diff options
Diffstat (limited to 'gnu/packages/maths.scm')
| -rw-r--r-- | gnu/packages/maths.scm | 229 |
1 files changed, 119 insertions, 110 deletions
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 5671b83c00..7370db5883 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -887,121 +887,130 @@ extremely large and complex data collections.") (define-public hdf-java (package - (name "hdf-java") - (version "3.3.2") - (source - (origin - (method url-fetch) - (uri (string-append - "http://www.hdfgroup.org/ftp/HDF5/releases/HDF-JAVA/hdfjni-" - version "/src/CMake-hdfjava-" version ".tar.gz")) - (sha256 - (base32 "0m1gp2aspcblqzmpqbdpfp6giskws85ds6p5gz8sx7asyp7wznpr")) - (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)))) - (build-system gnu-build-system) - (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))) - (inputs - `(("hdf4" ,hdf4) - ("hdf5" ,hdf5) - ("zlib" ,zlib) - ("libjpeg" ,libjpeg) - ("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=" (assoc-ref %build-inputs "zlib") "/lib/libz.so") - (string-append "JPEGLIB=" - (assoc-ref %build-inputs "libjpeg") "/lib/libjpeg.so") - "LLEXT=so") - - #:phases - (modify-phases %standard-phases - (add-before 'configure 'chdir-to-source - (lambda _ (chdir ,(string-append "hdfjava-" version)))) - (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") - (string-append (assoc-ref inputs "slf4j-api") - "/share/java/slf4j-api.jar"))) - ;; Replace outdated config.sub and config.guess: - (with-directory-excursion "config" - (for-each (lambda (file) - (copy-file - (string-append (assoc-ref inputs "automake") - "/share/automake-1.15/" file) file)) - '("config.sub" "config.guess"))) - (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 - (map (lambda (i) - (string-append (assoc-ref inputs i) - "/share/java/" i ".jar")) - '("junit" "hamcrest-core" "slf4j-api" "slf4j-simple"))) - (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") - (string-append (assoc-ref inputs "coreutils") - "/bin/test")) - (("/usr/bin/uname") - (string-append (assoc-ref inputs "coreutils") - "/bin/uname")) - (("CLASSPATH=[^\n]*") - (string-append "CLASSPATH=" class-path))) - (setenv "CLASSPATH" class-path)) - #t)) - (add-before 'check 'build-examples - (lambda _ - (zero? (apply system* `("javac" - ,@(find-files "examples" ".*\\.java"))))))) + (name "hdf-java") + (version "3.3.2") + (source + (origin + (method url-fetch) + (uri (string-append + "http://www.hdfgroup.org/ftp/HDF5/releases/HDF-JAVA/hdfjni-" + version "/src/CMake-hdfjava-" version ".tar.gz")) + (sha256 + (base32 "0m1gp2aspcblqzmpqbdpfp6giskws85ds6p5gz8sx7asyp7wznpr")) + (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)))) + (build-system gnu-build-system) + (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))) + (inputs + `(("hdf4" ,hdf4) + ("hdf5" ,hdf5) + ("zlib" ,zlib) + ("libjpeg" ,libjpeg) + ("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=" (assoc-ref %build-inputs "zlib") "/lib/libz.so") + (string-append "JPEGLIB=" + (assoc-ref %build-inputs "libjpeg") "/lib/libjpeg.so") + "LLEXT=so") - #:parallel-build? #f + #: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") + (string-append (assoc-ref inputs "slf4j-api") + "/share/java/slf4j-api.jar"))) + ;; Replace outdated config.sub and config.guess: + (with-directory-excursion "config" + (for-each (lambda (file) + (install-file + (string-append (assoc-ref inputs "automake") + "/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 + (map (lambda (i) + (string-append (assoc-ref inputs i) + "/share/java/" i ".jar")) + '("junit" "hamcrest-core" "slf4j-api" "slf4j-simple"))) + (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") + (string-append (assoc-ref inputs "coreutils") + "/bin/test")) + (("/usr/bin/uname") + (string-append (assoc-ref inputs "coreutils") + "/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-tests? #f )) - (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 + #:parallel-build? #f + + #:parallel-tests? #f )) + (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 the Java Native Interface to wrap the HDF4 and HDF5 libraries, which are implemented in C.") - ;; BSD-style license: - (license (license:x11-style - "https://support.hdfgroup.org/ftp/HDF5/hdf-java\ + ;; BSD-style license: + (license (license:x11-style + "https://support.hdfgroup.org/ftp/HDF5/hdf-java\ /current/src/unpacked/COPYING")))) (define-public hdf-eos2 |