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-rw-r--r--gnu/build/shepherd.scm19
-rw-r--r--gnu/image.scm3
-rw-r--r--gnu/installer/final.scm3
-rw-r--r--gnu/local.mk1
-rw-r--r--gnu/packages/bioconductor.scm1109
-rw-r--r--gnu/packages/bioinformatics.scm524
-rw-r--r--gnu/packages/c.scm97
-rw-r--r--gnu/packages/cran.scm170
-rw-r--r--gnu/packages/emacs-xyz.scm30
-rw-r--r--gnu/packages/engineering.scm58
-rw-r--r--gnu/packages/gnome.scm14
-rw-r--r--gnu/packages/gnuzilla.scm4
-rw-r--r--gnu/packages/graph.scm4
-rw-r--r--gnu/packages/guile.scm16
-rw-r--r--gnu/packages/java.scm6
-rw-r--r--gnu/packages/linux.scm6
-rw-r--r--gnu/packages/maven.scm8
-rw-r--r--gnu/packages/node.scm13
-rw-r--r--gnu/packages/patches/guile-sqlite3-fix-cross-compilation.patch55
-rw-r--r--gnu/packages/statistics.scm4
-rw-r--r--gnu/packages/web.scm2
-rw-r--r--gnu/packages/xorg.scm2
-rw-r--r--gnu/services/hurd.scm5
-rw-r--r--gnu/system/examples/bare-hurd.tmpl31
-rw-r--r--gnu/system/hurd.scm177
-rw-r--r--gnu/system/image.scm80
-rw-r--r--gnu/tests/install.scm9
27 files changed, 1481 insertions, 969 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
generated by cgit v1.2.3 (git 2.46.2) at 2024-11-16 07:07:04 +0000