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<h3>
Liubov Chuprikova pushed to branch master
at <a href="https://salsa.debian.org/med-team/bedtools">Debian Med / bedtools</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/bedtools/commit/75ec9125738229c886da4f93cf90a59fd6daa10d">75ec9125</a></strong>
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<span>by Liubov Chuprikova</span>
<i>at 2018-05-22T17:14:48+00:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Autopkgtest: fixed outdated run-unit-test
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<h4>2 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="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/bedtools/commit/75ec9125738229c886da4f93cf90a59fd6daa10d#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">bedtools (2.27.1+dfsg-2) 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"> [ Andreas Tille ]</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * Install autopkgtest script as /usr/share/doc/bedtools/run-unit-test</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> * Point Vcs fields to salsa.debian.org</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> [ Liubov Chuprikova ]</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * Fix "autopkgtest fails while it succeeded in the past"</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> updated run-unit-test to match new upstream tests</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> Closes: #894781</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Thu, 05 Apr 2018 09:00:44 +0200</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">bedtools (2.27.1+dfsg-1) unstable; urgency=medium</span>
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<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/bedtools/commit/75ec9125738229c886da4f93cf90a59fd6daa10d#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5" 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="5" 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">@@ -5,7 +5,6 @@ if [ "$ADTTMP" = "" ] ; then</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="nv" style="color: teal;">$ADTTMP</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: navy;">-x</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Copy test suite there</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="shell">cp <span class="nt" style="color: navy;">-a</span> /usr/share/bedtools/test <span class="nv" style="color: teal;">$ADTTMP</span></span>
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<td class="diff-line-num old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="shell"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -16,14 +15,5 @@ ln -s /usr/share/bedtools/genomes</td>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Enter the directory and run the tests</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: teal;">$ADTTMP</span>/test</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Test script is seeking for lower case dir</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-d</span> groupBy <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>ln <span class="nt" style="color: navy;">-s</span> groupBy groupby</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="shell"><span class="nv" style="color: teal;">DATA</span><span class="o" style="font-weight: 600;">=</span>/usr/share/bedtools/data <span class="nv" style="color: teal;">BT</span><span class="o" style="font-weight: 600;">=</span>/usr/bin/bedtools sh test.sh | tee test.sh.output</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="shell"></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;"># Did it fail ?</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="shell"><span class="nv" style="color: teal;">TESTFAILED</span><span class="o" style="font-weight: 600;">=</span>0</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="shell"><span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: navy;">-q</span> fail test.sh.output <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: teal;">TESTFAILED</span><span class="o" style="font-weight: 600;">=</span>1</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="nv" style="color: teal;">DATA</span><span class="o" style="font-weight: 600;">=</span>/usr/share/bedtools/data <span class="nv" style="color: teal;">BT</span><span class="o" style="font-weight: 600;">=</span>/usr/bin/bedtools sh test.sh</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="shell"></span></pre>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="shell"><span class="nb" style="color: #0086b3;">exit</span> <span class="nv" style="color: teal;">$TESTFAILED</span></span></pre>
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