcpp) ("r-rhdf5lib" ,r-rhdf5lib) ("r-zlibbioc" ,r-zlibbioc))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/sneumann/mzR/") (synopsis "Parser for mass spectrometry data files") (description @@ -9587,14 +9627,14 @@ previously been used in XCMS.") (define-public r-affyio (package (name "r-affyio") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affyio" version)) (sha256 (base32 - "0sbkadxdlx7qzxc8z8iv90y6j9b2f62mk3i54dijjh56x3hjy3hb")))) + "0j1f61409yq6hmkqrpzamfm7dx35rlq33ccs7wb1qcqx3d3nb75q")))) (build-system r-build-system) (propagated-inputs `(("r-zlibbioc" ,r-zlibbioc))) @@ -9611,14 +9651,14 @@ CDF file formats.") (define-public r-affy (package (name "r-affy") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affy" version)) (sha256 (base32 - "131za66wbaz9y86gvjqcc2yd1f2ngl2b796xw726g75djhdgxgap")))) + "0m6hkyjxmsf80n3anhwh9k26csxczv6v92fkb7klnchdski61pyc")))) (build-system r-build-system) (propagated-inputs `(("r-affyio" ,r-affyio) @@ -9639,14 +9679,14 @@ analysis.") (define-public r-vsn (package (name "r-vsn") - (version "3.54.0") + (version "3.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "vsn" version)) (sha256 (base32 - "1naqzb2m0km8fzr6chf9z71sisrwviy1fdi9b3hn4i8p18b4kqzh")))) + "1k82dikrv1gcync5y1131wg7z1kxv2z2jl4nndg20bixc3398h58")))) (build-system r-build-system) (propagated-inputs `(("r-affy" ,r-affy) @@ -9675,14 +9715,14 @@ and specific in detecting differential transcription.") (define-public r-mzid (package (name "r-mzid") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mzID" version)) (sha256 (base32 - "1glcv096bn6pxlw89dlij1nzpwnjvrbxysvw2gm6qgm7rhxlaxrw")))) + "0y50lzkdamkpz67f6r5whp246qsxpbammjil7g8vjprx0c4jk5n5")))) (properties `((upstream-name . "mzID"))) (build-system r-build-system) (propagated-inputs @@ -9693,6 +9733,8 @@ and specific in detecting differential transcription.") ("r-protgenerics" ,r-protgenerics) ("r-rcpp" ,r-rcpp) ("r-xml" ,r-xml))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/mzID") (synopsis "Parser for mzIdentML files") (description @@ -9705,14 +9747,14 @@ specific parser.") (define-public r-pcamethods (package (name "r-pcamethods") - (version "1.78.0") + (version "1.80.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pcaMethods" version)) (sha256 (base32 - "1wir67kfjm0m9gf0ki8qmvh45n4gx2k0wfl9pd1hp4g62fbrj1pj")))) + "10cww4jxyynkwxbbsx804nwac31j0hh8dgisygld0q663gaxkgni")))) (properties `((upstream-name . "pcaMethods"))) (build-system r-build-system) (propagated-inputs @@ -9735,14 +9777,14 @@ structure (pcaRes) to provide a common interface to the PCA results.") (define-public r-msnbase (package (name "r-msnbase") - (version "2.12.0") + (version "2.14.2") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnbase" version)) (sha256 (base32 - "1z889xkfphqqmv31i8hh5xqyclv660ic26rfck5bjpgk3s2zzwi6")))) + "17vlv9gh41s1hp043b7j1jfqiw52alh1misjzy1kxl0g90rld00l")))) (properties `((upstream-name . "MSnbase"))) (build-system r-build-system) (propagated-inputs @@ -9768,6 +9810,8 @@ structure (pcaRes) to provide a common interface to the PCA results.") ("r-scales" ,r-scales) ("r-vsn" ,r-vsn) ("r-xml" ,r-xml))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/lgatto/MSnbase") (synopsis "Base functions and classes for MS-based proteomics") (description @@ -9778,14 +9822,14 @@ of mass spectrometry based proteomics data.") (define-public r-msnid (package (name "r-msnid") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnID" version)) (sha256 (base32 - "0m71f2y12hmwvng45kzz4r4qrgc2jbd7j9gprmw8y5laawpdaifg")))) + "0dwa6j2nqb3223a8g4f453aznjh69wngrpvdi12iy69j1psbbjcc")))) (properties `((upstream-name . "MSnID"))) (build-system r-build-system) (propagated-inputs @@ -9878,14 +9922,14 @@ discovery of differentially expressed genes and markers.") (define-public r-aroma-light (package (name "r-aroma-light") - (version "3.16.0") + (version "3.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "aroma.light" version)) (sha256 (base32 - "0cgdg650j4dl0b45pwaw49ib97dwjazrv9sqzkygrjmcnnfxry8x")))) + "19y5f2minx2pp73zdh43v1qkwpkaxygkl8cwlnwja15i46s0bcyc")))) (properties `((upstream-name . "aroma.light"))) (build-system r-build-system) (propagated-inputs @@ -9905,14 +9949,14 @@ classes.") (define-public r-deseq (package (name "r-deseq") - (version "1.38.0") + (version "1.39.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DESeq" version)) (sha256 (base32 - "14pys93gsl50xmq5pc7pp1g20v3ywlg0yzkkhwb3kiy8573xn9nc")))) + "047hph5aqmjnz1aqprziw0smdn5lf96hmwpnvqrxv1j2yfvcf3h1")))) (properties `((upstream-name . "DESeq"))) (build-system r-build-system) (propagated-inputs @@ -9936,14 +9980,14 @@ distribution.") (define-public r-edaseq (package (name "r-edaseq") - (version "2.20.0") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EDASeq" version)) (sha256 (base32 - "19mgzbv8yxgvw86wpq401l27q55ygawlngl775yavwccz1zbhjnj")))) + "12gzxjh73qshlwvsf92lbrf4bi199kxg2snrkprh1z4yqf7bjfm4")))) (properties `((upstream-name . "EDASeq"))) (build-system r-build-system) (propagated-inputs @@ -9960,6 +10004,8 @@ distribution.") ("r-iranges" ,r-iranges) ("r-rsamtools" ,r-rsamtools) ("r-shortread" ,r-shortread))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/drisso/EDASeq") (synopsis "Exploratory data analysis and normalization for RNA-Seq") (description @@ -9975,20 +10021,23 @@ global-scaling and full-quantile normalization.") (define-public r-interactivedisplaybase (package (name "r-interactivedisplaybase") - (version "1.24.0") + (version "1.26.3") (source (origin (method url-fetch) (uri (bioconductor-uri "interactiveDisplayBase" version)) (sha256 (base32 - "0zwf3ma6wf4zypl6bgjp0n72k2hmp0g16gzl4v3y4157rxcbpl0n")))) + "1x5vipqa4pgwpd62c1c58shnlpv3zyzzpf4wdwr00q1swkdb7wv3")))) (properties `((upstream-name . "interactiveDisplayBase"))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) + ("r-dt" ,r-dt) ("r-shiny" ,r-shiny))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/interactiveDisplayBase") (synopsis "Base package for web displays of Bioconductor objects") (description @@ -9999,14 +10048,14 @@ Shiny-based display methods for Bioconductor objects.") (define-public r-annotationhub (package (name "r-annotationhub") - (version "2.18.0") + (version "2.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationHub" version)) (sha256 (base32 - "19vj3bk8jz68q84g3j8xs1s9bqz90lbwbciig1h45zvn2zc6087m")))) + "0r4xzf93bm9cpys5cg70wg0b8hxli80hvqwgh4hzbd45yyf5c4wz")))) (properties `((upstream-name . "AnnotationHub"))) (build-system r-build-system) (propagated-inputs @@ -10023,6 +10072,8 @@ Shiny-based display methods for Bioconductor objects.") ("r-rsqlite" ,r-rsqlite) ("r-s4vectors" ,r-s4vectors) ("r-yaml" ,r-yaml))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/AnnotationHub") (synopsis "Client to access AnnotationHub resources") (description @@ -10038,14 +10089,14 @@ by the user, helping with quick and reproducible access.") (define-public r-fastseg (package (name "r-fastseg") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fastseg" version)) (sha256 (base32 - "1cys6frmbizc8bf933mwvvnr31sfya9ahcc0wm66pbd1x3mygkmk")))) + "1d48n245pzmvcpsz93lxb4frqh222gfhpmlvm0sb74skn16way63")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -10068,20 +10119,22 @@ microarrays or GRanges for sequencing data.") (define-public r-keggrest (package (name "r-keggrest") - (version "1.26.1") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "KEGGREST" version)) (sha256 (base32 - "1cgjvv9n88y3ah21356mh8z2l08vjn42hjy8hcljsibknzc4v247")))) + "0q76w17fya2x0z7mvyhkk5kqh07flldgih13ma44vhcy1bdlm6j1")))) (properties `((upstream-name . "KEGGREST"))) (build-system r-build-system) (propagated-inputs `(("r-biostrings" ,r-biostrings) ("r-httr" ,r-httr) ("r-png" ,r-png))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/KEGGREST") (synopsis "Client-side REST access to KEGG") (description @@ -10092,14 +10145,14 @@ microarrays or GRanges for sequencing data.") (define-public r-gage (package (name "r-gage") - (version "2.36.0") + (version "2.37.