Subject: [bug#43400] [PATCH 09/12] gnu: r-rhdf5lib: Move to (gnu packages bioconductor).

From: zimoun <[email-masked]>
Date: Mon, 14 Sep 2020 18:07:44 +0200

* gnu/packages/bioinformatics.scm (r-rhdf5lib): Move from here...
* gnu/packages/bioconductor.scm (r-rhdf5lib): ...to here.
---
 gnu/packages/bioconductor.scm   | 83 +++++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 82 --------------------------------
 2 files changed, 83 insertions(+), 82 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 0ecb460bc4..0e63c486ee 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -5,6 +5,7 @@
 ;;; Copyright © 2019 Simon Tournier <[email-masked]>
 ;;; Copyright © 2020 Peter Lo <[email-masked]>
 ;;; Copyright © 2020 Mădălin Ionel Patrașcu <[email-masked]>
+;;; Copyright © 2020 Jakub Kądziołka <[email-masked]>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -8336,6 +8337,88 @@ routines.")
 objects from the @code{graph} package.")
     (license license:epl1.0)))
 
+(define-public r-rhdf5lib
+  (package
+    (name "r-rhdf5lib")
+    (version "1.10.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "Rhdf5lib" version))
+       (sha256
+        (base32
+         "0f45sqrvzj6x4mckalyp8366hm8v0rrmzklx3xd4gs6l2wallcn9"))
+       (modules '((guix build utils)))
+       (snippet
+        '(begin
+           ;; Delete bundled binaries
+           (delete-file-recursively "src/wininclude/")
+           (delete-file-recursively "src/winlib-4.9.3/")
+           (delete-file-recursively "src/winlib-8.3.0/")
+           (delete-file "src/hdf5small_cxx_hl_1.10.6.tar.gz")
+           #t))))
+    (properties `((upstream-name . "Rhdf5lib")))
+    (build-system r-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'do-not-use-bundled-hdf5
+           (lambda* (#:key inputs #:allow-other-keys)
+             (for-each delete-file '("configure" "configure.ac"))
+             ;; Do not make other packages link with the proprietary libsz.
+             (substitute* "R/zzz.R"
+               ((" \"%s/libsz.a\"") ""))
+             (with-directory-excursion "src"
+               (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source"))
+               (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10))
+                            "hdf5")
+               ;; Remove timestamp and host system information to make
+               ;; the build reproducible.
+               (substitute* "hdf5/src/libhdf5.settings.in"
+                 (("Configured on: @CONFIG_DATE@")
+                  "Configured on: Guix")
+                 (("Uname information:.*")
+                  "Uname information: Linux\n")
+                 ;; Remove unnecessary store reference.
+                 (("C Compiler:.*")
+                  "C Compiler: GCC\n"))
+               (rename-file "Makevars.in" "Makevars")
+               (substitute* "Makevars"
+                 (("@ZLIB_LIB@") "-lz")
+                 (("@ZLIB_INCLUDE@") "")
+                 (("HDF5_CXX_LIB=.*")
+                  (string-append "HDF5_CXX_LIB="
+                                 (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n"))
+                 (("HDF5_LIB=.*")
+                  (string-append "HDF5_LIB="
+                                 (assoc-ref inputs "hdf5") "/lib/libhdf5.a\n"))
+                 (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n")
+                 (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n")
+                 (("HDF5_HL_INCLUDE=.*") "HDF5_HL_INCLUDE=./hdf5/hl/src\n")
+                 (("HDF5_HL_CXX_INCLUDE=.*") "HDF5_HL_CXX_INCLUDE=./hdf5/hl/c++/src\n")
+                 (("HDF5_HL_LIB=.*")
+                  (string-append "HDF5_HL_LIB="
+                                 (assoc-ref inputs "hdf5") "/lib/libhdf5_hl.a\n"))
+                 (("HDF5_HL_CXX_LIB=.*")
+                  (string-append "HDF5_HL_CXX_LIB="
+                                 (assoc-ref inputs "hdf5") "/lib/libhdf5_hl_cpp.a\n"))
+                 ;; szip is non-free software
+                 (("cp \"\\$\\{SZIP_LIB\\}.*") "")
+                 (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n")))
+             #t)))))
+    (inputs
+     `(("zlib" ,zlib)))
+    (propagated-inputs
+     `(("hdf5" ,hdf5-1.10)))
+    (native-inputs
+     `(("hdf5-source" ,(package-source hdf5-1.10))
+       ("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/Rhdf5lib")
+    (synopsis "HDF5 library as an R package")
+    (description "This package provides C and C++ HDF5 libraries for use in R
+packages.")
+    (license license:artistic2.0)))
+
 (define-public r-beachmat
   (package
     (name "r-beachmat")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a84d19727c..8bd42c9429 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10684,88 +10684,6 @@ access and manipulation of HDF5 datasets.  It supports delayed operations and
 block processing.")
     (license license:artistic2.0)))
 
