Subject: [bug#48575] [PATCH 06/50] gnu: r-msnid: Move to (gnu packages bioconductor).

From: zimoun <[email-masked]>
Date: Fri, 21 May 2021 22:25:38 +0200

* gnu/packages/bioinformatics.scm (r-msnid): Move from here...
* gnu/packages/bioconductor.scm (r-msnid): ...to here.
---
 gnu/packages/bioconductor.scm   | 52 +++++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 52 ---------------------------------
 2 files changed, 52 insertions(+), 52 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 923413135b..b5787cb207 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2312,6 +2312,58 @@ and the assessment of differential expression.  The analysis methods apply to
 different technologies, including microarrays, RNA-seq, and quantitative PCR.")
     (license license:gpl2+)))
 
+(define-public r-msnid
+  (package
+    (name "r-msnid")
+    (version "1.24.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "MSnID" version))
+       (sha256
+        (base32
+         "05bncy7lw2a3h8xgnavjiz56pc6mk8q7l6qdd81197nawxs3j02d"))))
+    (properties `((upstream-name . "MSnID")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-annotationhub" ,r-annotationhub)
+       ("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocstyle" ,r-biocstyle)
+       ("r-biostrings" ,r-biostrings)
+       ("r-data-table" ,r-data-table)
+       ("r-doparallel" ,r-doparallel)
+       ("r-dplyr" ,r-dplyr)
+       ("r-foreach" ,r-foreach)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-iterators" ,r-iterators)
+       ("r-msnbase" ,r-msnbase)
+       ("r-msmstests" ,r-msmstests)
+       ("r-mzid" ,r-mzid)
+       ("r-mzr" ,r-mzr)
+       ("r-protgenerics" ,r-protgenerics)
+       ("r-purrr" ,r-purrr)
+       ("r-r-cache" ,r-r-cache)
+       ("r-rcpp" ,r-rcpp)
+       ("r-reshape2" ,r-reshape2)
+       ("r-rlang" ,r-rlang)
+       ("r-runit" ,r-runit)
+       ("r-stringr" ,r-stringr)
+       ("r-tibble" ,r-tibble)
+       ("r-xtable" ,r-xtable)))
+    (home-page "https://bioconductor.org/packages/MSnID")
+    (synopsis "Utilities for LC-MSn proteomics identifications")
+    (description
+     "This package extracts @dfn{tandem mass spectrometry} (MS/MS) ID data
+from mzIdentML (leveraging the mzID package) or text files.  After collating
+the search results from multiple datasets it assesses their identification
+quality and optimize filtering criteria to achieve the maximum number of
+identifications while not exceeding a specified false discovery rate.  It also
+contains a number of utilities to explore the MS/MS results and assess missed
+and irregular enzymatic cleavages, mass measurement accuracy, etc.")
+    (license license:artistic2.0)))
+
 (define-public r-rbgl
   (package
     (name "r-rbgl")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 9c9288c6b0..5c2abe6e94 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9275,58 +9275,6 @@ structure (pcaRes) to provide a common interface to the PCA results.")
 of mass spectrometry based proteomics data.")
     (license license:artistic2.0)))
 
-(define-public r-msnid
-  (package
-    (name "r-msnid")
-    (version "1.24.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "MSnID" version))
-       (sha256
-        (base32
-         "05bncy7lw2a3h8xgnavjiz56pc6mk8q7l6qdd81197nawxs3j02d"))))
-    (properties `((upstream-name . "MSnID")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-annotationhub" ,r-annotationhub)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocstyle" ,r-biocstyle)
-       ("r-biostrings" ,r-biostrings)
-       ("r-data-table" ,r-data-table)
-       ("r-doparallel" ,r-doparallel)
-       ("r-dplyr" ,r-dplyr)
-       ("r-foreach" ,r-foreach)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-iterators" ,r-iterators)
-       ("r-msnbase" ,r-msnbase)
-       ("r-msmstests" ,r-msmstests)
-       ("r-mzid" ,r-mzid)
-       ("r-mzr" ,r-mzr)
-       ("r-protgenerics" ,r-protgenerics)
-       ("r-purrr" ,r-purrr)
-       ("r-r-cache" ,r-r-cache)
-       ("r-rcpp" ,r-rcpp)
-       ("r-reshape2" ,r-reshape2)
-       ("r-rlang" ,r-rlang)
-       ("r-runit" ,r-runit)
-       ("r-stringr" ,r-stringr)
-       ("r-tibble" ,r-tibble)
-       ("r-xtable" ,r-xtable)))
-    (home-page "https://bioconductor.org/packages/MSnID")
-    (synopsis "Utilities for LC-MSn proteomics identifications")
-    (description
-     "This package extracts @dfn{tandem mass spectrometry} (MS/MS) ID data
-from mzIdentML (leveraging the mzID package) or text files.  After collating
-the search results from multiple datasets it assesses their identification
-quality and optimize filtering criteria to achieve the maximum number of
-identifications while not exceeding a specified false discovery rate.  It also
-contains a number of utilities to explore the MS/MS results and assess missed
-and irregular enzymatic cleavages, mass measurement accuracy, etc.")
-    (license license:artistic2.0)))
-
 (define-public r-aroma-light
   (package
     (name "r-aroma-light")
-- 
2.30.1