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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/khmer">Debian Med / khmer</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/khmer/-/commit/647094e88f38b49a44d36f04142d5f9f8668b863">647094e8</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-01-04T14:15:25+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix autopkgtests for newer pytest: s/pyarg/pyargs/
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/khmer/-/commit/59838ef4b7818c2ec480c7c4090974547f83baaf">59838ef4</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-01-04T14:18:00+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.5.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/khmer/-/commit/39ad852d088d70a1f088f8f33e4881f82586e27c">39ad852d</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-01-04T14:18:01+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: debhelper-compat 13
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/khmer/-/commit/7f0d97ab576aaf03e9141e6e59438d15d1f47236">7f0d97ab</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-01-04T14:18:11+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update renamed lintian tag names in lintian overrides.
Changes-By: lintian-brush
Fixes: lintian: renamed-tag
See-also: https://lintian.debian.org/tags/renamed-tag.html
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/khmer/-/commit/ef789e06e299792121c55389bc13445138ef58d8">ef789e06</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-01-04T14:18:11+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Replace use of deprecated $ADTTMP with $AUTOPKGTEST_TMP.
Changes-By: lintian-brush
Fixes: lintian: uses-deprecated-adttmp
See-also: https://lintian.debian.org/tags/uses-deprecated-adttmp.html
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/khmer/-/commit/1359150389fbab0ed6e9a0f554c638125fb91940">13591503</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-01-04T14:18:12+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
</pre>
</li>
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<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#1ecfa413953b6eab7ee70017897a75cd6b39d1f2">
debian/khmer.lintian-overrides
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<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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<li class="file-stats">
<a href="#a4360f3cb7376623ee88518c0d4e686d60834ac6">
debian/tests/test-liboxli-dev
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</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/khmer/-/compare/ed4b04f892fb1e19f275055fe523a304387cb7cb...1359150389fbab0ed6e9a0f554c638125fb91940#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">khmer (2.1.2+dfsg-8) 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"> * Fix autopkgtests for newer pytest: s/pyarg/pyargs/</span>
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<td class="diff-line-num new new_line" data-linenumber="4" 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="LC4" class="line" lang="plaintext"> * Standards-Version: 4.5.1 (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * debhelper-compat 13 (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Update renamed lintian tag names in lintian overrides.</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * Replace use of deprecated $ADTTMP with $AUTOPKGTEST_TMP.</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"> -- Michael R. Crusoe <crusoe@debian.org> Mon, 04 Jan 2021 14:18:12 +0100</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">khmer (2.1.2+dfsg-7) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> * Simplify autopkgtest. Closes: #955566</span>
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<a href="https://salsa.debian.org/med-team/khmer/-/compare/ed4b04f892fb1e19f275055fe523a304387cb7cb...1359150389fbab0ed6e9a0f554c638125fb91940#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">@@ -4,7 +4,7 @@ Uploaders: Michael R. Crusoe <crusoe@debian.org>,</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> Kevin Murray <spam@kdmurray.id.au></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-compat (= 1<span class="idiff left right">2</span>),</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">3</span>),</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> dh-python,</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> dh-exec,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> python3-guzzle-sphinx-theme,</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">@@ -22,7 +22,7 @@ Build-Depends: debhelper-compat (= 12),</td>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> libbz2-dev,</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> asciidoctor,</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> rdfind</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext">Standards-Version: 4.5.<span class="idiff left right">0</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">Standards-Version: 4.5.<span class="idiff left right">1</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/khmer</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/khmer.git</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">Homepage: https://khmer.readthedocs.org</span>
