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gnu: r-rhdf5lib: Update to 1.8.0. 

* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.8.0.
[arguments]: Update patches.
master
Ricardo Wurmus 2019-12-15 15:02:29 +01:00
parent 8804e4b48e
commit 1f5d262cfd
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GPG Key ID: 197A5888235FACAC
1 changed files with 18 additions and 6 deletions
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24
gnu/packages/bioinformatics.scm
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@ -10487,14 +10487,14 @@ block processing.")
(define-public r-rhdf5lib (define-public r-rhdf5lib
(package (package
(name "r-rhdf5lib") (name "r-rhdf5lib")
(version "1.6.3") (version "1.8.0")
(source (source
(origin (origin
(method url-fetch) (method url-fetch)
(uri (bioconductor-uri "Rhdf5lib" version)) (uri (bioconductor-uri "Rhdf5lib" version))
(sha256 (sha256
(base32 (base32
"0q68n5jm7w99paibj8vkxbdksbyrxilzwc9dkp3zf8zrdc5qfxzy")) "17lhwnm9rqsvbqkvwp0m07vjrk63a4389p2y39zffv8fgznxqzd7"))
(modules '((guix build utils))) (modules '((guix build utils)))
(snippet (snippet
'(begin '(begin
@ -10511,10 +10511,14 @@ block processing.")
(for-each delete-file '("configure" "configure.ac")) (for-each delete-file '("configure" "configure.ac"))
;; Do not make other packages link with the proprietary libsz. ;; Do not make other packages link with the proprietary libsz.
(substitute* "R/zzz.R" (substitute* "R/zzz.R"
(("'%s/libhdf5_cpp.a %s/libhdf5.a %s/libsz.a -lz'") (("'\"%s/libhdf5.a\" \"%s/libsz.a\" -lz'")
"'%s/libhdf5_cpp.a %s/libhdf5.a %s/libhdf5.a -lz'") "'\"%s/libhdf5.a\" \"%s/libhdf5.a\" -lz'")
(("'%s/libhdf5.a %s/libsz.a -lz'") (("'\"%s/libhdf5_cpp.a\" \"%s/libhdf5.a\" \"%s/libsz.a\" -lz'")
"'%s/libhdf5.a %s/libhdf5.a -lz'")) "'\"%s/libhdf5_cpp.a\" \"%s/libhdf5.a\" \"%s/libhdf5.a\" -lz'")
(("'%s/libhdf5_hl.a %s/libhdf5.a %s/libsz.a -lz'")
"'%s/libhdf5_hl.a %s/libhdf5.a %s/libhdf5.a -lz'")
(("'%s/libhdf5_hl_cpp.a %s/libhdf5_hl.a %s/libhdf5_cpp.a %s/libhdf5.a %s/libsz.a -lz'")
"'%s/libhdf5_hl_cpp.a %s/libhdf5_hl.a %s/libhdf5_cpp.a %s/libhdf5.a %s/libhdf5.a -lz'"))
(with-directory-excursion "src" (with-directory-excursion "src"
(invoke "tar" "xvf" (assoc-ref inputs "hdf5-source")) (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source"))
(rename-file (string-append "hdf5-" ,(package-version hdf5-1.10)) (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10))
@ -10539,6 +10543,14 @@ block processing.")
(assoc-ref inputs "hdf5") "/lib/libhdf5.a\n")) (assoc-ref inputs "hdf5") "/lib/libhdf5.a\n"))
(("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n") (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n")
(("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/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 ;; szip is non-free software
(("cp \"\\$\\{SZIP_LIB\\}.*") "") (("cp \"\\$\\{SZIP_LIB\\}.*") "")
(("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n"))) (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n")))