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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/0b94e119c811e67ce5c0ed3649bcd6a2c051da09">0b94e119</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-01-08T09:48:59Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix liboxli-dev autopkgtest.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/khmer/commit/254ca62b4632d94fbb9fce9005381ad8549bc237">254ca62b</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-01-08T10:43:45Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">skip the noroot tests
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/khmer/commit/0474ea70b8d717a48b004d2d4f15e6cf03f5f0a1">0474ea70</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-01-08T13:14:53Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fix metainfo-validation-issue
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/khmer/commit/82539b6a0401984f17e0d70571c2b200bcf066af">82539b6a</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-01-08T13:15:18Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Symlink to files in python3-guzzle-sphinx-theme
Instead of shipping them ourselves; thanks rdfind!
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/khmer/commit/f0ad030a4874da36c90619d767ec86b06b4bf8fa">f0ad030a</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-01-08T13:47:39Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Debian Buster's cython is > 0.26.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/khmer/commit/7428ae9d4813d52c8cbde9eff3a9627f74412ad8">7428ae9d</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-01-08T14:09:23Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">keep both copies of the CITATION file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/khmer/commit/2132761eba7b69c19444c17f28a28d9c2173358a">2132761e</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-01-08T14:16:43Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">upload to unstable
</pre>
</li>
</ul>
<h4>12 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#cf9802e192b48f765b1b5c8268d550d89c933053">
debian/README.source
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#f5f51601866c86e59a004bd93fa415f5675be8c5">
debian/clean
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#86b62191b1cc8e4240729754dd462b25b88e050e">
<span class="deleted-file">
−
debian/khmer-common.lintian-overrides
</span>
</a>
</li>
<li class="file-stats">
<a href="#1ecfa413953b6eab7ee70017897a75cd6b39d1f2">
debian/khmer.lintian-overrides
</a>
</li>
<li class="file-stats">
<a href="#b0f6dbcde4785d278e61d784b7cf80f389e87814">
debian/khmer.metainfo.xml
</a>
</li>
<li class="file-stats">
<a href="#7cab10cfa112c7374ebfef866a3aad2fca553d0e">
<span class="new-file">
+
debian/patches/fix_liboxli_test
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
</a>
</li>
<li class="file-stats">
<a href="#a4360f3cb7376623ee88518c0d4e686d60834ac6">
debian/tests/test-liboxli-dev
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="cf9802e192b48f765b1b5c8268d550d89c933053">
<a href="https://salsa.debian.org/med-team/khmer/compare/bfaee76542be628908ef3784d2f481afe604fac4...2132761eba7b69c19444c17f28a28d9c2173358a#cf9802e192b48f765b1b5c8268d550d89c933053"><strong>debian/README.source</strong></a>
<hr>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3" 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">@@ -3,7 +3,3 @@ khmer with changes they made. See third-party/seqan/ChangeLog for details. The</td>
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<td class="diff-line-num new_line" data-linenumber="3" 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 noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">most important change is a bugfix which was acknowledged by the SeqAn developers</span>
</pre>
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<td class="diff-line-num new_line" data-linenumber="4" 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 noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">but will not be fixed until the version 2.0 release of SeqAn:</span>
</pre>
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<td class="diff-line-num 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">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">https://github.com/seqan/seqan/issues/720</span></pre>
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<td class="diff-line-num new_line old" data-linenumber="6" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="7" 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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<td class="diff-line-num new_line old" data-linenumber="6" 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="LC7" class="line" lang="plaintext">Skip packaging khmer v2.1.2 until cython version 0.26.1 in in Debian or</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="8" 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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<td class="diff-line-num new_line old" data-linenumber="6" 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="LC8" class="line" lang="plaintext">https://github.com/cython/cython/commit/18bba8ff0261206db9243c2b1721633cb798af54</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="9" 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="LC9" class="line" lang="plaintext">is patched in</span></pre>
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<br>
</li>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/khmer/compare/bfaee76542be628908ef3784d2f481afe604fac4...2132761eba7b69c19444c17f28a28d9c2173358a#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-5) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
