diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 651b81d911b..9ccd609721a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -25662,59 +25662,64 @@ block processing.") . ("r-mockery")))) (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")) - (substitute* "R/zzz.R" - (("return\\(links\\)") "return(\" -lz\")")) - (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 "hdf5/src/libhdf5.settings.in" - "hdf5/src/libhdf5.settings") - (rename-file "Makevars.in" "Makevars") - (substitute* "Makevars" - (("@BUILD_HDF5@") "") - (("@COPY_SZIP@") "") - (("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")) - (("@ZLIB_LIB_PATH@") "-lz") - (("@ZLIB_INCLUDE_PATH@") "") + (list + #: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")) + (substitute* "R/zzz.R" + (("return\\(links\\)") "return(\" -lz\")")) + (with-directory-excursion "src" + (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source")) + (rename-file (string-append "hdf5-" #$(package-version hdf5-1.10)) + "hdf5") + ;; Remove timestamp and host system information to make + ;; the build reproducible. + (substitute* "hdf5/src/libhdf5.settings.in" + (("Configured on: @CONFIG_DATE@") + "Configured on: Guix") + (("Uname information:.*") + "Uname information: Linux\n") + ;; Remove unnecessary store reference. + (("C Compiler:.*") + "C Compiler: GCC\n")) + (rename-file "hdf5/src/libhdf5.settings.in" + "hdf5/src/libhdf5.settings") + (rename-file "Makevars.in" "Makevars") + (substitute* "Makevars" + (("@BUILD_HDF5@") "") + (("@COPY_SZIP@") "") + (("HDF5_CXX_LIB=.*") + (string-append "HDF5_CXX_LIB=" + #$(this-package-input "hdf5") "/lib/libhdf5_cpp.a\n")) + (("HDF5_LIB=.*") + (string-append "HDF5_LIB=" + #$(this-package-input "hdf5") "/lib/libhdf5.a\n")) + (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n") + (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n") + (("HDF5_HL_INCLUDE=.*") "HDF5_HL_INCLUDE=./hdf5/hl/src\n") + (("HDF5_HL_CXX_INCLUDE=.*") "HDF5_HL_CXX_INCLUDE=./hdf5/hl/c++/src\n") + (("HDF5_HL_LIB=.*") + (string-append "HDF5_HL_LIB=" + #$(this-package-input "hdf5") + "/lib/libhdf5_hl.a\n")) + (("HDF5_HL_CXX_LIB=.*") + (string-append "HDF5_HL_CXX_LIB=" + #$(this-package-input "hdf5") + "/lib/libhdf5_hl_cpp.a\n")) + (("@ZLIB_LIB_PATH@") "-lz") + (("@ZLIB_INCLUDE_PATH@") "") - ;; szip is non-free software - (("cp \"\\$\\{SZIP_LIB\\}.*") "") - (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n"))))) - (add-after 'unpack 'disable-bad-test - (lambda _ - ;; This tests for a specific minor version of HDF5. - (delete-file "inst/tinytest/test_library_version.R")))))) + ;; szip is non-free software + (("cp \"\\$\\{SZIP_LIB\\}.*") "") + (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n"))))) + (add-after 'unpack 'fix-bad-test + (lambda _ + ;; This tests for a specific minor version of HDF5. + (substitute* "inst/tinytest/test_library_version.R" + (("1.10.7") + #$(package-version (this-package-input "hdf5"))))))))) (propagated-inputs (list hdf5-1.10 zlib)) (native-inputs