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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/parsinsert">Debian Med / parsinsert</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/parsinsert/commit/7203c2afc6945cc289c7679bf6bafa1584f56aaf">7203c2af</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-04T15:27:53Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Run command from autopkgtest also as runtime-test to spot issues for certain architectures earlier
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/parsinsert/commit/dc2f0d1050c53027cff42dff35cc105fa0f3e448">dc2f0d10</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-04T15:28:11Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debhelper-compat 12
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/parsinsert/commit/6b9029ddeeb22f716ce243c01b352f67b1fe88b7">6b9029dd</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-04T15:28:14Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.4.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/parsinsert/commit/31435f7e467309c5ba7559cbb7111cc24668d70d">31435f7e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-04T15:28:14Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Secure URI in copyright format
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/parsinsert/commit/535662477314e76e1c38935197e587dd6fd8ae45">53566247</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-04T15:28:33Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/parsinsert/commit/fd4864669922b0a7ec57ab69d0b6646d88612e37">fd486466</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-04T15:28:33Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove trailing whitespace in debian/changelog
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/parsinsert/commit/8213c0f18b63c9ff365b44e5b82627b000242372">8213c0f1</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-04T15:28:38Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use secure URI in debian/watch.
Fixes lintian: debian-watch-uses-insecure-uri
See https://lintian.debian.org/tags/debian-watch-uses-insecure-uri.html for more details.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/parsinsert/commit/1fae9b23a5aabfdba67abb5b276157dc414c6a1a">1fae9b23</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-04T15:28:49Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Set upstream metadata fields: Archive.</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/parsinsert/commit/39bb9a5ecc762b2c25770603a532bd8835356ee1">39bb9a5e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-04T15:36:26Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>8 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="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<span class="deleted-file">
−
debian/compat
</span>
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
debian/upstream/metadata
</a>
</li>
<li class="file-stats">
<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">
debian/watch
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="cf9802e192b48f765b1b5c8268d550d89c933053">
<a href="https://salsa.debian.org/med-team/parsinsert/compare/bd39eade1c8ddbc0703416f20756424ef0d3c233...39bb9a5ecc762b2c25770603a532bd8835356ee1#cf9802e192b48f765b1b5c8268d550d89c933053"><strong>debian/README.source</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">parsinsert for Debian</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"></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">Usually we try to run thge upstream test suite. However, the upstream</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">tarball is missing the file Test.cpp so we can not run this. Upstream</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">is informed and we try to deliver the package including the test suite</span>
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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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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">in the future.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Usually we try to run the upstream test suite. However, the upstream</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">tarball is missing the file Test.cpp so we can not run this. Instead</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">the autopkgtest command is used as build time test.</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> <span class="idiff left right">Thu, 27 Feb 2014 16:50:26 +00</span>00</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> <span class="idiff left right">Wed, 04 Dec 2019 16:26:00 +01</span>00</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">The files in debian/tests/test_data was retrieved sourceforge</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">URL: https://sourceforge.net/projects/parsinsert/files</span>
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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/parsinsert/compare/bd39eade1c8ddbc0703416f20756424ef0d3c233...39bb9a5ecc762b2c25770603a532bd8835356ee1#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">parsinsert (1.04-5) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Run command from autopkgtest also as runtime-test to spot issues</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> for certain architectures earlier</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * debhelper-compat 12</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Standards-Version: 4.4.1</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * Secure URI in copyright format</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> * Remove trailing whitespace in debian/changelog</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> * Use secure URI in debian/watch.</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> * Set upstream metadata fields: Archive.</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"> -- Andreas Tille <tille@debian.org> Wed, 04 Dec 2019 16:28:50 +0100</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span>
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1
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">parsinsert (1.04-4) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> * debhelper 11</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="9" 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="23" 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">@@ -9,7 +23,7 @@ parsinsert (1.04-4) unstable; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">parsinsert (1.04-3) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> * Team upload.</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> [ Nadiya Sitdykova ]</span>