</pre>
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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 liboxli-dev autopkgtest.</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"> * debian/khmer.metainfo.xml: Use a component ID in reverse domain-name</span>
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<td class="diff-line-num new new_line" data-linenumber="5" 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="LC5" class="line" lang="plaintext"> format.</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * shrink khmer-common and silence many lintian warnings by symlinking to the</span>
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<td class="diff-line-num new new_line" data-linenumber="7" 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="LC7" class="line" lang="plaintext"> relevant files in python3-guzzle-sphinx-theme</span>
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<td class="diff-line-num new new_line" data-linenumber="8" 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="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> -- Michael R. Crusoe <michael.crusoe@gmail.com> Tue, 08 Jan 2019 06:16:30 -0800</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-4) 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"> * Team upload.</span>
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<a href="https://salsa.debian.org/med-team/khmer/compare/bfaee76542be628908ef3784d2f481afe604fac4...2132761eba7b69c19444c17f28a28d9c2173358a#f5f51601866c86e59a004bd93fa415f5675be8c5"><strong>debian/clean</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">fakehome/</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">debian/*.1</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">.pybuild/</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">.pytest_cache/</span>
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4
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">khmer.egg-info/</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">khmer/_oxli/*.cp*</span>
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6
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">khmer/_khmer.cpython*</span>
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<a href="https://salsa.debian.org/med-team/khmer/compare/bfaee76542be628908ef3784d2f481afe604fac4...2132761eba7b69c19444c17f28a28d9c2173358a#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_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">...</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">@@ -21,8 +21,7 @@ Build-Depends: debhelper (>= 11~),</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> zlib1g-dev,</span>
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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"> libjs-jquery,</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext"> libjs-twitter-bootstrap</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: 4.3.0</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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="33" 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">@@ -33,7 +32,8 @@ Architecture: all</td>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext">Multi-Arch: foreign</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext">Depends: file,</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext"> ${sphinxdoc:Depends}</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> ${sphinxdoc:Depends},</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> python3-guzzle-sphinx-theme</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext">Description: common files for the khmer project tools</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"> khmer is a library and suite of command line tools for working with DNA</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"> sequence. It is primarily aimed at short-read sequencing data such as</span>
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<a href="https://salsa.debian.org/med-team/khmer/compare/bfaee76542be628908ef3784d2f481afe604fac4...2132761eba7b69c19444c17f28a28d9c2173358a#86b62191b1cc8e4240729754dd462b25b88e050e"><strong>debian/khmer-common.lintian-overrides</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">khmer-common: extra-license-file usr/share/doc/khmer-common/html/_sources/LICENSE.rst.txt</span></pre>
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<a href="https://salsa.debian.org/med-team/khmer/compare/bfaee76542be628908ef3784d2f481afe604fac4...2132761eba7b69c19444c17f28a28d9c2173358a#1ecfa413953b6eab7ee70017897a75cd6b39d1f2"><strong>debian/khmer.lintian-overrides</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext"># These files are unchanged files from upstream tarball. There is no problem for a reproducible build</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">khmer: gzip-file-is-not-multi-arch-same-safe usr/lib/python3/dist-packages/khmer/tests/test-data/100-reads.fq.gz</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">khmer: gzip-file-is-not-multi-arch-same-safe usr/lib/python3/dist-packages/khmer/tests/test-data/100-reads.fq.truncated.gz</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">khmer: gzip-file-is-not-multi-arch-same-safe 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: gzip-file-is-not-multi-arch-same-safe 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: gzip-file-is-not-multi-arch-same-safe 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="LC7" class="line" lang="plaintext">khmer: gzip-file-is-not-multi-arch-same-safe 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="LC8" class="line" lang="plaintext">khmer: gzip-file-is-not-multi-arch-same-safe 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="LC9" class="line" lang="plaintext">khmer: gzip-file-is-not-multi-arch-same-safe usr/lib/python3/dist-packages/khmer/tests/test-data/test-reads.fq.gz</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="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: duplicated-compressed-file usr/lib/python3/dist-packages/khmer/tests/test-data/empty-file.bz2</span>
