diff options
| -rw-r--r-- | gnu/packages/maths.scm | 195 |
1 files changed, 81 insertions, 114 deletions
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index d3c48f8006..1e9de1f38c 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -1773,6 +1773,7 @@ extremely large and complex data collections.") (license (license:x11-style "https://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING")))) +;; When updating this package, please also update hdf-java. (define-public hdf5-1.10 (package (inherit hdf5-1.8) @@ -1835,131 +1836,97 @@ extremely large and complex data collections.") ;; Default version of HDF5. hdf5-1.10) +;; Keep this in sync with the current hdf5 package. (define-public hdf-java (package (name "hdf-java") - (version "3.3.2") + (version "1.10.9") (source (origin - (method url-fetch) - (uri (string-append - "https://www.hdfgroup.org/ftp/HDF5/releases/HDF-JAVA/hdfjni-" - version "/src/CMake-hdfjava-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/HDFGroup/hdf5") + (commit (string-append "hdf5-" + (string-map + (lambda (c) (if (char=? c #\.) #\_ c)) + version))))) + (file-name (git-file-name name version)) (sha256 - (base32 "0m1gp2aspcblqzmpqbdpfp6giskws85ds6p5gz8sx7asyp7wznpr")) + (base32 "1sjdcnafvzsy99vqhybkps8rnwmxb6fsvmkw89wb2mrrp4vi5z9v")) (modules '((guix build utils))) (snippet ; Make sure we don't use the bundled sources and binaries. - `(begin - (for-each delete-file - (list "SZip.tar.gz" "ZLib.tar.gz" "JPEG8d.tar.gz" - "HDF4.tar.gz" "HDF5.tar.gz")) - (delete-file-recursively ,(string-append "hdfjava-" version "/lib")) - #t)))) + '(for-each delete-file + (find-files "java/lib" "\\.jar$"))))) (build-system gnu-build-system) + (arguments + (list + #:configure-flags + #~(list "--enable-java" + "--disable-tools") + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'unbundle + (lambda* (#:key inputs #:allow-other-keys) + (let ((simple + (search-input-file + inputs "/lib/m2/org/slf4j/slf4j-simple/1.7.25/slf4j-simple-1.7.25.jar")) + (api + (search-input-file + inputs "/lib/m2/org/slf4j/slf4j-api/1.7.25/slf4j-api-1.7.25.jar")) + (junit + (search-input-file + inputs "/lib/m2/junit/junit/4.12/junit-4.12.jar")) + (hamcrest + (search-input-file + inputs "/lib/m2/org/hamcrest/hamcrest-core/1.3/hamcrest-core-1.3.jar"))) + (substitute* (append (find-files "java" "Makefile.am") + (find-files "java" "Makefile.in")) + (("\\$\\(top_srcdir\\)/java/lib/ext/slf4j-simple-1.7.33.jar") + simple) + (("\\$\\(top_srcdir\\)/java/lib/slf4j-api-1.7.33.jar") + api) + (("\\$\\(top_srcdir\\)/java/lib/junit.jar") + junit) + (("\\$\\(top_srcdir\\)/java/lib/hamcrest-core.jar") + hamcrest)) + (substitute* '("java/test/junit.sh.in" + "java/examples/datatypes/JavaDatatypeExample.sh.in" + "java/examples/datasets/JavaDatasetExample.sh.in" + "java/examples/intro/JavaIntroExample.sh.in" + "java/examples/groups/JavaGroupExample.sh.in") + (("^LIST_JAR_TESTFILES=\"" m) + (string-append m hamcrest "\n" + junit "\n" + api "\n" + simple "\n")) + (("^\\$HDFLIB_HOME/.*") "") + (("\"\\$BLDLIBDIR\"/junit.jar") + junit) + (("\"\\$BLDLIBDIR\"/hamcrest-core.jar") + hamcrest) + (("\"\\$BLDLIBDIR\"/slf4j-api-1.7.33.jar") + api) + (("\"\\$BLDLIBDIR\"/slf4j-simple-1.7.33.jar") + simple) + (("/usr/bin/test") + (search-input-file inputs "/bin/test")) + (("/usr/bin/uname") + (search-input-file inputs "/bin/uname"))) + (substitute* (find-files "java/test/testfiles/" ".