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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/bowtie2">Debian Med / bowtie2</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/bowtie2/-/commit/2a392383a9a35aeba764aecb3fdad53351270d56">2a392383</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-12-15T19:08:29+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Patch Makefile to set date for BUILD_TIME using SOURCE_DATE_EPOCH.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bowtie2/-/commit/cffbcd98f098c472951a25f4fd04101430e039af">cffbcd98</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-12-15T19:12:02+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Force same hostname to enable reproducible builds
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bowtie2/-/commit/55996a0cd1710ef072368d1a26b3efab4fdc55e0">55996a0c</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-12-15T19:12:31+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.5.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bowtie2/-/commit/98654ead45a7a03eb942c1c14d6662f22dd539fd">98654ead</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-12-15T19:12:31+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: debhelper-compat 13
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bowtie2/-/commit/b6d914ea2202b39991ebe2592903a7b619c276b1">b6d914ea</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-12-15T20:56:12+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">use binaries installed to debian/tmp
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bowtie2/-/commit/0e91df1ae1fad5da9353f7e386967b911c06446a">0e91df1a</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-12-15T21:23:01+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#e4a2623f2af550012f50a627aaec40ddaaad98d5">
debian/bowtie2.install
</a>
</li>
<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="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#64628a335264e9862b9b687ae70cddf5e153ea9b">
<span class="new-file">
+
debian/patches/use-source-date-epoch-in-Makefile.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="e4a2623f2af550012f50a627aaec40ddaaad98d5">
<a href="https://salsa.debian.org/med-team/bowtie2/-/compare/d81f9a835181d06d1ab4f4c1ae0233efe4b3ae0e...0e91df1ae1fad5da9353f7e386967b911c06446a#e4a2623f2af550012f50a627aaec40ddaaad98d5"><strong>debian/bowtie2.install</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="php"><span class="n" style="color: #333;">bowtie2</span> <span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">bin</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="php"><span class="n" style="color: #333;">bowtie2</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">align</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">l</span> <span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">bin</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="php"><span class="n" style="color: #333;">bowtie2</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">align</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">s</span> <span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">bin</span></span>
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4
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<td class="diff-line-num new_line old" data-linenumber="1" 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">
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="php"><span class="n" style="color: #333;">bowtie2</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">build</span> <span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">bin</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="php"><span class="n" style="color: #333;">bowtie2</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">build</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">l</span> <span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">bin</span></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="php"><span class="n" style="color: #333;">bowtie2</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">build</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">s</span> <span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">bin</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="php"><span class="n" style="color: #333;">bowtie2</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">inspect</span> <span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">bin</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="php"><span class="n" style="color: #333;">bowtie2</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">inspect</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">l</span> <span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">bin</span></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="php"><span class="n" style="color: #333;">bowtie2</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">inspect</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">s</span> <span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">bin</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">local</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">bin</span> <span class="n" style="color: #333;">usr</span></span></pre>
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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/bowtie2/-/compare/d81f9a835181d06d1ab4f4c1ae0233efe4b3ae0e...0e91df1ae1fad5da9353f7e386967b911c06446a#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">bowtie2 (2.4.2-2) unstable; urgency=medium</span>
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<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"> [ Vagrant Cascadian ]</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Patch Makefile to set date for BUILD_TIME using SOURCE_DATE_EPOCH.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> Closes: #977435</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Force same hostname to enable reproducible builds</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> Closes: #977436</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"> [ Andreas Tille ]</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> * Standards-Version: 4.5.1 (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> * debhelper-compat 13 (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> * use binaries installed to debian/tmp</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"> -- Andreas Tille <tille@debian.org> Tue, 15 Dec 2020 21:07:56 +0100</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">bowtie2 (2.4.2-1) unstable; urgency=medium</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"> * New upstream version 2.4.2</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/bowtie2/-/compare/d81f9a835181d06d1ab4f4c1ae0233efe4b3ae0e...0e91df1ae1fad5da9353f7e386967b911c06446a#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">@@ -4,7 +4,7 @@ Uploaders: Alexandre Mestiashvili <mestia@debian.org>,</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">2</span>),</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">3</span>),</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> help2man,</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> libtbb-dev,</span>
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> python3,</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">@@ -14,7 +14,7 @@ Build-Depends: debhelper-compat (= 12),</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> libfile-which-perl,</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> zlib1g-dev,</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> libsimde-dev</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">Standards-Version: 4.5.<span class="idiff left right">0</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Standards-Version: 4.5.<span class="idiff left right">1</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/bowtie2</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/bowtie2.git</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Homepage: http://bowtie-bio.sourceforge.net/bowtie2</span>
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<a href="https://salsa.debian.org/med-team/bowtie2/-/compare/d81f9a835181d06d1ab4f4c1ae0233efe4b3ae0e...0e91df1ae1fad5da9353f7e386967b911c06446a#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</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">@@ -8,3 +8,4 @@ silence_tbb_deprecation_warning.patch</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">simde</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">correct_64bit_test</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">no_sanity</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">use-source-date-epoch-in-Makefile.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/bowtie2/-/compare/d81f9a835181d06d1ab4f4c1ae0233efe4b3ae0e...0e91df1ae1fad5da9353f7e386967b911c06446a#64628a335264e9862b9b687ae70cddf5e153ea9b"><strong>debian/patches/use-source-date-epoch-in-Makefile.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">From: Vagrant Cascadian <vagrant@reproducible-builds.org></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Subject: Patch Makefile to set date for BUILD_TIME using SOURCE_DATE_EPOCH.</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Last-Update: Mon, 14 Dec 2020 19:56:00 -0800</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/977435</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">https://reproducible-builds.org/docs/source-date-epoch/</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff">Index: bowtie2/Makefile</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bowtie2.orig/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bowtie2/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="p">@@ -279,7 +279,7 @@</span> both-debug: bowtie2-align-s-debug bowtie</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> DEFS := -fno-strict-aliasing \</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" \</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> -DBUILD_HOST="\"$${HOSTNAME:-`hostname`}\"" \</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- -DBUILD_TIME="\"`date -u`\"" \</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ -DBUILD_TIME="\"`LC_ALL=C date -u -d@$(SOURCE_DATE_EPOCH)`\"" \</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> -DCOMPILER_VERSION="\"`$(CXX) -v 2>&1 | tail -1`\"" \</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> $(FILE_FLAGS) \</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> $(PREF_DEF) \</span></pre>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/bowtie2/-/compare/d81f9a835181d06d1ab4f4c1ae0233efe4b3ae0e...0e91df1ae1fad5da9353f7e386967b911c06446a#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">@@ -24,7 +24,7 @@ export EXTRA_OPTIONS</td>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> dh $@</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">override_dh_auto_build:</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext"> LD_PRELOAD= dh_auto_build -- EXTRA_FLAGS="-std=c++98 $(LDFLAGS)" $(EXTRA_OPTIONS)</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> LD_PRELOAD= dh_auto_build -- EXTRA_FLAGS="-std=c++98 $(LDFLAGS)" $(EXTRA_OPTIONS)<span class="idiff left right"> HOSTNAME=reproducible-hostname</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">override_dh_auto_test:</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext">ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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