Subject: [bug#48575] [PATCH 33/50] gnu: r-mzr: Move to (gnu packages bioconductor).

From: zimoun <[email-masked]>
Date: Fri, 21 May 2021 22:26:05 +0200

* gnu/packages/bioinformatics.scm (r-mzr): Move from here...
* gnu/packages/bioconductor.scm (r-mzr): ...to here.
---
 gnu/packages/bioconductor.scm   | 62 +++++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 61 --------------------------------
 2 files changed, 62 insertions(+), 61 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 7e86af7d21..5ceffd7b4d 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -36,6 +36,7 @@
   #:use-module (gnu packages)
   #:use-module (gnu packages base)
   #:use-module (gnu packages bioinformatics)
+  #:use-module (gnu packages boost)
   #:use-module (gnu packages cran)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages gcc)
@@ -3051,6 +3052,67 @@ mzIdentML files with the drawback of having less pretty output than a vendor
 specific parser.")
     (license license:gpl2+)))
 
+(define-public r-mzr
+  (package
+    (name "r-mzr")
+    (version "2.24.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "mzR" version))
+       (sha256
+        (base32
+         "0ik0yrjhvk8r5pm990chn2aadp0gqzzkkm0027682ky34xp142sg"))
+       (modules '((guix build utils)))
+       (snippet
+        '(begin
+           (delete-file-recursively "src/boost")
+           #t))))
+    (properties `((upstream-name . "mzR")))
+    (build-system r-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'use-system-boost
+           (lambda _
+             (substitute* "src/Makevars"
+               (("\\./boost/libs.*") "")
+               ;; This is to avoid having a plain directory on the list of
+               ;; libraries to link.
+               (("\\(RHDF5_LIBS\\)" match)
+                (string-append match "/libhdf5.a"))
+               (("PKG_LIBS=") "PKG_LIBS=$(BOOST_LIBS) ")
+               (("\\ARCH_OBJS=" line)
+                (string-append line
+                               "\nBOOST_LIBS=-lboost_system -lboost_regex \
+-lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n")))
+             #t)))))
+    (inputs
+     `(;; Our default boost package won't work here, unfortunately, even with
+       ;; mzR version 2.24.1.
+       ("boost" ,boost-for-mysql) ; use this instead of the bundled boost sources
+       ("zlib" ,zlib)))
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-ncdf4" ,r-ncdf4)
+       ("r-protgenerics" ,r-protgenerics)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rhdf5lib" ,r-rhdf5lib)
+       ("r-zlibbioc" ,r-zlibbioc)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://github.com/sneumann/mzR/")
+    (synopsis "Parser for mass spectrometry data files")
+    (description
+     "The mzR package provides a unified API to the common file formats and
+parsers available for mass spectrometry data.  It comes with a wrapper for the
+ISB random access parser for mass spectrometry mzXML, mzData and mzML files.
+The package contains the original code written by the ISB, and a subset of the
+proteowizard library for mzML and mzIdentML.  The netCDF reading code has
+previously been used in XCMS.")
+    (license license:artistic2.0)))
+
 (define-public r-organismdbi
   (package
     (name "r-organismdbi")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index baef88cd2e..a6321a179a 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8873,67 +8873,6 @@ trait.")
 proteomics packages.")
     (license license:artistic2.0)))
 
-(define-public r-mzr
-  (package
-    (name "r-mzr")
-    (version "2.24.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "mzR" version))
-       (sha256
-        (base32
-         "0ik0yrjhvk8r5pm990chn2aadp0gqzzkkm0027682ky34xp142sg"))
-       (modules '((guix build utils)))
-       (snippet
-        '(begin
-           (delete-file-recursively "src/boost")
-           #t))))
-    (properties `((upstream-name . "mzR")))
-    (build-system r-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'use-system-boost
-           (lambda _
-             (substitute* "src/Makevars"
-               (("\\./boost/libs.*") "")
-               ;; This is to avoid having a plain directory on the list of
-               ;; libraries to link.
-               (("\\(RHDF5_LIBS\\)" match)
-                (string-append match "/libhdf5.a"))
-               (("PKG_LIBS=") "PKG_LIBS=$(BOOST_LIBS) ")
-               (("\\ARCH_OBJS=" line)
-                (string-append line
-                               "\nBOOST_LIBS=-lboost_system -lboost_regex \
--lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n")))
-             #t)))))
-    (inputs
-     `(;; Our default boost package won't work here, unfortunately, even with
-       ;; mzR version 2.24.1.
-       ("boost" ,boost-for-mysql) ; use this instead of the bundled boost sources
-       ("zlib" ,zlib)))
-    (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-ncdf4" ,r-ncdf4)
-       ("r-protgenerics" ,r-protgenerics)
-       ("r-rcpp" ,r-rcpp)
-       ("r-rhdf5lib" ,r-rhdf5lib)
-       ("r-zlibbioc" ,r-zlibbioc)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://github.com/sneumann/mzR/")
-    (synopsis "Parser for mass spectrometry data files")
-    (description
-     "The mzR package provides a unified API to the common file formats and
-parsers available for mass spectrometry data.  It comes with a wrapper for the
-ISB random access parser for mass spectrometry mzXML, mzData and mzML files.
-The package contains the original code written by the ISB, and a subset of the
-proteowizard library for mzML and mzIdentML.  The netCDF reading code has
-previously been used in XCMS.")
-    (license license:artistic2.0)))
-
 (define-public r-dropbead
   (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
         (revision "2"))
-- 
2.30.1