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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/mapdamage">Debian Med / mapdamage</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/mapdamage/commit/b8b9e11fae938bea41777de7eb82f040792a4338">b8b9e11f</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-10-01T17:21:16Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix import statement in rescale_test.py
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</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mapdamage/commit/d0b6777584b4ead5b4c5bf84554c26370bd606d1">d0b67775</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-10-01T17:22:40Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Deactivate rescale_test.py in autopkgtest
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/mapdamage/commit/419c01c4ef5b11cd8447ab42cdeac2ec24a1b342">419c01c4</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-10-01T17:41:18Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Test-Depends: gfortran
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/mapdamage/commit/082127300ab8556a2e39232d06d300557539df7a">08212730</a></strong>
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<span>by Andreas Tille</span>
<i>at 2019-10-01T17:58:51Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
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<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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</li>
<li class="file-stats">
<a href="#147455c221c6114d6986278a930dc3b46df0c96c">
<span class="new-file">
+
debian/patches/fix_rescale_test.patch
</span>
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</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
debian/tests/control
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<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/mapdamage/compare/43e9ade9065122eb2e25f2be0a1f8f85f4ab1f28...082127300ab8556a2e39232d06d300557539df7a#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">mapdamage (2.1.0+dfsg-1) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">mapdamage (2.1.0+dfsg-1) <span class="idiff left right">unstable</span>; 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"> * New upstream version</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> Closes: #936989</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="7" 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="7" 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">@@ -7,8 +7,10 @@ mapdamage (2.1.0+dfsg-1) UNRELEASED; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> * Trim trailing whitespace.</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> * buildsystem=pybuild</span>
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<td class="diff-line-num 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">
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> * python3-pysam <!nocheck></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> * Deactivate rescale_test.py in autopkgtest</span>
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<td class="diff-line-num new new_line" data-linenumber="11" 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="LC11" class="line" lang="plaintext"> * Test-Depends: gfortran</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="LC11" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Tue, 01 Oct 2019 1<span class="idiff left right">7:13:12</span> +0200</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Tue, 01 Oct 2019 1<span class="idiff left right">9:41:25</span> +0200</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">mapdamage (2.0.9+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>
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<li id="147455c221c6114d6986278a930dc3b46df0c96c">
<a href="https://salsa.debian.org/med-team/mapdamage/compare/43e9ade9065122eb2e25f2be0a1f8f85f4ab1f28...082127300ab8556a2e39232d06d300557539df7a#147455c221c6114d6986278a930dc3b46df0c96c"><strong>debian/patches/fix_rescale_test.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Tue, 01 Oct 2019 17:13:12 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Description: Fix import statement in rescale_test.py</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">--- a/mapdamage/rescale_test.py</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/mapdamage/rescale_test.py</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -1,6 +1,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> import unittest</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> import optparse</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from . import rescale</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from mapdamage import rescale</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> import pysam</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> import filecmp</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> </span></pre>
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<a href="https://salsa.debian.org/med-team/mapdamage/compare/43e9ade9065122eb2e25f2be0a1f8f85f4ab1f28...082127300ab8556a2e39232d06d300557539df7a#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">use_debian_packaged_seqtk.patch</span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">fix_quantile_na_rm.patch</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">fix_rescale_test.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/mapdamage/compare/43e9ade9065122eb2e25f2be0a1f8f85f4ab1f28...082127300ab8556a2e39232d06d300557539df7a#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Tests: run-unit-test</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">Depends: @, r-cran-runit</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Depends: @, r-cran-runit<span class="idiff left right">, gfortran</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Restrictions: allow-stderr</span>
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4
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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">Tests: run-r-packages-check</span>
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<a href="https://salsa.debian.org/med-team/mapdamage/compare/43e9ade9065122eb2e25f2be0a1f8f85f4ab1f28...082127300ab8556a2e39232d06d300557539df7a#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12,8 +12,10 @@ cd $ADTTMP</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/tests/<span class="k" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">.</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/ref_T.fa <span class="nb" style="color: #0086b3;">.</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">gunzip</span> <span class="nt" style="color: #000080;">-r</span> <span class="k" style="font-weight: 600;">*</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="shell">python3 rescale_test.py</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># FIXME: rescale_test.py throws errors</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># will discuss with upstream</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># python3 rescale_test.py</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="shell">mapDamage <span class="nt" style="color: #000080;">-i</span> rescale_test/pe_test/pe.sam <span class="nt" style="color: #000080;">-r</span> ref_T.fa</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="shell"><span class="nv" style="color: #008080;">pdf_result</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"results_pe/Fragmisincorporation_plot.pdf"</span></span>
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