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gnu: r-rhdf5lib: Move to (gnu packages bioconductor).

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* gnu/packages/bioinformatics.scm (r-rhdf5lib): Move from here...
* gnu/packages/bioconductor.scm (r-rhdf5lib): ...to here.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
This commit is contained in:
zimoun 2020-09-14 18:07:44 +02:00 • committed by Ricardo Wurmus
parent 8863c14cd8
commit c61268c1b7
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GPG key ID: 197A5888235FACAC
2 changed files with 83 additions and 82 deletions
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83
gnu/packages/bioconductor.scm
View file

@ -5,6 +5,7 @@
;;; Copyright © 2019 Simon Tournier <zimon.toutoune@gmail.com>
;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
;;; Copyright © 2020 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
;;;
;;; This file is part of GNU Guix.
;;;
@ -8347,6 +8348,88 @@ 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")

82
gnu/packages/bioinformatics.scm
View file

@ -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"))