GNU bug report logs - #45399
[PATCH 00/10] Move some Bioconductor packages to (gnu packages bioconductor).

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Message #35 received at 45399 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: 45399 <at> debbugs.gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 09/10] gnu: r-gqtlstats: Move to (gnu packages bioconductor).
Date: Wed, 23 Dec 2020 19:06:34 +0100

* gnu/packages/bioinformatics.scm (r-gqtlstats): Move from here...
* gnu/packages/bioconductor.scm (r-gqtlstats): ...to here.
---
 gnu/packages/bioconductor.scm   | 47 +++++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 47 ---------------------------------
 2 files changed, 47 insertions(+), 47 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index ff9e26bbde..a3dd93e763 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9308,6 +9308,53 @@ metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines
 by Ernst and Kellis.")
     (license license:artistic2.0)))
 
+(define-public r-gqtlbase
+  (package
+    (name "r-gqtlbase")
+    (version "1.21.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "gQTLBase" version))
+       (sha256
+        (base32
+         "0nipibm1bk9k70ajbw1f6vjmz0dh7gk21l17q3m54bnawxsggrfh"))))
+    (properties `((upstream-name . "gQTLBase")))
+    (build-system r-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         ;; This is an upstream bug.
+         (add-after 'unpack 'fix-imports
+           (lambda _
+             (substitute* "NAMESPACE"
+               ((".*maxffmode.*") "")
+               (("importFrom\\(ff,.*") "import(ff)\n"))
+             #t)))))
+    (propagated-inputs
+     `(("r-batchjobs" ,r-batchjobs)
+       ("r-bbmisc" ,r-bbmisc)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-bit" ,r-bit)
+       ("r-doparallel" ,r-doparallel)
+       ("r-ff" ,r-ff)
+       ("r-ffbase" ,r-ffbase)
+       ("r-foreach" ,r-foreach)
+       ("r-genomicfiles" ,r-genomicfiles)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/gQTLBase")
+    (synopsis "Infrastructure for eQTL, mQTL and similar studies")
+    (description
+     "The purpose of this package is to simplify the storage and interrogation
+of @dfn{quantitative trait loci} (QTL) archives, such as eQTL, mQTL, dsQTL,
+and more.")
+    (license license:artistic2.0)))
+
 (define-public r-gqtlstats
   (package
     (name "r-gqtlstats")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 76236929de..bc483e6f13 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10549,53 +10549,6 @@ views.  High-level plots include sequence fragment length, edge-linked
 interval to data view, mismatch pileup, and several splicing summaries.")
     (license license:artistic2.0)))
 
-(define-public r-gqtlbase
-  (package
-    (name "r-gqtlbase")
-    (version "1.21.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "gQTLBase" version))
-       (sha256
-        (base32
-         "0nipibm1bk9k70ajbw1f6vjmz0dh7gk21l17q3m54bnawxsggrfh"))))
-    (properties `((upstream-name . "gQTLBase")))
-    (build-system r-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         ;; This is an upstream bug.
-         (add-after 'unpack 'fix-imports
-           (lambda _
-             (substitute* "NAMESPACE"
-               ((".*maxffmode.*") "")
-               (("importFrom\\(ff,.*") "import(ff)\n"))
-             #t)))))
-    (propagated-inputs
-     `(("r-batchjobs" ,r-batchjobs)
-       ("r-bbmisc" ,r-bbmisc)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-bit" ,r-bit)
-       ("r-doparallel" ,r-doparallel)
-       ("r-ff" ,r-ff)
-       ("r-ffbase" ,r-ffbase)
-       ("r-foreach" ,r-foreach)
-       ("r-genomicfiles" ,r-genomicfiles)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/gQTLBase")
-    (synopsis "Infrastructure for eQTL, mQTL and similar studies")
-    (description
-     "The purpose of this package is to simplify the storage and interrogation
-of @dfn{quantitative trait loci} (QTL) archives, such as eQTL, mQTL, dsQTL,
-and more.")
-    (license license:artistic2.0)))
-
 (define-public r-dropbead
   (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
         (revision "2"))
-- 
2.29.2

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