GNU bug report logs - #75727
[PATCH] gnu: Add r-sigfit.

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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#75727: closed ([PATCH] gnu: Add r-sigfit.)
Date: Wed, 22 Jan 2025 21:17:02 +0000

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Your message dated Wed, 22 Jan 2025 22:15:47 +0100
with message-id <87zfjia6t8.fsf <at> elephly.net>
and subject line [PATCH] gnu: Add r-sigfit.
has caused the debbugs.gnu.org bug report #75727,
regarding [PATCH] gnu: Add r-sigfit.
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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75727: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=75727
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From: Alexis Simon <alexis.simon <at> runbox.com>
To: guix-patches <at> gnu.org
Cc: Alexis Simon <alexis.simon <at> runbox.com>
Subject: [PATCH] gnu: Add r-sigfit.
Date: Tue, 21 Jan 2025 13:23:32 +0100

* gnu/packages/bioinformatics.scm (r-sigfit): New variable.

Change-Id: I9d63975d3512cf8583e7ec22f450bb4963c9ff2f
---
 gnu/packages/bioinformatics.scm | 36 +++++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c98f6022bf..899606b195 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1526,6 +1526,42 @@ (define-public r-saige
 tests in large cohorts and biobanks (SAIGE-GENE+).")
       (license license:gpl2+))))
 
+(define-public r-sigfit
+  (package
+    (name "r-sigfit")
+    (version "2.2.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/kgori/sigfit")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "16r6m8p90rnb4hxl86fz3kbals3626232i8fj0zhhd23p89z3w4v"))))
+    (properties `((upstream-name . "sigfit")))
+    (build-system r-build-system)
+    (native-inputs (list r-codetools))
+    (propagated-inputs (list r-rcpp
+                             r-rstan
+                             r-rstantools
+                             r-coda
+                             r-clue
+                             r-knitr
+                             r-rmarkdown
+                             r-bh
+                             r-rcppeigen
+                             r-stanheaders))
+    (home-page "https://github.com/kgori/sigfit")
+    (synopsis "Flexible Bayesian inference of mutational signatures")
+    (description
+     "R package to estimate signatures of mutational processes and their
+activities on mutation count data. Starting from a set of single-nucleotide
+variants (SNVs), it allows both estimation of the exposure of samples to
+predefined mutational signatures (including whether the signatures are
+present at all), and identification of signatures de novo from the mutation counts.")
+    (license license:gpl3)))
+
 (define-public r-singlet
   (let ((commit "765a6c45081807a1522f0e8983e2417822a36f36")
         (revision "1"))

base-commit: cf34ba66cf614358dfac925212d6a9074e318d80
-- 
2.45.2

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From: Ricardo Wurmus <rekado <at> elephly.net>
To: 75727-done <at> debbugs.gnu.org
Subject: [PATCH] gnu: Add r-sigfit.
Date: Wed, 22 Jan 2025 22:15:47 +0100

Thanks for the patch.  Applied with commit
cc678d0e4d67073943e75053c5e450c4df700b42 to the master branch.

-- 
Ricardo

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