From: zimoun <zimon.toutoune@gmail.com>
To: 48575@debbugs.gnu.org.
Cc: zimoun <zimon.toutoune@gmail.com>
Subject: [bug#48575] [PATCH 39/50] gnu: r-rhtslib: Move to (gnu packages bioconductor).
Date: Fri, 21 May 2021 22:26:11 +0200 [thread overview]
Message-ID: <20210521202622.26591-39-zimon.toutoune@gmail.com> (raw)
In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com>
* gnu/packages/bioinformatics.scm (r-rhtslib): Move from here...
* gnu/packages/bioconductor.scm (r-rhtslib): ...to here.
---
gnu/packages/bioconductor.scm | 32 ++++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 31 -------------------------------
2 files changed, 32 insertions(+), 31 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index e720d7bf6a..8e78a2a0ca 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -39,6 +39,7 @@
#:use-module (gnu packages boost)
#:use-module (gnu packages cran)
#:use-module (gnu packages compression)
+ #:use-module (gnu packages curl)
#:use-module (gnu packages gcc)
#:use-module (gnu packages graph)
#:use-module (gnu packages graphviz)
@@ -2832,6 +2833,37 @@ Enrichment Analysis} (GSEA).")
the Human Protein Atlas project.")
(license license:artistic2.0)))
+(define-public r-rhtslib
+ (package
+ (name "r-rhtslib")
+ (version "1.22.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "Rhtslib" version))
+ (sha256
+ (base32
+ "18wag2jnpda6078xjkpfdvar1gkb2myhw83gg03l39sabh35qya4"))))
+ (properties `((upstream-name . "Rhtslib")))
+ (build-system r-build-system)
+ ;; Without this a temporary directory ends up in the Rhtslib.so binary,
+ ;; which makes R abort the build.
+ (arguments '(#:configure-flags '("--no-staged-install")))
+ (propagated-inputs
+ `(("curl" ,curl)
+ ("zlib" ,zlib) ; packages using rhtslib need to link with zlib
+ ("r-zlibbioc" ,r-zlibbioc)))
+ (native-inputs
+ `(("pkg-config" ,pkg-config)
+ ("r-knitr" ,r-knitr)))
+ (home-page "https://github.com/nhayden/Rhtslib")
+ (synopsis "High-throughput sequencing library as an R package")
+ (description
+ "This package provides the HTSlib C library for high-throughput
+nucleotide sequence analysis. The package is primarily useful to developers
+of other R packages who wish to make use of HTSlib.")
+ (license license:lgpl2.0+)))
+
(define-public r-impute
(package
(name "r-impute")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 39c437f4a2..586efcf21e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7872,37 +7872,6 @@ including VCF header and contents in RDF and JSON.")
secondary structure and comparative analysis in R.")
(license license:gpl3+)))
-(define-public r-rhtslib
- (package
- (name "r-rhtslib")
- (version "1.22.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "Rhtslib" version))
- (sha256
- (base32
- "18wag2jnpda6078xjkpfdvar1gkb2myhw83gg03l39sabh35qya4"))))
- (properties `((upstream-name . "Rhtslib")))
- (build-system r-build-system)
- ;; Without this a temporary directory ends up in the Rhtslib.so binary,
- ;; which makes R abort the build.
- (arguments '(#:configure-flags '("--no-staged-install")))
- (propagated-inputs
- `(("curl" ,curl)
- ("zlib" ,zlib) ; packages using rhtslib need to link with zlib
- ("r-zlibbioc" ,r-zlibbioc)))
- (native-inputs
- `(("pkg-config" ,pkg-config)
- ("r-knitr" ,r-knitr)))
- (home-page "https://github.com/nhayden/Rhtslib")
- (synopsis "High-throughput sequencing library as an R package")
- (description
- "This package provides the HTSlib C library for high-throughput
-nucleotide sequence analysis. The package is primarily useful to developers
-of other R packages who wish to make use of HTSlib.")
- (license license:lgpl2.0+)))
-
(define-public r-bamsignals
(package
(name "r-bamsignals")
--
2.30.1
next prev parent reply other threads:[~2021-05-21 20:33 UTC|newest]
Thread overview: 52+ messages / expand[flat|nested] mbox.gz Atom feed top
2021-05-21 20:21 [bug#48575] [PATCH 00/50] Move some Bioconductor packages to (gnu packages bioconductor) zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 01/50] gnu: r-genomicalignments: Move " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 02/50] gnu: r-rtracklayer: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 03/50] gnu: r-genomicfeatures: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 04/50] gnu: r-topgo: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 05/50] gnu: r-bsgenome: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 06/50] gnu: r-msnid: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 07/50] gnu: r-msnbase: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 08/50] gnu: r-samr: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 09/50] gnu: r-impute: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 10/50] gnu: r-seqpattern: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 11/50] gnu: r-go-db: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 12/50] gnu: r-genomation: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 13/50] gnu: r-genomationdata: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 14/50] gnu: r-pcamethods: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 15/50] gnu: r-mzid: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 16/50] gnu: r-aroma-light: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 17/50] gnu: r-deseq: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 18/50] gnu: r-edaseq: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 19/50] gnu: r-interactivedisplaybase: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 20/50] gnu: r-annotationhub: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 21/50] gnu: r-fastseg: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 22/50] gnu: r-affy: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 23/50] gnu: r-keggrest: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 24/50] gnu: r-gage: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 25/50] gnu: r-complexheatmap: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 26/50] gnu: r-genomicfiles: " zimoun
2021-05-21 20:25 ` [bug#48575] [PATCH 27/50] gnu: r-dirichletmultinomial: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 28/50] gnu: r-organismdbi: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 29/50] gnu: r-affyio: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 30/50] gnu: r-vsn: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 31/50] gnu: r-biovizbase: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 32/50] gnu: r-ensembldb: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 33/50] gnu: r-mzr: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 34/50] gnu: r-protgenerics: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 35/50] gnu: r-sva: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 36/50] gnu: r-motifrg: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 37/50] gnu: r-seqlogo: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 38/50] gnu: r-zlibbioc: " zimoun
2021-05-21 20:26 ` zimoun [this message]
2021-05-21 20:26 ` [bug#48575] [PATCH 40/50] gnu: r-bamsignals: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 41/50] gnu: r-rcas: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 42/50] gnu: r-mutationalpatterns: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 43/50] gnu: r-tximport: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 44/50] gnu: r-rhdf5filters: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 45/50] gnu: r-annotationfilter: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 46/50] gnu: r-rhdf5: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 47/50] gnu: r-chipseq: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 48/50] gnu: r-copyhelper: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 49/50] gnu: r-copywriter: " zimoun
2021-05-21 20:26 ` [bug#48575] [PATCH 50/50] gnu: r-methylkit: " zimoun
2021-05-31 14:07 ` bug#48575: [PATCH 00/50] Move some Bioconductor packages " Ricardo Wurmus
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