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Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 83 |
1 files changed, 83 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2796f4f90e..e7db82741d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -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") |