Andreas Tille pushed to branch master at Debian Med / libsis-jhdf5-java
Commits: d6c6c49c by Andreas Tille at 2018-09-19T08:36:47Z args4j is now packaged - remove the means to work without it - - - - - 025bf9ad by Andreas Tille at 2018-09-19T10:57:32Z Drop unused patch, add -Ijni to includes - - - - - 5 changed files: - debian/README.source - debian/control - − debian/patches/fix_build_dir.patch - debian/patches/series - debian/rules Changes: ===================================== debian/README.source ===================================== @@ -11,25 +11,7 @@ also needs to link against the NCSA native library (via JNI) at runtime. So, trying to package sis-jhdf5: -The 'source' distribution' linked on the web page only have the Java source. -The real source you need is in SVN: - -svn co http://svncisd.ethz.ch/repos/cisd/jhdf5/trunk/ - -For compilation to succeed, we also need sis-base, not to be confused -with the entirely separate project at sis.apache.org! - -http://svncisd.ethz.ch/repos/cisd/base/trunk/ -See the libsis-base-java package for this. - -The code also depends on their own args4j library, but only for the CLI -under ch/systemsx/cisd/hdf5/h5ar/HDF5ArchiverMain.java which we can -simply leave out just now. I delete it from jsrc/ before compiling and -also leave out the h5ar.sh script which invokes it. Once args4j is packaged -this can be reinstated and the h5ar command can be added to /usr/bin -( http://bs-svn01.ethz.ch/repos/cisd/libraries/trunk/cisd-args4j/ ) - -So - can we exclude the ncsa.hdf.hdf5lib.* classes from sis-jhdf5 and +Can we exclude the ncsa.hdf.hdf5lib.* classes from sis-jhdf5 and compile it against the existing classes in /usr/share/java/jhdf5.jar? My conclusion is not, because... ===================================== debian/control ===================================== @@ -14,6 +14,7 @@ Build-Depends: debhelper (>= 11~), libcommons-io-java, libsis-base-java (>= 18.08.0~), libhdf5-dev (>> 1.8.13), + libargs4j-java, junit4, testng, libjmock2-java @@ -27,7 +28,8 @@ Architecture: all Depends: ${misc:Depends}, ${java:Depends}, libsis-jhdf5-jni (>= ${binary:Version}), - libsis-jhdf5-jni (<< ${source:Version}.1~) + libsis-jhdf5-jni (<< ${source:Version}.1~), + libargs4j-java Description: easy-to-use HDF library for Java JHDF5 is a Java binding to the HDF Group library for HDF5 focusing on ease-of-use, which was developed by CISD and is now maintained by ETH SIS. @@ -39,4 +41,9 @@ Architecture: any Depends: ${misc:Depends}, ${shlibs:Depends} Description: native libs used by libsis-jhdf5-java package - This package is only useful with libsis-jhdf5-java. + This package is only useful with libsis-jhdf5-java which is a + Java binding to the HDF Group library for HDF5 focusing on + ease-of-use, which was developed by CISD and is now maintained + by ETH SIS. + . + This package provides a native interface for the library. ===================================== debian/patches/fix_build_dir.patch deleted ===================================== @@ -1,21 +0,0 @@ -Author: Andreas Tille <[email protected]> -Last-Update: Mon, 13 Aug 2018 14:30:28 +0200 -Description: Do not make wrong assumptions about directory name - ---- a/javaproject.gradle -+++ b/javaproject.gradle -@@ -50,13 +50,9 @@ sourceSets { - buildDir = 'targets/gradle' - - buildscript { -- apply from: '../jhdf5/repository.gradle' -+ apply from: 'repository.gradle' - - repositories repositoryConfig -- -- dependencies { -- classpath 'cisd:cisd-ant-tasks:+' -- } - } - - repositories repositoryConfig ===================================== debian/patches/series ===================================== @@ -1,4 +1,3 @@ # fix_dodgy_cast.patch # remove_ch_rinn_imports.patch # load_native_debian.patch -fix_build_dir.patch ===================================== debian/rules ===================================== @@ -10,10 +10,9 @@ DPKG_EXPORT_BUILDFLAGS = 1 include /usr/share/dpkg/buildflags.mk include /usr/share/java/java_defaults.mk -CPPFLAGS += ${jvm_includes} +CPPFLAGS += ${jvm_includes} -Ijni TESTIGNORE = sourceTest/java/ch/systemsx/cisd/hdf5/HDF5RoundtripTest.java \ - sourceTest/java/ch/systemsx/cisd/hdf5/h5ar/HDF5ArchiverTest.java \ sourceTest/java/ch/systemsx/cisd/hdf5/io/HDF5DataSetRandomAccessFileTest.java %: @@ -37,13 +36,10 @@ override_dh_auto_build: $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -shared -fPIC -Wl,--exclude-libs,ALL \ -I/usr/lib/jvm/default-java/include/ -I/usr/include/hdf5/serial \ *.c jni/*.c -o libsis-jhdf5.so -lz -lhdf5_serial - # Java build - see README.source about the file being removed - mkdir jsrc ; cp -r source/java/ch source/java/ncsa jsrc - rm jsrc/ch/systemsx/cisd/hdf5/h5ar/HDF5ArchiverMain.java - # This line is still needed on Ubuntu 14.04 - jh_build sis-jhdf5.jar jsrc + jh_build sis-jhdf5.jar src override_dh_auto_test: +ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS))) # FIXME # Due to bug #842815 several tests are failing # To get at least some installable package these tests are ignored here @@ -72,3 +68,9 @@ override_dh_auto_test: # FIXME: Second part of hacking around bug #842815 mv debian/tmptestignore/* sourceTest/java/test/hdf5lib rmdir debian/tmptestignore +endif + +override_dh_install: + dh_install + mkdir -p debian/libsis-jhdf5-java/usr/bin + cp -a dist/bin/h5ar.sh debian/libsis-jhdf5-java/usr/bin View it on GitLab: https://salsa.debian.org/med-team/libsis-jhdf5-java/compare/fcbfbf7ccc76de73ae665cfb88e65d7e5626052c...025bf9add692f24ad7b07221ae5e9149bb5f2b47 -- View it on GitLab: https://salsa.debian.org/med-team/libsis-jhdf5-java/compare/fcbfbf7ccc76de73ae665cfb88e65d7e5626052c...025bf9add692f24ad7b07221ae5e9149bb5f2b47 You're receiving this email because of your account on salsa.debian.org.
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