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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/mrbayes">Debian Med / mrbayes</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/mrbayes/-/commit/b97f15d4f3d80e68c37958dfe4f82570668b7fa4">b97f15d4</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-07-18T14:31:34+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Avoid baseline violation by disabling AX_EXT
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mrbayes/-/commit/613a233a3dd8374f1bc6be3a83c113632f8a6fd0">613a233a</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-07-18T14:31:50+02:00</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/mrbayes/-/commit/993bc29b9cbff3bbbe69251f5b46a9ef9c67853d">993bc29b</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-07-18T14:31:55+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Add salsa-ci file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mrbayes/-/commit/0472b78a91b610def1f42670190e3d08523f7825">0472b78a</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-07-18T14:31:55+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Rules-Requires-Root: no
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mrbayes/-/commit/64b119f509a1cba53aff1897eb31993c10a37162">64b119f5</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-07-18T14:32:06+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse.
Changes-By: lintian-brush
Fixes: lintian: upstream-metadata-missing-bug-tracking
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html
Fixes: lintian: upstream-metadata-missing-repository
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-repository.html
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mrbayes/-/commit/074fbdbee6e49dbeeab825a9b2921c61561b5cf4">074fbdbe</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-07-18T14:41:20+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Override dh_missing with --list-missing
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mrbayes/-/commit/eea344b312147227ec57e07033fb2399bc792e1e">eea344b3</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-07-18T14:44:26+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>7 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#aee72e39293495ea3a7efc9fce5d096361fcd925">
<span class="new-file">
+
debian/patches/no_baseline_violation.patch
</span>
</a>
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<li class="file-stats">
<a href="#b1dbf22e88351ec0d5d1d1a7f53295504b480e61">
<span class="new-file">
+
debian/salsa-ci.yml
</span>
</a>
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<li class="file-stats">
<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
debian/upstream/metadata
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</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/mrbayes/-/compare/ebc09a0905f2007cff9ff640bc6832c3b3ac14b1...eea344b312147227ec57e07033fb2399bc792e1e#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">mrbayes (3.2.7a-3) unstable; urgency=medium</span>
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<td class="diff-line-num new new_line" data-linenumber="2" 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="LC2" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="3" 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="LC3" class="line" lang="plaintext"> * Avoid baseline violation by disabling AX_EXT</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"> Closes: #958125, #964787</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"> * debhelper-compat 13 (routine-update)</span>
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<td class="diff-line-num new new_line" data-linenumber="6" 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="LC6" class="line" lang="plaintext"> * Add salsa-ci file (routine-update)</span>
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<td class="diff-line-num new new_line" data-linenumber="7" 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="LC7" class="line" lang="plaintext"> * Rules-Requires-Root: no (routine-update)</span>
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<td class="diff-line-num new new_line" data-linenumber="8" 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="LC8" class="line" lang="plaintext"> * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,</span>
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<td class="diff-line-num new new_line" data-linenumber="9" 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="LC9" class="line" lang="plaintext"> Repository-Browse.</span>
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<td class="diff-line-num new new_line" data-linenumber="10" 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="LC10" class="line" lang="plaintext"> * Override dh_missing with --list-missing since due to the duplicate</span>
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<td class="diff-line-num new new_line" data-linenumber="11" 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="LC11" class="line" lang="plaintext"> build some examples would be installed twice otherwise</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></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"> -- Andreas Tille <tille@debian.org> Sat, 18 Jul 2020 14:41:26 +0200</span>
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<td class="diff-line-num new new_line" data-linenumber="14" 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="LC14" class="line" lang="plaintext"></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">mrbayes (3.2.7a-2) unstable; urgency=medium</span>
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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="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> * Fix binary-all build</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/mrbayes/-/compare/ebc09a0905f2007cff9ff640bc6832c3b3ac14b1...eea344b312147227ec57e07033fb2399bc792e1e#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: Steffen Moeller <moeller@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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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Section: science</span>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Priority: optional</span>
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7
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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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7
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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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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> libreadline-dev,</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">
9
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> mpi-default-dev,</span>
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> libhmsbeagle-dev,</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" 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="14" 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">@@ -14,6 +14,7 @@ Standards-Version: 4.5.0</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/mrbayes</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/mrbayes.git</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Homepage: http://mrbayes.csit.fsu.edu/</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Rules-Requires-Root: no</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">Package: mrbayes</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Architecture: any</span>
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<li id="aee72e39293495ea3a7efc9fce5d096361fcd925">
<a href="https://salsa.debian.org/med-team/mrbayes/-/compare/ebc09a0905f2007cff9ff640bc6832c3b3ac14b1...eea344b312147227ec57e07033fb2399bc792e1e#aee72e39293495ea3a7efc9fce5d096361fcd925"><strong>debian/patches/no_baseline_violation.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Avoid baseline violation by disabling AX_EXT</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/958125</span></span>
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<pre style="margin: 0;">+<span id="LC3" 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="LC4" class="line" lang="diff"><span class="p">Last-Update: Sat, 18 Jul 2020 14:29:31 +0200</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">--- a/configure.ac</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/configure.ac</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -241,7 +241,7 @@</span> AX_CFLAGS_WARN_ALL</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"> # Check for SIMD (etc.) extensions supported by hardware and compiler</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> # (-msse2 etc.)</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-AX_EXT</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# AX_EXT</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> AS_IF([test "x$enable_sse" = "xno"],</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> [AC_DEFINE([DISABLE_SSE], [1],</span></pre>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/mrbayes/-/compare/ebc09a0905f2007cff9ff640bc6832c3b3ac14b1...eea344b312147227ec57e07033fb2399bc792e1e#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">no_rpath.patch</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">autoreconf.patch</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">no_baseline_violation.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/mrbayes/-/compare/ebc09a0905f2007cff9ff640bc6832c3b3ac14b1...eea344b312147227ec57e07033fb2399bc792e1e#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">@@ -38,3 +38,6 @@ override_dh_installdeb:</td>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"> find debian/.debhelper/mrbayes-mpi/dbgsym-root/usr/lib/debug -name "*.debug" -delete ; \</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"> fi</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext"> dh_installdeb</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">override_dh_missing:</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> dh_missing --list-missing</span></pre>
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<a href="https://salsa.debian.org/med-team/mrbayes/-/compare/ebc09a0905f2007cff9ff640bc6832c3b3ac14b1...eea344b312147227ec57e07033fb2399bc792e1e#b1dbf22e88351ec0d5d1d1a7f53295504b480e61"><strong>debian/salsa-ci.yml</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="nn" style="color: #555;">---</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">include</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml</span></span></pre>
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<a href="https://salsa.debian.org/med-team/mrbayes/-/compare/ebc09a0905f2007cff9ff640bc6832c3b3ac14b1...eea344b312147227ec57e07033fb2399bc792e1e#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Bug-Database: https://github.com/NBISweden/MrBayes/issues</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Bug-Submit: https://github.com/NBISweden/MrBayes/issues/new</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Reference:</span>
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2
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> - Author: ></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> Fredrik Ronquist and Maxim Teslenko and Paul van der Mark and</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="47" 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="49" 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">@@ -47,3 +49,5 @@ Registry:</td>
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47
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49
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext"> Entry: OMICS_04237</span>
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48
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50
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext"> - Name: conda:bioconda</span>
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49
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext"> Entry: mrbayes</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">Repository: https://github.com/NBISweden/MrBayes.git</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">Repository-Browse: https://github.com/NBISweden/MrBayes</span></pre>
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