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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/pbgenomicconsensus">Debian Med / pbgenomicconsensus</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/pbgenomicconsensus/commit/b52deeaf90d7eeb912f9f48627d8526b8ab7af2f">b52deeaf</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-04-02T18:11:16Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Mark autopkgtest that is forced to succeed "superficial"
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pbgenomicconsensus/commit/5ed0a59d7f3ea6ca065000eaa3ec3d50fcff1d96">5ed0a59d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-04-02T18:32:08Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Make test more sensible
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pbgenomicconsensus/commit/60725a61f6d000fca4c7a9a7f2e2f1a35c449af7">60725a61</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-04-02T19:20:59Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Restore old autopkgtest file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pbgenomicconsensus/commit/23150713c126cf0f35dadae70b0636b0a535718f">23150713</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-04-02T19:23:36Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Document what really was done
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pbgenomicconsensus/commit/ee6d69fef18b0323a02d8113aa9916a209d291bf">ee6d69fe</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-04-02T19:25:08Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">No debugging noise
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pbgenomicconsensus/commit/304e988ecae787fc26b97888f681a276ec9922d0">304e988e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-04-02T19:33:06Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#e915a96d31118bd03d7869a1e348457a7999a648">
debian/patches/ignore_test_requiring_pbtestdata.patch
</a>
</li>
<li class="file-stats">
<a href="#18e6a4f3c4f9c0be09da6748c64846922df878da">
debian/patches/ignore_test_using_local_data.patch
</a>
</li>
<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
debian/tests/control
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</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/pbgenomicconsensus/compare/b10335c1c862e91e440b83b5941e2416386a28cd...304e988ecae787fc26b97888f681a276ec9922d0#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num new new_line" data-linenumber="1" 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="LC1" class="line" lang="plaintext">pbgenomicconsensus (2.3.2-3) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Really fix autopkgtest</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"> -- Andreas Tille <tille@debian.org> Tue, 02 Apr 2019 21:29:59 +0200</span>
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<td class="diff-line-num new new_line" data-linenumber="6" 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="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">pbgenomicconsensus (2.3.2-2) unstable; urgency=medium</span>
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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_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">
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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="LC9" class="line" lang="plaintext"> [ Afif Elghraoui ]</span>
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<li id="e915a96d31118bd03d7869a1e348457a7999a648">
<a href="https://salsa.debian.org/med-team/pbgenomicconsensus/compare/b10335c1c862e91e440b83b5941e2416386a28cd...304e988ecae787fc26b97888f681a276ec9922d0#e915a96d31118bd03d7869a1e348457a7999a648"><strong>debian/patches/ignore_test_requiring_pbtestdata.patch</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,15 +5,17 @@ Last-Update: Thu, 28 Mar 2019 13:40:21 +0100</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/Makefile</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -8,7 +8,1<span class="idiff left right">2</span> @@ tests: unit-tests basic-tests</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -8,7 +8,1<span class="idiff left right">4</span> @@ tests: unit-tests basic-tests</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> unit-tests:</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"> # Unit tests</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- py.test --junit-xml=nosetests.xml tests/unit</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # ignore tests requiring https://github.com/PacificBiosciences/PacBioTestData which is not packaged</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ set -e ; \</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;">+ TMPDIR=$$(mktemp -d /tmp/test_ignore_XXXXXX) ; \</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ mv tests/unit/test_tool_contract.py $${TMPDIR} ; \</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ py.test --junit-xml=nosetests.xml tests/unit ; \</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ rm -rf tests/unit/__pycache__ ; \</span></span>
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ mv $${TMPDIR}/* tests/unit ; \</span></span>
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ rmdir $${TMPDIR}</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="diff"> </span>
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<li id="18e6a4f3c4f9c0be09da6748c64846922df878da">
<a href="https://salsa.debian.org/med-team/pbgenomicconsensus/compare/b10335c1c862e91e440b83b5941e2416386a28cd...304e988ecae787fc26b97888f681a276ec9922d0#18e6a4f3c4f9c0be09da6748c64846922df878da"><strong>debian/patches/ignore_test_using_local_data.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">@@ -5,7 +5,7 @@ Last-Update: Thu, 28 Mar 2019 13:40:21 +0100</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/Makefile</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2<span class="idiff left right">0,8 +20,18</span> @@ unit-tests:</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2<span class="idiff left right">2,8 +22,19</span> @@ unit-tests:</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> </span>
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> basic-tests:</span>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"> # End-to-end tests</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,6 +13,7 @@ Last-Update: Thu, 28 Mar 2019 13:40:21 +0100</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- PATH=`pwd`:$(PATH) cram --verbose --xunit-file=gc-cram.xml `ls tests/cram/*.t | grep -v -e arrow -e bad_input`</span></span>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # some tests require a input files on a local mount of upstream</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;">+ # The test poa-all4mer.t contains a wrong syntax in calling poa - no idea how to fix this thus ignoring the test</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ set -e ; \</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ TMPDIR=$$(mktemp -d /tmp/test_ignore_XXXXXX) ; \</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for nt in $$(grep -Rl /mnt/secondary/Share/Quiver/ tests/*) ; do \</span></span>
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18
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ mkdir -p $${TMPDIR}/$$(dirname $${nt}) ; \</span></span>
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<a href="https://salsa.debian.org/med-team/pbgenomicconsensus/compare/b10335c1c862e91e440b83b5941e2416386a28cd...304e988ecae787fc26b97888f681a276ec9922d0#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</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">Test-Command:</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"> make unit-tests || true # due to warnings caused by python-pbcore some non-zero value is returned despite all tests are passing - thus adding '|| true'</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"> cp -r Makefile tests $AUTOPKGTEST_TMP</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> && cd $AUTOPKGTEST_TMP</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> && make tests</span>
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3
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Depends:</span>
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4
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> @,</span>
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5
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> python-nose,</span>
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6
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> python-cram,</span>
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7
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> make,</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> poa</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> poa<span class="idiff left right">,</span></span>
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9
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Restrictions: allow-stderr</span>
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10
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></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="plaintext">Test-Command:</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> make basic-tests</span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">Depends:</span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> @,</span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> python-nose,</span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> python-cram,</span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"> make,</span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> poa</span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">Restrictions: allow-stderr</span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext">Test-Command:</span>
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22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"> make extra-tests</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> cp -r Makefile tests $AUTOPKGTEST_TMP</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> && cd $AUTOPKGTEST_TMP</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> && make extra-tests</span>
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23
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Depends:</span>
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24
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> @,</span>
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25
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> python-cram,</span>
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