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<h3>
Julien Y. Dutheil pushed to branch master
at <a href="https://salsa.debian.org/med-team/physamp">Debian Med / physamp</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/physamp/commit/1fb8db55c8de3025018a5bd4182af6d4c86b7adc">1fb8db55</a></strong>
<div>
<span>by Julien Y. Dutheil</span>
<i>at 2017-09-04T20:13:21+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'upstream' of ssh://git.debian.org/git/debian-med/physamp into upstream
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/physamp/commit/62913cc63d6f099877a1a99b0d1fbf31cf746603">62913cc6</a></strong>
<div>
<span>by Julien Y. Dutheil</span>
<i>at 2018-04-18T16:05:29+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.1.0</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/physamp/commit/8c0f6598346160becc6b3ff03c988b5a9465c1fe">8c0f6598</a></strong>
<div>
<span>by Julien Y. Dutheil</span>
<i>at 2018-04-18T16:05:31+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/1.1.0'
Update to upstream version '1.1.0'
with Debian dir f6b44ccc8bc13c79e99d1ec09f2af68a25b143bb</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/physamp/commit/0f9aa36ad817145a2f563db298720039740259f6">0f9aa36a</a></strong>
<div>
<span>by Julien Y. Dutheil</span>
<i>at 2018-04-18T16:35:20+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Drafted version 1.1.0.
</pre>
</li>
</ul>
<h4>10 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">
CMakeLists.txt
</a>
</li>
<li class="file-stats">
<a href="#00fe7828d56d7a3ee4030d6cea057cf13f50e70c">
ChangeLog
</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="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#0b0bc73f3732038f9b84063ce13bdfb0570ad9bb">
docs/_config.yml
</a>
</li>
<li class="file-stats">
<a href="#d8da7e160dff5c85d568e01b91837ad248da8c01">
docs/physamp.texi
</a>
</li>
<li class="file-stats">
<a href="#eb90ea506343de121a819d4f8da53e3f22a32397">
physamp.spec
</a>
</li>
<li class="file-stats">
<a href="#5c96e3ebe415a6c6484e2da2761cd00425889fb5">
physamp/AlignmentOptimizer.cpp
</a>
</li>
<li class="file-stats">
<a href="#5ee57b55b516dc9afc2f61536ee25c46961d0356">
physamp/PhyloSampler.cpp
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9a2aa4db38d3115ed60da621e012c0efc0172aae">
<a href="https://salsa.debian.org/med-team/physamp/compare/e826a62c1ccf54fac927dddd3831a4c2e24452b8...0f9aa36ad817145a2f563db298720039740259f6#9a2aa4db38d3115ed60da621e012c0efc0172aae"><strong>CMakeLists.txt</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="59" 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="59" 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">@@ -59,6 +59,7 @@ else ()</td>
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<td class="diff-line-num new_line" data-linenumber="59" 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="LC59" class="line" lang="cmake"> <span class="c1" style="color: #998; font-style: italic;"># Generate command line args (always add -c to output compressed file to stdout)</span></span>
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<td class="diff-line-num old_line" data-linenumber="60" 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="60" 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="LC60" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">COMPRESS_PROGRAM</span><span class="si" style="color: #d14;">}</span> STREQUAL <span class="s2" style="color: #d14;">"gzip"</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="61" 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="61" 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="LC61" class="line" lang="cmake"> <span class="c1" style="color: #998; font-style: italic;"># -n for no timestamp in files (reproducible builds)</span></span>
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<td class="diff-line-num new old_line" data-linenumber="62" 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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<td class="diff-line-num new new_line" data-linenumber="62" 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="LC62" class="line" lang="cmake"> <span class="c1" style="color: #998; font-style: italic;"># -9 for maximum compression (lintian error)</span></span>
</pre>
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<td class="diff-line-num new_line" data-linenumber="63" 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="LC63" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span> <span class="p">(</span>COMPRESS_ARGS -c9n<span class="p">)</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="63" 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="64" 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="LC64" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">else</span> <span class="p">()</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="64" 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">
64
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<td class="diff-line-num new_line" data-linenumber="65" 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="LC65" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span> <span class="p">(</span>COMPRESS_ARGS -c<span class="p">)</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="73" 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="74" 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">@@ -73,7 +74,7 @@ IF (CMAKE_INSTALL_PREFIX)</td>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">ENDIF</span> <span class="p">(</span>CMAKE_INSTALL_PREFIX<span class="p">)</span></span>
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74
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<td class="diff-line-num new_line" data-linenumber="75" 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="LC75" class="line" lang="cmake"></span>
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<td class="diff-line-num new_line" data-linenumber="76" 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="LC76" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">include</span> <span class="p">(</span>GNUInstallDirs<span class="p">)</span></span>
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<td class="diff-line-num new_line old" data-linenumber="77" 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="LC76" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">find_package</span> <span class="p">(</span>bpp-phyl 1<span class="idiff left right">1</span>.0.0 REQUIRED<span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="77" 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="LC77" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">find_package</span> <span class="p">(</span>bpp-phyl 1<span class="idiff left right">2</span>.0.0 REQUIRED<span class="p">)</span></span>
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<td class="diff-line-num new_line" data-linenumber="78" 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="LC78" class="line" lang="cmake"></span>