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gage" version)) (sha256 (base32 - "1qxfmg0id19iy3ia8h5nrvk3d1azqb28kl7m08i23654wb6b45c6")))) + "1zfaas4x6g7wiml6cmxa7b4f43az9s0lrw80k6sf7c96hsh1jijr")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -10122,14 +10175,14 @@ analysis using other methods.") (define-public r-genomicfiles (package (name "r-genomicfiles") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFiles" version)) (sha256 (base32 - "1x6q827ms2l5lwzha1vsgfrshh35n9f19jq57xagrqlafxgpz86s")))) + "1k3824pzf9fdqvcv6cz2742q3mabpmncrc72hwa21ac8wy1b04n4")))) (properties `((upstream-name . "GenomicFiles"))) (build-system r-build-system) (propagated-inputs @@ -10155,14 +10208,14 @@ provide added flexibility for data combination and manipulation.") (define-public r-complexheatmap (package (name "r-complexheatmap") - (version "2.2.0") + (version "2.4.2") (source (origin (method url-fetch) (uri (bioconductor-uri "ComplexHeatmap" version)) (sha256 (base32 - "1pj6a6rmqckk033pkklk6hr4066rzavamy6w194rfdhind90rk0p")))) + "01jxxwxhf9n8baxgja4rb592p5210s4ppd7a5b4xby5aalhzkr0l")))) (properties `((upstream-name . "ComplexHeatmap"))) (build-system r-build-system) @@ -10174,6 +10227,8 @@ provide added flexibility for data combination and manipulation.") ("r-globaloptions" ,r-globaloptions) ("r-png" ,r-png) ("r-rcolorbrewer" ,r-rcolorbrewer))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/jokergoo/ComplexHeatmap") (synopsis "Making Complex Heatmaps") @@ -10187,14 +10242,14 @@ self-defined annotation graphics.") (define-public r-dirichletmultinomial (package (name "r-dirichletmultinomial") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DirichletMultinomial" version)) (sha256 (base32 - "0knmncmkkf2ypyqfcl5s8nmyyf9nrzkqprzn9w3w8182c0v49r0s")))) + "1m9dsrddrllb2i88qzik1867iv9mggrgdkn0dlp8sq7gl69vmalb")))) (properties `((upstream-name . "DirichletMultinomial"))) (build-system r-build-system) @@ -10216,14 +10271,14 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): (define-public r-ensembldb (package (name "r-ensembldb") - (version "2.10.2") + (version "2.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ensembldb" version)) (sha256 (base32 - "02lnpyp85zchmz404hr5381zmihvq4x9zgxdrbn2afi352vg0vab")))) + "1vvchc04nshxc768fp31rxb603aj3hmq8xlh5qabcwf2c3z9719g")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -10242,6 +10297,8 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): ("r-rsqlite" ,r-rsqlite) ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/jotsetung/ensembldb") (synopsis "Utilities to create and use Ensembl-based annotation databases") (description @@ -10259,14 +10316,14 @@ chromosome region or transcript models of lincRNA genes.") (define-public r-organismdbi (package (name "r-organismdbi") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "OrganismDbi" version)) (sha256 (base32 - "1bvfyh733mhka9zd00hrzpalgjs255c2blnxyf60ipzk5jg7yllb")))) + "194h5576inq44qr666snzq0ygnc77rk5ljkn9bn8zs6x6gb3cwaw")))) (properties `((upstream-name . "OrganismDbi"))) (build-system r-build-system) (propagated-inputs @@ -10291,14 +10348,14 @@ the fact that each of these packages implements a select methods.") (define-public r-biovizbase (package (name "r-biovizbase") - (version "1.34.1") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biovizBase" version)) (sha256 (base32 - "04vvj907bgs67w8rb7n1haf80p6cd0qj5fdxw0dwryb455y35vir")))) + "1vq2mxa2jkljgw75zqjdkyml0ppi5dspvwj4cznfhi31cq8ds0qh")))) (properties `((upstream-name . "biovizBase"))) (build-system r-build-system) (propagated-inputs @@ -10333,14 +10390,14 @@ effort and encourages consistency.") (define-public r-ggbio (package (name "r-ggbio") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ggbio" version)) (sha256 (base32 - "13wzwh40anh8l53yp19bg4w5cpxykcaf228dc8cxvjndyib711qb")))) + "11ggnqjq42fi2hm9xlvrrlr2xhy4kglvl1a0mycp1s4v67lxw5h5")))) (build-system r-build-system) (arguments `(#:phases @@ -10380,6 +10437,8 @@ effort and encourages consistency.") ("r-scales" ,r-scales) ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-variantannotation" ,r-variantannotation))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "http://www.tengfei.name/ggbio/") (synopsis "Visualization tools for genomic data") (description @@ -10393,41 +10452,17 @@ views. High-level plots include sequence fragment length, edge-linked interval to data view, mismatch pileup, and several splicing summaries.") (license license:artistic2.0))) -(define-public r-gprofiler - (package - (name "r-gprofiler") - (version "0.7.0") - (source - (origin - (method url-fetch) - (uri (cran-uri "gProfileR" version)) - (sha256 - (base32 - "1h1v0kgpsn04ald2izznh7fr2riwisj5hcgz4k7h3qc931rf0r4k")))) - (properties `((upstream-name . "gProfileR"))) - (build-system r-build-system) - (propagated-inputs - `(("r-plyr" ,r-plyr) - ("r-rcurl" ,r-rcurl))) - (home-page "https://cran.r-project.org/web/packages/gProfileR/") - (synopsis "Interface to the g:Profiler toolkit") - (description - "This package provides tools for functional enrichment analysis, -gene identifier conversion and mapping homologous genes across related -organisms via the @code{g:Profiler} toolkit.") - (license license:gpl2+))) - (define-public r-gqtlbase (package (name "r-gqtlbase") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gQTLBase" version)) (sha256 (base32 - "1qr8dqjbmj1mdjbzbnxwzfrm8f02wqfsgic8ws5kv7pmsby63y4x")))) + "06xvzp4fn3qfa46ggg8kxi267gbyd821vvx4040173xkqxpr0g5j")))) (properties `((upstream-name . "gQTLBase"))) (build-system r-build-system) (propagated-inputs @@ -10444,6 +10479,8 @@ organisms via the @code{g:Profiler} toolkit.") ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors) ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/gQTLBase") (synopsis "Infrastructure for eQTL, mQTL and similar studies") (description @@ -10455,14 +10492,14 @@ and more.") (define-public r-snpstats (package (name "r-snpstats") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "snpStats" version)) (sha256 (base32 - "1xq1rjljg70h5mshdza56dis0iv1a20sivs6dav3w5jbdd1l5qkh")))) + "1qv3nqqr30d3n66mawqd9dbl95dl89r4bcjvkc5iassy1yrwr8wq")))) (properties `((upstream-name . "snpStats"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) @@ -10514,14 +10551,14 @@ several related annotation packages.") (define-public r-erma (package (name "r-erma") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "erma" version)) (sha256 (base32 - "085qsr73p8nyp435f15l4l1jkfd64bfd9gl4z496nfxdnqn95srz")))) + "1ccfbq0r48sr3h8050w8zv8402h7nx09adr0xdyqlg7kwp9vd2l3")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -10538,6 +10575,8 @@ several related annotation packages.") ("r-s4vectors" ,r-s4vectors) ("r-shiny" ,r-shiny) ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/erma") (synopsis "Epigenomic road map adventures") (description @@ -10552,14 +10591,14 @@ by Ernst and Kellis.") (define-public r-ldblock (package (name "r-ldblock") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ldblock" version)) (sha256 (base32 - "0xpigfidmylfawy6vzshqnsw1lzjs4qms8q7zffij6bkvkv7920x")))) + "0plw00n2zfgh029ab41dnydzgv2yxrapjp770147rx9pff4dngrv")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) @@ -10572,6 +10611,8 @@ by Ernst and Kellis.") ("r-rsamtools" ,r-rsamtools) ("r-snpstats" ,r-snpstats) ("r-variantannotation" ,r-variantannotation))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/ldblock") (synopsis "Data structures for linkage disequilibrium measures in populations") (description @@ -10584,14 +10625,14 @@ defining LD blocks.") (define-public r-gqtlstats (package (name "r-gqtlstats") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gQTLstats" version)) (sha256 (base32 - "1dly4p9r4231hf31xg1nzqiyvjbcfjljfmhb88ic1jxwnvniyv2f")))) + "1jjqfpjp93nmxjn757j5mzcax96bzcqdd1gr3rsdxg7ap008l2w7")))) (properties `((upstream-name . "gQTLstats"))) (build-system r-build-system) (propagated-inputs @@ -10625,6 +10666,8 @@ defining LD blocks.") ("r-snpstats" ,r-snpstats) ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-variantannotation" ,r-variantannotation))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/gQTLstats") (synopsis "Computationally efficient analysis for eQTL and allied studies") (description @@ -10638,14 +10681,14 @@ family of feature/genome hypotheses.") (define-public r-gviz (package (name "r-gviz") - (version "1.30.3") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Gviz" version)) (sha256 (base32 - "0c9i26h5czm60n1bxzmdxxpywcj0sig6wcj913pb41mr83bbgra3")))) + "0cgkp0ciyy2qykqgh3vzp5mx9b4vsvacjh2jnsj3wldiapzlz08a")))) (properties `((upstream-name . "Gviz"))) (build-system r-build-system) (propagated-inputs @@ -10657,6 +10700,7 @@ family of feature/genome hypotheses.") ("r-biovizbase" ,r-biovizbase) ("r-bsgenome" ,r-bsgenome) ("r-digest" ,r-digest) + ("r-ensembldb" ,r-ensembldb) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicalignments" ,r-genomicalignments) ("r-genomicfeatures" ,r-genomicfeatures) @@ -10670,6 +10714,8 @@ family of feature/genome hypotheses.") ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors) ("r-xvector" ,r-xvector))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/Gviz") (synopsis "Plotting data and annotation information along genomic coordinates") (description @@ -10684,14 +10730,14 @@ with your data.") (define-public r-gwascat (package (name "r-gwascat") - (version "2.18.0") + (version "2.20.1") (source (origin (method url-fetch) (uri (bioconductor-uri "gwascat" version)) (sha256 (base32 - "038vhfsk2vs7inn5di093cmjbb81k7j0af385sg7l01jj70bdqq1")))) + "1cq5cmdrf0a0arr841yvkh6d8drc15p7mif1afr215l1s3y2dwd4")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -10700,11 +10746,13 @@ with your data.") ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicranges" ,r-genomicranges) - ("r-homo-sapiens" ,r-homo-sapiens) + ("r-ggplot2" ,r-ggplot2) ("r-iranges" ,r-iranges) ("r-rsamtools" ,r-rsamtools) ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/gwascat") (synopsis "Tools for data in the EMBL-EBI GWAS catalog") (description @@ -10715,13 +10763,13 @@ EMBL-EBI GWAS catalog.") (define-public r-sushi (package (name "r-sushi") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Sushi" version)) (sha256 (base32 - "15xng21hd09fb234ravrry3b872zg82w8x9lijxab9n96xihcpz5")))) + "17j3d5qjq5nbv99by5mq8rwr0jgh2jyyfn2nwxmwgzlmk3lgi1rb")))) (properties `((upstream-name . "Sushi"))) (build-system r-build-system) (propagated-inputs @@ -10737,19 +10785,21 @@ visualizations for publication-quality multi-panel figures.") (define-public r-fithic (package (name "r-fithic") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FitHiC" version)) (sha256 (base32 - "1irwkwi4afdj395134k31mvx7c2vpdd0rv8zrblnldascdsb04kc")))) + "1dffkdxm08wq4kjd9j2v2625x3p6vbrk33a2zx94pwpgkghr72yp")))) (properties `((upstream-name . "FitHiC"))) (build-system r-build-system) (propagated-inputs `(("r-data-table" ,r-data-table) ("r-fdrtool" ,r-fdrtool) ("r-rcpp" ,r-rcpp))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/FitHiC") (synopsis "Confidence estimation for intra-chromosomal contact maps") (description @@ -10761,13 +10811,13 @@ assays such as Hi-C.") (define-public r-hitc (package (name "r-hitc") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HiTC" version)) (sha256 (base32 - "0byahi0fz0dzjyklz8v9whax9ygg7gwb4pl1j3zbl6z8a9qx8pps")))) + "1jx2pfa7sbdz7xi466lz1h5xv126g56z73n0a5l2wrq28k47qaxy")))) (properties `((upstream-name . "HiTC"))) (build-system r-build-system) (propagated-inputs @@ -10790,14 +10840,14 @@ provided.") (define-public r-hdf5array (package (name "r-hdf5array") - (version "1.14.4") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HDF5Array" version)) (sha256 (base32 - "0ib0grhd9zbrn0dkrm4aa7qj7h0y6z1dvyx1ab3w6vczw7xghsfb")))) + "1g848s0qc6i4ipd7y2s5pk8k1xggk2kfy0gnr8wjjs2gq3914aw4")))) (properties `((upstream-name . "HDF5Array"))) (build-system r-build-system) (inputs @@ -10820,19 +10870,22 @@ block processing.") (define-public r-rhdf5lib (package (name "r-rhdf5lib") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhdf5lib" version)) (sha256 (base32 - "17lhwnm9rqsvbqkvwp0m07vjrk63a4389p2y39zffv8fgznxqzd7")) + "09ylwyk6a8sdrmi1mx7vpycpykqlqylmwa973g6jrcmk0h0qfa4w")) (modules '((guix build utils))) (snippet '(begin ;; Delete bundled binaries - (delete-file-recursively "src/winlib/") + (delete-file-recursively "src/wininclude/") + (delete-file-recursively "src/winlib-4.9.3/") + (delete-file-recursively "src/winlib-8.3.0/") + (delete-file "src/hdf5small_cxx_hl_1.10.6.tar.gz") #t)))) (properties `((upstream-name . "Rhdf5lib"))) (build-system r-build-system) @@ -10868,6 +10921,8 @@ block processing.") "C Compiler: GCC\n")) (rename-file "Makevars.in" "Makevars") (substitute* "Makevars" + (("@ZLIB_LIB@") "-lz") + (("@ZLIB_INCLUDE@") "") (("HDF5_CXX_LIB=.*") (string-append "HDF5_CXX_LIB=" (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n")) @@ -10893,7 +10948,8 @@ block processing.") (propagated-inputs `(("hdf5" ,hdf5-1.10))) (native-inputs - `(("hdf5-source" ,(package-source hdf5-1.10)))) + `(("hdf5-source" ,(package-source hdf5-1.10)) + ("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/Rhdf5lib") (synopsis "HDF5 library as an R package") (description "This package provides C and C++ HDF5 libraries for use in R @@ -10903,19 +10959,21 @@ packages.") (define-public r-beachmat (package (name "r-beachmat") - (version "2.2.1") + (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "beachmat" version)) (sha256 (base32 - "1bpnlw2kdy9yc2vq948k980r0j25ipb80llhvn0j3kxjiwyfgs3i")))) + "1vl6jbf9ia78cm4ikdb8vz04jv4b46zhvg5i006c63a9pzw7zhxi")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-delayedarray" ,r-delayedarray) ("r-matrix" ,r-matrix))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/beachmat") (synopsis "Compiling Bioconductor to handle each matrix type") (description "This package provides a consistent C++ class interface for a @@ -10926,14 +10984,14 @@ matrices.") (define-public r-singlecellexperiment (package (name "r-singlecellexperiment") - (version "1.8.0") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "SingleCellExperiment" version)) (sha256 (base32 - "11pqb3cigi9xbhxq2k3n7z23v1ibd03ws1lcrh5c5ffgb33nlyw5")))) + "092wvk11n7pa234vlwhxm3gdi4k3sbnz1splhxalbdhz3jf02zfp")))) (properties `((upstream-name . "SingleCellExperiment"))) (build-system r-build-system) @@ -10941,6 +10999,8 @@ matrices.") `(("r-biocgenerics" ,r-biocgenerics) ("r-s4vectors" ,r-s4vectors) ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/SingleCellExperiment") (synopsis "S4 classes for single cell data") (description "This package defines an S4 class for storing data from @@ -10953,13 +11013,13 @@ libraries.") (define-public r-scater (package (name "r-scater") - (version "1.14.6") + (version "1.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "scater" version)) (sha256 (base32 - "0sxd1s8wdlj9926bagq4crjrk1nnmh3j3bhgrw160zfgc3y8pzck")))) + "0pi4mpc3lvskj5biyhc9cskcnz9q2wjmfrz7xdnx8qqd8vpy84g3")))) (build-system r-build-system) (propagated-inputs `(("r-beachmat" ,r-beachmat) @@ -10973,10 +11033,13 @@ libraries.") ("r-ggplot2" ,r-ggplot2) ("r-matrix" ,r-matrix) ("r-rcpp" ,r-rcpp) + ("r-rlang" ,r-rlang) ("r-s4vectors" ,r-s4vectors) ("r-singlecellexperiment" ,r-singlecellexperiment) ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-viridis" ,r-viridis))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/davismcc/scater") (synopsis "Single-cell analysis toolkit for gene expression data in R") (description "This package provides a collection of tools for doing @@ -10987,14 +11050,14 @@ quality control.") (define-public r-scran (package (name "r-scran") - (version "1.14.6") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scran" version)) (sha256 (base32 - "1y8wlgk5zbv7c7gcp0ahfpbh9lifab7y3zwf0093fzaw7vr1y6cr")))) + "1gm4ys4aq8h1pn45k1rxk384wjyf55izivw8kgxbrflj6j4xvvsv")))) (build-system r-build-system) (propagated-inputs `(("r-beachmat" ,r-beachmat) @@ -11008,6 +11071,7 @@ quality control.") ("r-dqrng" ,r-dqrng) ("r-edger" ,r-edger) ("r-igraph" ,r-igraph) + ("r-iranges" ,r-iranges) ("r-limma" ,r-limma) ("r-matrix" ,r-matrix) ("r-rcpp" ,r-rcpp) @@ -11016,6 +11080,8 @@ quality control.") ("r-singlecellexperiment" ,r-singlecellexperiment) ("r-statmod" ,r-statmod) ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/scran") (synopsis "Methods for single-cell RNA-Seq data analysis") (description "This package implements a variety of low-level analyses of @@ -11027,14 +11093,14 @@ variable and significantly correlated genes.") (define-public r-delayedmatrixstats (package (name "r-delayedmatrixstats") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedMatrixStats" version)) (sha256 (base32 - "0mv2rl6a6l404piabcazxz1s6ars016pxhjf5v40hhr6y1r0wbqy")))) + "0i6gw8058gw9yajya3w9qq6l3p634fq9sv8dh8ifigxz0k9b98r6")))) (properties `((upstream-name . "DelayedMatrixStats"))) (build-system r-build-system) @@ -11046,6 +11112,8 @@ variable and significantly correlated genes.") ("r-matrix" ,r-matrix) ("r-matrixstats" ,r-matrixstats) ("r-s4vectors" ,r-s4vectors))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/PeteHaitch/DelayedMatrixStats") (synopsis "Functions that apply to rows and columns of DelayedMatrix objects") (description diff --git a/gnu/packages/c.scm b/gnu/packages/c.scm index 3e227decc9..c107a36c6a 100644 --- a/gnu/packages/c.scm +++ b/gnu/packages/c.scm @@ -8,6 +8,7 @@ ;;; Copyright © 2019 Andreas Enge <andreas@enge.fr> ;;; Copyright © 2020 Jan (janneke) Nieuwenhuizen <janneke@gnu.org> ;;; Copyright © 2020 Marius Bakke <marius@gnu.org> +;;; Copyright @ 2020 Katherine Cox-Buday <cox.katherine.e@gmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -41,6 +42,7 @@ #:use-module (gnu packages multiprecision) #:use-module (gnu packages pcre) #:use-module (gnu packages python) + #:use-module (gnu packages python-xyz) #:use-module (gnu packages autotools) #:use-module (gnu packages gettext) #:use-module (gnu packages pkg-config) @@ -339,3 +341,98 @@ address space pointers point to, or what locks a function acquires or releases.") (home-page "https://sparse.wiki.kernel.org/index.php/Main_Page") (license license:expat))) + +(define-public libestr + (package + (name "libestr") + (version "0.1.11") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rsyslog/libestr.