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-rw-r--r--gnu/packages/bioconductor.scm51
-rw-r--r--gnu/packages/bioinformatics.scm473
-rw-r--r--gnu/packages/emacs.scm4
-rw-r--r--gnu/packages/graph.scm4
-rw-r--r--gnu/packages/statistics.scm33
5 files changed, 288 insertions, 277 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 788e1e7def..ed35b4c61a 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -64,14 +64,14 @@ objects.")
(define-public r-hpar
(package
(name "r-hpar")
- (version "1.20.0")
+ (version "1.22.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "hpar" version))
(sha256
(base32
- "0s5v79mgxdx862v1jrdf5pdap81nz5vjx25ni8s3sl97ldckf6j8"))))
+ "1b72hvzasf6q739gmx6jblbzzyq22l7crrkbbfkihv3v7s94g388"))))
(build-system r-build-system)
(home-page "https://bioconductor.org/packages/hpar/")
(synopsis "Human Protein Atlas in R")
@@ -82,14 +82,14 @@ the Human Protein Atlas project.")
(define-public r-regioner
(package
(name "r-regioner")
- (version "1.10.0")
+ (version "1.12.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "regioneR" version))
(sha256
(base32
- "1vprp3l929hwzmvgskbhawfgnrymwc9n2rxd16rgagnv1dxnjxfp"))))
+ "09bzlaqdgy7wmzly3zc9y2da50d07mlixlnpaxdxpiwdk8qmhxsb"))))
(properties `((upstream-name . "regioneR")))
(build-system r-build-system)
(propagated-inputs
@@ -98,7 +98,8 @@ the Human Protein Atlas project.")
("r-bsgenome" ,r-bsgenome)
("r-rtracklayer" ,r-rtracklayer)
("r-genomeinfodb" ,r-genomeinfodb)
- ("r-iranges" ,r-iranges)))
+ ("r-iranges" ,r-iranges)
+ ("r-s4vectors" ,r-s4vectors)))
(home-page "https://bioconductor.org/packages/regioneR/")
(synopsis "Association analysis of genomic regions")
(description "This package offers a statistical framework based on
@@ -109,14 +110,14 @@ region sets and other genomic features.")
(define-public r-diffbind
(package
(name "r-diffbind")
- (version "2.6.6")
+ (version "2.8.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DiffBind" version))
(sha256
(base32
- "1sm5h6nq77hjfis6kr1nqyizcxgfz87dgpqc4fxlfqkmsd9n3vkp"))))
+ "1w1hybzd732ccg3q8zhirwfilq8sx3frv1x98zfyj3svzw98fish"))))
(properties `((upstream-name . "DiffBind")))
(build-system r-build-system)
(inputs
@@ -128,6 +129,8 @@ region sets and other genomic features.")
("r-dplyr" ,r-dplyr)
("r-edger" ,r-edger)
("r-genomicalignments" ,r-genomicalignments)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-ggplot2" ,r-ggplot2)
("r-ggrepel" ,r-ggrepel)
("r-gplots" ,r-gplots)
("r-iranges" ,r-iranges)
@@ -138,6 +141,7 @@ region sets and other genomic features.")
("r-rcpp" ,r-rcpp)
("r-rsamtools" ,r-rsamtools)
("r-s4vectors" ,r-s4vectors)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)
("r-systempiper" ,r-systempiper)
("r-zlibbioc" ,r-zlibbioc)))
(home-page "http://bioconductor.org/packages/DiffBind")
@@ -151,14 +155,14 @@ occupancy (overlap) analysis and plotting functions.")
(define-public r-ripseeker
(package
(name "r-ripseeker")
- (version "1.18.0")
+ (version "1.20.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "RIPSeeker" version))
(sha256
(base32
- "0bqkzwrncww7il36273chkd3gfxmii7p566ycki9qij419pwr35y"))))
+ "0y9cvzqslfxj3z9mnp47mknff0pky2g5x8x1z1s5yjcx35q89xfi"))))
(properties `((upstream-name . "RIPSeeker")))
(build-system r-build-system)
(propagated-inputs
@@ -222,23 +226,27 @@ expressed genes in DNA microarray experiments.")
(define-public r-chippeakanno
(package
(name "r-chippeakanno")
- (version "3.12.7")
+ (version "3.14.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ChIPpeakAnno" version))
(sha256
(base32
- "1zab489d7a6bh6ylc68x6yn47gdkmr7p3677grx9l2qafrryjr04"))))
+ "1kcnc3cnmrhdk1x7q3y6zsz09pgd3xn9xy1hfbxz48cajlb18ad0"))))
(properties `((upstream-name . "ChIPpeakAnno")))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
+ ("r-biostrings" ,r-biostrings)
+ ("r-delayedarray" ,r-delayedarray)
("r-go-db" ,r-go-db)
("r-biomart" ,r-biomart)
("r-bsgenome" ,r-bsgenome)
("r-genomicfeatures" ,r-genomicfeatures)
+ ("r-genomicranges" ,r-genomicranges)
("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-iranges" ,r-iranges)
("r-matrixstats" ,r-matrixstats)
("r-annotationdbi" ,r-annotationdbi)
("r-limma" ,r-limma)
@@ -250,6 +258,7 @@ expressed genes in DNA microarray experiments.")
("r-dbi" ,r-dbi)
("r-ensembldb" ,r-ensembldb)
("r-biobase" ,r-biobase)
+ ("r-s4vectors" ,r-s4vectors)
("r-seqinr" ,r-seqinr)
("r-idr" ,r-idr)
("r-genomicalignments" ,r-genomicalignments)
@@ -272,16 +281,15 @@ enrichedGO (addGeneIDs).")
(define-public r-marray
(package
(name "r-marray")
- (version "1.56.0")
+ (version "1.58.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "marray" version))
(sha256
- (base32 "14c93i86yc7jn4ax8p4l0z6v9xisw1bv7gzb4a0gbxhxn7mddaic"))))
+ (base32 "0539flh3y1qy5b1bamkfwbskis765c5s33v1y9j51n33mxb9h08d"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-limma" ,r-limma)))
+ `(("r-limma" ,r-limma)))
(home-page "http://bioconductor.org/packages/marray")
(synopsis "Exploratory analysis for two-color spotted microarray data")
(description "This package contains class definitions for two-color spotted
@@ -292,12 +300,12 @@ normalization and quality checking.")
(define-public r-cghbase
(package
(name "r-cghbase")
- (version "1.38.0")
+ (version "1.40.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "CGHbase" version))
(sha256
- (base32 "0fynvcsjdbgp69i0nxrc8ni58rhb1kx9k5r3nb91n9i8s43gjqlm"))))
+ (base32 "1hf44vma3kgwr61kjbszvfxkava8bjqnam1mdncqvczbypb2xwaq"))))
(properties `((upstream-name . "CGHbase")))
(build-system r-build-system)
(propagated-inputs
@@ -312,12 +320,12 @@ the @code{arrayCGH} packages.")
(define-public r-cghcall
(package
(name "r-cghcall")
- (version "2.40.0")
+ (version "2.42.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "CGHcall" version))
(sha256
- (base32 "11pi6awz3858yb4s0z3qf3kcmsdgp6d4aj41g4lfix1sv5amllch"))))
+ (base32 "0y71vfxv9x0am3xvv520yr95cb7m7y92dhdx1vkqki80jrmf12dz"))))
(properties `((upstream-name . "CGHcall")))
(build-system r-build-system)
(propagated-inputs
@@ -335,16 +343,17 @@ the @code{arrayCGH} packages.")
(define-public r-qdnaseq
(package
(name "r-qdnaseq")
- (version "1.14.0")
+ (version "1.16.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "QDNAseq" version))
(sha256
- (base32 "0lgbv4s0xqgrs7q6ynb3c273sf7pyrp51jnc8ravq1z5g0a2zshy"))))
+ (base32 "1pj69mfyxwfd0d7h4kls9xq96sdc55y3rv20qpla50hw9libcwwd"))))
(properties `((upstream-name . "QDNAseq")))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
+ ("r-biocparallel" ,r-biocparallel)
("r-cghbase" ,r-cghbase)
("r-cghcall" ,r-cghcall)
("r-dnacopy" ,r-dnacopy)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b4988aeb7b..a48288163f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6164,14 +6164,14 @@ data types as well.")
(define-public r-annotate
(package
(name "r-annotate")
- (version "1.56.2")
+ (version "1.58.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "annotate" version))
(sha256
(base32
- "0ybg9k1s289h15nj1kp9821i1rsk1gkn8i8blplmk7gsgpbw1f42"))))
+ "1qmncyvy147a1ll3iri45p822kcs3s7583jfnq9jf6sz9ilk8cjf"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
@@ -6191,13 +6191,13 @@ microarrays.")
(define-public r-copynumber
(package
(name "r-copynumber")
- (version "1.18.0")
+ (version "1.20.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "copynumber" version))
(sha256
(base32
- "01kcwzl485yjrkgyg8117b1il957ss0v6rq4bbxf4ksd5fzcjmyx"))))
+ "0y9nnwb0psphp3ix88wj2f8z5gr45r5znf55w892ysm27isdpmms"))))
(build-system r-build-system)
(propagated-inputs
`(("r-s4vectors" ,r-s4vectors)
@@ -6214,14 +6214,14 @@ penalized least squares regression method.")
(define-public r-geneplotter
(package
(name "r-geneplotter")
- (version "1.56.0")
+ (version "1.58.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "geneplotter" version))
(sha256
(base32
- "1z3g7frc1iviwrsv2dlm4nqvkc0685h4va0388yfxn102ln8wwma"))))
+ "055g28xgiazl4l0gkg8xiamks64f5yckjjyvw1abd6d6qjavwx0g"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotate" ,r-annotate)
@@ -6239,14 +6239,14 @@ penalized least squares regression method.")