*\\.txt$") + (("JUnit version 4.11") + "JUnit version 4.12-SNAPSHOT")))))))) (native-inputs - `(("jdk" ,icedtea "jdk") - ("automake" ,automake) ; For up to date 'config.guess' and 'config.sub'. - ;; For tests: - ("hamcrest-core" ,java-hamcrest-core) - ("junit" ,java-junit) - ("slf4j-simple" ,java-slf4j-simple))) + (list `(,icedtea "jdk") + ;; For tests: + java-hamcrest-core + java-junit + java-slf4j-simple)) (inputs - `(("hdf4" ,hdf4) - ("hdf5" ,hdf5-1.8) - ("zlib" ,zlib) - ("libjpeg" ,libjpeg-turbo) - ("slf4j-api" ,java-slf4j-api))) - (arguments - `(#:configure-flags - (list (string-append "--target=" ,(or (%current-target-system) (%current-system))) - (string-append "--with-jdk=" (assoc-ref %build-inputs "jdk") "/include," - (assoc-ref %build-inputs "jdk") "/lib" ) - (string-append "--with-hdf4=" (assoc-ref %build-inputs "hdf4") "/lib") - (string-append "--with-hdf5=" (assoc-ref %build-inputs "hdf5") "/lib")) - - #:make-flags - (list (string-append "HDFLIB=" (assoc-ref %build-inputs "hdf4") "/lib") - (string-append "HDF5LIB=" (assoc-ref %build-inputs "hdf5") "/lib") - (string-append "ZLIB=" (search-input-file %build-inputs "/lib/libz.so")) - (string-append "JPEGLIB=" - (search-input-file %build-inputs "/lib/libjpeg.so")) - "LLEXT=so") - - #:phases - (modify-phases %standard-phases - (add-before 'configure 'chdir-to-source - (lambda _ (chdir ,(string-append "hdfjava-" version)) #t)) - (add-before 'configure 'patch-build - (lambda* (#:key inputs outputs #:allow-other-keys) - (substitute* "configure" - (("COPT=\"") "COPT=\"-O2 ") ; CFLAGS is ignored in Makefiles - (("/bin/cat") (which "cat"))) - ;; Set classpath for compilation - (substitute* '("hdf/hdf5lib/Makefile.in" - "hdf/hdf5lib/exceptions/Makefile.in" - "hdf/hdflib/Makefile.in") - (("\\$\\(TOP\\)/lib/slf4j-api-1\\.7\\.5\\.jar") - ;; 'slf4j-api-X.Y.Z.jar' is installed in a Maven-style - ;; directory, so use 'find-files' to find it. - (car (find-files (assoc-ref inputs "slf4j-api") - "^slf4j-api.*\\.jar$")))) - ;; Replace outdated config.sub and config.guess: - (with-directory-excursion "config" - (for-each (lambda (file) - (install-file - (search-input-file inputs - (string-append - "/share/automake-" - ,(version-major+minor (package-version automake)) - "/" file)) - ".")) - '("config.sub" "config.guess"))) - - ;; Fix embedded version number - (let ((hdf5version (list ,@(string-split (package-version hdf5) #\.)))) - (substitute* "hdf/hdf5lib/H5.java" - (("1, 8, 19") - (string-join hdf5version ", ")))) - - (mkdir-p (string-append (assoc-ref outputs "out"))) - ;; Set classpath for tests - (let* ((build-dir (getcwd)) - (lib (string-append build-dir "/lib")) - (jhdf (string-append lib "/jhdf.jar")) - (jhdf5 (string-append lib "/jhdf5.jar")) - (testjars - (append - (map (lambda (i) - (car (find-files (assoc-ref inputs i) - (string-append "^" i - ".*\\.jar$")))) - '("slf4j-api" "slf4j-simple")) - (list - (car (find-files (assoc-ref inputs "junit") "jar$")) - (car (find-files (assoc-ref inputs "hamcrest-core") - "jar$"))))) - (class-path - (string-join `("." ,build-dir ,jhdf ,jhdf5 ,@testjars) ":"))) - - (substitute* '("test/hdf5lib/Makefile.in" - "test/hdf5lib/junit.sh.in" - "examples/runExample.sh.in") - (("/usr/bin/test") - (search-input-file inputs "/bin/test")) - (("/usr/bin/uname") - (search-input-file inputs "/bin/uname")) - (("CLASSPATH=[^\n]*") - (string-append "CLASSPATH=" class-path))) - (setenv "CLASSPATH" class-path)) - #t)) - (add-before 'check 'build-examples - (lambda _ - (apply invoke `("javac" - ,@(find-files "examples" ".*\\.java")))))) - - #:parallel-build? #f - - #:parallel-tests? #f )) + (list hdf4 + hdf5 + java-slf4j-api + libjpeg-turbo + zlib)) (home-page "https://support.hdfgroup.org/products/java") (synopsis "Java interface for the HDF4 and HDF5 libraries") (description "Java HDF Interface (JHI) and Java HDF5 Interface (JHI5) use |