From: zimoun <zimon.toutoune@gmail.com>
To: 48575@debbugs.gnu.org.
Cc: zimoun <zimon.toutoune@gmail.com>
Subject: [bug#48575] [PATCH 46/50] gnu: r-rhdf5: Move to (gnu packages bioconductor).
Date: Fri, 21 May 2021 22:26:18 +0200 [thread overview]
Message-ID: <20210521202622.26591-46-zimon.toutoune@gmail.com> (raw)
In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com>
* gnu/packages/bioinformatics.scm (r-rhdf5): Move from here...
* gnu/packages/bioconductor.scm (r-rhdf5): ...to here.
---
gnu/packages/bioconductor.scm | 39 +++++++++++++++++++++++++++++++++
gnu/packages/bioinformatics.scm | 39 ---------------------------------
2 files changed, 39 insertions(+), 39 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 87b879ad94..d027a24bf3 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3508,6 +3508,45 @@ reports together for a particular project that can be viewed in a web
browser.")
(license license:artistic2.0)))
+(define-public r-rhdf5
+ (package
+ (name "r-rhdf5")
+ (version "2.34.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "rhdf5" version))
+ (sha256
+ (base32
+ "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-rhdf5filters" ,r-rhdf5filters)
+ ("r-rhdf5lib" ,r-rhdf5lib)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/rhdf5")
+ (synopsis "HDF5 interface to R")
+ (description
+ "This R/Bioconductor package provides an interface between HDF5 and R.
+HDF5's main features are the ability to store and access very large and/or
+complex datasets and a wide variety of metadata on mass storage (disk) through
+a completely portable file format. The rhdf5 package is thus suited for the
+exchange of large and/or complex datasets between R and other software
+package, and for letting R applications work on datasets that are larger than
+the available RAM.")
+ (license license:artistic2.0)))
+
(define-public r-rhdf5filters
(package
(name "r-rhdf5filters")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 7ad51d3518..ef0d7b3007 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7990,45 +7990,6 @@ bound and non bound genomic regions to accurately identify transcription
factors bound at the specific regions.")
(license license:gpl2+)))
-(define-public r-rhdf5
- (package
- (name "r-rhdf5")
- (version "2.34.0")
- (source (origin
- (method url-fetch)
- (uri (bioconductor-uri "rhdf5" version))
- (sha256
- (base32
- "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-rhdf5filters" ,r-rhdf5filters)
- ("r-rhdf5lib" ,r-rhdf5lib)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://bioconductor.org/packages/rhdf5")
- (synopsis "HDF5 interface to R")
- (description
- "This R/Bioconductor package provides an interface between HDF5 and R.
-HDF5's main features are the ability to store and access very large and/or
-complex datasets and a wide variety of metadata on mass storage (disk) through
-a completely portable file format. The rhdf5 package is thus suited for the
-exchange of large and/or complex datasets between R and other software
-package, and for letting R applications work on datasets that are larger than
-the available RAM.")
- (license license:artistic2.0)))
-
(define-public emboss
(package
(name "emboss")
--
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 ` [bug#48575] [PATCH 39/50] gnu: r-rhtslib: " zimoun
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 ` zimoun [this message]
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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