(define-public r-genefilter
(package
(name "r-genefilter")
- (version "1.60.0")
+ (version "1.62.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "genefilter" version))
(sha256
(base32
- "173swlg6gj4kdllbqvyiw5dggbcxiwlwpqmllsv4dxzn7h25i3g7"))))
+ "14l0ff02spmjwxj0m1czhg5vlkgwcfi73cym8m2n9vn6i7bjdaqi"))))
(build-system r-build-system)
(native-inputs
`(("gfortran" ,gfortran)))
@@ -6266,14 +6266,14 @@ high-throughput sequencing experiments.")
(define-public r-deseq2
(package
(name "r-deseq2")
- (version "1.18.1")
+ (version "1.20.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DESeq2" version))
(sha256
(base32
- "1iyimg1s0x5pdmvl8x08s8h0v019y0nhjzs50chagbpk2x91fsmv"))))
+ "1wjnfpb41a9mmf9a22bz4zh7r1d4id50vpdc1mn5vfzrz7li9qik"))))
(properties `((upstream-name . "DESeq2")))
(build-system r-build-system)
(propagated-inputs
@@ -6303,14 +6303,14 @@ distribution.")
(define-public r-dexseq
(package
(name "r-dexseq")
- (version "1.24.4")
+ (version "1.26.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DEXSeq" version))
(sha256
(base32
- "1a80yv742fx5c7qav7imsdybphf0d5bixsqyf8w5zng7fk8j16d5"))))
+ "1mqb3mdxcsi3largsl7k27bvqrgps9ixv806xvmf29pw0xn05sg1"))))
(properties `((upstream-name . "DEXSeq")))
(build-system r-build-system)
(propagated-inputs
@@ -6346,14 +6346,14 @@ exploration of the results.")
(define-public r-annotationforge
(package
(name "r-annotationforge")
- (version "1.20.0")
+ (version "1.22.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "AnnotationForge" version))
(sha256
(base32
- "01vbrf76vqfvxh6vpfxkjwccxggnha3byqzj333glqz2b6kwx5q1"))))
+ "12ffj7h95adiya5mzyjxazqn1qgr434ajpabfcyhrj5v83s4vk65"))))
(properties
`((upstream-name . "AnnotationForge")))
(build-system r-build-system)
@@ -6376,14 +6376,14 @@ databases. Packages produced are intended to be used with AnnotationDbi.")
(define-public r-rbgl
(package
(name "r-rbgl")
- (version "1.54.0")
+ (version "1.56.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "RBGL" version))
(sha256
(base32
- "18jad23i3899ypv4bg3l47cvvs3qnj1pqis2p9x0135yv5y6wnv7"))))
+ "0hj972mmqpyi5fx1rq33kysavdyz4nspi6gcffzi3rv339m0anhf"))))
(properties `((upstream-name . "RBGL")))
(build-system r-build-system)
(propagated-inputs `(("r-graph" ,r-graph)))
@@ -6397,14 +6397,14 @@ the graph algorithms contained in the Boost library.")
(define-public r-gseabase
(package
(name "r-gseabase")
- (version "1.40.1")
+ (version "1.42.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "GSEABase" version))
(sha256
(base32
- "10cmjxahg2plwacfan6g0k8cwyzya96ypc7m1r79gwqkyykxw5fz"))))
+ "11bv92svik399q677jv96b71i4bq68xxyxn1yijpdik2lq4hgl7a"))))
(properties `((upstream-name . "GSEABase")))
(build-system r-build-system)
(propagated-inputs
@@ -6424,14 +6424,14 @@ Enrichment Analysis} (GSEA).")
(define-public r-category
(package
(name "r-category")
- (version "2.44.0")
+ (version "2.46.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Category" version))
(sha256
(base32
- "0mkav04vbla0xfa0dssxdd0rjs589sxi83xklf5iq5hj3dm8y0i8"))))
+ "03wfqa8d1dgwsm327zl2mpkq7dq3mzhq12598qz3ylfhrwplbgx0"))))
(properties `((upstream-name . "Category")))
(build-system r-build-system)
(propagated-inputs
@@ -6455,14 +6455,14 @@ analysis.")
(define-public r-gostats
(package
(name "r-gostats")
- (version "2.44.0")
+ (version "2.46.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "GOstats" version))
(sha256
(base32
- "04gqfdlx9fxf97qf0l28x4aaqvl10n6v58qiz5fiaw05sbj1pf1i"))))
+ "1i5mydz5d95w2k28qr9j01hmbnl2id55jq94jvcpcyp1pvinkdq0"))))
(properties `((upstream-name . "GOstats")))
(build-system r-build-system)
(propagated-inputs
@@ -6486,14 +6486,14 @@ testing and other simple calculations.")
(define-public r-shortread
(package
(name "r-shortread")
- (version "1.36.1")
+ (version "1.38.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ShortRead" version))
(sha256
(base32
- "1cyv47632m9ljkxfsvnvmd19sb607ys5kz8fwh6v39dnw16g0a6m"))))
+ "038z3z7qaw5bpgjzy91sjkybsny6jwjjsrnnq4gdqdw9ss1qy1fb"))))
(properties `((upstream-name . "ShortRead")))
(build-system r-build-system)
(inputs
@@ -6528,14 +6528,14 @@ ungapped alignment formats.")
(define-public r-systempiper
(package
(name "r-systempiper")
- (version "1.12.0")
+ (version "1.14.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "systemPipeR" version))
(sha256
(base32
- "11mj8pjq5vj25768vmagpzv74fvi3p3kdk5zdlznqyiaggri04cv"))))
+ "1550pd63mmky0vgkmpni7zf14kqz1741wv63nfaw29kcmhh3m5lm"))))
(properties `((upstream-name . "systemPipeR")))
(build-system r-build-system)
(propagated-inputs
@@ -6574,14 +6574,14 @@ annotation infrastructure.")
(define-public r-grohmm
(package
(name "r-grohmm")
- (version "1.12.0")
+ (version "1.14.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "groHMM" version))
(sha256
(base32
- "0cjkj0ypyc4dfi9s8dh88kh6q4xlpnc0wal7njg4b4gqj0l2hva7"))))
+ "1kjb14apyly44qdlx2ld6gr69wlazd4mbhs58l35hir12aphgrzp"))))
(properties `((upstream-name . "groHMM")))
(build-system r-build-system)
(propagated-inputs
@@ -6893,13 +6893,13 @@ barplots or heatmaps.")
(define-public r-biocgenerics
(package
(name "r-biocgenerics")
- (version "0.24.0")
+ (version "0.26.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BiocGenerics" version))
(sha256
(base32
- "03wxvhxyrhipbgcg83lqlfn7p9gbzzrnl48y0dq7303xgp232zai"))))
+ "19qxhy2cd3pykkhzbb5q3crgaxf65cpzf2mkfsz16gqhi8flj72p"))))
(properties
`((upstream-name . "BiocGenerics")))
(build-system r-build-system)
@@ -6913,13 +6913,13 @@ packages.")
(define-public r-biocinstaller
(package
(name "r-biocinstaller")
- (version "1.28.0")
+ (version "1.30.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BiocInstaller" version))
(sha256
(base32
- "19fga27bv6q9v5mpil74y76lahmnwvpg2h33rdx1r79nvljkd19d"))))
+ "1xg1gi1hf5vflp71ji21gnmr4kcjpx8a6c47cllpc7yqnjv5nfg0"))))
(properties
`((upstream-name . "BiocInstaller")))
(build-system r-build-system)
@@ -6932,13 +6932,13 @@ Bioconductor, CRAN, and Github.")
(define-public r-biocviews
(package
(name "r-biocviews")
- (version "1.46.0")
+ (version "1.48.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "biocViews" version))
(sha256
(base32
- "09zyqj1kqc089lmh9sliy0acanx9zimcasvp71dsrg2bqm08r1md"))))
+ "1yx2lir67ny0j150wyfqca0wsxp84byri8nscbs9qlndkh2jppq9"))))
(properties
`((upstream-name . "biocViews")))
(build-system r-build-system)
@@ -6983,13 +6983,13 @@ authoring books and technical documents with R Markdown.")
(define-public r-biocstyle
(package
(name "r-biocstyle")
- (version "2.6.1")
+ (version "2.8.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BiocStyle" version))
(sha256
(base32
- "03pp04pkcq99kdv2spzr995h2cxsza7l6w3d4gp4112m06prcybm"))))
+ "17m901ylz00w1a3nq5f910v55zixm1nr6rb3qrsbhqd94qzr0l2p"))))
(properties
`((upstream-name . "BiocStyle")))
(build-system r-build-system)
@@ -7008,13 +7008,13 @@ functionality.")
(define-public r-bioccheck
(package
(name "r-bioccheck")
- (version "1.14.0")
+ (version "1.16.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BiocCheck" version))
(sha256
(base32
- "1nzp8kgw13z9pgf885rplj6k37jcldfhbz0adqclxr2gq0yalmyx"))))
+ "1srp1g809f1nn0fyqknr7r6dq89bw1xpjvmygr7cw6ffknbc671s"))))
(properties
`((upstream-name . "BiocCheck")))
(build-system r-build-system)
@@ -7099,13 +7099,13 @@ that accept short and long options.")
(define-public r-dnacopy
(package
(name "r-dnacopy")
- (version "1.52.0")
+ (version "1.54.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "DNAcopy" version))
(sha256
(base32
- "127il5rlg1hzjlhwhs64x3nm18p00q1pd9ckb2b9ifl0rax95wai"))))
+ "03hfhmmc5y60r2gcgm367w2fr7qj115l74m9bp3h9qpn5yci0d8n"))))
(properties
`((upstream-name . "DNAcopy")))
(build-system r-build-system)
@@ -7121,13 +7121,13 @@ abnormal copy number.")
