gnu: r-rhdf5lib: Move to (gnu packages bioconductor).
* 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
Ricardo Wurmus
parent
8863c14cd8
commit
c61268c1b7
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@ -5,6 +5,7 @@
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;;; Copyright © 2019 Simon Tournier <zimon.toutoune@gmail.com>
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;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
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;;; Copyright © 2020 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
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;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
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;;;
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;;; This file is part of GNU Guix.
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;;;
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@ -8347,6 +8348,88 @@ (define-public r-rgraphviz
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objects from the @code{graph} package.")
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(license license:epl1.0)))
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(define-public r-rhdf5lib
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(package
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(name "r-rhdf5lib")
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(version "1.10.1")
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(source
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(origin
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(method url-fetch)
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(uri (bioconductor-uri "Rhdf5lib" version))
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(sha256
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(base32
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"0f45sqrvzj6x4mckalyp8366hm8v0rrmzklx3xd4gs6l2wallcn9"))
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(modules '((guix build utils)))
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(snippet
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'(begin
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;; Delete bundled binaries
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(delete-file-recursively "src/wininclude/")
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(delete-file-recursively "src/winlib-4.9.3/")
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(delete-file-recursively "src/winlib-8.3.0/")
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(delete-file "src/hdf5small_cxx_hl_1.10.6.tar.gz")
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#t))))
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(properties `((upstream-name . "Rhdf5lib")))
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(build-system r-build-system)
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(arguments
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`(#:phases
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(modify-phases %standard-phases
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(add-after 'unpack 'do-not-use-bundled-hdf5
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(lambda* (#:key inputs #:allow-other-keys)
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(for-each delete-file '("configure" "configure.ac"))
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;; Do not make other packages link with the proprietary libsz.
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(substitute* "R/zzz.R"
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((" \"%s/libsz.a\"") ""))
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(with-directory-excursion "src"
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(invoke "tar" "xvf" (assoc-ref inputs "hdf5-source"))
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(rename-file (string-append "hdf5-" ,(package-version hdf5-1.10))
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"hdf5")
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;; Remove timestamp and host system information to make
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;; the build reproducible.
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(substitute* "hdf5/src/libhdf5.settings.in"
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(("Configured on: @CONFIG_DATE@")
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"Configured on: Guix")
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(("Uname information:.*")
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"Uname information: Linux\n")
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;; Remove unnecessary store reference.
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(("C Compiler:.*")
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"C Compiler: GCC\n"))
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(rename-file "Makevars.in" "Makevars")
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(substitute* "Makevars"
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(("@ZLIB_LIB@") "-lz")
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(("@ZLIB_INCLUDE@") "")
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(("HDF5_CXX_LIB=.*")
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(string-append "HDF5_CXX_LIB="
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(assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n"))
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(("HDF5_LIB=.*")
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(string-append "HDF5_LIB="
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(assoc-ref inputs "hdf5") "/lib/libhdf5.a\n"))
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(("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n")
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(("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n")
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(("HDF5_HL_INCLUDE=.*") "HDF5_HL_INCLUDE=./hdf5/hl/src\n")
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(("HDF5_HL_CXX_INCLUDE=.*") "HDF5_HL_CXX_INCLUDE=./hdf5/hl/c++/src\n")
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(("HDF5_HL_LIB=.*")
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(string-append "HDF5_HL_LIB="
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(assoc-ref inputs "hdf5") "/lib/libhdf5_hl.a\n"))
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(("HDF5_HL_CXX_LIB=.*")
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(string-append "HDF5_HL_CXX_LIB="
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(assoc-ref inputs "hdf5") "/lib/libhdf5_hl_cpp.a\n"))
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;; szip is non-free software
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(("cp \"\\$\\{SZIP_LIB\\}.*") "")
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(("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n")))
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#t)))))
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(inputs
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`(("zlib" ,zlib)))
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(propagated-inputs
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`(("hdf5" ,hdf5-1.10)))
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(native-inputs
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`(("hdf5-source" ,(package-source hdf5-1.10))
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("r-knitr" ,r-knitr)))
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(home-page "https://bioconductor.org/packages/Rhdf5lib")
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(synopsis "HDF5 library as an R package")
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(description "This package provides C and C++ HDF5 libraries for use in R
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packages.")