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<td class="diff-line-num new_line" data-linenumber="79" 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="LC79" class="line" lang="cmake"></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># Subdirectories</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="86" 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="87" 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">@@ -86,10 +87,10 @@ ENDIF(NO_DEP_CHECK)</td>
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<td class="diff-line-num new_line" data-linenumber="87" 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="LC87" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># Packager</span></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>CPACK_PACKAGE_NAME <span class="s2" style="color: #d14;">"physamp"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>CPACK_PACKAGE_VENDOR <span class="s2" style="color: #d14;">"Julien Y. Dutheil"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>CPACK_PACKAGE_VERSION <span class="s2" style="color: #d14;">"1.<span class="idiff left right">0.3</span>"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>CPACK_PACKAGE_VERSION <span class="s2" style="color: #d14;">"1.<span class="idiff left right">1.0</span>"</span><span class="p">)</span></span>
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90
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91
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>CPACK_PACKAGE_VERSION_MAJOR <span class="s2" style="color: #d14;">"1"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>CPACK_PACKAGE_VERSION_MINOR <span class="s2" style="color: #d14;">"<span class="idiff left right">0</span>"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>CPACK_PACKAGE_VERSION_PATCH <span class="s2" style="color: #d14;">"<span class="idiff left right">3</span>"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>CPACK_PACKAGE_VERSION_MINOR <span class="s2" style="color: #d14;">"<span class="idiff left right">1</span>"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>CPACK_PACKAGE_VERSION_PATCH <span class="s2" style="color: #d14;">"<span class="idiff left right">0</span>"</span><span class="p">)</span></span>
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93
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94
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>CPACK_PACKAGE_DESCRIPTION_SUMMARY <span class="s2" style="color: #d14;">"The Phylogenetic Sampler package"</span><span class="p">)</span></span>
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94
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95
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>CPACK_RESOURCE_FILE_LICENSE <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">CMAKE_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">/LICENSE"</span><span class="p">)</span></span>
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96
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>CPACK_RESOURCE_FILE_AUTHORS <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">CMAKE_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">/AUTHORS"</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/physamp/compare/e826a62c1ccf54fac927dddd3831a4c2e24452b8...0f9aa36ad817145a2f563db298720039740259f6#00fe7828d56d7a3ee4030d6cea057cf13f50e70c"><strong>ChangeLog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">14/03/18 -*- Version 1.1.0 -*-</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">14/03/18 Julien Dutheil</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">* Compatibility update Bio++ 2.4.0.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">30/03/15 -*- Version 0.2.0 -*-</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">30/03/15 Julien Dutheil</span>
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<a href="https://salsa.debian.org/med-team/physamp/compare/e826a62c1ccf54fac927dddd3831a4c2e24452b8...0f9aa36ad817145a2f563db298720039740259f6#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">physamp (1.<span class="idiff left right">0.3-2</span>) UNRELEASED; urgency=medium</span>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">physamp (1.<span class="idiff left right">1.0-1</span>) UNRELEASED; 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"> [ Steffen Moeller ]</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * shortened single line description</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> * debian/upstream/metadata:</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> - reference to paper</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> - stated that there are no entries in catalogs</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="LC8" class="line" lang="plaintext"> -- Steffen Moeller <moeller@debian.org> Mon, 25 Sep 2017 14:46:05 +0200</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> [ Julien Y. Dutheil ]</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> * New upstream version.</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> * Compiles with -DCMAKE_BUILD_TYPE=RelWithDebInfo to generate debug info</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> (lintian warning)</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> * Point Vcs-fields to salsa.debian.org</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> * Standards-Version: 4.1.4</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"> -- Julien Dutheil <julien.dutheil@univ-montp2.fr> Wed, 18 Apr 2018 16:28:13 +0200</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">physamp (1.0.3-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/physamp/compare/e826a62c1ccf54fac927dddd3831a4c2e24452b8...0f9aa36ad817145a2f563db298720039740259f6#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">@@ -4,13 +4,13 @@ Uploaders: Andreas Tille <tille@debian.org>,</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> Julien Dutheil <julien.dutheil@univ-montp2.fr></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 (>= 1<span class="idiff left right">0</span>),</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper (>= 1<span class="idiff left right">1~</span>),</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> cmake,</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> texinfo,</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> libbpp-phyl-dev (>= 2.<span class="idiff left right">3.1</span>)</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">Standards-Version: 4.1.<span class="idiff left right">0</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">Vcs-Browser: https://<span class="idiff left right">anonscm.debian.org/cgit/debian-med</span>/physamp.git</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">Vcs-Git: https://<span class="idiff left right">anonscm.debian.org/git/debian-med</span>/physamp.git</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> libbpp-phyl-dev (>= 2.<span class="idiff left right">4.0</span>)</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">Standards-Version: 4.1.<span class="idiff left right">4</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Vcs-Browser: https://<span class="idiff left right">salsa.debian.org/med-team</span>/physamp.git</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Vcs-Git: https://<span class="idiff left right">salsa.debian.org/med-team</span>/physamp.git</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Homepage: https://jydu.github.io/physamp/</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">Package: physamp</span>
