GNU bug report logs - #54912
[PATCH] gnu: Add r-acme.

Previous Next

To add a comment to this bug, you must first unarchive it, by sending
a message to control AT debbugs.gnu.org, with unarchive 54912 in the body.
You can then email your comments to 54912 AT debbugs.gnu.org in the normal way.

Toggle the display of automated, internal messages from the tracker.

Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <guix-patches <at> gnu.org>
Subject: [PATCH] gnu: Add r-acme.
Date: Wed, 13 Apr 2022 16:12:58 +0200

* gnu/packages/bioconductor.scm (r-acme): 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 803437a033..69e9e14dd3 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -11642,6 +11642,36 @@ (define-public r-universalmotif
 motifs, and others.")
     (license license:gpl3)))
 
+;;  The homepage (http://watson.nci.nih.gov/~sdavis) seems to be inaccessible
+;; anymore so I changed it to the Bioconductor page of the package.
+(define-public r-acme
+  (package
+    (name "r-acme")
+    (version "2.50.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "ACME" version))
+              (sha256
+               (base32
+                "0h4bqbbqcwc938q7lysk5l35f64xz9d1bsniv2wshmlr4rr0zpcg"))))
+    (properties `((upstream-name . "ACME")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-biobase r-biocgenerics))
+    (home-page "https://bioconductor.org/packages/aCGH/")
+    (synopsis "Calculating microarray enrichment")
+    (description
+     "This package implements
+@dfn{algorithms for calculating microarray enrichment} (ACME), and it is a set
+of tools for analysing tiling array of
+@dfn{combined chromatin immunoprecipitation with DNA microarray} (ChIP/chip),
+DNAse hypersensitivity, or other experiments that result in regions of the
+genome showing enrichment.  It does not rely on a specific array technology
+(although the array should be a tiling array), is very general (can be applied
+in experiments resulting in regions of enrichment), and is very insensitive to
+array noise or normalization methods.  It is also very fast and can be applied
+on whole-genome tiling array experiments quite easily with enough memory.")
+    (license license:gpl2+)))
+
 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
 ;; it here.
 (define-public r-activedriverwgs
-- 
2.34.0

Message #10 received at 54912-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 54912-done <at> debbugs.gnu.org
Subject: [PATCH] gnu: Add r-acme.
Date: Thu, 14 Apr 2022 12:43:05 +0200

Applied, thanks!

I removed the comment at the top, because the bioc home page is fine to
use.  The importer just extracts the home page as it is declared in the
package’s DESCRIPTION file.  It’s not unusual that the home page there
has been abandoned as developers often forget about updating the
DESCRIPTION file.

-- 
Ricardo

Previous Next

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