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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/tree-puzzle">Debian Med / tree-puzzle</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/tree-puzzle/-/commit/c729e8b336de8caf69254b4d82648eddeb1b4ac0">c729e8b3</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-05-14T08:12:58+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Team upload
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/tree-puzzle/-/commit/ebcadc98d89f596170d75b0fc4cfc0cd574d4121">ebcadc98</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-05-14T08:13:51+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Another permissions fix
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/tree-puzzle/-/commit/8d6b2077538347ff704f419b623bedf20c660285">8d6b2077</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-05-14T08:33:49+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">DEP3
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/tree-puzzle/-/commit/a45d8eee4650085cb4929c4416bcb35924483f47">a45d8eee</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-05-14T08:34:33+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove my weak attempt to fix patch results which is not needed any more
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/tree-puzzle/-/commit/266d74687a5137ee1501a02ca8bfaea2a68b7505">266d7468</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-05-14T08:39:05+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#4d4a768106c2d60ca99f80e94bba2852f16941ba">
<span class="deleted-file">
−
debian/patches/patch_test_results.patch
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<li class="file-stats">
<a href="#6465ab63e7895d21eab6f9449464bbd8a9744d5e">
debian/patches/update_test_results.patch
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/tree-puzzle/-/compare/62de255c7949933fb1898221e44c44abd24681e5...266d74687a5137ee1501a02ca8bfaea2a68b7505#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">tree-puzzle (5.3~rc16+dfsg-1) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">tree-puzzle (5.3~rc16+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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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"> * Team upload.</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> [ Andreas Tille ]</span>
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<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> * New upstream pre-release</span>
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<td class="diff-line-num unfold js-unfold old_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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -17,9 +19,6 @@ tree-puzzle (5.3~rc16+dfsg-1) UNRELEASED; urgency=medium</td>
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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">
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> * debian/patches/fix-mpi3-build.patch:</span>
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<td class="diff-line-num old_line" data-linenumber="18" 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="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">
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> - Fix FTBFS due to the new MPI-3.0 API (Closes: #951984).</span>
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<td class="diff-line-num old_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">
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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">
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> [ Andreas Tille ]</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> * Fix more permissions</span>
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<td class="diff-line-num old old_line" data-linenumber="22" 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="LC22" class="line" lang="plaintext"></span>
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<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">
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> [ Pranav Ballaney ]</span>
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<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">
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> * Patch check-* files for tests (Closes: #806214)</span>
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<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">
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> * Enable build time tests</span>
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<li id="4d4a768106c2d60ca99f80e94bba2852f16941ba">
<a href="https://salsa.debian.org/med-team/tree-puzzle/-/compare/62de255c7949933fb1898221e44c44abd24681e5...266d74687a5137ee1501a02ca8bfaea2a68b7505#4d4a768106c2d60ca99f80e94bba2852f16941ba"><strong>debian/patches/patch_test_results.patch</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Wed, 25 Nov 2015 13:10:19 +0100</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Description: Some research was done why basically all tests are</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"> failing. It turned out that the results used for comparison</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"> really diverge from the actuall results. This patch might</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"> solve the may be simplest diversion - others are way more complex.</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"> .</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"> This needs to be discussed with upstream!</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"> This patch is not actually used in the packaging just provided</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"> here as an example for potential problems.</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"> .</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"> To check single patches by calling the scripts in dir tests</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"> make sure you call these by</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"> .</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"> VERSION=5.2 ./<scriptname></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"> .</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"> Otherwise you will simply get an sed error.</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff">--- a/tests/check-qp-pure-bin</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/check-qp-pure-bin</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"><span class="p">@@ -168,8 +168,8 @@</span> trees that have been generated in the 10</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"> Bipartitions included in the quartet puzzling tree:</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"> (bipartition with sequences in input order : number of times seen)</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- *..** : 1000</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"> *...* : 1000</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ *..** : 1000</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"> Congruent bipartitions occurred in 50% or less, not included in </span>
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31
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"> the consensus tree:</span></pre>
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<a href="https://salsa.debian.org/med-team/tree-puzzle/-/compare/62de255c7949933fb1898221e44c44abd24681e5...266d74687a5137ee1501a02ca8bfaea2a68b7505#6465ab63e7895d21eab6f9449464bbd8a9744d5e"><strong>debian/patches/update_test_results.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Pranav Ballaney <ballaneypranav@gmail.com></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: 2020-05-14 02:52:25 +0530</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Description: Test results to compare with are just wrong as discussed</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> with upstream</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"> See https://lists.debian.org/debian-med/2020/05/msg00118.html</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"></span>
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1
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff">--- a/tests/check-cons-pure-prot</span>
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2
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/check-cons-pure-prot</span></span>
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3
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"><span class="p">@@ -15,10 +15,36 @@</span> SEQUENCE ALIGNMENT</span>
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<a href="https://salsa.debian.org/med-team/tree-puzzle/-/compare/62de255c7949933fb1898221e44c44abd24681e5...266d74687a5137ee1501a02ca8bfaea2a68b7505#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -40,6 +40,7 @@ override_dh_fixperms:</td>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext"> -name "*.b" -o \</span>
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41
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext"> -name "*.ctrees" -o \</span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext"> -name "*.n" -o \</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> -name "*.nucl" -o \</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext"> -name "*.phy" -o \</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext"> -name "*.trees" -o \</span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext"> -name "check-*-bin" -o \</span>
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