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gnu: r-rhdf5lib: Update to 1.18.2.

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* gnu/packages/bioconductor.scm (r-rhdf5lib): Update to 1.18.2.
[source]: Adjust snippet.
[arguments]: Update build phase 'do-not-use-bundled-hdf5.
This commit is contained in:
Ricardo Wurmus 2022-05-28 12:45:21 +02:00
parent 59519a14de
commit 3db60a25a7
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1 changed files with 7 additions and 9 deletions
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gnu/packages/bioconductor.scm
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@ -13782,22 +13782,21 @@ block processing.")
(define-public r-rhdf5lib (define-public r-rhdf5lib
(package (package
(name "r-rhdf5lib") (name "r-rhdf5lib")
(version "1.16.0") (version "1.18.2")
(source (source
(origin (origin
(method url-fetch) (method url-fetch)
(uri (bioconductor-uri "Rhdf5lib" version)) (uri (bioconductor-uri "Rhdf5lib" version))
(sha256 (sha256
(base32 (base32
"0yly9s3wdnhd9ci2jxfkql38ibv35yzs38a6g6ashbg1m5kgwd9p")) "1jpb8h7c724yz51zjfqs90bsqxgmy1rry2ra9qamsgqpr2j9764g"))
(modules '((guix build utils))) (modules '((guix build utils)))
(snippet (snippet
'(begin '(begin
;; Delete bundled binaries ;; Delete bundled binaries
(delete-file-recursively "src/wininclude/") (delete-file-recursively "src/wininclude/")
(delete-file-recursively "src/winlib-8.3.0/") (delete-file-recursively "src/winlib/")
(delete-file "src/hdf5small_cxx_hl_1.10.7.tar.gz") (delete-file "src/hdf5small_cxx_hl_1.10.7.tar.gz")))))
#t))))
(properties `((upstream-name . "Rhdf5lib"))) (properties `((upstream-name . "Rhdf5lib")))
(build-system r-build-system) (build-system r-build-system)
(arguments (arguments
@ -13806,11 +13805,8 @@ block processing.")
(add-after 'unpack 'do-not-use-bundled-hdf5 (add-after 'unpack 'do-not-use-bundled-hdf5
(lambda* (#:key inputs #:allow-other-keys) (lambda* (#:key inputs #:allow-other-keys)
(for-each delete-file '("configure" "configure.ac")) (for-each delete-file '("configure" "configure.ac"))
;; Do not make other packages link with the proprietary libsz.
(substitute* "R/zzz.R" (substitute* "R/zzz.R"
((" \"%s/libsz.a\"") "") (("return\\(links\\)") "return(\" -lz\")"))
(("patharch, .getDynamicLinks")
".getDynamicLinks"))
(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))
@ -13829,6 +13825,8 @@ block processing.")
"hdf5/src/libhdf5.settings") "hdf5/src/libhdf5.settings")
(rename-file "Makevars.in" "Makevars") (rename-file "Makevars.in" "Makevars")
(substitute* "Makevars" (substitute* "Makevars"
(("@BUILD_HDF5@") "")
(("@COPY_SZIP@") "")
(("@ZLIB_LIB@") "-lz") (("@ZLIB_LIB@") "-lz")
(("@ZLIB_INCLUDE@") "") (("@ZLIB_INCLUDE@") "")
(("HDF5_CXX_LIB=.*") (("HDF5_CXX_LIB=.*")