gnu: Add java-cisd-jhdf5.
* gnu/packages/java.scm (java-cisd-jhdf5): New variable.
This commit is contained in:
Ricardo Wurmus
parent
04ddca26e6
commit
2f0d041816
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@ -59,6 +59,7 @@
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#:use-module (gnu packages image)
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#:use-module (gnu packages libffi)
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#:use-module (gnu packages linux) ;alsa
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#:use-module (gnu packages maths)
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#:use-module (gnu packages web)
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#:use-module (gnu packages wget)
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#:use-module (gnu packages pkg-config)
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@ -2347,6 +2348,181 @@ libraries from the SIS division at ETH Zurich like jHDF5.")
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(description "This package provides a parser for command line arguments.")
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(license license:asl2.0))))
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(define-public java-cisd-jhdf5
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(let ((revision 39162)
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(base-version "14.12.6"))
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(package
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(name "java-cisd-jhdf5")
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(version (string-append base-version "-" (number->string revision)))
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(source (origin
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(method svn-fetch)
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(uri (svn-reference
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(url (string-append "http://svnsis.ethz.ch/repos/cisd/"
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"jhdf5/tags/release/"
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(version-major+minor base-version)
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".x/" base-version "/jhdf5/"))
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(revision revision)))
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(file-name (string-append "java-cisd-jhdf5-" version "-checkout"))
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(sha256
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(base32
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"13i17s2hn0q9drdqvp8csy7770p3hdbh9rp30ihln2ldkfawdmz0"))
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(modules '((guix build utils)))
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(snippet
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'(begin
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;; Delete included gradle jar
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(delete-file-recursively "gradle/wrapper")
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;; Delete pre-built native libraries
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(delete-file-recursively "libs")
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#t))))
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(build-system ant-build-system)
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(arguments
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`(#:make-flags '("-file" "build/build.xml")
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#:build-target "jar-all"
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#:test-target "jar-test"
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#:jdk ,icedtea-8
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#:phases
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(modify-phases %standard-phases
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;; Don't erase results from the build phase when building tests.
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(add-after 'unpack 'separate-test-target-from-clean
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(lambda _
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(substitute* "build/build.xml"
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(("\"jar-test\" depends=\"clean, ")
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"\"jar-test\" depends=\""))
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#t))
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(add-after 'unpack 'unpack-build-resources
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(lambda* (#:key inputs #:allow-other-keys)
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(copy-recursively (assoc-ref inputs "build-resources")
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"../build_resources")
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(delete-file-recursively "../build_resources/lib/")
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(mkdir-p "../build_resources/lib")
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;; Remove dependency on classycle
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(substitute* "../build_resources/ant/build-common.xml"
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(("<taskdef name=\"dependency-checker.*") "")
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(("classname=\"classycle.*") "")
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(("classpath=\"\\$\\{lib\\}/classycle.*") ""))
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;; Remove dependency on svn
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(substitute* "build/build.xml"
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(("<build-info.*") "")
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(("\\$\\{revision.number\\}")
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,(number->string revision))
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(("\\$\\{version.number\\}") ,base-version))
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#t))
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(add-after 'unpack-build-resources 'fix-dependencies
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(lambda* (#:key inputs #:allow-other-keys)
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(substitute* "../build_resources/ant/build-common.xml"
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(("../libraries/testng/testng-jdk15.jar")
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(string-append (assoc-ref inputs "java-testng")
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"/share/java/java-testng.jar")))
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(substitute* "build/build.xml"
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(("\\$\\{lib\\}/sis-base/sis-base.jar")
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(string-append (assoc-ref inputs "java-cisd-base")
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"/share/java/sis-base.jar"))
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(("\\$\\{lib\\}/cisd-args4j/cisd-args4j.jar")
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(string-append (assoc-ref inputs "java-cisd-args4j")
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"/share/java/cisd-args4j.jar"))
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(("\\$\\{lib\\}/commons-lang/commons-lang.jar")
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(string-append (assoc-ref inputs "java-commons-lang")
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"/share/java/commons-lang-"
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,(package-version java-commons-lang) ".jar"))
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(("\\$\\{lib\\}/commons-io/commons-io.jar")
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(string-append (assoc-ref inputs "java-commons-io")
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"/share/java/commons-io-"
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,(package-version java-commons-io)
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"-SNAPSHOT.jar"))
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(("\\$\\{lib\\}/testng/testng-jdk15.jar")
