(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)
(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")
(propagated-inputs
`(("r-rhdf5filters" ,r-rhdf5filters)
("r-rhdf5lib" ,r-rhdf5lib)))
- (inputs
- `(("zlib" ,zlib)))
(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-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