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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/prottest">Debian Med / prottest</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/prottest/-/commit/fa47ffe07086565dba469982f81d35d04a2b40e4">fa47ffe0</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-10-29T18:05:12+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add patch to fix autopkgtests (Closes: #997886)
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<strong><a href="https://salsa.debian.org/med-team/prottest/-/commit/7c4fb9878df3898bd722ac9e4167442bfb7bebb5">7c4fb987</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-10-29T18:06:59+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/t/run-unit-tests: Remove un-necessary template
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/prottest/-/commit/37b0d72eff823911de381fc822af716e07dd9ad3">37b0d72e</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-10-29T18:06:59+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
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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="#02727f771798468c6dcb45df3bca81e95f90c4bc">
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+
debian/patches/read-stats-file.patch
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/prottest/-/compare/0078b6b6f9c161ca9fe2089b128794001ca1cc6b...37b0d72eff823911de381fc822af716e07dd9ad3#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">prottest (3.4.2+dfsg-7) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team Upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Add patch to fix autopkgtests (Closes: #997886)</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"> -- Nilesh Patra <nilesh@debian.org> Fri, 29 Oct 2021 18:05:16 +0530</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">prottest (3.4.2+dfsg-6) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> * Re-activate real test suggested by Tassia</span>
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<li id="02727f771798468c6dcb45df3bca81e95f90c4bc">
<a href="https://salsa.debian.org/med-team/prottest/-/compare/0078b6b6f9c161ca9fe2089b128794001ca1cc6b...37b0d72eff823911de381fc822af716e07dd9ad3#02727f771798468c6dcb45df3bca81e95f90c4bc"><strong>debian/patches/read-stats-file.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: properly resolve stats and tree files, add missing dot</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Author: Nilesh Patra <nilesh@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=997886</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: 2021-10-29</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/main/java/es/uvigo/darwin/prottest/exe/PhyMLv3AminoAcidRunEstimator.java</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/main/java/es/uvigo/darwin/prottest/exe/PhyMLv3AminoAcidRunEstimator.java</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -378,7 +378,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> if (!(statsFile.exists() && statsFile.canRead()))</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"> /* try with txt suffix */</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- statsFile = new File(workAlignment + STATS_FILE_SUFFIX + "txt");</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ statsFile = new File(workAlignment + STATS_FILE_SUFFIX + ".txt");</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> if (!(statsFile.exists() && statsFile.canRead()))</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> throw new StatsFileFormatException("PhyML", </span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> "Stats file does not exist. Please check if PhyML is working.");</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="p">@@ -389,7 +389,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> if (!(treeFile.exists() && treeFile.canRead()))</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> /* try with txt suffix */</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- treeFile = new File(workAlignment + TREE_FILE_SUFFIX + "txt");</span></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;">+ treeFile = new File(workAlignment + TREE_FILE_SUFFIX + ".txt");</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> if (!(treeFile.exists() && treeFile.canRead()))</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> throw new TreeFormatException(</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> "Tree file does not exist. Please check if PhyML is working correctly.");</span></pre>
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<a href="https://salsa.debian.org/med-team/prottest/-/compare/0078b6b6f9c161ca9fe2089b128794001ca1cc6b...37b0d72eff823911de381fc822af716e07dd9ad3#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">use_debian_packaged_phyml.patch</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">build.patch</span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">alter-import.patch</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">read-stats-file.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/prottest/-/compare/0078b6b6f9c161ca9fe2089b128794001ca1cc6b...37b0d72eff823911de381fc822af716e07dd9ad3#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</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">@@ -20,21 +20,6 @@ cd $AUTOPKGTEST_TMP</td>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/examples/<span class="k" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">.</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Run simulations with demo models</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Unfortunately there are issues with the Debian packaged phyml as described here</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># https://github.com/ddarriba/prottest3/issues/12</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working.</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Model................................ : FLU+I+G+F</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Number of parameters............... : 74 (21 + 53 branch length estimates)</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># ************************************************************</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Date : Sun Feb 21 14:44:46 UTC 2021</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Runtime: 0h:02:29</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Lk not initialized</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="shell">prottest <span class="nt" style="color: #000080;">-i</span> COX2_PF0016/alignment <span class="nt" style="color: #000080;">-t</span> COX2_PF0016/tree <span class="nt" style="color: #000080;">-S</span> 0 <span class="nt" style="color: #000080;">-all-distributions</span> <span class="nt" style="color: #000080;">-F</span> <span class="nt" style="color: #000080;">-AIC</span> <span class="nt" style="color: #000080;">-BIC</span> <span class="nt" style="color: #000080;">-tc</span> 0.5</span>
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="shell">prottest <span class="nt" style="color: #000080;">-i</span> Ribosomal_L5_PF00673/alignment <span class="nt" style="color: #000080;">-t</span> Ribosomal_L5_PF00673/tree <span class="nt" style="color: #000080;">-S</span> 0 <span class="nt" style="color: #000080;">-all-distributions</span> <span class="nt" style="color: #000080;">-F</span> <span class="nt" style="color: #000080;">-AIC</span> <span class="nt" style="color: #000080;">-BIC</span> <span class="nt" style="color: #000080;">-tc</span> 0.5</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="shell"></span>
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