(define-public r-biocviews
(package
(name "r-biocviews")
- (version "1.58.0")
+ (version "1.58.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "biocViews" version))
(sha256
(base32
- "0f0aa51h9x8n114zz6q6iw45d78i9wzl4ycbpiy0bdn23167pd84"))))
+ "1by2639z7n62z84dr8rj9jz12gsd1k8q42zsnxacxbwfwp6h0cl4"))))
(properties
`((upstream-name . "biocViews")))
(build-system r-build-system)
(define-public r-biocstyle
(package
(name "r-biocstyle")
- (version "2.18.0")
+ (version "2.18.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BiocStyle" version))
(sha256
(base32
- "1hfdvld0n9py45mxm05kbb0sq0s9p8yky3s6jb02gzhlxkk3q4fs"))))
+ "0rsxyna4dd99x42vc82mlkxx774vb9375llpakg53max1hhwkrqp"))))
(properties
`((upstream-name . "BiocStyle")))
(build-system r-build-system)
(define-public r-genomeinfodb
(package
(name "r-genomeinfodb")
- (version "1.26.0")
+ (version "1.26.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomeInfoDb" version))
(sha256
(base32
- "1xfhz7gmccijy2z015w07lh04g0ijh7zi6k7q6m4lripgban93g9"))))
+ "092izc49maxjhf6m4b0qx21ad16dz7bmxy5pysp3vkyhdrfa2f7v"))))
(properties
`((upstream-name . "GenomeInfoDb")))
(build-system r-build-system)
"1sl0l6v05lfglj281nszma0h5k234md7rn2pdah8vs2d4iq3kimw"))))
(properties
`((upstream-name . "VariantAnnotation")))
- (inputs
- `(("zlib" ,zlib)))
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
("r-biobase" ,r-biobase)
(substitute* "NAMESPACE"
(("import\\(zlibbioc\\)") ""))
#t)))))
- (inputs
- `(("zlib" ,zlib)))
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
("r-biocparallel" ,r-biocparallel)
(define-public r-genomationdata
(package
(name "r-genomationdata")
- (version "1.14.0")
+ (version "1.22.0")
(source (origin
(method url-fetch)
;; We cannot use bioconductor-uri here because this tarball is
"genomationData_" version ".tar.gz"))
(sha256
(base32
- "10xyb8akjrhmak2i0mnv1agny2ipy364q9nlibyplpzc7vdb6bw7"))))
+ "0igjsvfnws3498j65ifniw0kbxfqpfr59rcjddqvq4zsj453fx1g"))))
(build-system r-build-system)
;; As this package provides little more than large data files, it doesn't
;; make sense to build substitutes.
(arguments '(#:configure-flags '("--no-staged-install")))
(propagated-inputs
`(("curl" ,curl)
+ ("zlib" ,zlib) ; packages using rhtslib need to link with zlib
("r-zlibbioc" ,r-zlibbioc)))
- (inputs
- `(("zlib" ,zlib)))
(native-inputs
`(("pkg-config" ,pkg-config)
("r-knitr" ,r-knitr)))
("r-rcpp" ,r-rcpp)
("r-rhtslib" ,r-rhtslib)
("r-zlibbioc" ,r-zlibbioc)))
- (inputs
- `(("zlib" ,zlib)))
(native-inputs
`(("r-knitr" ,r-knitr)))
(home-page "https://bioconductor.org/packages/bamsignals")
of gene-level counts.")
(license license:gpl2+)))
+(define-public r-rhdf5filters
+ (package
+ (name "r-rhdf5filters")
+ (version "1.2.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "rhdf5filters" version))
+ (sha256
+ (base32
+ "1jvnss44liapbc6hk93yg1gknv0ahd5x86dydqiwq9l65jd03psq"))))
+ (properties `((upstream-name . "rhdf5filters")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-rhdf5lib" ,r-rhdf5lib)))
+ (inputs
+ `(("zlib" ,zlib)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://github.com/grimbough/rhdf5filters")
+ (synopsis "HDF5 compression filters")
+ (description
+ "This package provides a collection of compression filters for use with
+HDF5 datasets.")
+ (license license:bsd-2)))
+
(define-public r-rhdf5
(package
(name "r-rhdf5")
- (version "2.32.3")
+ (version "2.34.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "rhdf5" version))
(sha256
(base32
- "0fnx60dpf6s2qwq48lg98g18g8k7wgm66pw0kamlbb7l2hnwycvf"))))
+ "0almr1vscrgj5g4dyrags131wia2pmdbdidlpskbgm44ha6hpmqi"))))
(build-system r-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'fix-linking
+ (lambda _
+ (substitute* "src/Makevars"
+ ;; This is to avoid having a plain directory on the list of
+ ;; libraries to link.