(define-public r-s4vectors
(package
(name "r-s4vectors")
- (version "0.16.0")
+ (version "0.18.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "S4Vectors" version))
(sha256
(base32
- "03s8vz33nl6mivjb7dbvj702dkypi340lji1sjban03fyyls0hw0"))))
+ "0qvj2j0zl4djjl7vrwc6xak6h8dxr53iwypfbcvfb3sh7jwhdiz5"))))
(properties
`((upstream-name . "S4Vectors")))
(build-system r-build-system)
@@ -7173,13 +7173,13 @@ utilities for sequence data management under the ACNUC system.")
(define-public r-iranges
(package
(name "r-iranges")
- (version "2.12.0")
+ (version "2.14.10")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "IRanges" version))
(sha256
(base32
- "1vqczb9wlxsmpwpqig6j1dmiblcfpq6mgnq8qwzcrvddm4cp47m5"))))
+ "10ccw930vfmkskkrzbps14xglqlkxf588623dr7f1a9ckx7yr2p6"))))
(properties
`((upstream-name . "IRanges")))
(build-system r-build-system)
@@ -7225,13 +7225,13 @@ ID and species. It is used by functions in the GenomeInfoDb package.")
(define-public r-genomeinfodb
(package
(name "r-genomeinfodb")
- (version "1.14.0")
+ (version "1.16.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomeInfoDb" version))
(sha256
(base32
- "1jhm0imkac4gvchbjxj408aakk39xdv2fyh818d3lk295bz6bnyp"))))
+ "0yhnqhaydmmq7ihmhj3rbal4afq5p993l2qqrd0n5wmbyg7glg2d"))))
(properties
`((upstream-name . "GenomeInfoDb")))
(build-system r-build-system)
@@ -7253,13 +7253,13 @@ names in their natural, rather than lexicographic, order.")
(define-public r-edger
(package
(name "r-edger")
- (version "3.20.9")
+ (version "3.22.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "edgeR" version))
(sha256
(base32
- "0y52snwbz37xzdd7gihdkqczbndlfzmmypv6hri3ymjyfmlx6qaw"))))
+ "07py2g6vg9jbflwhc1hnzr2silbinrjwxq3mkq30nzjgf0n0hrf3"))))
(properties `((upstream-name . "edgeR")))
(build-system r-build-system)
(propagated-inputs
@@ -7281,13 +7281,13 @@ CAGE.")
(define-public r-variantannotation
(package
(name "r-variantannotation")
- (version "1.24.5")
+ (version "1.26.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "VariantAnnotation" version))
(sha256
(base32
- "07ywn3c4w83l3sr76d0z3b1nv9icgdh3phsjlc6cfx7i6nfmvxw2"))))
+ "06bccdf57vja7m63chmgc4539lwng3q3b8zxn285fj8524l6mcn7"))))
(properties
`((upstream-name . "VariantAnnotation")))
(inputs
@@ -7319,13 +7319,13 @@ coding changes and predict coding outcomes.")
(define-public r-limma
(package
(name "r-limma")
- (version "3.34.9")
+ (version "3.36.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "limma" version))
(sha256
(base32
- "1y2fm61g5i0fn0j3l31xvwh9zww9bpkc4nwzb1d0yv1cag20jkdc"))))
+ "1982g5v35ilfgxm2vkq1p3j1bbir795pjvfzx4nzam2rlqqymbqm"))))
(build-system r-build-system)
(home-page "http://bioinf.wehi.edu.au/limma")
(synopsis "Package for linear models for microarray and RNA-seq data")
@@ -7338,13 +7338,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.")
(define-public r-xvector
(package
(name "r-xvector")
- (version "0.18.0")
+ (version "0.20.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "XVector" version))
(sha256
(base32
- "1i4i3kdxr78lr1kcxq657p11ybi7kq10c8kyaqyh6gfc8i9rhvmk"))))
+ "1zjlhh9lsyhg0js1858csyw2389kbrzdqnqnha833wazkwxilp3f"))))
(properties
`((upstream-name . "XVector")))
(build-system r-build-system)
@@ -7374,13 +7374,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.")
(define-public r-genomicranges
(package
(name "r-genomicranges")
- (version "1.30.3")
+ (version "1.32.3")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomicRanges" version))
(sha256
(base32
- "07cszc9ri94nzk4dffwnsj247ih6pchnrzrvnb0q4dkk33gwy8n1"))))
+ "03gmka6rlz18vd4229796l5l3l6446v5cb90sn2nb5knjbp84hni"))))
(properties
`((upstream-name . "GenomicRanges")))
(build-system r-build-system)
@@ -7403,13 +7403,13 @@ manipulating genomic intervals and variables defined along a genome.")
(define-public r-biobase
(package
(name "r-biobase")
- (version "2.38.0")
+ (version "2.40.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "Biobase" version))
(sha256
(base32
- "1cgm1ja1kp56zdlzyy9ggbkfn8r2vbsd4hncmz8g4hjd47fg18kg"))))
+ "1iwds2a5ir29k19dbpynlc7nn836cw2gamchhgpi2jf2xar9m9jz"))))
(properties
`((upstream-name . "Biobase")))
(build-system r-build-system)
@@ -7425,13 +7425,13 @@ on Bioconductor or which replace R functions.")
(define-public r-annotationdbi
(package
(name "r-annotationdbi")
- (version "1.40.0")
+ (version "1.42.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "AnnotationDbi" version))
(sha256
(base32
- "1dh4qs1a757n640gs34lf6z2glc96nan86x0sqaw5csadl2rhnlc"))))
+ "0afkbzli08vq02r2pr9phrz3rxd6ilp1w7yw8y99nbjiz14f8b1c"))))
(properties
`((upstream-name . "AnnotationDbi")))
(build-system r-build-system)
@@ -7452,13 +7452,13 @@ annotation data packages using SQLite data storage.")
(define-public r-biomart
(package
(name "r-biomart")
- (version "2.34.2")
+ (version "2.36.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "biomaRt" version))
(sha256
(base32
- "1zlgs2zg0lmnk572p55n7m34nkxka8w10x8f2ndssjkffl2csy79"))))
+ "0b70s350ffc74v3xz5c3jpazr9zxdb7gjmjfj7aghlsrizrspill"))))
(properties
`((upstream-name . "biomaRt")))
(build-system r-build-system)
@@ -7485,13 +7485,13 @@ powerful online queries from gene annotation to database mining.")
(define-public r-biocparallel
(package
(name "r-biocparallel")
- (version "1.12.0")
+ (version "1.14.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BiocParallel" version))
(sha256
(base32
- "13ng3n2wsgl3fh0v6jnz3vg51k5c1sh44pqdvblcrcd1qyjmmqhd"))))
+ "00qg1kg2l9qqpyjaw5q910cmf84vwfiw1fhsx3ig784gwinwgj6n"))))
(properties
`((upstream-name . "BiocParallel")))
(build-system r-build-system)
@@ -7510,13 +7510,13 @@ objects.")
(define-public r-biostrings
(package
(name "r-biostrings")
- (version "2.46.0")
+ (version "2.48.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "Biostrings" version))
(sha256
(base32
- "0vg50qdlxqcm2d6axjnzg8wh8pr4c5gz03l8bdl0llmwzp0zclzk"))))
+ "118b490jk87ydigm6ln25ms4kskzkw0akmh77clzznhzpqnxsi6j"))))
(properties
`((upstream-name . "Biostrings")))
(build-system r-build-system)
@@ -7536,13 +7536,13 @@ biological sequences or sets of sequences.")
(define-public r-rsamtools
(package
(name "r-rsamtools")
- (version "1.30.0")
+ (version "1.32.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "Rsamtools" version))
(sha256
(base32
- "0pjny5fjvbnfdyhl3bwxin678sha2drvs00sivxh3l772cn6yams"))))
+ "1s65y5wn4d0x8zsljg2kmhcl6r9884h95kr041j7hp49bmxg3an6"))))
(properties
`((upstream-name . "Rsamtools")))
(build-system r-build-system)
@@ -7580,18 +7580,19 @@ files.")
(define-public r-delayedarray
(package
(name "r-delayedarray")
- (version "0.4.1")
+ (version "0.6.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "DelayedArray" version))
(sha256
(base32
- "0s7h2giyvz04cg6248kbbzpwhxdrpnsvl2s8k5c8ricisd9aaz4b"))))
+ "0n3w57cwy911q812wc8658y0v3xgpmg379sj98kfqdxa80z1mxdf"))))
(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-matrixstats" ,r-matrixstats)))
@@ -7610,13 +7611,13 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns),
(define-public r-summarizedexperiment
(package
(name "r-summarizedexperiment")
- (version "1.8.1")
+ (version "1.10.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "SummarizedExperiment" version))
(sha256
(base32
- "19vlwnby83fqjrilsxvnvgz0gvby7mrxvlmx18nb3p1w591ddfjh"))))
+ "0v3zxl9cqsv79ag5cnvzlhvgaz5cr8f4rn7flmwnwpqd508cznl1"))))
(properties
`((upstream-name . "SummarizedExperiment")))
(build-system r-build-system)
@@ -7641,13 +7642,13 @@ samples.")
(define-public r-genomicalignments
(package
(name "r-genomicalignments")
- (version "1.14.2")
+ (version "1.16.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomicAlignments" version))
(sha256
(base32
- "1659nj1xps7vliy5955i51x6hvrf16n1z0dfh10mmpaaswn2d2mv"))))
+ "00pi2cnkkbj2023fg2x2cmglkdalwzy1vr3glsikwz7ix9yylcaw"))))
(properties
`((upstream-name . "GenomicAlignments")))
(build-system r-build-system)
@@ -7674,13 +7675,13 @@ alignments.")
(define-public r-rtracklayer
(package
(name "r-rtracklayer")
- (version "1.38.3")
+ (version "1.40.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "rtracklayer" version))
(sha256
(base32
- "1khzfczm35k5lq9h0jlqrq01192spzjyh8s6is89spj006flwn4k"))))
+ "0l90jn4df3akxl0n1i9wvnbjqrzjc0d15r8vqr7b15q2117mrn5r"))))
(build-system r-build-system)
(arguments
`(#:phases
@@ -7692,6 +7693,8 @@ alignments.")