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<a href="https://salsa.debian.org/med-team/khmer/-/compare/ed4b04f892fb1e19f275055fe523a304387cb7cb...1359150389fbab0ed6e9a0f554c638125fb91940#1ecfa413953b6eab7ee70017897a75cd6b39d1f2"><strong>debian/khmer.lintian-overrides</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext"># The test data are provided in different compression methods intentionally to test different compression methods</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"># Since they are small anyway there is no reason to work around this</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">khmer: <span class="idiff left right">duplicated-compressed-fil</span>e usr/lib/python3/dist-packages/khmer/tests/test-data/empty-file.bz2</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">khmer: <span class="idiff left right">duplicated-compressed-fil</span>e usr/lib/python3/dist-packages/khmer/tests/test-data/empty-file.gz</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">khmer: <span class="idiff left right">duplicated-compressed-fil</span>e usr/lib/python3/dist-packages/khmer/tests/test-data/goodversion-k12.ht.gz</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">khmer: <span class="idiff left right">duplicated-compressed-fil</span>e usr/lib/python3/dist-packages/khmer/tests/test-data/random-20-a.fa.bz2</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">khmer: <span class="idiff left right">duplicated-compressed-fil</span>e usr/lib/python3/dist-packages/khmer/tests/test-data/random-20-a.fa.gz</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">khmer: <span class="idiff left right">duplicated-compressed-fil</span>e usr/lib/python3/dist-packages/khmer/tests/test-data/random-20-a.fq.bz2</span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">khmer: <span class="idiff left right">duplicated-compressed-fil</span>e usr/lib/python3/dist-packages/khmer/tests/test-data/random-20-a.fq.gz</span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">khmer: <span class="idiff left right">duplicated-compressed-fil</span>e usr/lib/python3/dist-packages/khmer/tests/test-data/test-abund-read-2.fa.bz2</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">khmer: <span class="idiff left right">duplicated-compressed-fil</span>e usr/lib/python3/dist-packages/khmer/tests/test-data/test-abund-read-2.fa.gz</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">khmer: <span class="idiff left right">duplicated-compressed-fil</span>e usr/lib/python3/dist-packages/khmer/tests/test-data/test-empty.fa.bz2</span></pre>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">khmer: <span class="idiff left right">compressed-duplicat</span>e usr/lib/python3/dist-packages/khmer/tests/test-data/empty-file.bz2</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">khmer: <span class="idiff left right">compressed-duplicat</span>e usr/lib/python3/dist-packages/khmer/tests/test-data/empty-file.gz</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">khmer: <span class="idiff left right">compressed-duplicat</span>e usr/lib/python3/dist-packages/khmer/tests/test-data/goodversion-k12.ht.gz</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">khmer: <span class="idiff left right">compressed-duplicat</span>e usr/lib/python3/dist-packages/khmer/tests/test-data/random-20-a.fa.bz2</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">khmer: <span class="idiff left right">compressed-duplicat</span>e usr/lib/python3/dist-packages/khmer/tests/test-data/random-20-a.fa.gz</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">khmer: <span class="idiff left right">compressed-duplicat</span>e usr/lib/python3/dist-packages/khmer/tests/test-data/random-20-a.fq.bz2</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">khmer: <span class="idiff left right">compressed-duplicat</span>e usr/lib/python3/dist-packages/khmer/tests/test-data/random-20-a.fq.gz</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">khmer: <span class="idiff left right">compressed-duplicat</span>e usr/lib/python3/dist-packages/khmer/tests/test-data/test-abund-read-2.fa.bz2</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">khmer: <span class="idiff left right">compressed-duplicat</span>e usr/lib/python3/dist-packages/khmer/tests/test-data/test-abund-read-2.fa.gz</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">khmer: <span class="idiff left right">compressed-duplicat</span>e usr/lib/python3/dist-packages/khmer/tests/test-data/test-empty.fa.bz2</span></pre>
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<a href="https://salsa.debian.org/med-team/khmer/-/compare/ed4b04f892fb1e19f275055fe523a304387cb7cb...1359150389fbab0ed6e9a0f554c638125fb91940#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">@@ -5,5 +5,5 @@ if [ "$AUTOPKGTEST_TMP" = "" ] ; then</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="si" style="color: #d14;">)</span></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 class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="shell"><span class="nv" style="color: #008080;">PATH</span><span class="o" style="font-weight: 600;">=</span>/usr/lib/khmer/bin/:<span class="nv" style="color: #008080;">$PATH</span> python3 <span class="nt" style="color: #000080;">-m</span> pytest <span class="nt" style="color: #000080;">--pyarg</span> khmer <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="nv" style="color: #008080;">PATH</span><span class="o" style="font-weight: 600;">=</span>/usr/lib/khmer/bin/:<span class="nv" style="color: #008080;">$PATH</span> python3 <span class="nt" style="color: #000080;">-m</span> pytest <span class="nt" style="color: #000080;">--pyarg<span class="idiff left right">s</span></span> khmer <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="shell"> <span class="nt" style="color: #000080;">-m</span> <span class="s1" style="color: #d14;">'not known_failing and not huge and not noroot'</span> <span class="nt" style="color: #000080;">-q</span></span></pre>
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<a href="https://salsa.debian.org/med-team/khmer/-/compare/ed4b04f892fb1e19f275055fe523a304387cb7cb...1359150389fbab0ed6e9a0f554c638125fb91940#a4360f3cb7376623ee88518c0d4e686d60834ac6"><strong>debian/tests/test-liboxli-dev</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/sh -ex</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span>khmer</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$A<span class="idiff left right">DT</span>TMP</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <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="LC4" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$A<span class="idiff left right">UTOPKGTEST_</span>TMP</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span><span class="s2" style="color: #d14;">"</span></span>
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