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gnu: r-rhtslib: Propagate zlib.

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* gnu/packages/bioinformatics.scm (r-rhtslib)[inputs]: Move zlib from here...
[propagated-inputs]: ...to here.
(r-variantannotation, r-rsamtools, r-bamsignals, r-rhdf5,
r-methylkit)[inputs]: Remove zlib.
* gnu/packages/bioconductor.scm (r-diffbind, r-quasr, r-cytolib, r-ncdfflow,
r-flowworkspace, r-seqbias)[inputs]: Remove zlib.
This commit is contained in:
Ricardo Wurmus 2020-12-07 16:44:23 +01:00
parent 7601015fc9
commit 4617cc7fd5
No known key found for this signature in database
GPG key ID: 197A5888235FACAC
2 changed files with 1 additions and 24 deletions
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12
gnu/packages/bioconductor.scm
View file

@ -1726,8 +1726,6 @@ (define-public r-diffbind
"0irhqsi6rrkrkc7dhwmfpqfd0mnigs17027czcx8vgbrbra4lcvd"))))
(properties `((upstream-name . "DiffBind")))
(build-system r-build-system)
(inputs
`(("zlib" ,zlib)))
(propagated-inputs
`(("r-amap" ,r-amap)
("r-apeglm" ,r-apeglm)
@ -5664,8 +5662,6 @@ (define-public r-quasr
"032m01q34nnmvbhcb2g3pz2fqmgcw5464m74m1m0h7x9bl04a5k8"))))
(properties `((upstream-name . "QuasR")))
(build-system r-build-system)
(inputs
`(("zlib" ,zlib)))
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
("r-biobase" ,r-biobase)
@ -6049,8 +6045,6 @@ (define-public r-cytolib
(("\\(RHDF5_LIBS\\)" match)
(string-append match "/libhdf5.a")))
#t)))))
(inputs
`(("zlib" ,zlib)))
(native-inputs
`(("r-knitr" ,r-knitr)
("pkg-config" ,pkg-config)))
@ -6150,8 +6144,6 @@ (define-public r-ncdfflow
(("\\(RHDF5_LIBS\\)" match)
(string-append match "/libhdf5.a")))
#t)))))
(inputs
`(("zlib" ,zlib)))
(propagated-inputs
`(("r-bh" ,r-bh)
("r-biobase" ,r-biobase)
@ -6332,8 +6324,6 @@ (define-public r-flowworkspace
(("\\{h5lib\\}" match)
(string-append match "/libhdf5.a")))
#t)))))
(inputs
`(("zlib" ,zlib)))
(propagated-inputs
`(("r-aws-s3" ,r-aws-s3)
("r-aws-signature" ,r-aws-signature)
@ -6997,8 +6987,6 @@ (define-public r-seqbias
`(("r-biostrings" ,r-biostrings)
("r-genomicranges" ,r-genomicranges)
("r-rhtslib" ,r-rhtslib)))
(inputs
`(("zlib" ,zlib))) ; This comes from rhtslib.
(home-page "https://bioconductor.org/packages/seqbias/")
(synopsis "Estimation of per-position bias in high-throughput sequencing data")
(description

13
gnu/packages/bioinformatics.scm
View file

@ -7980,8 +7980,6 @@ (define-public r-variantannotation
"1sl0l6v05lfglj281nszma0h5k234md7rn2pdah8vs2d4iq3kimw"))))
(properties
`((upstream-name . "VariantAnnotation")))
(inputs
`(("zlib" ,zlib)))
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
("r-biobase" ,r-biobase)
@ -8260,8 +8258,6 @@ (define-public r-rsamtools
(substitute* "NAMESPACE"
(("import\\(zlibbioc\\)") ""))
#t)))))
(inputs
`(("zlib" ,zlib)))
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
("r-biocparallel" ,r-biocparallel)
@ -8794,9 +8790,8 @@ (define-public r-rhtslib
(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)))
@ -8827,8 +8822,6 @@ (define-public r-bamsignals
("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")
@ -9127,8 +9120,6 @@ (define-public r-rhdf5
(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")
@ -9616,8 +9607,6 @@ (define-public r-methylkit
("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")