GNU bug report logs - #47156
[PATCH 00/10] Move some Bioconductor packages to (gnu packages bioconductor).

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Message #29 received at 47156 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: 47156 <at> debbugs.gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 07/10] gnu: r-genomeinfodbdata: Move to (gnu packages
 bioconductor).
Date: Mon, 15 Mar 2021 14:01:32 +0100

* gnu/packages/bioinformatics.scm (r-genomeinfodbdata): Move from here...
* gnu/packages/bioconductor.scm (r-genomeinfodbdata): ...to here.
[source]: Use 'bioconductor-uri'.
---
 gnu/packages/bioconductor.scm   | 20 ++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 23 -----------------------
 2 files changed, 20 insertions(+), 23 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 68c5ed7768..53f025ec61 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3,6 +3,7 @@
 ;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel <at> gnu.org>
 ;;; Copyright © 2016 Pjotr Prins <pjotr.guix <at> thebird.nl>
 ;;; Copyright © 2016 Ben Woodcroft <donttrustben <at> gmail.com>
+;;; Copyright © 2017 Efraim Flashner <efraim <at> flashner.co.il>
 ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me <at> tobias.gr>
 ;;; Copyright © 2019, 2020, 2021 Simon Tournier <zimon.toutoune <at> gmail.com>
 ;;; Copyright © 2020 Peter Lo <peterloleungyau <at> gmail.com>
@@ -391,6 +392,25 @@ musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored
 in Biostrings objects.")
     (license license:artistic2.0)))
 
+(define-public r-genomeinfodbdata
+  (package
+    (name "r-genomeinfodbdata")
+    (version "1.2.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "GenomeInfoDbData" version 'annotation))
+              (sha256
+               (base32
+                "0di6nlqpsyqf693k2na65ayqldih563x3zfrczpqc5q2hl5kg35c"))))
+    (properties
+     `((upstream-name . "GenomeInfoDbData")))
+    (build-system r-build-system)
+    (home-page "https://bioconductor.org/packages/GenomeInfoDbData")
+    (synopsis "Species and taxonomy ID look up tables for GenomeInfoDb")
+    (description "This package contains data for mapping between NCBI taxonomy
+ID and species.  It is used by functions in the GenomeInfoDb package.")
+    (license license:artistic2.0)))
+
 (define-public r-homo-sapiens
   (package
     (name "r-homo-sapiens")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 36ecf47467..25ade2b9db 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7691,29 +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-genomeinfodbdata
-  (package
-    (name "r-genomeinfodbdata")
-    (version "1.2.0")
-    (source (origin
-              (method url-fetch)
-              ;; We cannot use bioconductor-uri here because this tarball is
-              ;; located under "data/annotation/" instead of "bioc/".
-              (uri (string-append "https://bioconductor.org/packages/release/"
-                                  "data/annotation/src/contrib/GenomeInfoDbData_"
-                                  version ".tar.gz"))
-              (sha256
-               (base32
-                "0di6nlqpsyqf693k2na65ayqldih563x3zfrczpqc5q2hl5kg35c"))))
-    (properties
-     `((upstream-name . "GenomeInfoDbData")))
-    (build-system r-build-system)
-    (home-page "https://bioconductor.org/packages/GenomeInfoDbData")
-    (synopsis "Species and taxonomy ID look up tables for GenomeInfoDb")
-    (description "This package contains data for mapping between NCBI taxonomy
-ID and species.  It is used by functions in the GenomeInfoDb package.")
-    (license license:artistic2.0)))
-
 (define-public r-genomeinfodb
   (package
     (name "r-genomeinfodb")
-- 
2.30.1

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