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<a href="https://salsa.debian.org/med-team/khmer/compare/bfaee76542be628908ef3784d2f481afe604fac4...2132761eba7b69c19444c17f28a28d9c2173358a#b0f6dbcde4785d278e61d784b7cf80f389e87814"><strong>debian/khmer.metainfo.xml</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;"><?xml version="1.0" encoding="UTF-8"?></span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="xml"><span class="nt" style="color: navy;"><component></span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="xml"> <span class="nt" style="color: navy;"><id></span><span class="idiff left right">oxli</span><span class="nt" style="color: navy;"></id></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="xml"> <span class="nt" style="color: navy;"><id></span><span class="idiff left right">io.readthedocs.khmer</span><span class="nt" style="color: navy;"></id></span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="xml"> <span class="nt" style="color: navy;"><metadata_license></span>MIT<span class="nt" style="color: navy;"></metadata_license></span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="xml"> <span class="nt" style="color: navy;"><name></span>khmer<span class="nt" style="color: navy;"></name></span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="xml"> <span class="nt" style="color: navy;"><summary></span>in-memory DNA sequence kmer counting, filtering <span class="ni" style="color: purple;">&</span> graph traversal<span class="nt" style="color: navy;"></summary></span></span>
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<a href="https://salsa.debian.org/med-team/khmer/compare/bfaee76542be628908ef3784d2f481afe604fac4...2132761eba7b69c19444c17f28a28d9c2173358a#7cab10cfa112c7374ebfef866a3aad2fca553d0e"><strong>debian/patches/fix_liboxli_test</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">From: Michael R. Crusoe <michael.crusoe@gmail.com></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Subject: Fix liboxli sanity check test</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- khmer.orig/src/oxli/test-compile.cc</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ khmer/src/oxli/test-compile.cc</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -39,10 +39,10 @@</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> // This file is used to test compilation with liboxli.a/liboxli.so, after</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> // installation</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#include <oxli/hashtable.hh></span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include <oxli/hashgraph.hh></span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> int main()</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- oxli::Countgraph test(1,1);</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ oxli::Countgraph test(1,{1});</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> return 0;</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> }</span></pre>
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<a href="https://salsa.debian.org/med-team/khmer/compare/bfaee76542be628908ef3784d2f481afe604fac4...2132761eba7b69c19444c17f28a28d9c2173358a#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</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">@@ -10,3 +10,4 @@ cpython-bug-empty-exceptions</td>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">amend-skip</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">setup.py-py3</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">python3</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">fix_liboxli_test</span></pre>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/khmer/compare/bfaee76542be628908ef3784d2f481afe604fac4...2132761eba7b69c19444c17f28a28d9c2173358a#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</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">@@ -28,7 +28,8 @@ ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</td>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> PYBUILD_SYSTEM=custom \</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"> PYBUILD_TEST_ARGS="cd {dir}; export PATH={destdir}/usr/lib/khmer/bin:$$PATH ; \</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"> cd {build_dir}; export PYTHONPATH=$$(pwd); {interpreter} -m pytest \</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext"> -m 'not known_failing and not jenkins and not huge'" dh_auto_test</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> -m 'not known_failing and not jenkins and not huge and not noroot'\</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> -q" dh_auto_test</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext">endif</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext">override_dh_auto_clean:</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="42" 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">@@ -42,5 +43,10 @@ override_dh_install:</td>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext"> find debian/khmer -name .gitignore -delete</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext">override_dh_sphinxdoc:</span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="plaintext"> dh_sphinxdoc -X jquery.js</span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="plaintext"></span></pre>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> dh_sphinxdoc</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> rdfind -makesymlinks true -followsymlinks true\</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> /usr/lib/python3/dist-packages/guzzle_sphinx_theme \</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"> $(shell find debian/khmer-common | grep -i -v citation)</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> rm debian/khmer-common/usr/share/doc/khmer-common/html/_sources/citations.rst.txt</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"> cd debian/khmer-common/usr/share/doc/khmer-common/html/_sources/ && \</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"> ln -s ../../CITATION citations.rst.txt</span></pre>
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<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/khmer/compare/bfaee76542be628908ef3784d2f481afe604fac4...2132761eba7b69c19444c17f28a28d9c2173358a#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="shell"><span class="nv" style="color: teal;">pkg</span><span class="o" style="font-weight: 600;">=</span>khmer</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$ADTTMP</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 class="idiff left"> </span></span><span class="nv" style="color: teal;"><span class="idiff">ADTTMP</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="sb" style="color: #d14;"><span class="idiff">`</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">mktemp</span></span><span class="idiff"> </span><span class="nt" style="color: navy;"><span class="idiff">-d</span></span><span class="idiff"> /tmp/</span><span class="k" style="font-weight: 600;"><span class="idiff">${</span></span><span class="nv" style="color: teal;"><span class="idiff">pkg</span></span><span class="k" style="font-weight: 600;"><span class="idiff">}</span></span><span class="nt" style="color: navy;"><span class="idiff">-test</span></span><span class="idiff">.XXXXXX</span><span class="sb" style="color: #d14;"><span class="idiff right">`</span></span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="k" style="font-weight: 600;"><span class="idiff left"> </span></span><span class="nv" style="color: teal;"><span class="idiff">ADTTMP</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="k" style="font-weight: 600;"><span class="idiff">$(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">mktemp</span></span><span class="idiff"> </span><span class="nt" style="color: navy;"><span class="idiff">-d</span></span><span class="idiff"> /tmp/</span><span class="k" style="font-weight: 600;"><span class="idiff">${</span></span><span class="nv" style="color: teal;"><span class="idiff">pkg</span></span><span class="k" style="font-weight: 600;"><span class="idiff">}</span></span><span class="nt" style="color: navy;"><span class="idiff">-test</span></span><span class="idiff">.XXXXXX</span><span class="k" style="font-weight: 600;"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: teal;"><span class="idiff left right">$ADTTMP</span></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 class="idiff left">"</span></span><span class="nv" style="color: teal;"><span class="idiff">$ADTTMP</span></span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="shell"><span class="nv" style="color: teal;">PATH</span><span class="o" style="font-weight: 600;">=</span>/usr/lib/khmer/bin/:<span class="nv" style="color: teal;">$PATH</span> python3 <span class="nt" style="color: navy;">-m</span> pytest <span class="nt" style="color: navy;">--pyarg</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: navy;">-m</span> <span class="s1" style="color: #d14;">'not known_failing and not huge<span class="idiff left right">'</span></span></span></pre>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"> <span class="nt" style="color: navy;">-m</span> <span class="s1" style="color: #d14;">'not known_failing and not huge<span class="idiff left"> and not noroot'</span></span><span class="idiff"> </span><span class="nt" style="color: navy;"><span class="idiff right">-q</span></span></span></pre>
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<a href="https://salsa.debian.org/med-team/khmer/compare/bfaee76542be628908ef3784d2f481afe604fac4...2132761eba7b69c19444c17f28a28d9c2173358a#a4360f3cb7376623ee88518c0d4e686d60834ac6"><strong>debian/tests/test-liboxli-dev</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">@@ -2,17 +2,20 @@</td>
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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: teal;">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: teal;">$ADTTMP</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">ADTTMP</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;"><span class="idiff left">`</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">mktemp</span></span><span class="idiff"> </span><span class="nt" style="color: navy;"><span class="idiff">-d</span></span><span class="idiff"> /tmp/</span><span class="k" style="font-weight: 600;"><span class="idiff">${</span></span><span class="nv" style="color: teal;"><span class="idiff">pkg</span></span><span class="k" style="font-weight: 600;"><span class="idiff">}</span></span><span class="nt" style="color: navy;"><span class="idiff">-test</span></span><span class="idiff">.XXXXXX</span><span class="sb" style="color: #d14;"><span class="idiff right">`</span></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: teal;">ADTTMP</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;"><span