(substitute* "NAMESPACE"
(("import\\(zlibbioc\\)") ""))
#t)))))
+ (native-inputs
+ `(("pkg-config" ,pkg-config)))
(inputs
`(("zlib" ,zlib)))
(propagated-inputs
@@ -7719,13 +7722,13 @@ as well as query and modify the browser state, such as the current viewport.")
(define-public r-genomicfeatures
(package
(name "r-genomicfeatures")
- (version "1.30.3")
+ (version "1.32.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomicFeatures" version))
(sha256
(base32
- "010vn8hlwbnw12pd1d8pv6m12yp3xwx557gba5rbjq9p4qypnn3z"))))
+ "1cqcl72q0k5wylw1brn4g4h7xzys1v06piry19cvp0gjcvm5sp7a"))))
(properties
`((upstream-name . "GenomicFeatures")))
(build-system r-build-system)
@@ -7741,7 +7744,6 @@ as well as query and modify the browser state, such as the current viewport.")
("r-iranges" ,r-iranges)
("r-rcurl" ,r-rcurl)
("r-rsqlite" ,r-rsqlite)
- ("r-rmysql" ,r-rmysql)
("r-rtracklayer" ,r-rtracklayer)
("r-s4vectors" ,r-s4vectors)
("r-xvector" ,r-xvector)))
@@ -7785,13 +7787,13 @@ information about the latest version of the Gene Ontologies.")
(define-public r-graph
(package
(name "r-graph")
- (version "1.56.0")
+ (version "1.58.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "graph" version))
(sha256
(base32
- "15aajjp8h2z14p80c8hyd4rrmr9vqsm7bvwb989jxjl4k6g52an1"))))
+ "1zx445lk36g1s6i5dbhhf00nzzazyklfjxxjfax6q8hnhvgm9759"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)))
@@ -7804,13 +7806,13 @@ information about the latest version of the Gene Ontologies.")
(define-public r-topgo
(package
(name "r-topgo")
- (version "2.30.1")
+ (version "2.32.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "topGO" version))
(sha256
(base32
- "1cgz4knxr328xfqlhl6ypxl6x86rfrlqz748kn94ainxjzz55i6x"))))
+ "05yxnkid8bgw9lkm90if9fg63djhgvbailfa3qsfqa5c0zjmixw1"))))
(properties
`((upstream-name . "topGO")))
(build-system r-build-system)
@@ -7837,13 +7839,13 @@ dependencies between GO terms can be implemented and applied.")
(define-public r-bsgenome
(package
(name "r-bsgenome")
- (version "1.46.0")
+ (version "1.48.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BSgenome" version))
(sha256
(base32
- "1jbzq7lm2iajajn2bifxnkss0k9fdvgqr30mral17cbhp5f6w4lq"))))
+ "1rk2piqq5dppkd51ln3r872d7ng3rvq98071mnd0xdv2xwnyn5g8"))))
(properties
`((upstream-name . "BSgenome")))
(build-system r-build-system)
@@ -7898,13 +7900,13 @@ genome data packages and support for efficient SNP representation.")
(define-public r-impute
(package
(name "r-impute")
- (version "1.52.0")
+ (version "1.54.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "impute" version))
(sha256
(base32
- "0b8r4swvyx3cjcc2ky8yn0ncpzlbi1pgfsn3wpbjmhh7sqrffm2n"))))
+ "1d3cpfaqlq2gnb3hsc2yhxwkrnbd7m6ifif32yp0ya0jr5brl4hr"))))
(inputs
`(("gfortran" ,gfortran)))
(build-system r-build-system)
@@ -7918,13 +7920,13 @@ microarray data, using nearest neighbor averaging.")
(define-public r-seqpattern
(package
(name "r-seqpattern")
- (version "1.10.0")
+ (version "1.12.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "seqPattern" version))
(sha256
(base32
- "1kcm5w83q7w0v0vs7nyp4gq5z86c6n6pqy9zmyyhxcrns7f597pm"))))
+ "0dw0yldfcf0ibvpqxlpx1ijnjf9lma47w9w22siszzhw09i0wp3w"))))
(properties
`((upstream-name . "seqPattern")))
(build-system r-build-system)
@@ -7945,13 +7947,13 @@ reference point and sorted by a user defined feature.")
(define-public r-genomation
(package
(name "r-genomation")
- (version "1.11.3")
+ (version "1.12.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "genomation" version))
(sha256
(base32
- "1d2g1v6xhrf3gm86pv8ln22df5g6v6k6i4i39v4j82zn4apany6v"))))
+ "1vdmdyrq0n7pf8cvy2950v7hrcrcbd9zl4fg7dcmyly3iiwdyirp"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biostrings" ,r-biostrings)
@@ -8123,14 +8125,14 @@ annotations for the genome of the model mouse Mus musculus.")
(define-public r-seqlogo
(package
(name "r-seqlogo")
- (version "1.44.0")
+ (version "1.46.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "seqLogo" version))
(sha256
(base32
- "1ql4q4vx0j61a893dqc3c8zxmgs8sqhy3j1qhyfdvbd01vw9w1kq"))))
+ "16xvqcdknix9vjm8mrixi6nyfsr45jm844jh1x90m8044lwrsic1"))))
(properties `((upstream-name . "seqLogo")))
(build-system r-build-system)
(home-page "https://bioconductor.org/packages/seqLogo")
@@ -8369,14 +8371,14 @@ Biostrings objects.")
(define-public r-motifrg
(package
(name "r-motifrg")
- (version "1.22.0")
+ (version "1.24.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "motifRG" version))
(sha256
(base32
- "193zl2rlzwxv9p9q5i7rilj3w05ndqfyp9bdpvagp5s5cin4hf44"))))
+ "0mxhyidkyd2zqahdbg69y20r550z78lvr1r3pbjymnwfg4hcfq1p"))))
(properties `((upstream-name . "motifRG")))
(build-system r-build-system)
(propagated-inputs
@@ -8421,13 +8423,13 @@ two-dimensional genome scans.")
(define-public r-zlibbioc
(package
(name "r-zlibbioc")
- (version "1.24.0")
+ (version "1.26.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "zlibbioc" version))
(sha256
(base32
- "1zr9hbh55hglfpy15cpxwmddxblhyb0an15953l3rbhmlh2vpy92"))))
+ "1rwr0mci8a712q0isavi4jmhm94gwivc4nr8j7r4kw05flp4g7gz"))))
(properties
`((upstream-name . "zlibbioc")))
(build-system r-build-system)
@@ -8463,14 +8465,14 @@ secondary structure and comparative analysis in R.")
(define-public r-rhtslib
(package
(name "r-rhtslib")
- (version "1.10.0")
+ (version "1.12.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Rhtslib" version))
(sha256
(base32
- "1dw3p44bfr0m7w39ckc2k37sjcp1zz0b9g12mr8am15jaj6v0q2j"))))
+ "16ywnb8cmr2xabd1i21b92rfziw7xfbv25yv16ipw617p41wa39z"))))
(properties `((upstream-name . "Rhtslib")))
(build-system r-build-system)
(propagated-inputs
@@ -8478,7 +8480,7 @@ secondary structure and comparative analysis in R.")
(inputs
`(("zlib" ,zlib)))
(native-inputs
- `(("autoconf" ,autoconf)))
+ `(("pkg-config" ,pkg-config)))
(home-page "https://github.com/nhayden/Rhtslib")
(synopsis "High-throughput sequencing library as an R package")
(description
@@ -8490,14 +8492,14 @@ of other R packages who wish to make use of HTSlib.")
(define-public r-bamsignals
(package
(name "r-bamsignals")
- (version "1.10.0")
+ (version "1.12.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "bamsignals" version))
(sha256
(base32
- "15id6mkj95skb4kfafvfs2j7ylydal60c3pspcl7llhwpq6vcqvl"))))
+ "09l4v414ijkjpkvcv2580v13v18ky196f0lv27ldblpa8bddvmns"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
@@ -8612,18 +8614,19 @@ library implementing most of the pipeline's features.")
(define-public r-mutationalpatterns
(package
(name "r-mutationalpatterns")
- (version "1.4.3")
+ (version "1.6.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MutationalPatterns" version))
(sha256
(base32
- "0ml4gsp5dfv23xqrknxh25q8q65hly1xb1215lcwyc8hj9z8f941"))))
+ "1yq7351j42mjxn8fd3c5bdxzb2l5s4lvqhjdvv4rwj4f600n6wj9"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
("r-biostrings" ,r-biostrings)
+ ;; These two packages are suggested packages
("r-bsgenome-hsapiens-1000g" ,r-bsgenome-hsapiens-1000genomes-hs37d5)
("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
("r-genomicranges" ,r-genomicranges)
@@ -8787,13 +8790,13 @@ kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
(define-public r-tximport
(package
(name "r-tximport")
- (version "1.6.0")
+ (version "1.8.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "tximport" version))
(sha256
(base32
- "1gyqcm91hxg1kgjqcz2qw1n56yp9pymjzs50rwcpb2893dr8sp2h"))))
+ "1qjc7ah9dzccpvcjrp9k4qnaz13x6kvy1c1xpdj503km6k528lip"))))
(build-system r-build-system)
(home-page "https://bioconductor.org/packages/tximport")
(synopsis "Import and summarize transcript-level estimates for gene-level analysis")
@@ -8809,39 +8812,18 @@ of gene-level counts.")