-(define-public r-rhdf5lib
-  (package
-    (name "r-rhdf5lib")
-    (version "1.10.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "Rhdf5lib" version))
-       (sha256
-        (base32
-         "0f45sqrvzj6x4mckalyp8366hm8v0rrmzklx3xd4gs6l2wallcn9"))
-       (modules '((guix build utils)))
-       (snippet
-        '(begin
-           ;; Delete bundled binaries
-           (delete-file-recursively "src/wininclude/")
-           (delete-file-recursively "src/winlib-4.9.3/")
-           (delete-file-recursively "src/winlib-8.3.0/")
-           (delete-file "src/hdf5small_cxx_hl_1.10.6.tar.gz")
-           #t))))
-    (properties `((upstream-name . "Rhdf5lib")))
-    (build-system r-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'do-not-use-bundled-hdf5
-           (lambda* (#:key inputs #:allow-other-keys)
-             (for-each delete-file '("configure" "configure.ac"))
-             ;; Do not make other packages link with the proprietary libsz.
-             (substitute* "R/zzz.R"
-               ((" \"%s/libsz.a\"") ""))
-             (with-directory-excursion "src"
-               (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source"))
-               (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10))
-                            "hdf5")
-               ;; Remove timestamp and host system information to make
-               ;; the build reproducible.
-               (substitute* "hdf5/src/libhdf5.settings.in"
-                 (("Configured on: @CONFIG_DATE@")
-                  "Configured on: Guix")
-                 (("Uname information:.*")
-                  "Uname information: Linux\n")
-                 ;; Remove unnecessary store reference.
-                 (("C Compiler:.*")
-                  "C Compiler: GCC\n"))
-               (rename-file "Makevars.in" "Makevars")
-               (substitute* "Makevars"
-                 (("@ZLIB_LIB@") "-lz")
-                 (("@ZLIB_INCLUDE@") "")
-                 (("HDF5_CXX_LIB=.*")
-                  (string-append "HDF5_CXX_LIB="
-                                 (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n"))
-                 (("HDF5_LIB=.*")
-                  (string-append "HDF5_LIB="
-                                 (assoc-ref inputs "hdf5") "/lib/libhdf5.a\n"))
-                 (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n")
-                 (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n")
-                 (("HDF5_HL_INCLUDE=.*") "HDF5_HL_INCLUDE=./hdf5/hl/src\n")
-                 (("HDF5_HL_CXX_INCLUDE=.*") "HDF5_HL_CXX_INCLUDE=./hdf5/hl/c++/src\n")
-                 (("HDF5_HL_LIB=.*")
-                  (string-append "HDF5_HL_LIB="
-                                 (assoc-ref inputs "hdf5") "/lib/libhdf5_hl.a\n"))
-                 (("HDF5_HL_CXX_LIB=.*")
-                  (string-append "HDF5_HL_CXX_LIB="
-                                 (assoc-ref inputs "hdf5") "/lib/libhdf5_hl_cpp.a\n"))
-                 ;; szip is non-free software
-                 (("cp \"\\$\\{SZIP_LIB\\}.*") "")
-                 (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n")))
-             #t)))))
-    (inputs
-     `(("zlib" ,zlib)))
-    (propagated-inputs
-     `(("hdf5" ,hdf5-1.10)))
-    (native-inputs
-     `(("hdf5-source" ,(package-source hdf5-1.10))
-       ("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/Rhdf5lib")
-    (synopsis "HDF5 library as an R package")
-    (description "This package provides C and C++ HDF5 libraries for use in R
-packages.")
-    (license license:artistic2.0)))
-
 (define-public r-dropbead
   (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
         (revision "2"))
-- 
2.28.0