GNU bug report logs - #47171
[PATCH 00/10] Move some Bioconductor packages to (gnu packages bioconductor).

Previous Next

Full log

Message #23 received at 47171 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: 47171 <at> debbugs.gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 06/10] gnu: r-biomart: Move to (gnu packages bioconductor).
Date: Mon, 15 Mar 2021 19:09:00 +0100

* gnu/packages/bioinformatics.scm (r-biomart): Move from here...
* gnu/packages/bioconductor.scm (r-biomart): ...to here.
---
 gnu/packages/bioconductor.scm   | 38 +++++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 38 ---------------------------------
 2 files changed, 38 insertions(+), 38 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 2ae212dfac..897e85dfe3 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1621,6 +1621,44 @@ databases.  Packages produced are intended to be used with AnnotationDbi.")
 on Bioconductor or which replace R functions.")
     (license license:artistic2.0)))
 
+(define-public r-biomart
+  (package
+    (name "r-biomart")
+    (version "2.46.3")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "biomaRt" version))
+              (sha256
+               (base32
+                "0gwmd0ykpv0gyh34c56g5m12lil20fvig49f3ih1jxrxf3q4wmq7"))))
+    (properties
+     `((upstream-name . "biomaRt")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-biocfilecache" ,r-biocfilecache)
+       ("r-httr" ,r-httr)
+       ("r-openssl" ,r-openssl)
+       ("r-progress" ,r-progress)
+       ("r-rappdirs" ,r-rappdirs)
+       ("r-stringr" ,r-stringr)
+       ("r-xml" ,r-xml)
+       ("r-xml2" ,r-xml2)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/biomaRt")
+    (synopsis "Interface to BioMart databases")
+    (description
+     "biomaRt provides an interface to a growing collection of databases
+implementing the @url{BioMart software suite, http://www.biomart.org}.  The
+package enables retrieval of large amounts of data in a uniform way without
+the need to know the underlying database schemas or write complex SQL queries.
+Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene,
+Wormbase and dbSNP mapped to Ensembl.  These major databases give biomaRt
+users direct access to a diverse set of data and enable a wide range of
+powerful online queries from gene annotation to database mining.")
+    (license license:artistic2.0)))
+
 (define-public r-category
   (package
     (name "r-category")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a45196bc5b..289a96f572 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7691,44 +7691,6 @@ including VCF header and contents in RDF and JSON.")
     (home-page "https://github.com/vcflib/bio-vcf")
     (license license:expat)))
 
-(define-public r-biomart
-  (package
-    (name "r-biomart")
-    (version "2.46.3")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "biomaRt" version))
-              (sha256
-               (base32
-                "0gwmd0ykpv0gyh34c56g5m12lil20fvig49f3ih1jxrxf3q4wmq7"))))
-    (properties
-     `((upstream-name . "biomaRt")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-biocfilecache" ,r-biocfilecache)
-       ("r-httr" ,r-httr)
-       ("r-openssl" ,r-openssl)
-       ("r-progress" ,r-progress)
-       ("r-rappdirs" ,r-rappdirs)
-       ("r-stringr" ,r-stringr)
-       ("r-xml" ,r-xml)
-       ("r-xml2" ,r-xml2)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/biomaRt")
-    (synopsis "Interface to BioMart databases")
-    (description
-     "biomaRt provides an interface to a growing collection of databases
-implementing the @url{BioMart software suite, http://www.biomart.org}.  The
-package enables retrieval of large amounts of data in a uniform way without
-the need to know the underlying database schemas or write complex SQL queries.
-Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene,
-Wormbase and dbSNP mapped to Ensembl.  These major databases give biomaRt
-users direct access to a diverse set of data and enable a wide range of
-powerful online queries from gene annotation to database mining.")
-    (license license:artistic2.0)))
-
 (define-public r-biocparallel
   (package
     (name "r-biocparallel")
-- 
2.30.1

Previous Next

GNU bug tracking system
Copyright (C) 1999 Darren O. Benham, 1997,2003 nCipher Corporation Ltd, 1994-97 Ian Jackson.