(define-public r-rhdf5
(package
(name "r-rhdf5")
- (version "2.22.0")
+ (version "2.24.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "rhdf5" version))
(sha256
(base32
- "145858qg1xan6imxcbprzq3yn3mdf532aahdr6cibvdjg47hs4c1"))))
+ "15cmmchhk8bnp94gxg0zk9qyzdjx5kv16dzpbnb62mkq7ydmifx6"))))
(build-system r-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'unpack-smallhdf5
- (lambda* (#:key outputs #:allow-other-keys)
- (system* "tar" "-xzvf"
- "src/hdf5source/hdf5small.tgz" "-C" "src/" )
- (substitute* "src/hdf5/configure"
- (("/bin/mv") "mv"))
- ;; Remove timestamp and host system information to make
- ;; the build reproducible.
- (substitute* "src/hdf5/src/libhdf5.settings.in"
- (("Configured on: @CONFIG_DATE@")
- "Configured on: Guix")
- (("Uname information:.*")
- "Uname information: Linux\n")
- ;; Remove unnecessary store reference.
- (("C Compiler:.*")
- "C Compiler: GCC\n"))
- #t)))))
(propagated-inputs
- `(("r-zlibbioc" ,r-zlibbioc)))
+ `(("r-rhdf5lib" ,r-rhdf5lib)))
(inputs
- `(("perl" ,perl)
- ("zlib" ,zlib)))
+ `(("zlib" ,zlib)))
(home-page "https://bioconductor.org/packages/rhdf5")
(synopsis "HDF5 interface to R")
(description
@@ -8857,13 +8839,13 @@ the available RAM.")
(define-public r-annotationfilter
(package
(name "r-annotationfilter")
- (version "1.2.0")
+ (version "1.4.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "AnnotationFilter" version))
(sha256
(base32
- "04zf864c1fvdlaay2r5cn30fc1n5i3czh31fs62qlrvs61wjiscs"))))
+ "1w8ypfdz4g7vnwfrvnhjcpm8waciqyq2cn883ajdwg4vv7a5mj9a"))))
(properties
`((upstream-name . "AnnotationFilter")))
(build-system r-build-system)
@@ -9160,14 +9142,14 @@ common bioinformatics tools.")
(define-public r-chipseq
(package
(name "r-chipseq")
- (version "1.28.0")
+ (version "1.30.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "chipseq" version))
(sha256
(base32
- "1ymcq77krwjzrkzzcw7i9909cmkqa7c0675z9wzvrrk81hgdssfq"))))
+ "09f8dgl5ni75qkf7nvvppwr3irpplv4xb3ks59ld7l8i2mplcrx7"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
@@ -9212,14 +9194,14 @@ GenomicRanges Bioconductor package.")
(define-public r-copywriter
(package
(name "r-copywriter")
- (version "2.10.0")
+ (version "2.12.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "CopywriteR" version))
(sha256
(base32
- "17fy2lc5yf3nh6v077kv87h53n263hqz2540lzrl0vjiqrl2plca"))))
+ "0b7xwq1va2zclb54f07c5ipmmq4iv2hrlph3j93jz5hmyayv50z3"))))
(properties `((upstream-name . "CopywriteR")))
(build-system r-build-system)
(propagated-inputs
@@ -9252,13 +9234,13 @@ number detection tools.")
(define-public r-methylkit
(package
(name "r-methylkit")
- (version "1.4.1")
+ (version "1.6.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "methylKit" version))
(sha256
(base32
- "1k0nfn9318sgwm4z963bhnbp4c3zv85v3f9886vc5hgaisr0yvai"))))
+ "01qmndm5z21p78w7xfp8ynan6jpfg54rnkpj8b86rc081qh0sgjj"))))
(properties `((upstream-name . "methylKit")))
(build-system r-build-system)
(propagated-inputs
@@ -9298,14 +9280,14 @@ TAB-Seq.")
(define-public r-sva
(package
(name "r-sva")
- (version "3.26.0")
+ (version "3.28.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "sva" version))
(sha256
(base32
- "0q5xb68wfcnchy8rkv5ma67pmz1i91lsnvmwmj8f1c3w4xan3pgw"))))
+ "0a3jqbz0jp1jxrnjkqfpmca840yqcdwxprdl608bzzx2zb4jl52s"))))
(build-system r-build-system)
(propagated-inputs
`(("r-genefilter" ,r-genefilter)
@@ -9408,14 +9390,14 @@ as allowing spectra with different resolutions.")
(define-public r-protgenerics
(package
(name "r-protgenerics")
- (version "1.10.0")
+ (version "1.12.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ProtGenerics" version))
(sha256
(base32
- "16ijp50448wnabp43klx943rhdvh7x45hvy7cnpq1s4dckxhhyni"))))
+ "05jbadw2aiwy8vi2ia0jxg06cmwhly2cq4dy1ag7kdxf1c5i9ccn"))))
(properties `((upstream-name . "ProtGenerics")))
(build-system r-build-system)
(home-page "https://github.com/lgatto/ProtGenerics")
@@ -9428,14 +9410,14 @@ proteomics packages.")
(define-public r-mzr
(package
(name "r-mzr")
- (version "2.12.0")
+ (version "2.14.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "mzR" version))
(sha256
(base32
- "1x3gp30sfxz2v3k3swih9kff9b2rvk7hzhnlkp6ywlnn2wgb0q8c"))
+ "190m2bq5bqxhljaj4f7vz9wj5h5laaxd8zp5jampnql6xc4zmarg"))
(modules '((guix build utils)))
(snippet
'(begin
@@ -9457,12 +9439,14 @@ proteomics packages.")
#t)))))
(inputs
`(("boost" ,boost) ; use this instead of the bundled boost sources
- ("netcdf" ,netcdf)))
+ ("netcdf" ,netcdf)
+ ("zlib" ,zlib)))
(propagated-inputs
`(("r-biobase" ,r-biobase)
("r-biocgenerics" ,r-biocgenerics)
("r-protgenerics" ,r-protgenerics)
("r-rcpp" ,r-rcpp)
+ ("r-rhdf5lib" ,r-rhdf5lib)
("r-zlibbioc" ,r-zlibbioc)))
(home-page "https://github.com/sneumann/mzR/")
(synopsis "Parser for mass spectrometry data files")
@@ -9478,14 +9462,14 @@ previously been used in XCMS.")
(define-public r-affyio
(package
(name "r-affyio")
- (version "1.48.0")
+ (version "1.50.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "affyio" version))
(sha256
(base32
- "1pzzp3d3dbmyf34gvivfiprkpscn36rgvhrq853a1d3avcwr5ak9"))))
+ "0sh5wnnchyfpq5n6rchbqmb27byn7kdzn5rgran6i39c81i5z22n"))))
(build-system r-build-system)
(propagated-inputs
`(("r-zlibbioc" ,r-zlibbioc)))
@@ -9502,14 +9486,14 @@ CDF file formats.")
(define-public r-affy
(package
(name "r-affy")
- (version "1.56.0")
+ (version "1.58.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "affy" version))
(sha256
(base32
- "0jmbkimma5ffsdkk3xp03g4lpz84gd95nkqakif2nqq6wmx0syrj"))))
+ "0sxq875sigm21sf3qncrfrwfdz9nqw1vldxn3d3hj6aq64jg1ki6"))))
(build-system r-build-system)
(propagated-inputs
`(("r-affyio" ,r-affyio)
@@ -9518,6 +9502,8 @@ CDF file formats.")
("r-biocinstaller" ,r-biocinstaller)
("r-preprocesscore" ,r-preprocesscore)
("r-zlibbioc" ,r-zlibbioc)))
+ (inputs
+ `(("zlib" ,zlib)))
(home-page "https://bioconductor.org/packages/affy")
(synopsis "Methods for affymetrix oligonucleotide arrays")
(description
@@ -9528,14 +9514,14 @@ analysis.")
(define-public r-vsn
(package
(name "r-vsn")
- (version "3.46.0")
+ (version "3.48.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "vsn" version))
(sha256
(base32
- "18y62phzirj75gg6v5l41jwybmk23ia6w7qhch0kxc4bl2rysw6j"))))
+ "0k6mah3g3zqbfap31xmvig4fn452a18xwwa5y0mfj5mj8588p57h"))))
(build-system r-build-system)
(propagated-inputs
`(("r-affy" ,r-affy)
@@ -9562,14 +9548,14 @@ and specific in detecting differential transcription.")
(define-public r-mzid
(package
(name "r-mzid")
- (version "1.16.0")
+ (version "1.18.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "mzID" version))
(sha256
(base32
- "0yk70dka56zd8w62f03ggx3mandj91gfa767h9ajj0sd3mjmfqb9"))))
+ "060k0xlhg8q802c6zsb4b8ps0ccd9ybyaz0gnsvqkxb786i2vk40"))))
(properties `((upstream-name . "mzID")))
(build-system r-build-system)
(propagated-inputs
@@ -9592,14 +9578,14 @@ specific parser.")
(define-public r-pcamethods
(package
(name "r-pcamethods")
- (version "1.70.0")
+ (version "1.72.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "pcaMethods" version))
(sha256
(base32
- "0ii235g0x0492kh8cfrf28ni0b6vd6fh7kizkqmczzqggd6b1bk8"))))
+ "0v99yf8m7ryh6z0r3z0ggpqfnflcq5bn1q1i1cl9b7q4p6b4sa07"))))
(properties `((upstream-name . "pcaMethods")))
(build-system r-build-system)
(propagated-inputs
@@ -9622,14 +9608,14 @@ structure (pcaRes) to provide a common interface to the PCA results.")
(define-public r-msnbase
(package
(name "r-msnbase")
- (version "2.4.2")
+ (version "2.6.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MSnbase" version))
(sha256
(base32
- "1ig64bf881p118dwqfr0ry41m7yhnyv165smv8fdwfv7sb6sagif"))))
+ "0zrpx9r93q5ca2zdak5rs2m9sjm0wjdra1xfj3d3sx6p5gzfyg6n"))))
(properties `((upstream-name . "MSnbase")))
(build-system r-build-system)
(propagated-inputs
@@ -9643,6 +9629,7 @@ structure (pcaRes) to provide a common interface to the PCA results.")
