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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/pbbam">Debian Med / pbbam</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/pbbam/commit/eb33a6d6e195e224643cec68fc5558bc2df4ddb7">eb33a6d6</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-09-06T11:52:03Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">DEP3
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pbbam/commit/bf39bf82b564908853795dd489747c3ac168cc44">bf39bf82</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-09-06T12:27:26Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove paragraph with removed files
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pbbam/commit/f21b69b1d5408863d7f08f60ea5e42ba4245f1b4">f21b69b1</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-09-06T12:28:33Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Respect DEB_BUILD_OPTIONS in override_dh_auto_test
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pbbam/commit/9e07afdc1c0499add380f4ec92f1fcb5cf17eb6c">9e07afdc</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-09-06T12:29:30Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">hardening=+all
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pbbam/commit/bebb30604c1b1cd2fec217641e835e68f4ec453f">bebb3060</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-09-06T12:39:17Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
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<li class="file-stats">
<a href="#ff915ae138b6737d7ec8867ad801818d7c99e76a">
debian/patches/fix_gtest_depcheck.patch
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/pbbam/compare/7ee473fe6b0d840b1fc3b4ccc7ce4a0713962dd3...bebb30604c1b1cd2fec217641e835e68f4ec453f#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">pbbam (0.18.0+dfsg-1) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">pbbam (0.18.0+dfsg-1) <span class="idiff left right">unstable</span>; urgency=medium</span>
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<td class="line_content noteable_line" 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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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> [ Andreas Tille ]</span>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * Team upload.</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -10,11 +10,13 @@ pbbam (0.18.0+dfsg-1) UNRELEASED; urgency=medium</td>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> * Standards-Version: 4.2.1</span>
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<td class="diff-line-num old_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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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> * Use d-shlibs</span>
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<td class="diff-line-num old_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">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> * Remove unneeded trigger</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> * Respect DEB_BUILD_OPTIONS in override_dh_auto_test</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> * hardening=+all</span>
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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"> [ Fabian Kloetzl ]</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> * fix dependency check for meson</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="LC17" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> T<span class="idiff left right">ue, 21 Aug 2018 21:31:37</span> +0200</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> T<span class="idiff left right">hu, 06 Sep 2018 14:29:53</span> +0200</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">pbbam (0.7.4+ds-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/pbbam/compare/7ee473fe6b0d840b1fc3b4ccc7ce4a0713962dd3...bebb30604c1b1cd2fec217641e835e68f4ec453f#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">@@ -9,16 +9,6 @@ Files: *</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Copyright: 2014-2016 Pacific Biosciences of California, Inc. <devnet@pacificbiosciences.com></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">License: PacBio-BSD-3-Clause</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">Files: cmake/FindCSharp.cmake</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> cmake/FindMono.cmake</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> cmake/UseCSharp.cmake</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> cmake/UseDotNetFrameworkSdk.cmake</span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> cmake/UseMono.cmake</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">Copyright: 2006-2010 Mathieu Malaterre <mathieu.malaterre@gmail.com></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">Comment: These files are from GDCM (as indicated in the file headers).</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"> The license terms have been retrieved from there.</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext">License: MM-BSD-3-Clause</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="LC12" class="line" lang="plaintext">Files: src/pugixml/*</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Copyright: 2006-2014 Arseny Kapoulkine <arseny.kapoulkine@gmail.com></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> 2003 Kristen Wegner <kristen@tima.net></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">@@ -61,30 +51,6 @@ License: PacBio-BSD-3-Clause</td>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext"> OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF</span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="plaintext"> SUCH DAMAGE.</span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="plaintext">License: MM-BSD-3-clause</span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="plaintext"> Redistribution and use in source and binary forms, with or without</span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="plaintext"> modification, are permitted provided that the following conditions are met:</span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="plaintext"> 1. Redistributions of source code must retain the above copyright notice,</span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="plaintext"> this list of conditions and the following disclaimer.</span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="plaintext"> 3. Neither name of Mathieu Malaterre, or CREATIS, nor the names of any</span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="plaintext"> contributors (CNRS, INSERM, UCB, Universite Lyon I), may be used to</span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="plaintext">License: BSD-3-Clause</span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="plaintext"> Redistribution and use in source and binary forms, with or without</span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="plaintext"> modification, are permitted provided that the following conditions</span>
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<a href="https://salsa.debian.org/med-team/pbbam/compare/7ee473fe6b0d840b1fc3b4ccc7ce4a0713962dd3...bebb30604c1b1cd2fec217641e835e68f4ec453f#ff915ae138b6737d7ec8867ad801818d7c99e76a"><strong>debian/patches/fix_gtest_depcheck.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Author: Andreas Tille, Fabian Klötzl</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Last-Update: 2018-09-05 14:50:07 +0000</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Description: Use Debian packaged gtest</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"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/meson.build</span></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/tests/meson.build</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -6,7 +6,7 @@ if not pbbam_cram_script.found()</span></span>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/pbbam/compare/7ee473fe6b0d840b1fc3b4ccc7ce4a0713962dd3...bebb30604c1b1cd2fec217641e835e68f4ec453f#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">@@ -4,6 +4,8 @@</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">export LC_ALL=C.UTF-8</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">include /usr/share/dpkg/default.mk</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">export DEB_BUILD_MAINT_OPTIONS=hardening=+all</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">DEB_VERSION_UPSTREAM := $(subst +ds,,$(DEB_VERSION_UPSTREAM))</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">generated_data_dir = $(CURDIR)/gendata</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></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">@@ -23,6 +25,7 @@ generated_data_dir = $(CURDIR)/gendata</td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">## -DPacBioBAM_wrap_r=ON</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_test: $(subst .t.in,.deb.t,$(wildcard tests/src/cram/pb*.t.in))</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"> mkdir -p $(generated_data_dir)</span>
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27
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"> python tests/scripts/generate_data.py $(CURDIR)/tests/data $(generated_data_dir)</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"> # Fix broken PATH</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="32" 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="35" 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">@@ -32,6 +35,7 @@ override_dh_auto_test: $(subst .t.in,.deb.t,$(wildcard tests/src/cram/pb*.t.in))</td>
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32
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext"> LIBDIR=`find $$PWD -name lib -type d`; \</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext"> PATH="$$BINDIR:$(PATH)" LD_LIBRARY_PATH="$$LIBDIR:$(LD_LIBRARY_PATH)" \</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext"> cram -v $^</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">endif</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext">override_dh_installchangelogs:</span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext"> dh_installchangelogs CHANGELOG.md</span>
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