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1ca4rj90c0dn7kqpbcchkflxjw88a7rxcnwbr0gply4a28i01nd8")))) + (build-system gnu-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + ;; autogen.sh calls configure at the end of the script. + (replace 'bootstrap + (lambda _ (invoke "autoreconf" "-vfi")))))) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("pkg-config" ,pkg-config) + ("libtool" ,libtool))) + (home-page "https://github.com/rsyslog/libestr") + (synopsis "Helper functions for handling strings") + (description + "This C library contains some essential string manipulation functions and +more, like escaping special characters.") + (license license:lgpl2.1+))) + +(define-public libfastjson + (package + (name "libfastjson") + (version "0.99.8") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rsyslog/libfastjson.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0qhs0g9slj3p0v2z4s3cnsx44msrlb4k78ljg7714qiziqbrbwyl")))) + (build-system gnu-build-system) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("libtool" ,libtool))) + (home-page "https://github.com/rsyslog/libfastjson") + (synopsis "Fast JSON library for C") + (description + "libfastjson is a fork from json-c aiming to provide: a small library +with essential JSON handling functions, sufficiently good JSON support (not +100% standards compliant), and very fast processing.") + (license license:expat))) + +(define-public liblogging + (package + (name "liblogging") + (version "1.0.6") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rsyslog/liblogging.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1l32m0y65svf5vxsgw935jnqs6842rcqr56dmzwqvr00yfrjhjkp")))) + (build-system gnu-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + ;; autogen.sh calls configure at the end of the script. + (replace 'bootstrap + (lambda _ (invoke "autoreconf" "-vfi")))))) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("pkg-config" ,pkg-config) + ("libtool" ,libtool) + ;; For rst2man.py + ("python-docutils" ,python-docutils))) + (home-page "https://github.com/rsyslog/liblogging") + (synopsis "Easy to use and lightweight signal-safe logging library") + (description + "Liblogging is an easy to use library for logging. It offers an enhanced +replacement for the syslog() call, but retains its ease of use.") + (license license:bsd-2))) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 7fa47aee1c..0a502a6063 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -72,6 +72,7 @@ #:use-module (gnu packages mpi) #:use-module (gnu packages multiprecision) #:use-module (gnu packages networking) + #:use-module (gnu packages node) #:use-module (gnu packages pcre) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) @@ -103,6 +104,76 @@ The package provides functions for point generation, arc length estimation, degree elevation and curve fitting.") (license license:gpl2+))) +(define-public r-v8 + (package + (name "r-v8") + (version "3.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "V8" version)) + (sha256 + (base32 + "0xdljralgwyivdhx2a7kqf3yv4ijl4rdrz2p7p59lj2x5d2qyanf")))) + (properties `((upstream-name . "V8"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'find-v8 + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "configure" + (("^PKG_LIBS=.*") + (string-append "PKG_LIBS=" + (assoc-ref inputs "node") + "/lib/libnode.so.64\n"))) + (setenv "INCLUDE_DIR" + (string-append + (assoc-ref inputs "node") + "/include/node")) + (setenv "LIB_DIR" + (string-append + (assoc-ref inputs "node") "/lib")) + #t))))) + (inputs + `(("node" ,libnode))) + (propagated-inputs + `(("r-curl" ,r-curl) + ("r-jsonlite" ,r-jsonlite) + ("r-rcpp" ,r-rcpp))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://jeroen.cran.dev/V8") + (synopsis "Embedded JavaScript and WebAssembly engine for R") + (description + "This package provides an R interface to V8: Google's JavaScript and +WebAssembly engine.") + (license license:expat))) + +(define-public r-dot + (package + (name "r-dot") + (version "0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "DOT" version)) + (sha256 + (base32 + "0qh5n57cp9c2n5yn59q4wggz82943pwfanp3kx869aba2x3sj30i")))) + (properties `((upstream-name . "DOT"))) + (build-system r-build-system) + (propagated-inputs + `(("r-v8" ,r-v8))) + (home-page "http://haghish.com/dot") + (synopsis "Render and Export DOT Graphs in R") + (description + "This package provides tools to render DOT diagram markup language in R +and also provides the possibility to export the graphs in PostScript and +SVG (Scalable Vector Graphics) formats. In addition, it supports literate +programming packages such as @code{knitr} and @code{rmarkdown}.") + (license license:expat))) + (define-public r-clipr (package (name "r-clipr") @@ -158,6 +229,77 @@ the system clipboards.") respecting the grammar of its graphics paradigm.") (license license:gpl2+))) +(define-public r-gprofiler + (package + (name "r-gprofiler") + (version "0.7.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "gProfileR" version)) + (sha256 + (base32 + "1h1v0kgpsn04ald2izznh7fr2riwisj5hcgz4k7h3qc931rf0r4k")))) + (properties `((upstream-name . "gProfileR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-plyr" ,r-plyr) + ("r-rcurl" ,r-rcurl))) + (home-page "https://cran.r-project.org/web/packages/gProfileR/") + (synopsis "Interface to the g:Profiler toolkit") + (description + "This package provides tools for functional enrichment analysis, +gene identifier conversion and mapping homologous genes across related +organisms via the @code{g:Profiler} toolkit.") + (license license:gpl2+))) + +(define-public r-gprofiler2 + (package + (name "r-gprofiler2") + (version "0.1.9") + (source + (origin + (method url-fetch) + (uri (cran-uri "gprofiler2" version)) + (sha256 + (base32 + "112hmmvdwg8xz90w1bsbzc55y4xi9jj4dqy0q4bsgp49x58r92rb")))) + (properties `((upstream-name . "gprofiler2"))) + (build-system r-build-system) + (propagated-inputs + `(("r-crosstalk" ,r-crosstalk) + ("r-dplyr" ,r-dplyr) + ("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-jsonlite" ,r-jsonlite) + ("r-plotly" ,r-plotly) + ("r-rcurl" ,r-rcurl) + ("r-tidyr" ,r-tidyr) + ("r-viridislite" ,r-viridislite))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://cran.r-project.org/web/packages/gprofiler2/") + (synopsis "Interface to the g:Profiler toolset") + (description + "This package provides a toolset for functional enrichment analysis and +visualization, gene/protein/SNP identifier conversion and mapping orthologous +genes across species via @url{https://biit.cs.ut.ee/gprofiler,g:Profiler}. +The main tools are: + +@enumerate +@item @code{g:GOSt}, functional enrichment analysis and visualization of gene + lists; +@item @code{g:Convert}, gene/protein/transcript identifier conversion across + various namespaces; +@item @code{g:Orth}, orthology search across species; +@item @code{g:SNPense}, mapping SNP rs identifiers to chromosome positions, + genes and variant effects. +@end enumerate + +This package is an R interface corresponding to the 2019 update of +@code{g:Profiler} and provides access to versions @code{e94_eg41_p11} and +higher.") + (license license:gpl2+))) + (define-public r-oenb (package (name "r-oenb") @@ -21853,3 +21995,31 @@ with posterior predictive checks and leave-one-out cross-validation.") and prediction with Aalen-Johansen or simulation in competing risks and multi-state models.") (license license:gpl2+))) + +(define-public r-scatterpie + (package + (name "r-scatterpie") + (version "0.1.