Subject: bug#36792: closed (patches merged)

From: [email-masked] (GNU bug Tracking System)
Date: Fri, 21 Feb 2020 17:08:03 +0000

Your bug report

#36797: [PATCH 03/11] gnu: Add r-all.

which was filed against the guix-patches package, has been closed.

The explanation is attached below, along with your original report.
If you require more details, please reply to [email-masked].

-- 
36797: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=36797
GNU Bug Tracking System
Contact [email-masked] with problems

Subject: patches merged
From: zimoun <[email-masked]>
To: [email-masked]
Date: Fri, 21 Feb 2020 18:07:33 +0100
List-Id: <debbugs-submit.debbugs.gnu.org>

Dear,

All the patches are merged now; except r-flowpeaks. Because this
package use Artistic1.0 which is not enough clear to be considered
"free" [1,2] (GNU's point of view [3]) and upstream are not
responsive, let clean the bug tracker. :-)

[1] https://debbugs.gnu.org/cgi/bugreport.cgi?bug=36797#16
[2] https://lists.gnu.org/archive/html/guix-devel/2019-12/msg00286.html
[3] https://www.gnu.org/licenses/license-list.en.html#ArtisticLicense

All the best,
simon

Subject: [PATCH 03/11] gnu: Add r-all.
From: zimoun <[email-masked]>
To: [email-masked]
Cc: zimoun <[email-masked]>
Date: Wed, 24 Jul 2019 20:21:56 +0200
List-Id: <debbugs-submit.debbugs.gnu.org>

* gnu/packages/bioconductor.scm (r-all): New variable.
---
 gnu/packages/bioconductor.scm | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index e5a2d66b2d..18b5711496 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -865,6 +865,36 @@ which were then sequenced to a depth of ~4 million reads per library,
 resulting in a complete gene expression profile for each cell.")
     (license license:artistic2.0)))
 
+(define-public r-all
+  (package
+    (name "r-all")
+    (version "1.26.0")
+    (source (origin
+              (method url-fetch)
+              ;; We cannot use bioconductor-uri here because this tarball is
+              ;; located under "data/experiment/" instead of "bioc/".
+              (uri (string-append "https://www.bioconductor.org/packages/"
+                                  "release/data/experiment/src/contrib/"
+                                  "ALL_" version ".tar.gz"))
+              (sha256
+               (base32
+                "1z7kpjw4ndj6fkxwvhqf3gawhrn26ksrlns7j2c78qzxqmjndik9"))))
+    (properties
+      `((upstream-name . "ConsensusClusterPlus")))
+    (build-system r-build-system)
+    (propagated-inputs
+      `(("r-biobase" ,r-biobase)))
+    (home-page
+      "https://bioconductor.org/packages/ALL")
+    (synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory")
+    (description
+      "The data consist of microarrays from 128 different individuals with
+acute lymphoblastic leukemia (ALL). A number of additional covariates are
+available. The data have been normalized (using rma) and it is the jointly
+normalized data that are available here. The data are presented in the form of
+an exprSet object.")
+    (license license:artistic2.0)))
+
 
 ;;; Packages
 
-- 
2.21.0