diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 82 |
1 files changed, 0 insertions, 82 deletions
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")) |