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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/bamtools">Debian Med / bamtools</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/bamtools/-/commit/d168122823bd3993c886d2d9199fc2fd8e6e0ba5">d1681228</a></strong>
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<span>by Andreas Tille</span>
<i>at 2021-04-15T21:27:14+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Extend means to prevent timeouts from amd64 also to armhf and s390x
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<strong><a href="https://salsa.debian.org/med-team/bamtools/-/commit/54022a84bdccaa816c36541f01ba1196609b92a5">54022a84</a></strong>
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<span>by Andreas Tille</span>
<i>at 2021-04-15T21:28:43+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update changelog
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<h4>2 changed files:</h4>
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<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/bamtools/-/compare/37913b3e5b1cc8cefd990698632d69f4d7e96fc3...54022a84bdccaa816c36541f01ba1196609b92a5#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">bamtools (2.5.1+dfsg-9) 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"> [ Steffen Möller ]</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Update metadata - indent and ref to guix</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> [ Andreas Tille ]</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * Extend means to prevent timeouts from amd64 also to armhf and s390x</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> Closes: #987023</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"> -- Andreas Tille <tille@debian.org> Thu, 15 Apr 2021 21:28:36 +0200</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">bamtools (2.5.1+dfsg-8) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> * Exclude test that times out on arm64</span>
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<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/bamtools/-/compare/37913b3e5b1cc8cefd990698632d69f4d7e96fc3...54022a84bdccaa816c36541f01ba1196609b92a5#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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<td class="diff-line-num unfold js-unfold old_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="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">@@ -23,13 +23,13 @@ bamtools coverage -in sam_spec_example.bam -out out</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># This test fails on ppc64el for whatever reason and is for the moment (see bug #933505)</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="shell"><span class="nv" style="color: #008080;">ARCH</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span>dpkg <span class="nt" style="color: #000080;">--print-architecture</span><span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$ARCH</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s2" style="color: #d14;">"ppc64el"</span> <span class="nt" style="color: #000080;">-a</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$ARCH</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s2" style="color: #d14;">"arm64"</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$ARCH</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s2" style="color: #d14;">"ppc64el"</span> <span class="nt" style="color: #000080;">-a</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$ARCH</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s2" style="color: #d14;">"arm64"</span> <span class="nt" style="color: #000080;"><span class="idiff left">-a</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="nv" style="color: #008080;"><span class="idiff">$ARCH</span></span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"armhf"</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-a</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="nv" style="color: #008080;"><span class="idiff">$ARCH</span></span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"s390x"</span></span><span class="idiff right"> </span><span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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27
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>bamtools filter <span class="nt" style="color: #000080;">-script</span> filter_script <span class="nt" style="color: #000080;">-in</span> sam_spec_example.bam <span class="nt" style="color: #000080;">-out</span> out.bam</span>
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28
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28
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>
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29
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29
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$ARCH</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">"ppc64el"</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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30
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"The following test is known to fail on ppc64el architecture (see bug #933505)"</span></span>
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31
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31
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="shell"> <span class="k" style="font-weight: 600;">else</span></span>
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32
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"The following test is known to time out on <span class="idiff left right">arm64</span> architecture (see bug #953939)"</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"The following test is known to time out on </span><span class="nv" style="color: #008080;"><span class="idiff left right">$ARCH</span></span><span class="s2" style="color: #d14;"> architecture (see bug #953939)"</span></span>
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33
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33
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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34
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"bamtools filter -script filter_script -in sam_spec_example.bam -out out.bam"</span></span>
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35
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35
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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