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "scatterpie" version)) + (sha256 + (base32 + "0g5sn0iv6c1q7y51j4gbbbnil5089dgk1w4q94c7h5y3x7wfrzqb")))) + (properties `((upstream-name . "scatterpie"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggforce" ,r-ggforce) + ("r-ggplot2" ,r-ggplot2) + ("r-rlang" ,r-rlang) + ("r-rvcheck" ,r-rvcheck) + ("r-tidyr" ,r-tidyr))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://cran.r-project.org/web/packages/scatterpie/") + (synopsis "Scatter pie plot") + (description + "This package creates scatterpie plots, especially useful for plotting +pies on a map.") + (license license:artistic2.0))) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 946d01cba5..af379902a1 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -74,6 +74,7 @@ ;;; Copyright © 2020 Ryan Desfosses <rdes@protonmail.com> ;;; Copyright © 2020 Marcin Karpezo <sirmacik@wioo.waw.pl> ;;; Copyright © 2020 Fredrik Salomonsson <plattfot@gmail.com> +;;; Copyright © 2020 Ryan Desfosses <rdes@protonmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -4072,14 +4073,14 @@ source code using IPython.") (define-public emacs-debbugs (package (name "emacs-debbugs") - (version "0.22") + (version "0.23") (source (origin (method url-fetch) (uri (string-append "https://elpa.gnu.org/packages/debbugs-" version ".tar")) (sha256 (base32 - "05ik9qv539b5c1nzxkk3lk23bqj4vqgmfmd8x367abhb7c9gix2z")))) + "0mcz97b3sddrc68wi8dz95b2rq7ky88pr2i1ghyhy28as16chmz5")))) (build-system emacs-build-system) (arguments '(#:include '("\\.el$" "\\.wsdl$" "\\.info$"))) (propagated-inputs @@ -23155,3 +23156,28 @@ files.") sources. It features syntax highlighting, autocompletion, preview of buffer or region and use of locally installed binaries.") (license license:gpl3+))) + +(define-public emacs-shell-pop + (let ((commit "4b4394037940a890a313d715d203d9ead2d156a6") + (revision "0")) + (package + (name "emacs-shell-pop") + (version (git-version "0.64" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/kyagi/shell-pop-el.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0s77n6b9iw1x3dv91ybkpgy3zvqd12si7zw3lg0m2b6j1akrawsg")))) + (build-system emacs-build-system) + (home-page "https://github.com/kyagi/shell-pop-el") + (synopsis "Utility which helps with pop up shell buffer") + (description + "This Emacs utility helps you pop up and pop out shell buffer window +easily. Four pre-set options are: @samp{shell}, @samp{terminal}, +@samp{ansi-term}, and @samp{eshell}. You can also set your custom shell if +you use some other configuration.") + (license license:gpl3+)))) diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm index 9d9c67b861..fe3c87edd5 100644 --- a/gnu/packages/engineering.scm +++ b/gnu/packages/engineering.scm @@ -105,6 +105,7 @@ #:use-module (gnu packages version-control) #:use-module (gnu packages wxwidgets) #:use-module (gnu packages xml) + #:use-module (gnu packages openkinect) #:use-module (gnu packages xorg)) (define-public librecad @@ -2619,3 +2620,60 @@ accessible through a simple API") model files. Its main goal is to simplify the creation of 3DS import and export filters.") (license license:lgpl2.1+))) + +(define-public meshlab + (package + (name "meshlab") + (version "2020.05") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/cnr-isti-vclab/meshlab") + (commit (string-append "Meshlab-" version)) + (recursive? #t))) + (file-name (git-file-name name version)) + (sha256 + (base32 "00sim20ka9vjwljixdj4cqd285j21mpaq05ari7nqq2w8yyglp5m")))) + (build-system cmake-build-system) + (inputs + `(("qtbase" ,qtbase) + ("qtscript" ,qtscript) + ("qtxmlpatterns" ,qtxmlpatterns) + ("mesa" ,mesa) + ("glu" ,glu) + ("glew" ,glew) + ("muparser" ,muparser) + ("gmp" ,gmp) + ("eigen" ,eigen) + ("libfreenect" ,libfreenect) + ("lib3ds" ,lib3ds) + ("openctm" ,openctm) + ;; FIXME: Compilation fails with system qhull: + ;; https://github.com/cnr-isti-vclab/meshlab/issues/678 + ;; ("qhull" ,qhull) + )) + (arguments + `(#:tests? #f ; Has no tests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'go-to-source-dir + (lambda _ (chdir "src") #t)) + (add-after 'install 'move-files + (lambda* (#:key outputs #:allow-other-keys) + (let ((lib (string-append (assoc-ref outputs "out") + "/lib"))) + (rename-file + (string-append lib "/meshlab/libmeshlab-common.so") + (string-append lib "/libmeshlab-common.so")) + #t)))))) + (synopsis "3D triangular mesh processing and editing software") + (home-page "https://www.meshlab.net/") + (description "MeshLab is a system for the processing and +editing of unstructured large 3D triangular meshes. It is aimed to help the +processing of the typical not-so-small unstructured models arising in 3D +scanning, providing a set of tools for editing, cleaning, healing, inspecting, +rendering and converting this kind of meshes. These tools include MeshLab +proper, a versatile program with a graphical user interface, and meshlabserver, +a program that can perform mesh processing tasks in batch mode, without a +GUI.") + (license license:gpl3+))) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index f48c4aa59a..213eacecd7 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -1286,6 +1286,19 @@ offline sources, providing a centralized place for managing your contacts.") (("\"locale\"") (string-append "\"" libc "/bin/locale\""))) #t))) + (add-before 'configure 'patch-bubblewrap + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "libgnome-desktop/gnome-desktop-thumbnail-script.c" + (("\"bwrap\",") + (string-append "\"" (which "bwrap") "\",")) + (("\"--ro-bind\", \"/usr\", \"/usr\",") + (string-append "\"--ro-bind\", \"" + (%store-directory) + "\", \"" + (%store-directory) + "\",")) + (("\"--ro-bind\", \"/etc/ld.so.cache\", \"/etc/ld.so.cache\",") "")) + #t)) (add-before 'check 'pre-check (lambda* (#:key inputs #:allow-other-keys) ;; Tests require a running X server and locales. @@ -1315,6 +1328,7 @@ offline sources, providing a centralized place for managing your contacts.") (inputs `(("gdk-pixbuf" ,gdk-pixbuf) ("glib" ,glib) + ("bubblewrap" ,bubblewrap) ("libxext" ,libxext) ("libxkbfile" ,libxkbfile) ("libxrandr" ,libxrandr))) diff --git a/gnu/packages/gnuzilla.scm b/gnu/packages/gnuzilla.scm index 1f5deb3302..0a8edcb1e4 100644 --- a/gnu/packages/gnuzilla.scm +++ b/gnu/packages/gnuzilla.scm @@ -1112,11 +1112,13 @@ from forcing GEXP-PROMISE." (lib (string-append out "/lib")) (gtk (assoc-ref inputs "gtk+")) (gtk-share (string-append gtk "/share")) + (mesa (assoc-ref inputs "mesa")) + (mesa-lib (string-append mesa "/lib")) (pulseaudio (assoc-ref inputs "pulseaudio")) (pulseaudio-lib (string-append pulseaudio "/lib"))) (wrap-program (car (find-files lib "^icecat$")) `("XDG_DATA_DIRS" prefix (,gtk-share)) - `("LD_LIBRARY_PATH" prefix (,pulseaudio-lib))) + `("LD_LIBRARY_PATH" prefix (,pulseaudio-lib ,mesa-lib))) #t)))))) (home-page "https://www.gnu.org/software/gnuzilla/") (synopsis "Entirely free browser derived from Mozilla Firefox") diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm index a999b1cdfa..dc8f2c64a2 100644 --- a/gnu/packages/graph.scm +++ b/gnu/packages/graph.scm @@ -181,14 +181,14 @@ model.") (define-public r-rgraphviz (package (name "r-rgraphviz") - (version "2.30.0") + (version "2.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rgraphviz" version)) (sha256 (base32 - "00lrkbgbb4payybckcmazsv8skysgdlglyqbl7yjb37vv3gnfc6c")))) + "1calpvzgcz6v7s4x6bf35kj83sga95zjp7x87p5d3qnbv7q2wz5y")))) (properties `((upstream-name . "Rgraphviz"))) (build-system r-build-system) ;; FIXME: Rgraphviz bundles the sources of an older variant of diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm index c2dc7f6d5f..34d348c344 100644 --- a/gnu/packages/guile.scm +++ b/gnu/packages/guile.scm @@ -633,7 +633,7 @@ Guile's foreign function interface.") (define-public guile-sqlite3 (package (name "guile-sqlite3") - (version "0.1.0") + (version "0.1.2") (home-page "https://notabug.org/guile-sqlite3/guile-sqlite3.git") (source (origin (method git-fetch) @@ -642,18 +642,8 @@ Guile's foreign function interface.") (commit (string-append "v" version)))) (sha256 (base32 - "1nv8j7wk6b5n4p22szyi8lv8fs31rrzxhzz16gyj8r38c1fyp9qp")) - (file-name (string-append name "-" version "-checkout")) - (patches - (search-patches "guile-sqlite3-fix-cross-compilation.patch")) - (modules '((guix build utils))) - (snippet - '(begin - ;; Allow builds with Guile 3.0. - (substitute* "configure.ac" - (("^GUILE_PKG.