GNU bug report logs - #44311
[PATCH] gnu: Add r-deconstructsigs.

Previous Next

Full log

View this message in rfc822 format

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#44311: closed ([PATCH] gnu: Add r-deconstructsigs.)
Date: Tue, 22 Dec 2020 22:39:01 +0000

[Message part 1 (text/plain, inline)]

Your message dated Tue, 22 Dec 2020 23:38:30 +0100
with message-id <87wnx9mpp5.fsf <at> elephly.net>
and subject line Re: [bug#44311] [PATCH] gnu: Add r-deconstructsigs.
has caused the debbugs.gnu.org bug report #44311,
regarding [PATCH] gnu: Add r-deconstructsigs.
to be marked as done.

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


-- 
44311: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=44311
GNU Bug Tracking System
Contact help-debbugs <at> gnu.org with problems

[Message part 2 (message/rfc822, inline)]

From: Aniket Patil <aniket112.patil <at> gmail.com>
To: guix-patches <at> gnu.org
Cc: Aniket Patil <aniket112.patil <at> gmail.com>
Subject: [PATCH] gnu: Add r-deconstructsigs.
Date: Thu, 29 Oct 2020 22:39:49 +0530

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 82caaf54f6..75d9ae7de2 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -24715,3 +24715,33 @@ modal regression and conditional density estimation in the
 presence/absence of measurement error. Bandwidth selection is 
 also provided for each method.")
     (license license:gpl2+)))
+
+(define-public r-deconstructsigs
+  (package
+    (name "r-deconstructsigs")
+    (version "1.8.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "deconstructSigs" version))
+        (sha256
+          (base32
+            "014x0nb23jb98666kaav2phkvmkr38pi38jv0dqd4jv7zp0gdf1a"))))
+    (properties
+      `((upstream-name . "deconstructSigs")))
+    (build-system r-build-system)
+    (propagated-inputs
+      `(("r-bsgenome" ,r-bsgenome)
+        ("r-bsgenome-hsapiens-ucsc-hg19"
+         ,r-bsgenome-hsapiens-ucsc-hg19)
+        ("r-genomeinfodb" ,r-genomeinfodb)
+        ("r-reshape2" ,r-reshape2)))
+    (home-page
+      "https://github.com/raerose01/deconstructSigs")
+    (synopsis "Identifies Signatures Present in a Tumor Sample")
+    (description
+      "Takes sample information in the form of the fraction of 
+mutations in each of 96 trinucleotide contexts and identifies 
+the weighted combination of published signatures that, when summed, 
+most closely reconstructs the mutational profile.")
+    (license license:gpl2+)))
-- 
2.28.0

[Message part 3 (message/rfc822, inline)]

From: Ricardo Wurmus <rekado <at> elephly.net>
To: Aniket Patil <aniket112.patil <at> gmail.com>
Cc: 44311-done <at> debbugs.gnu.org, zimoun <zimon.toutoune <at> gmail.com>
Subject: Re: [bug#44311] [PATCH] gnu: Add r-deconstructsigs.
Date: Tue, 22 Dec 2020 23:38:30 +0100

Hi Aniket,

> * gnu/packages/cran.scm (r-deconstructsigs): New variable.

I’m sorry, but we need to drop this patch because
gnu/packages/bioconductor.scm already contains this definition.

“Already” really isn’t quite the right word, because you submitted your
patch before I added the definition to the bioconductor module when
Simon and I upgraded our CRAN and Bioconductor packages.

This package is in the bioconductor module because it depends on the
Bioconductor package r-bsgenome-hsapiens-ucsc-hg19.

-- 
Ricardo

Previous Next

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