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<h3>
Pierre Gruet pushed to branch master
at <a href="https://salsa.debian.org/med-team/artemis">Debian Med / artemis</a>
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<h4>
Commits:
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<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/artemis/-/commit/fbf905bd533da6b28f2e1441a06e7342c9206932">fbf905bd</a></strong>
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<span>by Pierre Gruet</span>
<i>at 2021-04-26T17:28:35+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Removing useless dependency on jarwrapper
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<strong><a href="https://salsa.debian.org/med-team/artemis/-/commit/896db2097b9be77e7d77e5e386d883d42b680d76">896db209</a></strong>
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<span>by Pierre Gruet</span>
<i>at 2021-04-26T17:30:40+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Using my debian.org email address
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<h4>9 changed files:</h4>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
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<li class="file-stats">
<a href="#79008705e3f8eca0d134ef96cd41d3ab55fcb6c6">
debian/patches/debianize_launcher_scripts.patch
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<li class="file-stats">
<a href="#371597159c0cb7b9fc4a4cfefb5d408b03e81d8d">
debian/patches/missing_htsjdk_dependency_in_pom.patch
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<li class="file-stats">
<a href="#2d79086d21603902d1d606d9054e60986e8341a4">
debian/patches/no_install_of_provided_jars.patch
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<li class="file-stats">
<a href="#a778d0965cd7524f3455d4369ab7818dcbf5d585">
debian/patches/running_build_tests.patch
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<li class="file-stats">
<a href="#6f2db47d73b2ca08518b115254bc36c6823bf067">
debian/patches/using_system_jars_in_pom.patch
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<li class="file-stats">
<a href="#c5bb453025139c6c27fffc2b83d2ba1b570ac0ed">
debian/tests/run-some-unit-tests
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/artemis/-/compare/d96dcd20e930faf20a28c897a7b7f6f19d2abc43...896db2097b9be77e7d77e5e386d883d42b680d76#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">artemis (18.1.0+dfsg-4) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Removing useless dependency on jarwrapper</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Pierre Gruet <pgt@debian.org> Mon, 26 Apr 2021 17:27:18 +0200</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">artemis (18.1.0+dfsg-3) unstable; urgency=medium</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"> * Changing homepage in d/control and manpages (Closes: #974680)</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/artemis/-/compare/d96dcd20e930faf20a28c897a7b7f6f19d2abc43...896db2097b9be77e7d77e5e386d883d42b680d76#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Source: artemis</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org>,</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> Pierre Gruet <pgtdebian<span class="idiff left right">@free.fr</span>></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Pierre Gruet <pgt<span class="idiff left">@</span>debian<span class="idiff right">.org</span>></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 (= 13),</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="59" 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">@@ -59,8 +59,7 @@ Depends: ${misc:Depends},</td>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="plaintext"> libpicard-java,</span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="plaintext"> jemboss,</span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="plaintext"> libcglib-java,</span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="plaintext"> default-jre,</span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="plaintext"> jarwrapper</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext"> default-jre</span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="plaintext">Description: genome browser and annotation tool</span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="plaintext"> Artemis is a genome browser and annotation tool that allows visualisation of</span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="plaintext"> sequence features, next generation data and the results of analyses within the</span>
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<a href="https://salsa.debian.org/med-team/artemis/-/compare/d96dcd20e930faf20a28c897a7b7f6f19d2abc43...896db2097b9be77e7d77e5e386d883d42b680d76#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</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">@@ -49,7 +49,7 @@ License: Apache-2.0</td>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext">Files: debian/*</span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext">Copyright: 2015-2016 Afif Elghraoui <afif@debian.org></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="plaintext"> 2020 Pierre Gruet <pgtdebian<span class="idiff left right">@free.fr</span>></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"> 2020 Pierre Gruet <pgt<span class="idiff left">@</span>debian<span class="idiff right">.org</span>></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="plaintext">License: GPL-2+</span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="plaintext">License: Expat</span>
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<a href="https://salsa.debian.org/med-team/artemis/-/compare/d96dcd20e930faf20a28c897a7b7f6f19d2abc43...896db2097b9be77e7d77e5e386d883d42b680d76#79008705e3f8eca0d134ef96cd41d3ab55fcb6c6"><strong>debian/patches/debianize_launcher_scripts.patch</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff"><span class="p">Description: Simplifying the provided launchers</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"> Many options or tricks are useless on a Debian system.</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"> The paths are also adapted to the Debian install.</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="p">Author: Pierre Gruet <pgtdebian<span class="idiff left right">@free.fr</span>></span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Author: Pierre Gruet <pgt<span class="idiff left">@</span>debian<span class="idiff right">.org</span>></span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="p">Last-Update: 2020-09-06</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"></span>