class="idiff left">$(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">mktemp</span></span><span class="idiff"> </span><span class="nt" style="color: navy;"><span class="idiff">-d</span></span><span class="idiff"> /tmp/</span><span class="k" style="font-weight: 600;"><span class="idiff">${</span></span><span class="nv" style="color: teal;"><span class="idiff">pkg</span></span><span class="k" style="font-weight: 600;"><span class="idiff">}</span></span><span class="nt" style="color: navy;"><span class="idiff">-test</span></span><span class="idiff">.XXXXXX</span><span class="k" style="font-weight: 600;"><span class="idiff right">)</span></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="nv" style="color: teal;"><span class="idiff left right">$ADTTMP</span></span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="nv" style="color: teal;"><span class="idiff">$ADTTMP</span></span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span></span>
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8
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="shell"></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="shell">c++ <span class="nt" style="color: navy;">-o</span> test-prog-static <span class="nt" style="color: navy;">-static</span> <span class="nt" style="color: navy;">-std</span><span class="o" style="font-weight: 600;">=</span>c++11 <span class="sb" style="color: #d14;">`</span>pkg-config oxli <span class="nt" style="color: navy;">--static</span> <span class="nt" style="color: navy;">--cflags</span><span class="sb" style="color: #d14;">`</span> <span class="nt" style="color: navy;">-I</span>/usr/include/oxli/smhasher <span class="se" style="color: #d14;">\</span></span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="shell"> /usr/share/doc/khmer-common/test-compile.cc <span class="sb" style="color: #d14;">`</span>pkg-config oxli <span class="nt" style="color: navy;">--static</span> <span class="nt" style="color: navy;">--libs</span><span class="sb" style="color: #d14;">`</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell">c++ <span class="nt" style="color: navy;">-o</span> test-prog-static <span class="nt" style="color: navy;">-static</span> <span class="nt" style="color: navy;">-std</span><span class="o" style="font-weight: 600;">=</span>c++11 <span class="se" style="color: #d14;">\</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"> <span class="k" style="font-weight: 600;">$(</span>pkg-config oxli <span class="nt" style="color: navy;">--static</span> <span class="nt" style="color: navy;">--cflags</span><span class="k" style="font-weight: 600;">)</span> <span class="nt" style="color: navy;">-I</span>/usr/include/oxli/smhasher <span class="se" style="color: #d14;">\</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"> /usr/share/doc/khmer-common/test-compile.cc <span class="se" style="color: #d14;">\</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"> <span class="k" style="font-weight: 600;">$(</span>pkg-config oxli <span class="nt" style="color: navy;">--static</span> <span class="nt" style="color: navy;">--libs</span><span class="k" style="font-weight: 600;">)</span></span>
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11
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell"></span>
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12
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="shell">./test-prog-static</span>
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13
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell"></span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="shell">c++ <span class="nt" style="color: navy;">-o</span> test-prog-dynamic <span class="nt" style="color: navy;">-std</span><span class="o" style="font-weight: 600;">=</span>c++11 <span class="sb" style="color: #d14;">`</span>pkg-config oxli <span class="nt" style="color: navy;">--cflags</span><span class="sb" style="color: #d14;">`</span> <span class="nt" style="color: navy;">-I</span>/usr/include/oxli/smhasher <span class="se" style="color: #d14;">\</span></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="shell"> /usr/share/doc/khmer-common/test-compile.cc <span class="sb" style="color: #d14;">`</span>pkg-config oxli <span class="nt" style="color: navy;">--libs</span><span class="sb" style="color: #d14;">`</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell">c++ <span class="nt" style="color: navy;">-o</span> test-prog-dynamic <span class="nt" style="color: navy;">-std</span><span class="o" style="font-weight: 600;">=</span>c++11 <span class="k" style="font-weight: 600;">$(</span>pkg-config oxli <span class="nt" style="color: navy;">--cflags</span><span class="k" style="font-weight: 600;">)</span> <span class="se" style="color: #d14;">\</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"> <span class="nt" style="color: navy;">-I</span>/usr/include/oxli/smhasher <span class="se" style="color: #d14;">\</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"> /usr/share/doc/khmer-common/test-compile.cc <span class="k" style="font-weight: 600;">$(</span>pkg-config oxli <span class="nt" style="color: navy;">--libs</span><span class="k" style="font-weight: 600;">)</span></span>
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16
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="shell"></span>
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17
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="shell">./test-prog-dynamic</span>
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18
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="shell"></span>
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