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<a href="https://salsa.debian.org/med-team/physamp/compare/e826a62c1ccf54fac927dddd3831a4c2e24452b8...0f9aa36ad817145a2f563db298720039740259f6#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">@@ -7,3 +7,8 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+bindnow</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></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"> dh $@</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">override_dh_auto_configure:</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> dh_auto_configure -- -DCMAKE_BUILD_TYPE=RelWithDebInfo</span>
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<a href="https://salsa.debian.org/med-team/physamp/compare/e826a62c1ccf54fac927dddd3831a4c2e24452b8...0f9aa36ad817145a2f563db298720039740259f6#0b0bc73f3732038f9b84063ce13bdfb0570ad9bb"><strong>docs/_config.yml</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="yaml"><span class="na" style="color: teal;">theme</span><span class="pi">:</span> <span class="s" style="color: #d14;">jekyll-theme-slate</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="na" style="color: teal;">theme</span><span class="pi">:</span> <span class="s" style="color: #d14;">jekyll-theme-slate</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"><span class="na" style="color: teal;">title</span><span class="pi">:</span> <span class="s" style="color: #d14;">PhySamp</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml"><span class="na" style="color: teal;">description</span><span class="pi">:</span> <span class="s" style="color: #d14;">Phylogenetic Sampling and Optimization of Sequence Alignments</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"><span class="na" style="color: teal;">show_downloads</span><span class="pi">:</span> <span class="no" style="color: teal;">true</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="yaml"><span class="na" style="color: teal;">share</span><span class="pi">:</span> <span class="no" style="color: teal;">true</span></span></pre>
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<a href="https://salsa.debian.org/med-team/physamp/compare/e826a62c1ccf54fac927dddd3831a4c2e24452b8...0f9aa36ad817145a2f563db298720039740259f6#d8da7e160dff5c85d568e01b91837ad248da8c01"><strong>docs/physamp.texi</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="objective_c"><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="n" style="color: #333;">input</span> <span class="n" style="color: #333;">texinfo</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">@c</span> <span class="o" style="font-weight: 600;">-*-</span><span class="n" style="color: #333;">texinfo</span><span class="o" style="font-weight: 600;">-*-</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="objective_c"><span class="err" style="color: #a61717; background-color: #e3d2d2;">@c</span> <span class="o" style="font-weight: 600;">%**</span><span class="n" style="color: #333;">start</span> <span class="n" style="color: #333;">of</span> <span class="n" style="color: #333;">header</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="objective_c"><span class="err" style="color: #a61717; background-color: #e3d2d2;">@setfilename</span> <span class="n" style="color: #333;">physamp</span><span class="p">.</span><span class="n" style="color: #333;">info</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="objective_c"><span class="err" style="color: #a61717; background-color: #e3d2d2;">@settitle</span> <span class="n" style="color: #333;">PhySamp</span> <span class="n" style="color: #333;">Manual</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;"><span class="idiff left">0</span></span><span class="p"><span class="idiff">.</span></span><span class="mi" style="color: #099;"><span class="idiff right">3</span></span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="objective_c"><span class="err" style="color: #a61717; background-color: #e3d2d2;">@settitle</span> <span class="n" style="color: #333;">PhySamp</span> <span class="n" style="color: #333;">Manual</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;"><span class="idiff left">1</span></span><span class="p"><span class="idiff">.</span></span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="objective_c"><span class="err" style="color: #a61717; background-color: #e3d2d2;">@documentencoding</span> <span class="n" style="color: #333;">UTF</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="objective_c"><span class="err" style="color: #a61717; background-color: #e3d2d2;">@afourpaper</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="objective_c"><span class="err" style="color: #a61717; background-color: #e3d2d2;">@dircategory</span> <span class="n" style="color: #333;">Science</span> <span class="n" style="color: #333;">Biology</span> <span class="n" style="color: #333;">Genetics</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,9 +13,9 @@</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="objective_c"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="objective_c"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="objective_c"><span class="err" style="color: #a61717; background-color: #e3d2d2;">@copying</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="objective_c"><span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">manual</span> <span class="n" style="color: #333;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">PhySamp</span> <span class="n" style="color: #333;">package</span><span class="p">,</span> <span class="n" style="color: #333;">version</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;"><span class="idiff left">0</span></span><span class="p"><span class="idiff">.</span></span><span class="mi" style="color: #099;"><span class="idiff right">3</span></span><span class="p">.</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="objective_c"><span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">manual</span> <span class="n" style="color: #333;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">PhySamp</span> <span class="n" style="color: #333;">package</span><span class="p">,</span> <span class="n" style="color: #333;">version</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;"><span class="idiff left">1</span></span><span class="p"><span class="idiff">.</span></span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">.