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<li id="371597159c0cb7b9fc4a4cfefb5d408b03e81d8d">
<a href="https://salsa.debian.org/med-team/artemis/-/compare/d96dcd20e930faf20a28c897a7b7f6f19d2abc43...896db2097b9be77e7d77e5e386d883d42b680d76#371597159c0cb7b9fc4a4cfefb5d408b03e81d8d"><strong>debian/patches/missing_htsjdk_dependency_in_pom.patch</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff"><span class="p">Description: adding missing dependency on htsjdk in pom</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Author: Pierre Gruet <pgtdebian<span class="idiff left right">@free.fr</span>></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Author: Pierre Gruet <pgt<span class="idiff left">@</span>debian<span class="idiff right">.org</span>></span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Forwarded: https://github.com/sanger-pathogens/Artemis/issues/313</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="p">Last-Update: 2020-09-04</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"></span>
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<a href="https://salsa.debian.org/med-team/artemis/-/compare/d96dcd20e930faf20a28c897a7b7f6f19d2abc43...896db2097b9be77e7d77e5e386d883d42b680d76#2d79086d21603902d1d606d9054e60986e8341a4"><strong>debian/patches/no_install_of_provided_jars.patch</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff"><span class="p">Description: avoid installing embedded jars as we removed them</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"> Author relies on jars that are embedded in their source archive. Instead, we</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"> use the ones that are packaged in Debian.</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="p">Author: Pierre Gruet <pgtdebian<span class="idiff left right">@free.fr</span>></span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Author: Pierre Gruet <pgt<span class="idiff left">@</span>debian<span class="idiff right">.org</span>></span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="p">Last-Update: 2020-09-04</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"></span>
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<a href="https://salsa.debian.org/med-team/artemis/-/compare/d96dcd20e930faf20a28c897a7b7f6f19d2abc43...896db2097b9be77e7d77e5e386d883d42b680d76#a778d0965cd7524f3455d4369ab7818dcbf5d585"><strong>debian/patches/running_build_tests.patch</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 @@ Description: changes in pom and in test definitions when they cannot be run</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"> We also remove the lines allowing to skip tests or to ignore failures.</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"> In the definitions of the tests, we add @Ignore for the ones that require a</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"> X11 instance to run.</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="p">Author: Pierre Gruet <pgtdebian<span class="idiff left right">@free.fr</span>></span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">Author: Pierre Gruet <pgt<span class="idiff left">@</span>debian<span class="idiff right">.org</span>></span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"><span class="p">Last-Update: 2020-09-05</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"></span>
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<a href="https://salsa.debian.org/med-team/artemis/-/compare/d96dcd20e930faf20a28c897a7b7f6f19d2abc43...896db2097b9be77e7d77e5e386d883d42b680d76#6f2db47d73b2ca08518b115254bc36c6823bf067"><strong>debian/patches/using_system_jars_in_pom.patch</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff"><span class="p">Description: specifying paths on Debian system for some dependencies</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"> For those dependencies, no maven-repo tree is available, we are therefore</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"> giving their path with system scope.</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="p">Author: Pierre Gruet <pgtdebian<span class="idiff left right">@free.fr</span>></span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Author: Pierre Gruet <pgt<span class="idiff left">@</span>debian<span class="idiff right">.org</span>></span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="p">Last-Update: 2020-09-04</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"></span>
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<a href="https://salsa.debian.org/med-team/artemis/-/compare/d96dcd20e930faf20a28c897a7b7f6f19d2abc43...896db2097b9be77e7d77e5e386d883d42b680d76#c5bb453025139c6c27fffc2b83d2ba1b570ac0ed"><strong>debian/tests/run-some-unit-tests</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 @@ set -e</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># autopkgtest check: run some unit tests. Some other tests try to launch X11</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># or connect through ssh, having the selected one run should be good enough.</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># (C) 2020 Pierre Gruet.</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Author: Pierre Gruet <pgtdebian<span class="idiff left right">@free.fr</span>></span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Author: Pierre Gruet <pgt<span class="idiff left">@</span>debian<span class="idiff right">.org</span>></span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span>artemis</span>
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