Subject: bug#44311: closed (Re: [bug#44311] [PATCH] gnu: Add r-deconstructsigs.)

From: [email-masked] (GNU bug Tracking System)
Date: Tue, 22 Dec 2020 22:39:02 +0000

Your bug report

#44311: [PATCH] gnu: Add r-deconstructsigs.

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].

-- 
44311: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=44311
GNU Bug Tracking System
Contact [email-masked] with problems

Subject: Re: [bug#44311] [PATCH] gnu: Add r-deconstructsigs.
From: Ricardo Wurmus <[email-masked]>
To: Aniket Patil <[email-masked]>
Cc: [email-masked], zimoun <[email-masked]>
Date: Tue, 22 Dec 2020 23:38:30 +0100
List-Id: <debbugs-submit.debbugs.gnu.org>

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

Subject: [PATCH] gnu: Add r-deconstructsigs.
From: Aniket Patil <[email-masked]>
To: [email-masked]
Cc: Aniket Patil <[email-masked]>
Date: Thu, 29 Oct 2020 22:39:49 +0530
List-Id: <debbugs-submit.debbugs.gnu.org>

* 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