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<h3>
Pierre Gruet pushed to branch master
at <a href="https://salsa.debian.org/med-team/libsis-jhdf5-java">Debian Med / libsis-jhdf5-java</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/libsis-jhdf5-java/-/commit/4d1d27836208c0a4a36a18df2826ffbdd95861c1">4d1d2783</a></strong>
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<span>by Pierre Gruet</span>
<i>at 2020-05-07T23:19:04+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Changing the name of generated .so to avoid name collisions
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<h4>3 changed files:</h4>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<a href="#47333971d6f08d8864c87124d2db3c6e159b4145">
debian/patches/loading_jni_in_java_file.patch
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/libsis-jhdf5-java/-/commit/4d1d27836208c0a4a36a18df2826ffbdd95861c1#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="mosel"><span class="n" style="color: #333;">libsis</span><span class="p">-</span><span class="n" style="color: #333;">jhdf5</span><span class="p">-</span><span class="n" style="color: #333;">java</span> <span class="p">(</span><span class="m" style="color: #099;">19.04.0</span><span class="p">+</span><span class="n" style="color: #333;">dfsg</span><span class="p">-</span><span class="m" style="color: #099;">2</span><span class="p">)</span> <span class="n" style="color: #333;">UNRELEASED</span><span class="p">;</span> <span class="n" style="color: #333;">urgency</span><span class="p">=</span><span class="n" style="color: #333;">medium</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="mosel"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Changing</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">name</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="p">.</span><span class="n" style="color: #333;">so</span> <span class="n" style="color: #333;">file</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">libsis</span><span class="p">-</span><span class="n" style="color: #333;">jhdf5</span><span class="p">-</span><span class="n" style="color: #333;">jni</span> <span class="p">(</span><span class="n" style="color: #333;">Closes</span><span class="p">:</span> <span class="p">#</span><span class="m" style="color: #099;">959955</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="mosel"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="mosel"> <span class="p">--</span> <span class="n" style="color: #333;">Pierre</span> <span class="n" style="color: #333;">Gruet</span> <span class="p"><</span><span class="n" style="color: #333;">pgtdebian</span><span class="p">@</span><span class="n" style="color: #333;">free</span><span class="p">.</span><span class="n" style="color: #333;">fr</span><span class="p">></span> <span class="n" style="color: #333;">Thu</span><span class="p">,</span> <span class="m" style="color: #099;">07</span> <span class="n" style="color: #333;">May</span> <span class="m" style="color: #099;">2020</span> <span class="m" style="color: #099;">21</span><span class="p">:</span><span class="m" style="color: #099;">46</span><span class="p">:</span><span class="m" style="color: #099;">07</span> <span class="p">+</span><span class="m" style="color: #099;">0200</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="mosel"></span>
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<td class="diff-line-num new_line" data-linenumber="7" 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">
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="mosel"><span class="n" style="color: #333;">libsis</span><span class="p">-</span><span class="n" style="color: #333;">jhdf5</span><span class="p">-</span><span class="n" style="color: #333;">java</span> <span class="p">(</span><span class="m" style="color: #099;">19.04.0</span><span class="p">+</span><span class="n" style="color: #333;">dfsg</span><span class="p">-</span><span class="m" style="color: #099;">1</span><span class="p">)</span> <span class="n" style="color: #333;">unstable</span><span class="p">;</span> <span class="n" style="color: #333;">urgency</span><span class="p">=</span><span class="n" style="color: #333;">medium</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="mosel"> <span class="p">[</span> <span class="n" style="color: #333;">Andreas</span> <span class="n" style="color: #333;">Tille</span> <span class="p">]</span></span>
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<li id="47333971d6f08d8864c87124d2db3c6e159b4145">
<a href="https://salsa.debian.org/med-team/libsis-jhdf5-java/-/commit/4d1d27836208c0a4a36a18df2826ffbdd95861c1#47333971d6f08d8864c87124d2db3c6e159b4145"><strong>debian/patches/loading_jni_in_java_file.patch</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff"><span class="p">Description: adding loading of jni part in Java code</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> In two files, the library has to be loaded by calling System.loadLibrary.</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"> In two other ones, the library call has to be changed.</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="p">Author: Pierre Gruet <pgtdebian@free.fr></span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Last-Update: 2020-05-0<span class="idiff left right">3</span></span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">Last-Update: 2020-05-0<span class="idiff left right">7</span></span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff">--- a/source/java/ch/systemsx/cisd/hdf5/io/HDF5DataSetRandomAccessFile.java</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/source/java/ch/systemsx/cisd/hdf5/io/HDF5DataSetRandomAccessFile.java</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,7 +10,7 @@ Last-Update: 2020-05-03</td>
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> {</span>
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9
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<td class="diff-line-num new_line" data-linenumber="11" 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">
