GNU bug report logs - #48575
[PATCH 00/50] Move some Bioconductor packages to (gnu packages bioconductor).

Previous Next

Full log

Message #26 received at 48575 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: 48575 <at> debbugs.gnu.org.
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 08/50] gnu: r-samr: Move to (gnu packages bioconductor).
Date: Fri, 21 May 2021 22:25:40 +0200

* gnu/packages/cran.scm (r-samr): Move from here...
* gnu/packages/bioconductor.scm (r-samr): ...to here.
---
 gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++
 gnu/packages/cran.scm         | 30 ------------------------------
 2 files changed, 31 insertions(+), 30 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 58c8336ce5..f9aa34d254 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -10,6 +10,7 @@
 ;;; Copyright © 2020, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu <at> mdc-berlin.de>
 ;;; Copyright © 2020 Jakub Kądziołka <kuba <at> kadziolka.net>
 ;;; Copyright © 2021 Hong Li <hli <at> mdc-berlin.de>
+;;; Copyright © 2021 Tim Howes <timhowes <at> lavabit.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -2604,6 +2605,36 @@ built-in).  The user may export/import tracks to/from the supported browsers,
 as well as query and modify the browser state, such as the current viewport.")
     (license license:artistic2.0)))
 
+;; This is a CRAN package, but it depends on a Bioconductor package.
+(define-public r-samr
+  (package
+    (name "r-samr")
+    (version "3.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "samr" version))
+       (sha256
+        (base32
+         "01km0f7qgm73x19vbvsxl083hs1dq4dj8qm5h64cxbf20b08my15"))))
+    (properties `((upstream-name . "samr")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-gsa" ,r-gsa)
+       ("r-impute" ,r-impute)
+       ("r-matrixstats" ,r-matrixstats)
+       ("r-openxlsx" ,r-openxlsx)
+       ("r-shiny" ,r-shiny)
+       ("r-shinyfiles" ,r-shinyfiles)))
+    (native-inputs `(("gfortran" ,gfortran)))
+    (home-page "https://statweb.stanford.edu/~tibs/SAM/")
+    (synopsis "Significance analysis of Microarrays")
+    (description
+     "This is a package for significance analysis of Microarrays for
+differential expression analysis, RNAseq data and related problems.")
+    ;; Any version of the LGPL
+    (license license:lgpl3+)))
+
 (define-public r-shortread
   (package
     (name "r-shortread")
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 8709cd21fa..e5d1db7cb6 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -33,7 +33,6 @@
 ;;; Copyright © 2020 Magali Lemes <magalilemes00 <at> gmail.com>
 ;;; Copyright © 2020 Simon Tournier <zimon.toutoune <at> gmail.com>
 ;;; Copyright © 2020 Aniket Patil <aniket112.patil <at> gmail.com>
-;;; Copyright © 2021 Tim Howes <timhowes <at> lavabit.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -28629,35 +28628,6 @@ indicator, a quantitative variable or a survival time.")
     ;; Any version of the LGPL
     (license license:lgpl3+)))
 
-(define-public r-samr
-  (package
-    (name "r-samr")
-    (version "3.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (cran-uri "samr" version))
-       (sha256
-        (base32
-         "01km0f7qgm73x19vbvsxl083hs1dq4dj8qm5h64cxbf20b08my15"))))
-    (properties `((upstream-name . "samr")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-gsa" ,r-gsa)
-       ("r-impute" ,r-impute)
-       ("r-matrixstats" ,r-matrixstats)
-       ("r-openxlsx" ,r-openxlsx)
-       ("r-shiny" ,r-shiny)
-       ("r-shinyfiles" ,r-shinyfiles)))
-    (native-inputs `(("gfortran" ,gfortran)))
-    (home-page "https://statweb.stanford.edu/~tibs/SAM/")
-    (synopsis "Significance analysis of Microarrays")
-    (description
-     "This is a package for significance analysis of Microarrays for
-differential expression analysis, RNAseq data and related problems.")
-    ;; Any version of the LGPL
-    (license license:lgpl3+)))
-
 (define-public r-randomforestsrc
   (package
     (name "r-randomforestsrc")
-- 
2.30.1

Previous Next

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