GNU bug report logs - #36797
[PATCH 08/11] gnu: Add r-flowpeaks.

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From: help-debbugs <at> gnu.org (GNU bug Tracking System)
To: zimoun <zimon.toutoune <at> gmail.com>
Cc: tracker <at> debbugs.gnu.org
Subject: bug#36798: closed ([PATCH 09/11] gnu: Add r-flowsom.)
Date: Fri, 21 Feb 2020 17:08:04 +0000

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Your message dated Fri, 21 Feb 2020 18:07:33 +0100
with message-id <CAJ3okZ2GnkOKAPNwz8FwmRbZ+W+pYHiwB=xD4qocRuuwEgtM4w <at> mail.gmail.com>
and subject line patches merged
has caused the debbugs.gnu.org bug report #36797,
regarding [PATCH 09/11] gnu: Add r-flowsom.
to be marked as done.

(If you believe you have received this mail in error, please contact
help-debbugs <at> gnu.org.)


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36797: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=36797
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From: zimoun <zimon.toutoune <at> gmail.com>
To: guix-patches <at> gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 09/11] gnu: Add r-flowsom.
Date: Wed, 24 Jul 2019 20:22:02 +0200

* gnu/packages/bioconductor.scm (r-flowsom): New variable.
---
 gnu/packages/bioconductor.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index ab4d9f4075..dd6570ed17 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4930,3 +4930,32 @@ and to both short and long sequence reads.")
       "This package provides a fast and automatic clustering to classify the cells into subpopulations based on finding the peaks from the overall density function generated by K-means.")
     (license license:artistic2.0)))     ;TODO: artistic1.0 does not exist
 
+(define-public r-flowsom
+  (package
+    (name "r-flowsom")
+    (version "1.16.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (bioconductor-uri "FlowSOM" version))
+        (sha256
+          (base32
+            "03wl3xk7g7vajc4kkrqa0gsbjfxlqr918qi849h5nir31963398l"))))
+    (properties `((upstream-name . "FlowSOM")))
+    (build-system r-build-system)
+    (propagated-inputs
+      `(("r-biocgenerics" ,r-biocgenerics)
+        ("r-consensusclusterplus"
+         ,r-consensusclusterplus)
+        ("r-flowcore" ,r-flowcore)
+        ("r-flowutils" ,r-flowutils)
+        ("r-igraph" ,r-igraph)
+        ("r-tsne" ,r-tsne)
+        ("r-xml" ,r-xml)))
+    (home-page "http://www.r-project.org")
+    (synopsis
+      "Using self-organizing maps for visualization and interpretation of cytometry data")
+    (description
+      "FlowSOM offers visualization options for cytometry data, by using Self-Organizing Map clustering and Minimal Spanning Trees.")
+    (license license:gpl2+)))
+
-- 
2.21.0

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From: zimoun <zimon.toutoune <at> gmail.com>
To: 36797-done <at> debbugs.gnu.org
Subject: patches merged
Date: Fri, 21 Feb 2020 18:07:33 +0100

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

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