("r-iranges" ,r-iranges)
("r-lattice" ,r-lattice)
("r-maldiquant" ,r-maldiquant)
+ ("r-mass" ,r-mass)
("r-mzid" ,r-mzid)
("r-mzr" ,r-mzr)
("r-pcamethods" ,r-pcamethods)
@@ -9651,6 +9638,7 @@ structure (pcaRes) to provide a common interface to the PCA results.")
("r-protgenerics" ,r-protgenerics)
("r-rcpp" ,r-rcpp)
("r-s4vectors" ,r-s4vectors)
+ ("r-scales" ,r-scales)
("r-vsn" ,r-vsn)
("r-xml" ,r-xml)))
(home-page "https://github.com/lgatto/MSnbase")
@@ -9663,14 +9651,14 @@ of mass spectrometry based proteomics data.")
(define-public r-msnid
(package
(name "r-msnid")
- (version "1.12.1")
+ (version "1.14.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MSnID" version))
(sha256
(base32
- "1zw508kk4f8brg69674wp18gqkpx2kpya5f6x9cl3qng7v4h5pxx"))))
+ "172q5chi44104iz4y0g42wrimfp7hlhrfa8vzybx6m0ccrkkhl17"))))
(properties `((upstream-name . "MSnID")))
(build-system r-build-system)
(propagated-inputs
@@ -9795,14 +9783,14 @@ discovery of differentially expressed genes and markers.")
(define-public r-aroma-light
(package
(name "r-aroma-light")
- (version "3.8.0")
+ (version "3.10.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "aroma.light" version))
(sha256
(base32
- "0crnk6851jwypqr5l5jcbbay0vi5vvdjyisaf6z2d69c39wmr6sc"))))
+ "1dxsiwsrwcq9mj573f9vpdzrhagdqzal328ma8076px4gg6khxkn"))))
(properties `((upstream-name . "aroma.light")))
(build-system r-build-system)
(propagated-inputs
@@ -9822,14 +9810,14 @@ classes.")
(define-public r-deseq
(package
(name "r-deseq")
- (version "1.30.0")
+ (version "1.32.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DESeq" version))
(sha256
(base32
- "0mn5w3cy16iwwk8zxs7za6aa6cnrca75z0g45zd5zh1py5d7nfv9"))))
+ "0ykxw8ksif026xy25wx50j2sdsrp156aqkmhcgfjkpgcw699glnm"))))
(properties `((upstream-name . "DESeq")))
(build-system r-build-system)
(propagated-inputs
@@ -9853,14 +9841,14 @@ distribution.")
(define-public r-edaseq
(package
(name "r-edaseq")
- (version "2.12.0")
+ (version "2.14.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "EDASeq" version))
(sha256
(base32
- "07zm89zcivyn2261aq9grqmly8ji482kr9h9dyfknfdfrpv7jpwv"))))
+ "1832pb3jkim4vrqzb8lajwx9r482bhww5n9nz3s6crvyamlp2dj0"))))
(properties `((upstream-name . "EDASeq")))
(build-system r-build-system)
(propagated-inputs
@@ -9891,14 +9879,14 @@ global-scaling and full-quantile normalization.")
(define-public r-interactivedisplaybase
(package
(name "r-interactivedisplaybase")
- (version "1.16.0")
+ (version "1.18.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "interactiveDisplayBase" version))
(sha256
(base32
- "01yb945jqqimwjgriza6yy4dnp303cdirxrhl4hjyprfdlmnz5p5"))))
+ "05w58z3i9vkma4jd6rhjaxls4yiq4kwrppgcdq9xrr1pxp99k575"))))
(properties
`((upstream-name . "interactiveDisplayBase")))
(build-system r-build-system)
@@ -9915,14 +9903,14 @@ Shiny-based display methods for Bioconductor objects.")
(define-public r-annotationhub
(package
(name "r-annotationhub")
- (version "2.10.1")
+ (version "2.12.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "AnnotationHub" version))
(sha256
(base32
- "14v8g44a6zg9j2rwn9x9y8509k0wr2cw8yccliz24glplb40wva4"))))
+ "11gh7qkgazs90czdqgv74gh2hz26xrmdp6wsz9x5pygbxls8xdw3"))))
(properties `((upstream-name . "AnnotationHub")))
(build-system r-build-system)
(propagated-inputs
@@ -9950,14 +9938,14 @@ by the user, helping with quick and reproducible access.")
(define-public r-fastseg
(package
(name "r-fastseg")
- (version "1.24.0")
+ (version "1.26.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "fastseg" version))
(sha256
(base32
- "0dd7nr3klwz9ailwshnbynhd62lwb8zbbpj6jf3igpb94yi6x2jp"))))
+ "1yw6hai6hb8qy7akdm4frfp6h4zy93zb68kdj094sanm7kgqmgik"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
@@ -9980,14 +9968,14 @@ microarrays or GRanges for sequencing data.")
(define-public r-keggrest
(package
(name "r-keggrest")
- (version "1.18.1")
+ (version "1.20.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "KEGGREST" version))
(sha256
(base32
- "02gwmm79djj55a90dzc80hlgwc6bafl7xd7fnx2q59pk945k3z9c"))))
+ "1349vidgl9m10l1rbrp3pkwwgi2xcbsw9h9z2xqbvg97lmqc4r8j"))))
(properties `((upstream-name . "KEGGREST")))
(build-system r-build-system)
(propagated-inputs
@@ -10004,14 +9992,14 @@ microarrays or GRanges for sequencing data.")
(define-public r-gage
(package
(name "r-gage")
- (version "2.28.2")
+ (version "2.30.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "gage" version))
(sha256
(base32
- "0h0mlhns9j7cpfksvdlvx9jb7szm3r1dwqb3s4s8p8hmkb9byyii"))))
+ "0j3cqxy97lpf146wkmdfaq9680gicmzxvhp6w5pxq3j7ipiy7262"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
@@ -10033,14 +10021,14 @@ analysis using other methods.")
(define-public r-genomicfiles
(package
(name "r-genomicfiles")
- (version "1.14.0")
+ (version "1.16.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "GenomicFiles" version))
(sha256
(base32
- "0r0wmrs5jycf1kckhnc2sgjmp336srlcjdkpbb1ymm7kazdd0s9n"))))
+ "0bhsq5czigrjyl9gkb2kpkpl367b3ac5g8s280adkcxggn9g7sxq"))))
(properties `((upstream-name . "GenomicFiles")))
(build-system r-build-system)
(propagated-inputs
@@ -10066,14 +10054,14 @@ provide added flexibility for data combination and manipulation.")
(define-public r-complexheatmap
(package
(name "r-complexheatmap")
- (version "1.17.1")
+ (version "1.18.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ComplexHeatmap" version))
(sha256
(base32
- "1x6kp55iqqsd8bhdl3qch95nfiy2y46ldbbsx1sj1v8f0b0ywwcy"))))
+ "0z57mrginzd40niy51dvnyqgbrij05ji0dbwqs3x2as80sq28i3q"))))
(properties
`((upstream-name . "ComplexHeatmap")))
(build-system r-build-system)
@@ -10096,14 +10084,14 @@ self-defined annotation graphics.")
(define-public r-dirichletmultinomial
(package
(name "r-dirichletmultinomial")
- (version "1.20.0")
+ (version "1.22.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DirichletMultinomial" version))
(sha256
(base32
- "1c4s6x0qm20556grcd1xys9kkpnlzpasaai474malwcg6qvgi4x1"))))
+ "0vcyp81b90in4ls5nbadc66cw2g9aydr94aqifq5j4b7diq74yfs"))))
(properties
`((upstream-name . "DirichletMultinomial")))
(build-system r-build-system)
@@ -10125,19 +10113,18 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2):
(define-public r-ensembldb
(package
(name "r-ensembldb")
- (version "2.2.2")
+ (version "2.4.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ensembldb" version))
(sha256
(base32
- "1yngndkf3588z91z0a2fvkg423p26ajm6xv1p27x0l9mzhhaqq3k"))))
+ "1l2b4cxiycv05mz4z4f3dhx57r9ksha02psc114h30ldm5rxz8w6"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
("r-annotationfilter" ,r-annotationfilter)
- ("r-annotationhub" ,r-annotationhub)
("r-biobase" ,r-biobase)
("r-biocgenerics" ,r-biocgenerics)
("r-biostrings" ,r-biostrings)
@@ -10169,14 +10156,14 @@ chromosome region or transcript models of lincRNA genes.")
(define-public r-organismdbi
(package
(name "r-organismdbi")
- (version "1.20.0")
+ (version "1.22.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "OrganismDbi" version))
(sha256
(base32
- "0yxvhwn0m53wfwp0zi81x96argdf7cf1lpymc2as51apvfcnjdl8"))))
+ "0hb9ni41bjfy5s5ryw2qmqs2sx3i7j47w1g0l8g1pvn7ppnxb6cv"))))
(properties `((upstream-name . "OrganismDbi")))
(build-system r-build-system)
(propagated-inputs
@@ -10201,14 +10188,14 @@ the fact that each of these packages implements a select methods.")
(define-public r-biovizbase
(package
(name "r-biovizbase")
- (version "1.26.0")
+ (version "1.28.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "biovizBase" version))
(sha256
(base32
- "14l4vhj0a4ssr9m9zdzz3qpd4qw1mhgq5bmxq7jhrq3j9kmd6i2f"))))
+ "0lkiqdr3ics6hgv47lwkykcy761823bbkhffbn4ykyfzyqwl4p67"))))
(properties `((upstream-name . "biovizBase")))
(build-system r-build-system)
(propagated-inputs
@@ -10242,14 +10229,14 @@ effort and encourages consistency.")