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14
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> * add autopkgtest test</span>
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15
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"> * add info about source of test_data</span>
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<a href="https://salsa.debian.org/med-team/parsinsert/compare/bd39eade1c8ddbc0703416f20756424ef0d3c233...39bb9a5ecc762b2c25770603a532bd8835356ee1#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">11</span></pre>
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<a href="https://salsa.debian.org/med-team/parsinsert/compare/bd39eade1c8ddbc0703416f20756424ef0d3c233...39bb9a5ecc762b2c25770603a532bd8835356ee1#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">@@ -4,8 +4,8 @@ Uploaders: Tim Booth <tbooth@ceh.ac.uk>,</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> Andreas Tille <tille@debian.org></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<span class="idiff left right"> (>= 11~</span>)</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">2</span>.1</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper<span class="idiff left right">-compat (= 12</span>)</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">4</span>.1</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/parsinsert</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/parsinsert.git</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Homepage: http://sourceforge.net/projects/parsinsert/</span>
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<a href="https://salsa.debian.org/med-team/parsinsert/compare/bd39eade1c8ddbc0703416f20756424ef0d3c233...39bb9a5ecc762b2c25770603a532bd8835356ee1#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Format: http<span class="idiff left right">s</span>://www.debian.org/doc/packaging-manuals/copyright-format/1.0/</span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Upstream-Name: ParsInsert</span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Upstream-Contact: David Knox <david.knox@colorado.edu></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Source: http://parsinsert.sourceforge.net</span>
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<a href="https://salsa.debian.org/med-team/parsinsert/compare/bd39eade1c8ddbc0703416f20756424ef0d3c233...39bb9a5ecc762b2c25770603a532bd8835356ee1#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">@@ -16,7 +16,12 @@ override_dh_auto_clean:</td>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> dh_auto_clean</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">override_dh_auto_test:</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"> echo "Upstream tarball lacks Test.cpp so we can not run the test."</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> cd debian/tests/test_data && \</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> $(CURDIR)/parsinsert -d0 -c80 -n1 set1000.fasta -m lanemask.txt -x rdp.taxonomy \</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> -l set1000.log -o set1000.results -t core_rdp.ntree \</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> -s core_rdp.fasta</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">endif</span>
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20
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25
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"></span>
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21
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26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"># Note a manpage was generated using:</span>
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22
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"># help2man -N ./parsinsert --version-string=1.04 > debian/parsinsert.1</span>
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<li id="f5606a935d95a2f20059a7ac1136f47b2edadbf6">
<a href="https://salsa.debian.org/med-team/parsinsert/compare/bd39eade1c8ddbc0703416f20756424ef0d3c233...39bb9a5ecc762b2c25770603a532bd8835356ee1#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</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">Registry:</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"> - Name: OMICtools</span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"> Entry: OMICS_21460</span>
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<td class="diff-line-num old old_line" data-linenumber="4" 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">
4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> - Name: SciCrunch</span>
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5
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<td class="diff-line-num new_line old" data-linenumber="2" 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="LC5" class="line" lang="plaintext"> Entry: NA</span>
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<td class="diff-line-num old old_line" 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">
6
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<td class="diff-line-num new_line old" data-linenumber="2" 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="LC6" class="line" lang="plaintext"> - Name: bio.tools</span>
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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">
7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> Entry: NA</span></pre>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">- Name: OMICtools</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> Entry: OMICS_21460</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">- Name: SciCrunch</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> Entry: NA</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">- Name: bio.tools</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> Entry: NA</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">Archive: SourceForge</span></pre>
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<a href="https://salsa.debian.org/med-team/parsinsert/compare/bd39eade1c8ddbc0703416f20756424ef0d3c233...39bb9a5ecc762b2c25770603a532bd8835356ee1#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</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">version=3</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">http://sf.net/parsinsert/ParsInsert\.([\d\.]+)\.tgz</span></pre>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">http<span class="idiff left right">s</span>://sf.net/parsinsert/ParsInsert\.([\d\.]+)\.tgz</span></pre>
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