</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="objective_c"></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="objective_c"><span class="n" style="color: #333;">Copyright</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">@copyright</span><span class="p">{}</span> <span class="mi" style="color: #099;">201<span class="idiff left right">7</span></span> <span class="n" style="color: #333;">Julien</span> <span class="n" style="color: #333;">Y</span><span class="p">.</span> <span class="n" style="color: #333;">Dutheil</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="objective_c"><span class="n" style="color: #333;">Copyright</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">@copyright</span><span class="p">{}</span> <span class="mi" style="color: #099;">201<span class="idiff left right">8</span></span> <span class="n" style="color: #333;">Julien</span> <span class="n" style="color: #333;">Y</span><span class="p">.</span> <span class="n" style="color: #333;">Dutheil</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="objective_c"><span class="k" style="font-weight: 600;">@end</span> <span class="n" style="color: #333;">copying</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="objective_c"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="objective_c"><span class="err" style="color: #a61717; background-color: #e3d2d2;">@titlepage</span></span>
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<a href="https://salsa.debian.org/med-team/physamp/compare/e826a62c1ccf54fac927dddd3831a4c2e24452b8...0f9aa36ad817145a2f563db298720039740259f6#eb90ea506343de121a819d4f8da53e3f22a32397"><strong>physamp.spec</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">%define _basename physamp</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">%define _version 1.0.1</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">%define _release 1</span>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">%define _prefix /usr</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="LC6" class="line" lang="plaintext">URL: https://github.com/jydu/<span class="idiff left right">maffilter</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">URL: https://github.com/jydu/<span class="idiff left right">physamp</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">Name: <span class="idiff left right">%{_basename}</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">Version: <span class="idiff left right">%{_version}</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">Release: <span class="idiff left right">%{_release</span>}</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Name: <span class="idiff left right">physamp</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Version: <span class="idiff left right">1.1.0</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Release: <span class="idiff left right">1%{?dist</span>}</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">License: GPL-3.0</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Vendor: Julien Dutheil</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">Source: %{<span class="idiff left right">_basename}-%{_</span>version}.tar.gz</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Source: %{<span class="idiff left right">name}-%{</span>version}.tar.gz</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Summary: The PhySamp package</span>
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15
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Group: Productivity/Scientific/Other</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="LC13" class="line" lang="plaintext"></span>
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<td class="diff-line-num old old_line" data-linenumber="17" 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">
17
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<td class="diff-line-num new_line old" data-linenumber="14" 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="LC17" class="line" lang="plaintext">Requires: libbpp-phyl1<span class="idiff left right">1 = 2.3.1</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="18" 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">
18
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<td class="diff-line-num new_line old" data-linenumber="14" 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="LC18" class="line" lang="plaintext">Requires: libbpp-seq1<span class="idiff left right">1 = 2.3.1</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="19" 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">
19
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<td class="diff-line-num new_line old" data-linenumber="14" 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="LC19" class="line" lang="plaintext">Requires: libbpp-core<span class="idiff left right">3 = 2.3.1</span></span>
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<td class="diff-line-num new old_line" data-linenumber="20" 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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<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">
14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Requires: libbpp-phyl1<span class="idiff left right">2 = 2.4.0</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="20" 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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<td class="diff-line-num new new_line" data-linenumber="15" 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">
15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Requires: libbpp-seq1<span class="idiff left right">2 = 2.4.0</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="20" 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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<td class="diff-line-num new new_line" data-linenumber="16" 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">
16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">Requires: libbpp-core<span class="idiff left right">4 = 2.4.0</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="20" 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">
20
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<td class="diff-line-num new_line" data-linenumber="17" 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">
17
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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="LC17" class="line" lang="plaintext"></span>
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<td class="diff-line-num old old_line" data-linenumber="21" 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">
21
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<td class="diff-line-num new_line old" data-linenumber="18" 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="LC21" class="line" lang="plaintext">BuildRoot: %{_builddir}/%{<span class="idiff left right">_base</span>name}-root</span>
