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322/323: gnu: r-rhtslib: Propagate zlib.
From: |
guix-commits |
Subject: |
322/323: gnu: r-rhtslib: Propagate zlib. |
Date: |
Wed, 9 Dec 2020 06:48:04 -0500 (EST) |
rekado pushed a commit to branch master
in repository guix.
commit 4617cc7fd509cc73703e5b273c634f995bb69a5d
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Mon Dec 7 16:44:23 2020 +0100
gnu: r-rhtslib: Propagate zlib.
* 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.
---
gnu/packages/bioconductor.scm | 12 ------------
gnu/packages/bioinformatics.scm | 13 +------------
2 files changed, 1 insertion(+), 24 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 5f524f3..5a3d638 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1726,8 +1726,6 @@ signal in the input, that lead to spurious peaks during
peak calling.")
"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 @@ index.")
"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 @@ cluster count and membership by stability evidence in
unsupervised analysis.")
(("\\(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 @@ change point detection.")
(("\\(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 @@ for other R packages to compile and link against.")
(("\\{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 @@ with multiple R processes supported by the package
@code{parallel}.")
`(("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
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 9cf5c0a..9edf75a 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7980,8 +7980,6 @@ CAGE.")
"1sl0l6v05lfglj281nszma0h5k234md7rn2pdah8vs2d4iq3kimw"))))
(properties
`((upstream-name . "VariantAnnotation")))
- (inputs
- `(("zlib" ,zlib)))
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
("r-biobase" ,r-biobase)
@@ -8260,8 +8258,6 @@ biological sequences or sets of sequences.")
(substitute* "NAMESPACE"
(("import\\(zlibbioc\\)") ""))
#t)))))
- (inputs
- `(("zlib" ,zlib)))
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
("r-biocparallel" ,r-biocparallel)
@@ -8794,9 +8790,8 @@ secondary structure and comparative analysis in R.")
(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 @@ of other R packages who wish to make use of HTSlib.")
("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 @@ HDF5 datasets.")
(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 @@ number detection tools.")
("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")
- 284/323: gnu: r-ggbio: Update to 1.38.0., (continued)
- 284/323: gnu: r-ggbio: Update to 1.38.0., guix-commits, 2020/12/09
- 272/323: gnu: r-edaseq: Update to 2.24.0., guix-commits, 2020/12/09
- 296/323: gnu: r-genomicinteractions: Update to 1.24.0., guix-commits, 2020/12/09
- 292/323: gnu: Add r-bluster., guix-commits, 2020/12/09
- 297/323: gnu: r-biocsingular: Update to 1.6.0., guix-commits, 2020/12/09
- 307/323: gnu: r-pcatools: Update to 2.2.0., guix-commits, 2020/12/09
- 309/323: gnu: r-scdd: Update to 1.14.0., guix-commits, 2020/12/09
- 314/323: gnu: r-lumi: Update to 2.42.0., guix-commits, 2020/12/09
- 318/323: gnu: r-bigmelon: Update to 1.16.0., guix-commits, 2020/12/09
- 319/323: gnu: r-gqtlbase: Update to 1.21.1., guix-commits, 2020/12/09
- 322/323: gnu: r-rhtslib: Propagate zlib.,
guix-commits <=
- 182/323: gnu: r-experimenthub: Update to 1.16.0., guix-commits, 2020/12/09
- 186/323: gnu: r-biocpkgtools: Update to 1.8.0., guix-commits, 2020/12/09
- 220/323: gnu: r-category: Update to 2.56.0., guix-commits, 2020/12/09
- 231/323: gnu: r-genomicranges: Update to 1.42.0., guix-commits, 2020/12/09
- 234/323: gnu: r-biomart: Update to 2.46.0., guix-commits, 2020/12/09
- 235/323: gnu: r-biocparallel: Update to 1.24.1., guix-commits, 2020/12/09
- 242/323: gnu: r-genomicfeatures: Update to 1.42.1., guix-commits, 2020/12/09
- 198/323: gnu: r-fithic: Update to 1.16.0., guix-commits, 2020/12/09
- 171/323: gnu: r-biggr: Update to 1.26.0., guix-commits, 2020/12/09
- 178/323: gnu: r-reactomepa: Update to 1.34.0., guix-commits, 2020/12/09