[med-svn] [Git][med-team/libsis-jhdf5-java][master] 2 commits: args4j is now packaged - remove the means to work without it
Andreas Tille
gitlab at salsa.debian.org
Wed Sep 19 12:57:45 BST 2018
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 <tille at debian.org>
-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
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