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<h3>
Andreas Tille 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/fbbbfaa8c714ee7d84af258399fd38bbfc850ade">fbbbfaa8</a></strong>
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<span>by Andreas Tille</span>
<i>at 2021-02-21T15:52:35+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Unfortunately we can only do a superficial for the moment
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<strong><a href="https://salsa.debian.org/med-team/prottest/-/commit/4fb1f6138726ee947b043fac7f156cd005d5f582">4fb1f613</a></strong>
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<span>by Andreas Tille</span>
<i>at 2021-02-21T15:58:15+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
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<h4>3 changed files:</h4>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
debian/tests/control
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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/006ef64028fe70f877338d448b31d83bd46581ed...4fb1f6138726ee947b043fac7f156cd005d5f582#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-5) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">prottest (3.4.2+dfsg-5) <span class="idiff left right">unstable</span>; 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"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="8" 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="8" 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">@@ -8,6 +8,9 @@ prottest (3.4.2+dfsg-5) UNRELEASED; urgency=medium</td>
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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"> [ Tassia Camoes Araujo ]</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> * Add functional test</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> Unfortunately we can only do a superficial for the moment until there</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> will be a way to run with phyml provided in Debian (see</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> https://github.com/ddarriba/prottest3/issues/12 )</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> [ Pierre Gruet ]</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> * Adding libbetter-appframework-java in runtime dependencies and its</span>
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<li id="83223a554d33ba7e1888274ff8ac43adb8147ba0">
<a href="https://salsa.debian.org/med-team/prottest/-/compare/006ef64028fe70f877338d448b31d83bd46581ed...4fb1f6138726ee947b043fac7f156cd005d5f582#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Tests: run-unit-test</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Depends: @</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Restrictions: allow-stderr</span></pre>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Restrictions: allow-stderr<span class="idiff left right">, superficial</span></span></pre>
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<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/prottest/-/compare/006ef64028fe70f877338d448b31d83bd46581ed...4fb1f6138726ee947b043fac7f156cd005d5f582#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">@@ -21,7 +21,22 @@ cd $AUTOPKGTEST_TMP</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</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">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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<pre style="margin: 0;">-<span id="LC25" 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="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="LC38" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># For the moment we'll leave the trivial test</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#prottest -i COX2_PF0016/alignment -t COX2_PF0016/tree -S 0 -all-distributions -F -AIC -BIC -tc 0.5</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#prottest -i Ribosomal_L5_PF00673/alignment -t Ribosomal_L5_PF00673/tree -S 0 -all-distributions -F -AIC -BIC -tc 0.5</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"PASS"</span></span></pre>
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