*") - "GUILE_PKG([3.0 2.2 2.0])\n")) - #t)))) + "1nryy9j3bk34i0alkmc9bmqsm0ayz92k1cdf752mvhyjjn8nr928")) + (file-name (string-append name "-" version "-checkout")))) (build-system gnu-build-system) (native-inputs `(("autoconf" ,autoconf) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index 885086fe30..d5bc713c70 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -276,7 +276,7 @@ JNI.") (version "1.8.4") (source (origin (method url-fetch) - (uri (string-append "mirror://apache/dist/" + (uri (string-append "mirror://apache/" "ant/source/apache-ant-" version "-src.tar.bz2")) (sha256 @@ -10832,7 +10832,7 @@ graphs, and pie charts.") (version "3.1") (source (origin (method url-fetch) - (uri (string-append "mirror://apache/dist/httpcomponents/" + (uri (string-append "mirror://apache/httpcomponents/" "commons-httpclient/source/commons-httpclient-" version "-src.tar.gz")) (sha256 @@ -10928,7 +10928,7 @@ inside a Zip archive.") (version "2.0.8") (source (origin (method url-fetch) - (uri (string-append "mirror://apache/dist/jakarta/oro/" + (uri (string-append "mirror://apache/jakarta/oro/" "jakarta-oro-" version ".tar.gz")) (sha256 (base32 diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index a3b1b9d1c0..20c17144a3 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -3720,11 +3720,7 @@ in a digital read-out.") #t))) #:make-flags (list (string-append "prefix=" (assoc-ref %outputs "out")) - ;; Make sure the kernel headers are treated as system - ;; headers to suppress warnings from those. - (string-append "C_INCLUDE_PATH=" - (assoc-ref %build-inputs "kernel-headers") - "/include") + "CC=gcc" "WERROR=0" ;; By default, 'config/Makefile' uses lib64 on diff --git a/gnu/packages/maven.scm b/gnu/packages/maven.scm index a62eb7469e..66c6e3adfa 100644 --- a/gnu/packages/maven.scm +++ b/gnu/packages/maven.scm @@ -340,7 +340,7 @@ Maven Wagon, for use in Maven."))) (version "3.2.1") (source (origin (method url-fetch) - (uri (string-append "mirror://apache/dist/maven/shared/" + (uri (string-append "mirror://apache/maven/shared/" "maven-shared-utils-" version "-source-release.zip")) (sha256 (base32 @@ -380,7 +380,7 @@ replacement with improvements.") (version "3.5") (source (origin (method url-fetch) - (uri (string-append "mirror://apache/dist/maven/" + (uri (string-append "mirror://apache/maven/" "plugin-tools/maven-plugin-tools-" version "-source-release.zip")) (sha256 (base32 "1ryqhs62j5pas93brhf5dsnvp99hxbvssf681yj5rk3r9h24hqm2")))) @@ -404,7 +404,7 @@ replacement with improvements.") (version "3.1.0") (source (origin (method url-fetch) - (uri (string-append "mirror://apache/dist/maven/wagon/" + (uri (string-append "mirror://apache/maven/wagon/" "wagon-" version "-source-release.zip")) (sha256 (base32 "0r07j6xdzdnrvqnv8ida7dx1m05pznh5qgmcfcfpyvg9nxbj3l1n")))) (build-system ant-build-system) @@ -691,7 +691,7 @@ gets and puts artifacts through HTTP(S) using Apache HttpClient-4.x."))) (version "3.6.1") (source (origin (method url-fetch) - (uri (string-append "mirror://apache/dist/maven/" + (uri (string-append "mirror://apache/maven/" "maven-3/" version "/source/" "apache-maven-" version "-src.tar.gz")) (sha256 (base32 "0grw9zp166ci53rd7qkyy2qmwmik37xhiz1z84jpm0msyvzj2n82")) diff --git a/gnu/packages/node.scm b/gnu/packages/node.scm index a3cf3c9199..1adb2cd07f 100644 --- a/gnu/packages/node.scm +++ b/gnu/packages/node.scm @@ -27,6 +27,7 @@ #:use-module (guix packages) #:use-module (guix derivations) #:use-module (guix download) + #:use-module (guix utils) #:use-module (guix build-system gnu) #:use-module (gnu packages) #:use-module (gnu packages adns) @@ -197,3 +198,15 @@ devices.") (license expat) (properties '((max-silent-time . 7200) ;2h, needed on ARM (timeout . 21600))))) ;6h + +(define-public libnode + (package + (inherit node) + (name "libnode") + (arguments + (substitute-keyword-arguments (package-arguments node) + ((#:configure-flags flags ''()) + `(cons* "--shared" "--without-npm" ,flags)) + ((#:phases phases '%standard-phases) + `(modify-phases ,phases + (delete 'patch-npm-shebang))))))) diff --git a/gnu/packages/patches/guile-sqlite3-fix-cross-compilation.patch b/gnu/packages/patches/guile-sqlite3-fix-cross-compilation.patch deleted file mode 100644 index 9ea9a47677..0000000000 --- a/gnu/packages/patches/guile-sqlite3-fix-cross-compilation.patch +++ /dev/null @@ -1,55 +0,0 @@ -From a6e9e62a77ecc5012929613e20da23b2636450a5 Mon Sep 17 00:00:00 2001 -From: Mathieu Othacehe <mathieu.othacehe@parrot.com> -Date: Mon, 25 Mar 2019 11:00:38 +0100 -Subject: [PATCH] cross compile - ---- - build-aux/guile.am | 2 +- - configure.ac | 19 ++++++++++++------- - 2 files changed, 13 insertions(+), 8 deletions(-) - -diff --git a/build-aux/guile.am b/build-aux/guile.am -index dc1e63f..3126372 100644 ---- a/build-aux/guile.am -+++ b/build-aux/guile.am -@@ -16,4 +16,4 @@ EXTRA_DIST = $(SOURCES) $(NOCOMP_SOURCES) - GUILE_WARNINGS = -Wunbound-variable -Warity-mismatch -Wformat - SUFFIXES = .scm .go - .scm.go: -- $(AM_V_GEN)$(top_builddir)/env $(GUILE_TOOLS) compile $(GUILE_WARNINGS) -o "$@" "$<" -+ $(AM_V_GEN)$(top_builddir)/env $(GUILE_TOOLS) compile $(GUILE_TARGET) $(GUILE_WARNINGS) -o "$@" "$<" -diff --git a/configure.ac b/configure.ac -index f648fcb..2d34d0a 100644 ---- a/configure.ac -+++ b/configure.ac -@@ -21,15 +21,20 @@ PKG_CHECK_MODULES([SQLITE], [sqlite3]) - SQLITE_LIBDIR="`"$PKG_CONFIG" sqlite3 --variable libdir`" - AC_SUBST([SQLITE_LIBDIR]) - --AC_MSG_CHECKING([whether '$SQLITE_LIBDIR/libsqlite3' is usable]) --GUILE_CHECK([retval], -- [(dynamic-func \"sqlite3_open_v2\" -+if test "$cross_compiling" = "no"; then -+ AC_MSG_CHECKING([whether '$SQLITE_LIBDIR/libsqlite3' is usable]) -+ GUILE_CHECK([retval], -+ [(dynamic-func \"sqlite3_open_v2\" - (dynamic-link \"$SQLITE_LIBDIR/libsqlite3\"))]) --if test "$retval" != 0; then -- AC_MSG_RESULT([no]) -- AC_MSG_ERROR([failed to load '$SQLITE_LIBDIR/libsqlite3']) -+ if test "$retval" != 0; then -+ AC_MSG_RESULT([no]) -+ AC_MSG_ERROR([failed to load '$SQLITE_LIBDIR/libsqlite3']) -+ else -+ AC_MSG_RESULT([yes]) -+ fi - else -- AC_MSG_RESULT([yes]) -+ GUILE_TARGET="--target=$host_alias" -+ AC_SUBST([GUILE_TARGET]) - fi - - AC_CONFIG_FILES([Makefile sqlite3.scm]) --- -2.17.1 - diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index cd60ce87b0..1e7e235136 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4076,14 +4076,14 @@ hierarchical clustering dendrograms.") (define-public r-preprocesscore (package (name "r-preprocesscore") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "preprocessCore" version)) (sha256 (base32 - "0zrb9hx60vppkg0priczdb301nhq5f0dj8lkc8rcc4xrqqr915qm")))) + "0q1406kswylc8zn5k3wyd34p34pfzbhi1ggkfsh30zcjp6adbwjl")))) (properties `((upstream-name . "preprocessCore"))) (build-system r-build-system) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 26396fd59d..8d1c668b8e 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -1588,7 +1588,7 @@ from streaming URLs. It is a command-line wrapper for the libquvi library.") (source (origin (method url-fetch) - (uri (string-append "mirror://apache/dist/serf/serf-" + (uri (string-append "mirror://apache/serf/serf-" version ".tar.bz2")) (sha256 (base32 "1k47gbgpp52049andr28y28nbwh9m36bbb0g8p0aka3pqlhjv72l")))) diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm index 9a7b856791..e5fe3e14cf 100644 --- a/gnu/packages/xorg.scm +++ b/gnu/packages/xorg.scm @@ -2556,7 +2556,7 @@ including most mice, keyboards, tablets and touchscreens.") (native-inputs `(("pkg-config" ,pkg-config))) (inputs - `(("libinput" ,libinput) + `(("libinput" ,libinput-minimal) ("xorg-server" ,xorg-server))) (home-page "https://www.x.org/wiki/") (synopsis "Input driver for X server based on libinput") diff --git a/gnu/services/hurd.scm b/gnu/services/hurd.scm index 1ccf164223..61d92b4bda 100644 --- a/gnu/services/hurd.scm +++ b/gnu/services/hurd.scm @@ -115,9 +115,4 @@ (description "Provide console login using the Hurd @command{getty} program."))) -(define* (hurd-getty-service config) - "Return a service to run the Hurd getty according to @var{config}, which -specifies the tty to run, among other things." - (service hurd-getty-service-type config)) - ;;; hurd.scm ends here diff --git a/gnu/system/examples/bare-hurd.tmpl b/gnu/system/examples/bare-hurd.tmpl index 16f20416aa..414a9379c8 100644 --- a/gnu/system/examples/bare-hurd.tmpl +++ b/gnu/system/examples/bare-hurd.tmpl @@ -5,12 +5,27 @@ ;; To build a disk image for a virtual machine, do ;; -;; ./pre-inst-env guix system disk-image --target=i586-pc-gnu --no-grafts \ +;; ./pre-inst-env guix system disk-image --target=i586-pc-gnu \ ;; gnu/system/examples/bare-hurd.tmpl ;; -;; it boots, but needs activation, more setup and services to be useful. +;; You may run it like so +;; +;; guix environment --ad-hoc qemu -- qemu-system-i386 -enable-kvm -m 512M \ +;; -device rtl8139,netdev=net0 -netdev user,id=net0,hostfwd=tcp:127.0.0.1:10022-:2222 \ +;; -snapshot -hda <the-image> +;; +;; and use it like +;; +;; ssh -p 10022 root@localhost +;; guix build -e '(@@ (gnu packages commencement) gnu-make-boot0)' +;; +;; or even (if you use --image-size=3G) +;; +;; guix build hello (use-modules (gnu) (gnu system hurd) (guix utils)) +(use-service-modules ssh) +(use-package-modules ssh) (define %hurd-os (operating-system @@ -25,7 +40,15 @@ %base-file-systems)) (host-name "guixygnu") (timezone "Europe/Amsterdam") - (packages %base-packages/hurd) - (services %base-services/hurd))) + (packages (cons openssh-sans-x %base-packages/hurd)) + (services (cons (service