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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/libsis-jhdf5-java">Debian Med / libsis-jhdf5-java</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/libsis-jhdf5-java/commit/e323eda668e2b8bafc29ba8c212c099651c7890a">e323eda6</a></strong>
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<span>by Andreas Tille</span>
<i>at 2018-09-27T12:11:51Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Clean up rules and document current issue with private header of hdf5 lib H5private.h
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<h4>1 changed file:</h4>
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/libsis-jhdf5-java/commit/e323eda668e2b8bafc29ba8c212c099651c7890a#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -16,31 +16,22 @@ TESTIGNORE = sourceTest/java/ch/systemsx/cisd/hdf5/HDF5RoundtripTest.java \</td>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> sourceTest/java/ch/systemsx/cisd/hdf5/io/HDF5DataSetRandomAccessFileTest.java</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">%:</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"> dh $@ --with javahelper<span class="idiff left right"> --buildsystem=gradle</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> dh $@ --with javahelper</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext">override_jh_installlibs:</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"> mv targets/gradle/libs/sis-jhdf5-1.jar targets/gradle/libs/sis-jhdf5.jar</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"> jh_installlibs --version-strip='[~pre1]*[+]git[.0-9a-f]*[+]dfsg[.0-9]*'</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext">_override_dh_auto_clean:</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext"> rm -rf build *.jar</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext"> rm -rf source/c/*.log</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext"> rm -rf source/c/*.so</span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext"> # Stuff generated during testing</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext"> find sourceTest/java -name '*.class' -delete</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext"> cd sourceTest/java && rm -f *.hdf *.h5</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext"> rm -f sourceTest/java/sourceTest/java/test/hdf5lib/h5ex_g_iterate.hdf</span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext"> rm -rf test-output targets</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext"> #Things that we'd probably exclude from the orig.tar.gz anyway</span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext"> rm -rf jsrc lib ./sourceTest/java/jni</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="plaintext">_override_dh_auto_build:</span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="plaintext"> # C build</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">override_dh_auto_build:</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> dh_auto_build</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> # Create JNI manually since this is not part of the build system</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> # Upsteam seems to `cd source/c` and call a script which in turn calls compile_hdf5_gcc.sh</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> # In this script hdf5 source is unpacked, possibly patched, build and used for the JNI build</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> # Most problematic issue is that private header H5private.h is used</span>
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39
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> cd source/c && \</span>
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40
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -shared -fPIC -Wl,--exclude-libs,ALL \</span>
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41
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"> -I/usr/lib/jvm/default-java/include/ -I/usr/include/hdf5/serial \</span>
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42
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext"> *.c jni/*.c -o libsis-jhdf5.so -lz -lhdf5_serial</span>
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43
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext"> jh_build sis-jhdf5.jar src</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> *.c jni/*.c -o libsis-jhdf5.so -lz -lhdf5_serial</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">override_jh_installlibs:</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> mv targets/gradle/libs/sis-jhdf5-1.jar targets/gradle/libs/sis-jhdf5.jar</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> jh_installlibs --version-strip='[~pre1]*[+]git[.0-9a-f]*[+]dfsg[.0-9]*'</span>
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44
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext"></span>
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45
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext">_override_dh_auto_test:</span>
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46
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext">ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -73,8 +64,3 @@ ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</td>
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73
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64
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="plaintext"> mv debian/tmptestignore/* sourceTest/java/test/hdf5lib</span>
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<td class="diff-line-num old_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
74
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65
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="plaintext"> rmdir debian/tmptestignore</span>
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75
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="plaintext">endif</span></pre>
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76
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="plaintext"></span>
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77
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="plaintext">_override_dh_install:</span>
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<td class="diff-line-num old old_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="plaintext"> dh_install</span>
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<td class="diff-line-num old old_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="plaintext"> mkdir -p debian/libsis-jhdf5-java/usr/bin</span>
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80
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="plaintext"> cp -a dist/bin/h5ar.sh debian/libsis-jhdf5-java/usr/bin</span></pre>
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