11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"> this(createHDF5ReaderOrWriter(hdf5File, readOnly), dataSetPath, creationStorageFeature,</span>
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10
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<td class="diff-line-num new_line" data-linenumber="12" 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">
12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"> size, opaqueTagOrNull, true);</span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ System.loadLibrary("jhdf5");</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ System.loadLibrary("<span class="idiff left right">sis-</span>jhdf5");</span></span>
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12
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"> }</span>
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13
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<td class="diff-line-num new_line" data-linenumber="15" 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">
15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"> </span>
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14
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<td class="diff-line-num 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">
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="diff"> private static IHDF5Reader createHDF5ReaderOrWriter(File hdf5File, boolean readOnly)</span>
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<td class="diff-line-num unfold js-unfold old_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="diff-line-num unfold js-unfold new_line" data-linenumber="18" 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">@@ -16,7 +18,29 @@ Last-Update: 2020-05-03</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="diff"> HDF5GenericStorageFeatures creationStorageFeature, int size, String opaqueTagOrNull,</span>
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17
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="diff"> boolean closeReaderOnCloseFile) throws IOExceptionUnchecked</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="diff"> {</span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ System.loadLibrary("jhdf5");</span></span>
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<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ System.loadLibrary("<span class="idiff left right">sis-</span>jhdf5");</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="diff"> this.closeReaderOnCloseFile = closeReaderOnCloseFile;</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="diff"> final boolean readOnly = (reader instanceof IHDF5Writer) == false;</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="diff"> try</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/source/java/ch/systemsx/cisd/hdf5/BuildAndEnvironmentInfo.java</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/source/java/ch/systemsx/cisd/hdf5/BuildAndEnvironmentInfo.java</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="p">@@ -26,7 +26,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> */</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> public class BuildAndEnvironmentInfo extends AbstractBuildAndEnvironmentInfo</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- private final static String BASE = "jhdf5";</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ private final static String BASE = "sis-jhdf5";</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> public final static BuildAndEnvironmentInfo INSTANCE = new BuildAndEnvironmentInfo();</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/source/java/hdf/hdf5lib/H5.java</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/source/java/hdf/hdf5lib/H5.java</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="p">@@ -235,7 +235,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> return;</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if (NativeLibraryUtilities.loadNativeLibrary("jhdf5") == false)</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (NativeLibraryUtilities.loadNativeLibrary("sis-jhdf5") == false)</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> throw new UnsupportedOperationException("No suitable HDF5 native library found for this platform.");</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> }</span></pre>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/libsis-jhdf5-java/-/commit/4d1d27836208c0a4a36a18df2826ffbdd95861c1#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -20,7 +20,7 @@ override_dh_auto_clean:</td>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> -rm -rf debian/libsis-jhdf5-java/ debian/libsis-jhdf5-jni/ debian/tmp/ debian/.debhelper/</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> -rm debian/*debhelper* debian/files debian/*.substvars</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> -rm -rf targets/ test-output/</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"> -rm source/c/libjhdf5.so</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> -rm source/c/lib<span class="idiff left right">sis-</span>jhdf5.so</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_build:</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> dh_auto_build</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -32,7 +32,7 @@ override_dh_auto_build:</td>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"> cd source/c && \</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"> $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -shared -fPIC -Wl,--exclude-libs,ALL \</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"> -I/usr/lib/jvm/default-java/include/ -I/usr/include/hdf5/serial \</span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext"> *.c jni/*.c -o libjhdf5.so -lz -lhdf5_serial</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> *.c jni/*.c -o lib<span class="idiff left right">sis-</span>jhdf5.so -lz -lhdf5_serial</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_jh_installlibs:</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"> # The jar that is build is placed in targets/gradle/libs, and its name</span>
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