+ (("\\(RHDF5_LIBS\\)" match)
+ (string-append match "/libhdf5.a")))
+ #t)))))
(propagated-inputs
- `(("r-rhdf5lib" ,r-rhdf5lib)))
- (inputs
- `(("zlib" ,zlib)))
+ `(("r-rhdf5filters" ,r-rhdf5filters)
+ ("r-rhdf5lib" ,r-rhdf5lib)))
(native-inputs
`(("r-knitr" ,r-knitr)))
(home-page "https://bioconductor.org/packages/rhdf5")
("r-zlibbioc" ,r-zlibbioc)))
(native-inputs
`(("r-knitr" ,r-knitr))) ; for vignettes
- (inputs
- `(("zlib" ,zlib)))
(home-page "https://github.com/al2na/methylKit")
(synopsis
"DNA methylation analysis from high-throughput bisulfite sequencing results")
(define-public r-keggrest
(package
(name "r-keggrest")
- (version "1.30.0")
+ (version "1.30.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "KEGGREST" version))
(sha256
(base32
- "0awg0hmxj25rpmqyf6jz6kbkswmimz3h352xx15xhkamwcxykng6"))))
+ "0k9z85xf9la2y98xqmdmjb8mci9fh2fdybkl77x1yl26hyalip0s"))))
(properties `((upstream-name . "KEGGREST")))
(build-system r-build-system)
(propagated-inputs
(define-public r-gqtlbase
(package
(name "r-gqtlbase")
- (version "1.20.4")
+ (version "1.21.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "gQTLBase" version))
(sha256
(base32
- "1ly14vhhqxjpbxjypi6ppd37dycabdhf4ny4nsvp9969k418zv41"))))
+ "0nipibm1bk9k70ajbw1f6vjmz0dh7gk21l17q3m54bnawxsggrfh"))))
(properties `((upstream-name . "gQTLBase")))
(build-system r-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ ;; This is an upstream bug.
+ (add-after 'unpack 'fix-imports
+ (lambda _
+ (substitute* "NAMESPACE"
+ ((".*maxffmode.*") "")
+ (("importFrom\\(ff,.*") "import(ff)\n"))
+ #t)))))
(propagated-inputs
`(("r-batchjobs" ,r-batchjobs)
("r-bbmisc" ,r-bbmisc)
(define-public r-snpstats
(package
(name "r-snpstats")
- (version "1.38.0")
+ (version "1.40.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "snpStats" version))
(sha256
(base32
- "1qv3nqqr30d3n66mawqd9dbl95dl89r4bcjvkc5iassy1yrwr8wq"))))
+ "1298a71swwav53yf9kfqkdpach3818plqcbw0lgb6sibs8y8ff24"))))
(properties `((upstream-name . "snpStats")))
(build-system r-build-system)
(inputs `(("zlib" ,zlib)))
(define-public r-erma
(package
(name "r-erma")
- (version "1.4.0")
+ (version "1.6.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "erma" version))
(sha256
(base32
- "1ccfbq0r48sr3h8050w8zv8402h7nx09adr0xdyqlg7kwp9vd2l3"))))
+ "1k2j1xhv0vwn45xmh8ds0gz812px5hnpgzvp37ngsdn4j5ai1l0k"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
(define-public r-ldblock
(package
(name "r-ldblock")
- (version "1.18.0")
+ (version "1.20.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ldblock" version))
(sha256
(base32
- "0plw00n2zfgh029ab41dnydzgv2yxrapjp770147rx9pff4dngrv"))))
+ "09i3ikv0axks9g842z1pjsc8x0fba51zyyc218h0bylbi1n9cdkm"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
(define-public r-gqtlstats
(package
(name "r-gqtlstats")
- (version "1.20.0")
+ (version "1.21.3")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "gQTLstats" version))
(sha256
(base32
- "1jjqfpjp93nmxjn757j5mzcax96bzcqdd1gr3rsdxg7ap008l2w7"))))
+ "1h78l23idf867djmdk97b02jxgmz4vfr2dai01fp648d0lsx5mkl"))))
(properties `((upstream-name . "gQTLstats")))
(build-system r-build-system)
(propagated-inputs
(define-public r-gviz
(package
(name "r-gviz")
- (version "1.32.0")
+ (version "1.34.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Gviz" version))
(sha256
(base32
- "0cgkp0ciyy2qykqgh3vzp5mx9b4vsvacjh2jnsj3wldiapzlz08a"))))
+ "0v7bz46b91dnrr55ah42ljj1i2xs3090s4w0lw8098pag00p4vh2"))))
(properties `((upstream-name . "Gviz")))
(build-system r-build-system)
(propagated-inputs
(define-public r-gwascat
(package
(name "r-gwascat")
- (version "2.20.1")
+ (version "2.22.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "gwascat" version))
(sha256
(base32
- "1cq5cmdrf0a0arr841yvkh6d8drc15p7mif1afr215l1s3y2dwd4"))))
+ "1aqi1ny93virnzsxkh9ccx3mws70bgv0r8nwgla09vffb7f16nna"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
- ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocfilecache" ,r-biocfilecache)
("r-biostrings" ,r-biostrings)
("r-genomeinfodb" ,r-genomeinfodb)
("r-genomicfeatures" ,r-genomicfeatures)
("r-genomicranges" ,r-genomicranges)
- ("r-ggplot2" ,r-ggplot2)
("r-iranges" ,r-iranges)
- ("r-rsamtools" ,r-rsamtools)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)))
+ ("r-readr" ,r-readr)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-snpstats" ,r-snpstats)
+ ("r-variantannotation" ,r-variantannotation)))
(native-inputs
`(("r-knitr" ,r-knitr)))
(home-page "https://bioconductor.org/packages/gwascat")
(define-public r-sushi
(package
(name "r-sushi")
- (version "1.26.0")
+ (version "1.28.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "Sushi" version))
(sha256
(base32
- "17j3d5qjq5nbv99by5mq8rwr0jgh2jyyfn2nwxmwgzlmk3lgi1rb"))))
+ "0ksj4f9z14mjsv6ssg5dwhpldw4r7wpdsln2if5g486mm1c56r8p"))))
(properties `((upstream-name . "Sushi")))
(build-system r-build-system)
(propagated-inputs