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(string-append (assoc-ref inputs "java-testng")
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"/share/java/java-testng.jar"))
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(("\\$\\{lib\\}/junit4/junit.jar")
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(string-append (assoc-ref inputs "java-junit")
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"/share/java/junit.jar"))
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(("\\$\\{lib\\}/jmock/hamcrest/hamcrest-core.jar")
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(string-append (assoc-ref inputs "java-hamcrest-core")
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"/share/java/hamcrest-core.jar")))
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;; Remove dependency on ch.rinn.restrictions
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(with-directory-excursion "source/java/ch/systemsx/cisd/hdf5/"
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(substitute* '("BitSetConversionUtils.java"
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"HDF5Utils.java")
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(("import ch.rinn.restrictions.Private;") "")
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(("@Private") "")))
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(with-directory-excursion "sourceTest/java/ch/systemsx/cisd/hdf5/"
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(substitute* '("BitSetConversionTest.java"
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"h5ar/HDF5ArchiverTest.java")
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(("import ch.rinn.restrictions.Friend;") "")
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(("@Friend.*") ""))
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;; Remove leftovers from removing @Friend
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(substitute* "h5ar/HDF5ArchiverTest.java"
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(("\\{ HDF5Archiver.class, IdCache.class, LinkRecord.class \\}\\)")
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"")))
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#t))
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(add-before 'configure 'build-native-library
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(lambda* (#:key inputs #:allow-other-keys)
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(let ((jdk (assoc-ref inputs "jdk"))
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(hdf5 (assoc-ref inputs "hdf5"))
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(dir ,(match (%current-system)
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("i686-linux"
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"i386-Linux")
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((or "armhf-linux" "aarch64-linux")
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"arm-Linux")
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((or "x86_64-linux")
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"amd64-Linux")
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(_ "unknown-Linux"))))
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(with-directory-excursion "source/c"
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(apply invoke `("gcc" "-shared" "-O3"
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"-fPIC"
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"-Wl,--exclude-libs,ALL"
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,@(find-files "jhdf5" "\\.c$")
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,@(find-files "hdf-java" "\\.c$")
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,(string-append "-I" hdf5 "/include")
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,(string-append "-I" jdk "/include")
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,(string-append "-I" jdk "/include/linux")
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,(string-append hdf5 "/lib/libhdf5.a")
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"-o" "libjhdf5.so" "-lz")))
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(install-file "source/c/libjhdf5.so"
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(string-append "libs/native/jhdf5/" dir))
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#t)))
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;; In the "check" phase we only build the test executable.
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(add-after 'check 'run-tests
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(lambda _
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(invoke "java" "-jar" "targets/dist/sis-jhdf5-test.jar")
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(delete-file "targets/dist/sis-jhdf5-test.jar")
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#t))
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(replace 'install
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(install-jars "targets/dist")))))
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(inputs
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`(("java-cisd-base" ,java-cisd-base)
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("java-cisd-args4j" ,java-cisd-args4j)
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("java-commons-lang" ,java-commons-lang)
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("java-commons-io" ,java-commons-io)
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("hdf5" ,hdf5)
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("zlib" ,zlib)))
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(native-inputs
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`(("jdk" ,icedtea-8)
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("java-testng" ,java-testng)
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("java-junit" ,java-junit)
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("java-jmock" ,java-jmock)
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("java-hamcrest-core" ,java-hamcrest-core)
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("build-resources"
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,(origin
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(method svn-fetch)
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(uri (svn-reference
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(url (string-append "http://svnsis.ethz.ch/repos/cisd/"
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"jhdf5/tags/release/"
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(version-major+minor base-version)
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".x/" base-version
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"/build_resources/"))
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(revision revision)))
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(sha256
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(base32
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"0b6335gkm4x895rac6kfg9d3rpq0sy19ph4zpg2gyw6asfsisjhk"))))))
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(home-page "https://wiki-bsse.ethz.ch/display/JHDF5/")
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(synopsis "Java binding for HDF5")
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(description "JHDF5 is a high-level API in Java for reading and writing
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HDF5 files, building on the libraries provided by the HDF Group.")
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;; The C sources are under a non-copyleft license, which looks like a
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;; variant of the BSD licenses. The whole package is under the ASL2.0.
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(license (list license:asl2.0
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(license:non-copyleft "file://source/c/COPYING"))))))
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(define-public java-classpathx-servletapi
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(package
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(name "java-classpathx-servletapi")
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