openssh-service-type + (openssh-configuration + (openssh openssh-sans-x) + (use-pam? #f) + (port-number 2222) + (permit-root-login #t) + (allow-empty-passwords? #t) + (password-authentication? #t))) + %base-services/hurd)))) %hurd-os diff --git a/gnu/system/hurd.scm b/gnu/system/hurd.scm index 956682357e..2205def577 100644 --- a/gnu/system/hurd.scm +++ b/gnu/system/hurd.scm @@ -39,16 +39,15 @@ #:use-module (gnu system) #:use-module (gnu system shadow) #:use-module (gnu system vm) - #:export (cross-hurd-image - %base-packages/hurd + #:export (%base-packages/hurd %base-services/hurd %hurd-default-operating-system %hurd-default-operating-system-kernel)) ;;; Commentary: ;;; -;;; This module provides tools to (cross-)build GNU/Hurd virtual machine -;;; images. +;;; This module provides system-specifics for the GNU/Hurd operating system +;;; and virtual machine. ;;; ;;; Code: @@ -104,173 +103,3 @@ (pam-services '()) (setuid-programs '()) (sudoers-file #f))) - -(define* (cross-hurd-image #:key (hurd hurd) (gnumach gnumach)) - "Return a cross-built GNU/Hurd image." - - (define (cross-built thing) - (with-parameters ((%current-target-system "i586-pc-gnu")) - thing)) - - (define (cross-built-entry entry) - (manifest-entry - (inherit entry) - (item (cross-built (manifest-entry-item entry))) - (dependencies (map cross-built-entry - (manifest-entry-dependencies entry))))) - - (define system-profile - (profile - (content - (map-manifest-entries cross-built-entry - (packages->manifest %base-packages/hurd))))) - - (define grub.cfg - (let ((hurd (cross-built hurd)) - (mach (with-parameters ((%current-system "i686-linux")) - gnumach)) - (libc (cross-libc "i586-pc-gnu"))) - (computed-file "grub.cfg" - #~(call-with-output-file #$output - (lambda (port) - (format port " -set timeout=2 -search.file ~a/boot/gnumach - -menuentry \"GNU\" { - multiboot ~a/boot/gnumach root=device:hd0s1 - module ~a/hurd/ext2fs.static ext2fs \\ - --multiboot-command-line='${kernel-command-line}' \\ - --host-priv-port='${host-port}' \\ - --device-master-port='${device-port}' \\ - --exec-server-task='${exec-task}' -T typed '${root}' \\ - '$(task-create)' '$(task-resume)' - module ~a/lib/ld.so.1 exec ~a/hurd/exec '$(exec-task=task-create)' -}\n" - #+mach #+mach #+hurd - #+libc #+hurd)))))) - - (define fstab - (plain-file "fstab" - "# This file was generated from your Guix configuration. Any changes -# will be lost upon reboot or reconfiguration. - -/dev/hd0s1 / ext2 defaults -")) - - (define passwd - (plain-file "passwd" - "root:x:0:0:root:/root:/bin/sh -guixbuilder:x:1:1:guixbuilder:/var/empty:/bin/no-sh -")) - - (define group - (plain-file "group" - "guixbuild:x:1:guixbuilder -")) - - (define shadow - (plain-file "shadow" - "root::0:0:0:0::: -")) - - (define etc-profile - (plain-file "profile" - "\ -export PS1='\\u@\\h\\$ ' - -GUIX_PROFILE=\"/run/current-system/profile\" -. \"$GUIX_PROFILE/etc/profile\" - -GUIX_PROFILE=\"$HOME/.guix-profile\" -if [ -f \"$GUIX_PROFILE/etc/profile\" ]; then - . \"$GUIX_PROFILE/etc/profile\" -fi\n")) - - (define hurd-directives - `((directory "/servers") - ,@(map (lambda (server) - `(file ,(string-append "/servers/" server))) - '("startup" "exec" "proc" "password" - "default-pager" "crash-dump-core" - "kill" "suspend")) - ("/servers/crash" -> "crash-dump-core") - (directory "/servers/socket") - (file "/servers/socket/1") - (file "/servers/socket/2") - (file "/servers/socket/16") - ("/servers/socket/local" -> "1") - ("/servers/socket/inet" -> "2") - ("/servers/socket/inet6" -> "16") - (directory "/boot") - ("/boot/grub.cfg" -> ,grub.cfg) ;XXX: not strictly needed - ("/hurd" -> ,(file-append (with-parameters ((%current-target-system - "i586-pc-gnu")) - hurd) - "/hurd")) - - ;; TODO: Create those during activation, eventually. - (directory "/root") - (file "/root/.guile" - ,(object->string - '(begin - (use-modules (ice-9 readline) (ice-9 colorized)) - (activate-readline) (activate-colorized)))) - (directory "/run") - (directory "/run/current-system") - ("/run/current-system/profile" -> ,system-profile) - ("/etc/profile" -> ,etc-profile) - ("/etc/fstab" -> ,fstab) - ("/etc/group" -> ,group) - ("/etc/passwd" -> ,passwd) - ("/etc/shadow" -> ,shadow) - (file "/etc/hostname" "guixygnu") - (file "/etc/resolv.conf" - "nameserver 10.0.2.3\n") - ("/etc/services" -> ,(file-append (with-parameters ((%current-target-system - "i586-pc-gnu")) - net-base) - "/etc/services")) - ("/etc/protocols" -> ,(file-append (with-parameters ((%current-target-system - "i586-pc-gnu")) - net-base) - "/etc/protocols")) - ("/etc/motd" -> ,(file-append (with-parameters ((%current-target-system - "i586-pc-gnu")) - hurd) - "/etc/motd")) - ("/etc/login" -> ,(file-append (with-parameters ((%current-target-system - "i586-pc-gnu")) - hurd) - "/etc/login")) - - - ;; XXX can we instead, harmlessly set _PATH_TTYS (from glibc) in runttys.c? - ("/etc/ttys" -> ,(file-append (with-parameters ((%current-target-system - "i586-pc-gnu")) - hurd) - "/etc/ttys")) - ("/bin/sh" -> ,(file-append (with-parameters ((%current-target-system - "i586-pc-gnu")) - bash) - "/bin/sh")))) - - (qemu-image #:file-system-type "ext2" - #:file-system-options '("-o" "hurd") - #:device-nodes 'hurd - #:inputs `(("system" ,system-profile) - ("grub.cfg" ,grub.cfg) - ("fstab" ,fstab) - ("passwd" ,passwd) - ("group" ,group) - ("etc-profile" ,etc-profile) - ("shadow" ,shadow)) - #:copy-inputs? #t - #:os system-profile - #:bootcfg-drv grub.cfg - #:bootloader grub-bootloader - #:register-closures? #f - #:extra-directives hurd-directives)) - -;; Return this thunk so one can type "guix build -f gnu/system/hurd.scm". -cross-hurd-image diff --git a/gnu/system/image.scm b/gnu/system/image.scm index a0e6bf31f1..1bda25fd7f 100644 --- a/gnu/system/image.scm +++ b/gnu/system/image.scm @@ -1,5 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2020 Mathieu Othacehe <m.othacehe@gmail.com> +;;; Copyright © 2020 Jan (janneke) Nieuwenhuizen <janneke@gnu.org> ;;; ;;; This file is part of GNU Guix. ;;; @@ -103,6 +104,7 @@ (define hurd-disk-image (image (format 'disk-image) + (target "i586-pc-gnu") (partitions (list (partition (size 'guess) @@ -525,42 +527,54 @@ image, depending on IMAGE format." (let* ((os (operating-system-for-image image)) (image* (image-with-os image os)) + (target (image-target image)) (register-closures? (has-guix-service-type? os)) (bootcfg (operating-system-bootcfg os)) (bootloader (bootloader-configuration-bootloader (operating-system-bootloader os)))) - (case (image-format image) - ((disk-image) - (system-disk-image image* - #:bootcfg bootcfg - #:bootloader bootloader - #:register-closures? register-closures? - #:inputs `(("system" ,os) - ("bootcfg" ,bootcfg)))) - ((iso9660) - (system-iso9660-image image* - #:bootcfg bootcfg - #:bootloader bootloader - #:register-closures? register-closures? - #:inputs `(("system" ,os) - ("bootcfg" ,bootcfg)) - #:grub-mkrescue-environment - '(("MKRESCUE_SED_MODE" . "mbr_hfs"))))))) - -(define (find-image file-system-type) - "Find and return an image that could match the given FILE-SYSTEM-TYPE. This -is useful to adapt to interfaces written before the addition of the <image> -record." - (mlet %store-monad ((target (current-target-system))) - (mbegin %store-monad - (return - (match file-system-type - ("iso9660" iso9660-image) - (_ (cond - ((and target - (hurd-triplet? target)) - hurd-disk-image) - (else - efi-disk-image)))))))) + (with-parameters ((%current-target-system target)) + (case (image-format image) + ((disk-image) + (system-disk-image image* + #:bootcfg bootcfg + #:bootloader bootloader + #:register-closures? register-closures? + #:inputs `(("system" ,os) + ("bootcfg" ,bootcfg)))) + ((iso9660) + (system-iso9660-image + image* + #:bootcfg bootcfg + #:bootloader bootloader + #:register-closures? register-closures? + #:inputs `(("system" ,os) + ("bootcfg" ,bootcfg)) + ;; Make sure to use a mode that does no imply + ;; HFS+ tree creation that may fail with: + ;; + ;; "libisofs: FAILURE : Too much files to mangle, + ;; cannot guarantee unique file names" + ;; + ;; This happens if some limits are exceeded, see: + ;; https://lists.gnu.org/archive/html/grub-devel/2020-06/msg00048.html + #:grub-mkrescue-environment + '(("MKRESCUE_SED_MODE" . "mbr_only")))))))) + +(define (find-image file-system-type target) + "Find and return an image built that could match the given FILE-SYSTEM-TYPE, +built for TARGET. This is useful to adapt to interfaces written before the +addition of the <image> record." + (match file-system-type + ("iso9660" iso9660-image) + (_ (cond + ((and target + (hurd-triplet? target)) + hurd-disk-image) + (else + efi-disk-image))))) + +;;; Local Variables: +;;; eval: (put 'maybe-with-target 'scheme-indent-function 1) +;;; End: ;;; image.scm ends here diff --git a/gnu/tests/install.scm b/gnu/tests/install.scm index 6bd8c7d3d2..db355b85ca 100644 --- a/gnu/tests/install.scm +++ b/gnu/tests/install.scm @@ -3,6 +3,7 @@ ;;; Copyright © 2017, 2019 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2020 Mathieu Othacehe <m.othacehe@gmail.com> ;;; Copyright © 2020 Danny Milosavljevic <dannym@scratchpost.org> +;;; Copyright © 2020 Jan (janneke) Nieuwenhuizen <janneke@gnu.org> ;;; ;;; This file is part of GNU Guix. ;;; @@ -227,15 +228,17 @@ packages defined in installation-os." (mlet* %store-monad ((_ (set-grafting #f)) (system (current-system)) - (target (operating-system-derivation target-os)) - (base-image (find-image - installation-disk-image-file-system-type)) + (target (current-target-system)) + (base-image -> (find-image + installation-disk-image-file-system-type + target)) ;; Since the installation system has no network access, ;; we cheat a little bit by adding TARGET to its GC ;; roots. This way, we know 'guix system init' will ;; succeed. Also add guile-final, which is pulled in ;; through provenance.drv and may not always be present. + (target (operating-system-derivation target-os)) (image -> (system-image (image diff --git a/guix/build-system/r.scm b/guix/build-system/r.scm index 2d328764b0..c8ec9abd0d 100644 --- a/guix/build-system/r.scm +++ b/guix/build-system/r.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2015, 2017, 2018 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2015, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net> ;;; ;;; This file is part of GNU Guix. ;;; @@ -59,7 +59,7 @@ release corresponding to NAME and VERSION." "/src/contrib/" name "_" version ".tar.gz") ;; TODO: use %bioconductor-version from (guix import cran) - (string-append "https://bioconductor.org/packages/3.10" + (string-append "https://bioconductor.org/packages/3.11" type-url-part "/src/contrib/Archive/" name "_" version ".tar.gz")))) diff --git a/guix/download.scm b/guix/download.scm index c3dc5a208c..7d6edddbdd 100644 --- a/guix/download.scm +++ b/guix/download.scm @@ -141,8 +141,12 @@ "http://www.eu.apache.org/dist/" "http://www.us.apache.org/dist/" "http://apache.belnet.be/" + "http://apache.mirror.iweb.ca/" "http://mirrors.ircam.fr/pub/apache/" + "http://apache.mirrors.ovh.net/ftp.apache.org/dist/" "http://apache-mirror.rbc.ru/pub/apache/" + "ftp://ftp.osuosl.org/pub/apache/" + "http://mirrors.ibiblio.org/apache/" ;; As a last resort, try the archive. "http://archive.apache.org/dist/") diff --git a/guix/git-authenticate.scm b/guix/git-authenticate.scm index c333717136..0d6f696a0b 100644 --- a/guix/git-authenticate.scm +++ b/guix/git-authenticate.scm @@ -85,9 +85,11 @@ (signature missing-key-error-signature)) -(define (commit-signing-key repo commit-id keyring) +(define* (commit-signing-key repo commit-id keyring + #:key (disallowed-hash-algorithms '(sha1))) "Return the OpenPGP key that signed COMMIT-ID (an OID). Raise an exception -if the commit is unsigned, has an invalid signature, or if its signing key is +if the commit is unsigned, has an invalid signature, has a signature using one +of the hash algorithms in DISALLOWED-HASH-ALGORITHMS, or if its signing key is not in KEYRING." (let-values (((signature signed-data) (catch 'git-error @@ -103,6 +105,17 @@ not in KEYRING." (oid->string commit-id))))))) (let ((signature (string->openpgp-packet signature))) + (when (memq (openpgp-signature-hash-algorithm signature) + `(,@disallowed-hash-algorithms md5)) + (raise (condition + (&unsigned-commit-error (commit commit-id)) + (&message + (message (format #f (G_ "commit ~a has a ~a signature, \ +which is not permitted") + (oid->string commit-id) + (openpgp-signature-hash-algorithm + signature))))))) + (with-fluids ((%default-port-encoding "UTF-8")) (let-values (((status data) (verify-openpgp-signature signature keyring @@ -198,8 +211,18 @@ not specify anything, fall back to DEFAULT-AUTHORIZATIONS." (define id (commit-id commit)) + (define recent-commit? + (false-if-git-not-found + (tree-entry-bypath (commit-tree commit) ".guix-authorizations"))) + (define signing-key - (commit-signing-key repository id keyring)) + (commit-signing-key repository id keyring + ;; Reject SHA1 signatures unconditionally as suggested + ;; by the authors of "SHA-1 is a Shambles" (2019). + ;; Accept it for "historical" commits (there are such + ;; signatures from April 2020 in the repository). + #:disallowed-hash-algorithms + (if recent-commit? '(sha1) '()))) (unless (member (openpgp-public-key-fingerprint signing-key) (commit-authorized-keys repository commit diff --git a/guix/import/cran.scm b/guix/import/cran.scm index ad66a644ee..b822fbc0ae 100644 --- a/guix/import/cran.scm +++ b/guix/import/cran.scm @@ -141,9 +141,9 @@ package definition." (define %cran-url "https://cran.r-project.org/web/packages/") (define %bioconductor-url "https://bioconductor.org/packages/") -;; The latest Bioconductor release is 3.10. Bioconductor packages should be +;; The latest Bioconductor release is 3.11. Bioconductor packages should be ;; updated together. -(define %bioconductor-version "3.10") +(define %bioconductor-version "3.11") (define* (bioconductor-packages-list-url #:optional type) (string-append "https://bioconductor.org/packages/" diff --git a/guix/lint.scm b/guix/lint.scm index 6271894360..82861b8a27 100644 --- a/guix/lint.scm +++ b/guix/lint.scm @@ -9,6 +9,7 @@ ;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2017, 2018, 2020 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2018, 2019 Arun Isaac <arunisaac@systemreboot.net> +;;; Copyright © 2020 Chris Marusich <cmmarusich@gmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -669,13 +670,17 @@ patch could not be found." (or (and=> (package-source package) origin-patches) '())) + (define (starts-with-package-name? file-name) + (and=> (string-contains file-name (package-name package)) + zero?)) + (append (if (every (match-lambda ;patch starts with package name? ((? string? patch) - (and=> (string-contains (basename patch) - (package-name package)) - zero?)) - (_ #f)) ;must be an <origin> or something like that. + (starts-with-package-name? (basename patch))) + ((? origin? patch) + (starts-with-package-name? (origin-actual-file-name patch))) + (_ #f)) ;must be some other file-like object patches) '() (list diff --git a/guix/scripts/system.scm b/guix/scripts/system.scm index 3d7aa77cb7..6769a602b1 100644 --- a/guix/scripts/system.scm +++ b/guix/scripts/system.scm @@ -5,6 +5,7 @@ ;;; Copyright © 2017, 2019 Mathieu Othacehe <m.othacehe@gmail.com> ;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2019 Christopher Baines <mail@cbaines.net> +;;; Copyright © 2020 Jan (janneke) Nieuwenhuizen <janneke@gnu.org> ;;; ;;; This file is part of GNU Guix. ;;; @@ -801,7 +802,8 @@ static checks." (check-initrd-modules os))) (mlet* %store-monad - ((image (find-image file-system-type)) + ((target (current-target-system)) + (image -> (find-image file-system-type target)) (sys (system-derivation-for-action os image action #:file-system-type file-system-type #:image-size image-size diff --git a/tests/git-authenticate.scm b/tests/git-authenticate.scm index 84689d628e..97990acaea 100644 --- a/tests/git-authenticate.scm +++ b/tests/git-authenticate.scm @@ -81,6 +81,35 @@ #:keyring-reference "master") 'failed))))) +(unless (which (git-command)) (test-skip 1)) +(test-assert "signed commits, SHA1 signature" + (with-fresh-gnupg-setup (list %ed25519-public-key-file + %ed25519-secret-key-file) + ;; Force use of SHA1 for signatures. + (call-with-output-file (string-append (getenv "GNUPGHOME") "/gpg.conf") + (lambda (port) + (display "digest-algo sha1" port))) + + (with-temporary-git-repository directory + `((add "a.txt" "A") + (add "signer.key" ,(call-with-input-file %ed25519-public-key-file + get-string-all)) + (add ".guix-authorizations" + ,(object->string + `(authorizations (version 0) + ((,(key-fingerprint %ed25519-public-key-file) + (name "Charlie")))))) + (commit "first commit" + (signer ,(key-fingerprint %ed25519-public-key-file)))) + (with-repository directory repository + (let ((commit (find-commit repository "first"))) + (guard (c ((unsigned-commit-error? c) + (oid=? (git-authentication-error-commit c) + (commit-id commit)))) + (authenticate-commits repository (list commit) + #:keyring-reference "master") + 'failed)))))) + (unless (gpg+git-available?) (test-skip 1)) (test-assert "signed commits, default authorizations" (with-fresh-gnupg-setup (list %ed25519-public-key-file |