GNU bug report logs - #61250
[PATCH 1/3] gnu: Add r-viper.

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From: help-debbugs <at> gnu.org (GNU bug Tracking System)
To: Ricardo Wurmus <rekado <at> elephly.net>
Cc: tracker <at> debbugs.gnu.org
Subject: bug#61250: closed ([PATCH 1/3] gnu: Add r-viper.)
Date: Fri, 03 Feb 2023 15:50:01 +0000

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Your message dated Fri, 03 Feb 2023 16:47:28 +0100
with message-id <87ilgi92c2.fsf <at> elephly.net>
and subject line [PATCH 1/3] gnu: Add r-viper.
has caused the debbugs.gnu.org bug report #61250,
regarding [PATCH 1/3] gnu: Add r-viper.
to be marked as done.

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


-- 
61250: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=61250
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Contact help-debbugs <at> gnu.org with problems

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From: Navid Afkhami <navid.afkhami <at> mdc-berlin.de>
To: <guix-patches <at> gnu.org>
Subject: [PATCH 1/3] gnu: Add r-viper.
Date: Fri, 3 Feb 2023 13:18:52 +0100

* gnu/packages/bioconductor.scm (r-viper): New variable.
---
 gnu/packages/bioconductor.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 711b988e7f..aeef6f4106 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8307,6 +8307,27 @@ (define-public r-variantannotation
 coding changes and predict coding outcomes.")
     (license license:artistic2.0)))
 
+(define-public r-viper
+  (package
+    (name "r-viper")
+    (version "1.32.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "viper" version))
+              (sha256
+               (base32
+                "11i2q9nakh534nx2l736id7k1yqhk7jpg32sbfl4vrnh398q86h6"))))
+    (properties `((upstream-name . "viper")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-biobase r-e1071 r-kernsmooth r-mixtools))
+    (home-page "https://bioconductor.org/packages/viper")
+    (synopsis
+     "Virtual inference of protein-activity by enriched regulon analysis")
+    (description
+     "Inference of protein activity from gene expression data.
+Including the VIPER and msVIPER algorithms")
+    (license license:gpl2+)))
+
 (define-public r-vsn
   (package
     (name "r-vsn")
-- 
2.34.1

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From: Ricardo Wurmus <rekado <at> elephly.net>
To: 61250-done <at> debbugs.gnu.org
Subject: [PATCH 1/3] gnu: Add r-viper.
Date: Fri, 03 Feb 2023 16:47:28 +0100

Unfortunately, we cannot add this to Guix.   The license says:

  c. You agree that You will only use the Program and Documentation for
     non-commercial internal academic or educational research purposes
     only. You will not (i) reproduce or copy the Program (ii) use, or
     cause or permit the use of, the Program in whole or in part for any
     purpose other than as permitted under this License; (iii)
     distribute, sell, lease, license or otherwise make the Program
     available to a third party outside Your organization; or (iv)
     reverse engineer, decompile, or disassemble the Program.

I have instead added the package to guix-science-nonfree.

-- 
Ricardo

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