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(license license:artistic2.0)))
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(define-public r-beachmat
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(package
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(name "r-beachmat")
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@ -10684,88 +10684,6 @@ (define-public r-hdf5array
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block processing.")
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(license license:artistic2.0)))
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(define-public r-rhdf5lib
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(package
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(name "r-rhdf5lib")
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(version "1.10.1")
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(source
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(origin
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(method url-fetch)
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(uri (bioconductor-uri "Rhdf5lib" version))
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(sha256
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(base32
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"0f45sqrvzj6x4mckalyp8366hm8v0rrmzklx3xd4gs6l2wallcn9"))
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(modules '((guix build utils)))
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(snippet
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'(begin
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;; Delete bundled binaries
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(delete-file-recursively "src/wininclude/")
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(delete-file-recursively "src/winlib-4.9.3/")
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(delete-file-recursively "src/winlib-8.3.0/")
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(delete-file "src/hdf5small_cxx_hl_1.10.6.tar.gz")
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#t))))
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(properties `((upstream-name . "Rhdf5lib")))
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(build-system r-build-system)
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(arguments
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`(#:phases
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(modify-phases %standard-phases
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(add-after 'unpack 'do-not-use-bundled-hdf5
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(lambda* (#:key inputs #:allow-other-keys)
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(for-each delete-file '("configure" "configure.ac"))
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;; Do not make other packages link with the proprietary libsz.
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(substitute* "R/zzz.R"
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((" \"%s/libsz.a\"") ""))
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(with-directory-excursion "src"
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(invoke "tar" "xvf" (assoc-ref inputs "hdf5-source"))
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(rename-file (string-append "hdf5-" ,(package-version hdf5-1.10))
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"hdf5")
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;; Remove timestamp and host system information to make
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;; the build reproducible.
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(substitute* "hdf5/src/libhdf5.settings.in"
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(("Configured on: @CONFIG_DATE@")
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"Configured on: Guix")
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(("Uname information:.*")
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"Uname information: Linux\n")
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;; Remove unnecessary store reference.
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(("C Compiler:.*")
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"C Compiler: GCC\n"))
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(rename-file "Makevars.in" "Makevars")
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(substitute* "Makevars"
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(("@ZLIB_LIB@") "-lz")
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(("@ZLIB_INCLUDE@") "")
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(("HDF5_CXX_LIB=.*")
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(string-append "HDF5_CXX_LIB="
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(assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n"))
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(("HDF5_LIB=.*")
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(string-append "HDF5_LIB="
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(assoc-ref inputs "hdf5") "/lib/libhdf5.a\n"))
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(("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n")
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(("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n")
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(("HDF5_HL_INCLUDE=.*") "HDF5_HL_INCLUDE=./hdf5/hl/src\n")
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(("HDF5_HL_CXX_INCLUDE=.*") "HDF5_HL_CXX_INCLUDE=./hdf5/hl/c++/src\n")
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(("HDF5_HL_LIB=.*")
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(string-append "HDF5_HL_LIB="
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(assoc-ref inputs "hdf5") "/lib/libhdf5_hl.a\n"))
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(("HDF5_HL_CXX_LIB=.*")
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(string-append "HDF5_HL_CXX_LIB="
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(assoc-ref inputs "hdf5") "/lib/libhdf5_hl_cpp.a\n"))
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;; szip is non-free software
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(("cp \"\\$\\{SZIP_LIB\\}.*") "")
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(("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n")))
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#t)))))
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(inputs
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`(("zlib" ,zlib)))
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(propagated-inputs
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`(("hdf5" ,hdf5-1.10)))
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(native-inputs
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`(("hdf5-source" ,(package-source hdf5-1.10))
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("r-knitr" ,r-knitr)))
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(home-page "https://bioconductor.org/packages/Rhdf5lib")
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(synopsis "HDF5 library as an R package")
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(description "This package provides C and C++ HDF5 libraries for use in R
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packages.")
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(license license:artistic2.0)))
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(define-public r-dropbead
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(let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
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(revision "2"))
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