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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/pbseqlib">Debian Med / pbseqlib</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/pbseqlib/commit/8663c859a14b607ef327e5e566b2ffc509607a6e">8663c859</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-19T10:30:58Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.4.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pbseqlib/commit/0d538a07c6fbbd9a155719b98413d44aa97bc116">0d538a07</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-19T10:31:00Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debian/copyright: use spaces rather than tabs to start continuation lines.
Fixes lintian: tab-in-licence-text
See https://lintian.debian.org/tags/tab-in-licence-text.html for more details.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pbseqlib/commit/ab4105e5cf11dbe5028d77cd86dc32d68fc42c39">ab4105e5</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-19T11:17:38Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">There is no point to check for gtest since its installed via Build-Depends
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pbseqlib/commit/07290a0d439204f3880621f11d57a55ea639b73b">07290a0d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-19T16:55:39Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Make sure hdf5 headers will be included, todo: link to hdf5 lib
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pbseqlib/commit/2b5192df0d9df3a3babb85a7853f52ab5c7c54e4">2b5192df</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-19T16:56:36Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Polish changelog
</pre>
</li>
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<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
</a>
</li>
<li class="file-stats">
<a href="#8d9aad5fc2842ec6547b13e57733b48a1b48bf26">
<span class="new-file">
+
debian/patches/meson.patch
</span>
</a>
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/pbseqlib/compare/c856ecf05cf78f6b4e58452ce0b97ad76dac4e16...2b5192df0d9df3a3babb85a7853f52ab5c7c54e4#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">pbseqlib (5.3.3+dfsg-1) UNRELEASED; urgency=medium</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> [ Helmut Grohne ]</span>
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<td class="diff-line-num new new_line" data-linenumber="4" 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">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Covnert libpbseq-dev to Architecture: any. (Closes: #940327)</span>
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<td class="diff-line-num new new_line" data-linenumber="5" 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">
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="6" 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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> [ Andreas Tille ]</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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> * Add myself to Uploaders to have at least one human uploader after</span>
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<td class="diff-line-num new_line" data-linenumber="8" 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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> Afif removed himself.</span>
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<td class="diff-line-num new_line" data-linenumber="9" 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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> * New upstream version</span>
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<td class="diff-line-num new_line" data-linenumber="10" 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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> * debhelper-compat 12</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> * Standards-Version: 4.4.0</span>
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<td class="diff-line-num old_line" data-linenumber="9" 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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<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">
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> * Add new Build-Depends needed for testing</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> <span class="idiff left right">[ Helmut Grohne ]</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> <span class="idiff left right">* Covnert libpbseq-dev to Architecture: any. (Closes: #940327)</span></span>
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<td class="diff-line-num new old_line" data-linenumber="13" 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">
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> * Standards-Version: 4.4.1</span>
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<td class="diff-line-num new new_line" data-linenumber="13" 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">
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> <span class="idiff left right">* debian/copyright: use spaces rather than tabs to start continuation</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> <span class="idiff left right"> lines.</span></span>
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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">
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Mon, 05 Aug 2019 16:53:23 +0200</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/pbseqlib/compare/c856ecf05cf78f6b4e58452ce0b97ad76dac4e16...2b5192df0d9df3a3babb85a7853f52ab5c7c54e4#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -16,7 +16,7 @@ Build-Depends: debhelper-compat (= 12),</td>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> libpbbam-dev (>= 0.18.0+dfsg-1~),</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> libhts-dev,</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> libgtest-dev <!nocheck></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">Standards-Version: 4.4.<span class="idiff left right">0</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">Standards-Version: 4.4.<span class="idiff left right">1</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/pbseqlib</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/pbseqlib.git</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">Homepage: https://github.com/PacificBiosciences/blasr_libcpp</span>
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<a href="https://salsa.debian.org/med-team/pbseqlib/compare/c856ecf05cf78f6b4e58452ce0b97ad76dac4e16...2b5192df0d9df3a3babb85a7853f52ab5c7c54e4#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</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">@@ -22,7 +22,7 @@ License: Larsson</td>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">Files: pbdata/MD5Utils.cpp</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> pbdata/MD5Utils.hpp</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">Copyright: 1991-1992 RSA Data Security, Inc.</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext"><span class="idiff left right"> </span> 1995 Mordechai T. Abzug</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"><span class="idiff left right"> </span> 1995 Mordechai T. Abzug</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">License: RSA</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">Files: debian/*</span>
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<a href="https://salsa.debian.org/med-team/pbseqlib/compare/c856ecf05cf78f6b4e58452ce0b97ad76dac4e16...2b5192df0d9df3a3babb85a7853f52ab5c7c54e4#8d9aad5fc2842ec6547b13e57733b48a1b48bf26"><strong>debian/patches/meson.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Fri, 13 Dec 2019 22:17:15 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Description: There is no point to check for gtest since its installed via Build-Depends</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">--- a/unittest/meson.build</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/unittest/meson.build</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -11,7 +11,7 @@</span> subdir('pbdata')</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> # Sources #</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> ###########</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-libblasr_gtest_dep = dependency('gtest_main', fallback : ['gtest', 'gtest_main_dep'])</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+libblasr_gtest_dep = dependency('gtest', main: true)</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> libblasr_unittest = executable(</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> 'libblasr_unittest', [</span></pre>
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<a href="https://salsa.debian.org/med-team/pbseqlib/compare/c856ecf05cf78f6b4e58452ce0b97ad76dac4e16...2b5192df0d9df3a3babb85a7853f52ab5c7c54e4#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">hdf5-1.10.1-support.patch</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">hdf5-1.10.0-support.patch</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">meson.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/pbseqlib/compare/c856ecf05cf78f6b4e58452ce0b97ad76dac4e16...2b5192df0d9df3a3babb85a7853f52ab5c7c54e4#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">@@ -8,7 +8,7 @@ export HDF5_LIB = /usr/lib/$(DEB_HOST_MULTIARCH)/hdf5/serial</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">export GTEST_INC = /usr/include</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">export GTEST_SRCDIR = /usr/src/gtest</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">export DEB_CFLAGS_MAINT_APPEND=-O3</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">export DEB_CFLAGS_MAINT_APPEND=-O3<span class="idiff left right"> -I$(HDF5_INC)</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">export DEB_CXXFLAGS_MAINT_APPEND=-O3</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">export LDLIBS += -lpbbam</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">@@ -16,7 +16,7 @@ export LDLIBS += -lpbbam</td>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"># Needed for patch hdf5-1.10.1-support.patch</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">HDF5_VERSION := $(shell grep 'HDF5 Version' $(HDF5_LIB)/libhdf5.settings | awk '{print $$3}')</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">ifeq (yes,$(shell dpkg --compare-versions $(HDF5_VERSION) '>=' 1.10.1 && echo yes))</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">export DEB_CPPFLAGS_MAINT_APPEND<span class="idiff left right">=-DHAVE_HDF5_1_10_1</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">export DEB_CPPFLAGS_MAINT_APPEND<span class="idiff left right">+=-DHAVE_HDF5_1_10_1 $(DEB_CFLAGS_MAINT_APPEND)</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">endif</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">export DEB_BUILD_MAINT_OPTIONS=hardening=+all</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="24" 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>
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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">@@ -24,9 +24,6 @@ export DEB_BUILD_MAINT_OPTIONS=hardening=+all</td>
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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"> dh $@</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext">override_dh_auto_build:</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext"> dh_auto_build -- PREFIX_INC=..</span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">override_dh_auto_test:</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"># Ignore the return code because some tests</span>
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