(define-public r-ggbio
(package
(name "r-ggbio")
- (version "1.26.1")
+ (version "1.28.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ggbio" version))
(sha256
(base32
- "1xlmlngn27iwnr21s9di4059kav1a7c1sajx08wja8yn8f7j06hp"))))
+ "0wszh3w8yia5zw758h837i1q35k99sn444y2hahcxqbdmmlbf7in"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
@@ -10318,14 +10305,14 @@ organisms via the @code{g:Profiler} toolkit.")
(define-public r-gqtlbase
(package
(name "r-gqtlbase")
- (version "1.10.0")
+ (version "1.12.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "gQTLBase" version))
(sha256
(base32
- "1756vfcj2dkkgcmfkkg7qdaig36dv9gfvpypn9rbrky56wm1p035"))))
+ "1m3ajpqjhw1nwwsn372r44xfxq0a9a0pzsnrprzdjp6mh52p9b5m"))))
(properties `((upstream-name . "gQTLBase")))
(build-system r-build-system)
(propagated-inputs
@@ -10353,14 +10340,14 @@ and more.")
(define-public r-snpstats
(package
(name "r-snpstats")
- (version "1.28.0")
+ (version "1.30.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "snpStats" version))
(sha256
(base32
- "1x9qwynh2hwl24vq02naf4mchpch7xi2pkdrlgw896k28kx0lvir"))))
+ "0iydgfnm053iw860qa1bbh4f6nwzlsf3vhgq92gvl2v4xsz1jbbs"))))
(properties `((upstream-name . "snpStats")))
(build-system r-build-system)
(inputs `(("zlib" ,zlib)))
@@ -10412,24 +10399,26 @@ several related annotation packages.")
(define-public r-erma
(package
(name "r-erma")
- (version "0.10.1")
+ (version "0.12.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "erma" version))
(sha256
(base32
- "1fi8nc6fbd7i4p9i9hli31xplmdpsxqcdrb8v3nf8fx9klllbdav"))))
+ "1ka68n18yizlyvb8bpwwcl4hqbsasg8hw8jb3vgy3cd4szji87hh"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
("r-biobase" ,r-biobase)
("r-biocgenerics" ,r-biocgenerics)
- ("r-foreach" ,r-foreach)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-genomeinfodb" ,r-genomeinfodb)
("r-genomicfiles" ,r-genomicfiles)
("r-genomicranges" ,r-genomicranges)
("r-ggplot2" ,r-ggplot2)
("r-homo-sapiens" ,r-homo-sapiens)
+ ("r-iranges" ,r-iranges)
("r-rtracklayer" ,r-rtracklayer)
("r-s4vectors" ,r-s4vectors)
("r-shiny" ,r-shiny)
@@ -10448,17 +10437,18 @@ by Ernst and Kellis.")
(define-public r-ldblock
(package
(name "r-ldblock")
- (version "1.8.1")
+ (version "1.10.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ldblock" version))
(sha256
(base32
- "1q8dz8wcq1r7kr635s9q21g36sxkdybk8khhpa4p57qv8r0gppl0"))))
+ "0c24zvnwsp39d3q0bps13sc441jj9ms2zi34xsb8c392lqmbypvd"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-erma" ,r-erma)
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-erma" ,r-erma)
("r-genomeinfodb" ,r-genomeinfodb)
("r-genomicfiles" ,r-genomicfiles)
("r-go-db" ,r-go-db)
@@ -10479,14 +10469,14 @@ defining LD blocks.")
(define-public r-gqtlstats
(package
(name "r-gqtlstats")
- (version "1.10.1")
+ (version "1.12.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "gQTLstats" version))
(sha256
(base32
- "0gvq1sf2zjbkk431x40z6wql3c1rpclnnwa2f1hvykb8mmw70kmq"))))
+ "19g8qhfgngdc14cw9k4i44cxhs3qva87x56gjzmn25k1yj8qgsp1"))))
(properties `((upstream-name . "gQTLstats")))
(build-system r-build-system)
(propagated-inputs
@@ -10509,8 +10499,8 @@ defining LD blocks.")
("r-ggplot2" ,r-ggplot2)
("r-gqtlbase" ,r-gqtlbase)
("r-hardyweinberg" ,r-hardyweinberg)
+ ("r-homo-sapiens" ,r-homo-sapiens)
("r-iranges" ,r-iranges)
- ("r-ldblock" ,r-ldblock)
("r-limma" ,r-limma)
("r-mgcv" ,r-mgcv)
("r-plotly" ,r-plotly)
@@ -10533,14 +10523,14 @@ family of feature/genome hypotheses.")
(define-public r-gviz
(package
(name "r-gviz")
- (version "1.22.3")
+ (version "1.24.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Gviz" version))
(sha256
(base32
- "1grjzrjpzkw572pbvpsvdnfkfgwybl0cnjd7nnk2xdr26wnbsi9a"))))
+ "1fhli7ahkl5r43j0hc89ib41mfadj6qyrg36i03ncz8zs6iqwpx4"))))
(properties `((upstream-name . "Gviz")))
(build-system r-build-system)
(propagated-inputs
@@ -10579,14 +10569,14 @@ with your data.")
(define-public r-gwascat
(package
(name "r-gwascat")
- (version "2.10.0")
+ (version "2.12.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "gwascat" version))
(sha256
(base32
- "0n5x5i5v6a8wpn5mxmlpkl34b4kyypmymiwww6g61zch7xqrgywi"))))
+ "08ba9il4vbjjwlbwmqg4ai6ya1p09js9agn95sw0dhc9gqln42hx"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
@@ -10619,13 +10609,13 @@ EMBL-EBI GWAS catalog.")
(define-public r-sushi
(package
(name "r-sushi")
- (version "1.16.0")
+ (version "1.18.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "Sushi" version))
(sha256
(base32
- "0axaqm480z8d0b2ldgxwm0swava1p4irc62bpl17p2k8k78g687g"))))
+ "1m15hmg4k0qhshyn65xfj5hx7xbaf0kxqw70lxisak6pj1w00l41"))))
(properties `((upstream-name . "Sushi")))
(build-system r-build-system)
(propagated-inputs
@@ -10641,13 +10631,13 @@ visualizations for publication-quality multi-panel figures.")
(define-public r-fithic
(package
(name "r-fithic")
- (version "1.4.0")
+ (version "1.6.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "FitHiC" version))
(sha256
(base32
- "12ylhrppi051m7nqsgq95kzd9g9wmp34i0zzfi55cjqawlpx7c6n"))))
+ "06w4q836bi1mvkbl1saghv4r5p4hxpjg8cp7kgad13ls450kqmyd"))))
(properties `((upstream-name . "FitHiC")))
(build-system r-build-system)
(propagated-inputs
@@ -10665,13 +10655,13 @@ assays such as Hi-C.")
(define-public r-hitc
(package
(name "r-hitc")
- (version "1.22.1")
+ (version "1.24.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "HiTC" version))
(sha256
(base32
- "0da1jw9my2n2gihs31zyn14wwr23d8v2vij39ll7rm6fma3ydfbl"))))
+ "0qkk5139f51lwwy1yh7nbkflh5d69prirmhniwam34nlg9rzjm2z"))))
(properties `((upstream-name . "HiTC")))
(build-system r-build-system)
(propagated-inputs
@@ -10694,14 +10684,14 @@ provided.")
(define-public r-qvalue
(package
(name "r-qvalue")
- (version "2.10.0")
+ (version "2.12.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "qvalue" version))
(sha256
(base32
- "1rd9rnf16kh8wc076kahd9hsb9rfwsbzmz3kjmp0pj6rbiq0051i"))))
+ "1ndwkj0hh7v4lwylq1v0fkxqs7mfmbcj8kxbdpj1wkvf131z2ns8"))))
(build-system r-build-system)
(propagated-inputs
`(("r-ggplot2" ,r-ggplot2)
@@ -10723,14 +10713,14 @@ problems in genomics, brain imaging, astrophysics, and data mining.")
(define-public r-hdf5array
(package
(name "r-hdf5array")
- (version "1.6.0")
+ (version "1.8.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "HDF5Array" version))
(sha256
(base32
- "0kcdza41saqv6vlpvqd841awbiwkg84lh0plx6c7fmfgbqv7a0jh"))))
+ "1l0276qxkhgdxsfck3jmi8jvnsr20g10gjki53g0mqa45wnhm3ck"))))
(properties `((upstream-name . "HDF5Array")))
(build-system r-build-system)
(propagated-inputs
@@ -10749,14 +10739,14 @@ block processing.")
(define-public r-rhdf5lib
(package
(name "r-rhdf5lib")
- (version "1.0.0")
+ (version "1.2.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Rhdf5lib" version))
(sha256
(base32
- "0kkc4rprjbqn2wvbx4d49kk9l91vihccxbl4843qr1wqk6v33r1w"))))
+ "1y59acac6v8hrhv84gghn9ifsni9xxxacaj177rrl4frmkrz4x3c"))))
(properties `((upstream-name . "Rhdf5lib")))
(build-system r-build-system)
(arguments
@@ -10767,10 +10757,10 @@ block processing.")
(for-each delete-file '("configure" "configure.ac"))
;; Do not make other packages link with the proprietary libsz.
(substitute* "R/zzz.R"
- (("'%s/libhdf5_cpp.a %s/libhdf5.a %s/libsz.a'")
- "'%s/libhdf5_cpp.a %s/libhdf5.a %s/libhdf5.a'")
- (("'%s/libhdf5.a %s/libsz.a'")
- "'%s/libhdf5.a %s/libhdf5.a'"))
+ (("'%s/libhdf5_cpp.a %s/libhdf5.a %s/libsz.a -lz'")
+ "'%s/libhdf5_cpp.a %s/libhdf5.a %s/libhdf5.a -lz'")
+ (("'%s/libhdf5.a %s/libsz.a -lz'")
+ "'%s/libhdf5.a %s/libhdf5.a -lz'"))
(with-directory-excursion "src"
(invoke "tar" "xvf" (assoc-ref inputs "hdf5-source"))
(rename-file (string-append "hdf5-" ,(package-version hdf5))
@@ -10797,8 +10787,7 @@ block processing.")
