Subject: bug#36793: closed (patches merged)

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

Your bug report

#36797: [PATCH 04/11] gnu: Add r-flowcore.

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 04/11] gnu: Add r-flowcore.
From: zimoun <[email-masked]>
To: [email-masked]
Cc: zimoun <[email-masked]>
Date: Wed, 24 Jul 2019 20:21:57 +0200
List-Id: <debbugs-submit.debbugs.gnu.org>

* gnu/packages/bioconductor.scm (r-flowcore): 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 18b5711496..3a38042537 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4799,3 +4799,33 @@ read mapping, read counting, SNP calling, structural variant detection and
 gene fusion discovery.  It can be applied to all major sequencing techologies
 and to both short and long sequence reads.")
     (license license:gpl3)))
+
+(define-public r-flowcore
+  (package
+    (name "r-flowcore")
+    (version "1.50.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (bioconductor-uri "flowCore" version))
+        (sha256
+          (base32
+            "0pvcyzycsmgc8iw60q9xnhllfan6ihwpz3gvk8h1n9jmhpxzylan"))))
+    (properties `((upstream-name . "flowCore")))
+    (build-system r-build-system)
+    (propagated-inputs
+      `(("r-bh" ,r-bh)
+        ("r-biobase" ,r-biobase)
+        ("r-biocgenerics" ,r-biocgenerics)
+        ("r-corpcor" ,r-corpcor)
+        ("r-graph" ,r-graph)
+        ("r-mass" ,r-mass)
+        ("r-matrixstats" ,r-matrixstats)
+        ("r-rcpp" ,r-rcpp)
+        ("r-rrcov" ,r-rrcov)))
+    (home-page
+      "https://bioconductor.org/packages/flowCore")
+    (synopsis "Basic structures for flow cytometry data")
+    (description
+      "Provides S4 data structures and basic functions to deal with flow cytometry data.")
+    (license license:artistic2.0)))
-- 
2.21.0