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<td class="diff-line-num new old_line" data-linenumber="22" 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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<td class="diff-line-num new new_line" data-linenumber="18" 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">
18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">BuildRoot: %{_builddir}/%{name}-root</span>
</pre>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="22" 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">
22
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<td class="diff-line-num new_line" data-linenumber="19" 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">
19
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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="LC19" class="line" lang="plaintext">BuildRequires: cmake >= 2.8.11</span>
</pre>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="23" 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">
23
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<td class="diff-line-num new_line" data-linenumber="20" 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">
20
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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="LC20" class="line" lang="plaintext">BuildRequires: gcc-c++ >= 4.7.0</span>
</pre>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num 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">
24
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<td class="diff-line-num new_line" data-linenumber="21" 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">
21
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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="LC21" class="line" lang="plaintext">BuildRequires: groff</span>
</pre>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="25" 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">
25
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<td class="diff-line-num new_line" data-linenumber="22" 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">
22
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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="LC22" class="line" lang="plaintext">BuildRequires: texinfo >= 4.0.0</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="26" 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">
26
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<td class="diff-line-num new_line old" data-linenumber="23" 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="LC26" class="line" lang="plaintext">BuildRequires: libbpp-core<span class="idiff left right">3 = 2.3.1</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="27" 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">
27
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<td class="diff-line-num new_line old" data-linenumber="23" 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="LC27" class="line" lang="plaintext">BuildRequires: libbpp-core-devel = 2.<span class="idiff left right">3.1</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="28" 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">
28
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<td class="diff-line-num new_line old" data-linenumber="23" 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="LC28" class="line" lang="plaintext">BuildRequires: libbpp-seq1<span class="idiff left right">1 = 2.3.1</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="29" 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">
29
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<td class="diff-line-num new_line old" data-linenumber="23" 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="LC29" class="line" lang="plaintext">BuildRequires: libbpp-seq-devel = 2.<span class="idiff left right">3.1</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="30" 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">
30
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<td class="diff-line-num new_line old" data-linenumber="23" 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="LC30" class="line" lang="plaintext">BuildRequires: libbpp-phyl1<span class="idiff left right">1 = 2.3.1</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="31" 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">
31
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext">BuildRequires: libbpp-phyl-devel = 2.<span class="idiff left right">3.1</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="32" 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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<td class="diff-line-num new new_line" data-linenumber="23" 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">
23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">BuildRequires: libbpp-core<span class="idiff left right">4 = 2.4.0</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="32" 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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24
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">BuildRequires: libbpp-core-devel = 2.<span class="idiff left right">4.0</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="32" 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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<td class="diff-line-num new new_line" data-linenumber="25" 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">
25
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">BuildRequires: libbpp-seq1<span class="idiff left right">2 = 2.4.0</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="32" 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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<td class="diff-line-num new new_line" data-linenumber="26" 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">
26
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">BuildRequires: libbpp-seq-devel = 2.<span class="idiff left right">4.0</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="32" 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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<td class="diff-line-num new new_line" data-linenumber="27" 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">
27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">BuildRequires: libbpp-phyl1<span class="idiff left right">2 = 2.4.0</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="32" 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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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">BuildRequires: libbpp-phyl-devel = 2.<span class="idiff left right">4.0</span></span>
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29
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"></span>
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30
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"></span>
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34
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31