(("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n")
;; szip is non-free software
(("cp \\$\\{SZIP_LIB\\}.*") "")
- (("PKG_LIBS = \\$\\{HDF5_LIB\\} \\$\\{SZIP_LIB\\}")
- "PKG_LIBS = ${HDF5_LIB}\n")))
+ (("\\$\\{USER_LIB_DIR\\}libsz.a") "")))
#t)))))
(inputs
`(("zlib" ,zlib)))
@@ -10815,17 +10804,18 @@ packages.")
(define-public r-beachmat
(package
(name "r-beachmat")
- (version "1.0.2")
+ (version "1.2.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "beachmat" version))
(sha256
(base32
- "0b6dzja5fbx4dawb7ixj67mlhw4fy62pfp20mfp918fy96zmdwqz"))))
+ "1w90v0jx1zgrfxzx99gdkk0dz2vi25hr51jml1bvq33i64rj7996"))))
(build-system r-build-system)
(inputs
- `(("hdf5" ,hdf5)))
+ `(("hdf5" ,hdf5)
+ ("zlib" ,zlib)))
(propagated-inputs
`(("r-delayedarray" ,r-delayedarray)
("r-hdf5array" ,r-hdf5array)
@@ -10842,14 +10832,14 @@ matrices.")
(define-public r-singlecellexperiment
(package
(name "r-singlecellexperiment")
- (version "1.0.0")
+ (version "1.2.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "SingleCellExperiment" version))
(sha256
(base32
- "1r276i97w64a5vdlg6952gkj7bls909p42zl8fn8yz87cdwyaars"))))
+ "0mz3chia250v8v6q8r5cqv5fc4bpcw1hhrfr3p7l5i4xi85scpka"))))
(properties
`((upstream-name . "SingleCellExperiment")))
(build-system r-build-system)
@@ -10869,27 +10859,27 @@ libraries.")
(define-public r-scater
(package
(name "r-scater")
- (version "1.6.3")
+ (version "1.8.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "scater" version))
(sha256
(base32
- "0q3s96gf8saa1dq2fvmpl0jyj7bx3wrdfck3hanb8pxkcir2p7dn"))))
+ "0bhpikgz3b9f510dawsay4zry9rlp8vjx5n6zvwbcpwrd94p3903"))))
(build-system r-build-system)
(propagated-inputs
`(("r-beachmat" ,r-beachmat)
("r-biobase" ,r-biobase)
("r-biocgenerics" ,r-biocgenerics)
- ("r-biomart" ,r-biomart)
("r-data-table" ,r-data-table)
+ ("r-delayedarray" ,r-delayedarray)
+ ("r-delayedmatrixstats" ,r-delayedmatrixstats)
("r-dplyr" ,r-dplyr)
("r-edger" ,r-edger)
("r-ggbeeswarm" ,r-ggbeeswarm)
("r-ggplot2" ,r-ggplot2)
("r-limma" ,r-limma)
("r-matrix" ,r-matrix)
- ("r-matrixstats" ,r-matrixstats)
("r-plyr" ,r-plyr)
("r-rcpp" ,r-rcpp)
("r-reshape2" ,r-reshape2)
@@ -10913,19 +10903,21 @@ quality control.")
(define-public r-scran
(package
(name "r-scran")
- (version "1.6.9")
+ (version "1.8.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "scran" version))
(sha256
(base32
- "0cs64cnf0xjcgmawr210y99j3gxs6aqgh8081n9827kkqnx2y5dm"))))
+ "0nbn5x75gf9d0p18w7vpkbv30cpdqvp5bz8xvila0h7jla7xdyih"))))
(build-system r-build-system)
(propagated-inputs
`(("r-beachmat" ,r-beachmat)
("r-biocgenerics" ,r-biocgenerics)
("r-biocparallel" ,r-biocparallel)
+ ("r-delayedarray" ,r-delayedarray)
+ ("r-delayedmatrixstats" ,r-delayedmatrixstats)
("r-dt" ,r-dt)
("r-dynamictreecut" ,r-dynamictreecut)
("r-edger" ,r-edger)
@@ -10942,8 +10934,7 @@ quality control.")
("r-singlecellexperiment" ,r-singlecellexperiment)
("r-statmod" ,r-statmod)
("r-summarizedexperiment" ,r-summarizedexperiment)
- ("r-viridis" ,r-viridis)
- ("r-zoo" ,r-zoo)))
+ ("r-viridis" ,r-viridis)))
(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
@@ -10955,14 +10946,14 @@ variable and significantly correlated genes.")
(define-public r-delayedmatrixstats
(package
(name "r-delayedmatrixstats")
- (version "1.0.3")
+ (version "1.2.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DelayedMatrixStats" version))
(sha256
(base32
- "1cxjbjdq9hg9cm95rci0al7a4pk2h73ym276ahw9q4977zbg6381"))))
+ "1dasghfy8x27zzmd0igag4mc1gxxxbchsl4hpc1050dj3wnw9w3y"))))
(properties
`((upstream-name . "DelayedMatrixStats")))
(build-system r-build-system)
diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index 02d597d82c..e9c8fa443b 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -4188,7 +4188,7 @@ If you want to mark a folder manually as a project just create an empty
(define-public emacs-elfeed
(package
(name "emacs-elfeed")
- (version "2.3.0")
+ (version "3.0.0")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/skeeto/elfeed/archive/"
@@ -4196,7 +4196,7 @@ If you want to mark a folder manually as a project just create an empty
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "1fd1mx0q1qb9vgdzls5ppxfriyid48blg8smgjspiazp7kxakzxv"))))
+ "1wkdrxr6zzqb48czqqv34l87bx8aqjk1739ddqg933aqh241kfvn"))))
(build-system emacs-build-system)
(arguments
`(#:tests? #t
diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm
index a9ee949855..b393919e66 100644
--- a/gnu/packages/graph.scm
+++ b/gnu/packages/graph.scm
@@ -155,14 +155,14 @@ model.")
(define-public r-rgraphviz
(package
(name "r-rgraphviz")
- (version "2.22.0")
+ (version "2.24.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Rgraphviz" version))
(sha256
(base32
- "1y9nyjffa9644jch0p2i3w302fmnyc2kb0c3z1f3d5zp1p4qmyqv"))))
+ "1037hzfxxcn46w6y88wm3kk2nixj0s8bk0hkmnshpxih3kmnvqby"))))
(properties `((upstream-name . "Rgraphviz")))
(build-system r-build-system)
;; FIXME: Rgraphviz bundles the sources of an older variant of
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 434f26dbe3..3996eb91e4 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -113,10 +113,10 @@ be output in text, PostScript, PDF or HTML.")
;; Update this package together with the set of recommended packages: r-boot,
;; r-class, r-cluster, r-codetools, r-foreign, r-kernsmooth, r-lattice,
;; r-mass, r-matrix, r-mgcv, r-nlme, r-nnet, r-rpart, r-spatial, r-survival.
-(define-public r-minimal
+(define r-with-tests
(package
- (name "r-minimal")
- (version "3.4.4")
+ (name "r-with-tests")
+ (version "3.5.0")
(source (origin
(method url-fetch)
(uri (string-append "mirror://cran/src/base/R-"
@@ -124,7 +124,7 @@ be output in text, PostScript, PDF or HTML.")
version ".tar.gz"))
(sha256
(base32
- "0dq3jsnwsb5j3fhl0wi3p5ycv8avf8s5j1y4ap3d2mkjmcppvsdk"))))
+ "0w38865laqg28cdhikxdxhx4rfp0kgcn72gakwypsy91br9ja5zx"))))
(build-system gnu-build-system)
(arguments
`(#:disallowed-references (,tzdata-for-tests)
@@ -217,11 +217,9 @@ as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\
(add-after 'build 'install-info
(lambda _ (zero? (system* "make" "install-info")))))
#:configure-flags
- `(;; Do not build the recommended packages. The build system creates
- ;; random temporary directories and embeds their names in some
- ;; package files. We build these packages with the r-build-system
- ;; instead.
- "--without-recommended-packages"
+ `(;; We build the recommended packages here, because they are needed in
+ ;; order to run the test suite. We disable them in the r-minimal
+ ;; package.
"--with-cairo"
"--with-blas=-lopenblas"
"--with-libpng"
@@ -292,6 +290,19 @@ publication-quality data plots. A large amount of 3rd-party packages are
available, greatly increasing its breadth and scope.")
(license license:gpl3+)))
+(define-public r-minimal
+ (package (inherit r-with-tests)
+ (name "r-minimal")
+ (arguments
+ `(#:tests? #f
+ ,@(substitute-keyword-arguments (package-arguments r-with-tests)
+ ((#:configure-flags flags)
+ ;; Do not build the recommended packages. The build system creates
+ ;; random temporary directories and embeds their names in some
+ ;; package files. We build these packages with the r-build-system
+ ;; instead.
+ `(cons "--without-recommended-packages" ,flags)))))))
+
(define-public rmath-standalone
(package (inherit r-minimal)
(name "rmath-standalone")
@@ -3522,13 +3533,13 @@ vignettes.")
(define-public r-mvtnorm
(package
(name "r-mvtnorm")
- (version "1.0-7")
+ (version "1.0-8")
(source (origin
(method url-fetch)
(uri (cran-uri "mvtnorm" version))
(sha256
(base32
- "0f7hzflygdnbwvzadr3knhybhanwg7agqddclj6mhbvwqpgb0qyh"))))
+ "0la42lylb7cjrcrc285bn69bz9kyg556xw317iz139dp1yswl410"))))
(build-system r-build-system)
(inputs
`(("gfortran" ,gfortran)))
generated by cgit v1.2.3 (git 2.45.0) at 2024-11-23 09:40:13 +0000