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext">AutoReq: yes</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">@@ -80,6 +77,9 @@ rm -rf $RPM_BUILD_ROOT</td>
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80
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77
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="plaintext">%{_prefix}/share/man/man1/bppphysamp.1.*</span>
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81
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78
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="plaintext"></span>
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82
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79
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="plaintext">%changelog</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext">* Wed Mar 14 2018 Julien Dutheil <dutheil@evolbio.mpg.de> 1.1.0-1</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext">- Compatibility update with Bio++ 2.4.0</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">- More options in branch panel</span>
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83
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83
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="plaintext">* Tue Jun 06 2017 Julien Dutheil <dutheil@evolbio.mpg.de> 1.0.1-1</span>
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84
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="plaintext">- Compatibility update with Bio++ 2.3.1</span>
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85
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="plaintext">* Fri May 26 2017 Julien Dutheil <dutheil@evolbio.mpg.de> 1.0.0-1</span>
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<li id="5c96e3ebe415a6c6484e2da2761cd00425889fb5">
<a href="https://salsa.debian.org/med-team/physamp/compare/e826a62c1ccf54fac927dddd3831a4c2e24452b8...0f9aa36ad817145a2f563db298720039740259f6#5c96e3ebe415a6c6484e2da2761cd00425889fb5"><strong>physamp/AlignmentOptimizer.cpp</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">@@ -401,8 +401,8 @@ class InputSelector: public Selector {</td>
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401
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401
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<pre style="margin: 0;"> <span id="LC401" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">argv</span><span class="p">)</span></span>
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402
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402
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<pre style="margin: 0;"> <span id="LC402" class="line" lang="cpp"><span class="p">{</span></span>
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403
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403
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<pre style="margin: 0;"> <span id="LC403" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"******************************************************************"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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404
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<pre style="margin: 0;">-<span id="LC404" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"* Bio++ Alignment Optimizer, version 1.<span class="idiff left right">0.2</span>. *"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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405
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<pre style="margin: 0;">-<span id="LC405" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"* Author: J. Dutheil Last Modif. <span class="idiff left right">20/07/17</span> *"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"* Bio++ Alignment Optimizer, version 1.<span class="idiff left right">1.0</span>. *"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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405
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"* Author: J. Dutheil Last Modif. <span class="idiff left right">14/03/18</span> *"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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406
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406
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<pre style="margin: 0;"> <span id="LC406" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"* E. Figuet *"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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407
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407
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<pre style="margin: 0;"> <span id="LC407" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"******************************************************************"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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408
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408
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<pre style="margin: 0;"> <span id="LC408" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/physamp/compare/e826a62c1ccf54fac927dddd3831a4c2e24452b8...0f9aa36ad817145a2f563db298720039740259f6#5ee57b55b516dc9afc2f61536ee25c46961d0356"><strong>physamp/PhyloSampler.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="83" 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">@@ -83,8 +83,8 @@ class Test {</td>
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83
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">argv</span><span class="p">)</span></span>
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84
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="cpp"><span class="p">{</span></span>
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85
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85
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"******************************************************************"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"* Bio++ Phylogenetic Sampler, version 1.<span class="idiff left right">0.2</span>. *"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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87
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"* Author: J. Dutheil Last Modif. <span class="idiff left right">20/07/17</span> *"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"* Bio++ Phylogenetic Sampler, version 1.<span class="idiff left right">1.0</span>. *"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"* Author: J. Dutheil Last Modif. <span class="idiff left right">14/03/18</span> *"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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88
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"******************************************************************"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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89
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="cpp"> </span>
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