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<h3>
Graham Inggs pushed to branch master
at <a href="https://salsa.debian.org/med-team/gffread">Debian Med / gffread</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/gffread/-/commit/66b7741a740cc24fbe6f46b5fb6cf48edce4dd96">66b7741a</a></strong>
<div>
<span>by Graham Inggs</span>
<i>at 2020-12-06T01:48:55+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Skip two failing tests from gff2aplot
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gffread/-/commit/e10e18146fc4772bcbe8bdc65b20701d42a0285d">e10e1814</a></strong>
<div>
<span>by Graham Inggs</span>
<i>at 2020-12-06T01:51:13+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adjust autopkgtest dependencies for various architectures
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gffread/-/commit/4f9c20911a84c968243dc407710c17010219e2a5">4f9c2091</a></strong>
<div>
<span>by Graham Inggs</span>
<i>at 2020-12-06T01:56:24+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Bump Standards-Version to 4.5.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gffread/-/commit/d8d253ff657804ccf719deb8135fcd71af4cb2c2">d8d253ff</a></strong>
<div>
<span>by Graham Inggs</span>
<i>at 2020-12-06T01:57:12+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Prepare for upload to unstable
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gffread/-/commit/e814fa3541aa2bc0365228cbe8b72aa5f6a001a9">e814fa35</a></strong>
<div>
<span>by Graham Inggs</span>
<i>at 2020-12-06T08:11:21+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix a typo in ppc64el autopkgtest, upload to unstable
</pre>
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
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<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
debian/tests/control
</a>
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<li class="file-stats">
<a href="#aab2726ed6daf419caf178b1480b6d7da8a85af6">
debian/tests/run-tests
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/gffread/-/compare/d719fba162be014938c92a2cad7558260fe37731...e814fa3541aa2bc0365228cbe8b72aa5f6a001a9#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">gffread (0.12.1-3) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Fix a typo in ppc64el autopkgtest</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"> -- Graham Inggs <ginggs@debian.org> Sun, 06 Dec 2020 06:09:58 +0000</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="LC8" class="line" lang="plaintext">gffread (0.12.1-2) unstable; urgency=medium</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"> * Team upload</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> * Skip two failing tests from gff2aplot that were not run</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> previously due to being compressed (Closes: #962553)</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> * Adjust autopkgtest dependencies for various architectures</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> * Bump Standards-Version to 4.5.1, no changes</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> -- Graham Inggs <ginggs@debian.org> Sat, 05 Dec 2020 23:56:29 +0000</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">gffread (0.12.1-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> * Team upload.</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">@@ -7,7 +7,7 @@ Section: science</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 13),</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> libgclib-dev (>= 0.11.10)</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">Standards-Version: 4.5.<span class="idiff left right">0</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Standards-Version: 4.5.<span class="idiff left right">1</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/gffread</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/gffread.git</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Homepage: https://ccb.jhu.edu/software/stringtie/gff.shtml</span>
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<a href="https://salsa.debian.org/med-team/gffread/-/compare/d719fba162be014938c92a2cad7558260fe37731...e814fa3541aa2bc0365228cbe8b72aa5f6a001a9#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Tests: run-tests</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">Depends: gffread, bash, augustus-doc, bedtools-test, cnvkit<span class="idiff left right">, emboss-data, emboss-test, gbrowse, genometools-common, gff2aplot, gff2ps, htslib-test, libbio-graphics-perl, optimir, proteinortho, python3-gffutils, python3-pybedtools</span>, r-bioc-genomicfeatures, r-bioc-gviz, r-bioc-rhtslib, r-bioc-rtracklayer, seqan-apps, spades [amd64], trinityrnaseq-examples, dpkg-dev</span></pre>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Depends: gffread, bash, augustus-doc, bedtools-test, cnvkit<span class="idiff left right"> [amd64 arm64 ppc64el], emboss-data, emboss-test, gbrowse, genometools-common, gff2aplot, gff2ps, htslib-test, libbio-graphics-perl, optimir [amd64 arm64 ppc64el], proteinortho [amd64 arm64 ppc64el s390x], python3-gffutils, python3-pybedtools [amd64 arm64 ppc64el]</span>, r-bioc-genomicfeatures, r-bioc-gviz, r-bioc-rhtslib, r-bioc-rtracklayer, seqan-apps, spades [amd64], trinityrnaseq-examples, dpkg-dev</span></pre>
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<a href="https://salsa.debian.org/med-team/gffread/-/compare/d719fba162be014938c92a2cad7558260fe37731...e814fa3541aa2bc0365228cbe8b72aa5f6a001a9#aab2726ed6daf419caf178b1480b6d7da8a85af6"><strong>debian/tests/run-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">@@ -10,10 +10,22 @@ cd "$AUTOPKGTEST_TMP"</td>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># generated via</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># apt-file search --package-only --regexp '\.gff.?$' | grep -v -E "bedops|cct|ugene|gbrowse-data"</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="shell"><span class="nv" style="color: #008080;">PACKAGES</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"augustus-doc, bedtools-test, <span class="idiff left right">cnvkit, emboss-data, emboss-test, gbrowse, genometools-common, gff2aplot, gff2ps, htslib-test, libbio-graphics-perl, optimir, proteinortho, python3-gffutils, python3-pybedtoo</span>ls, r-bioc-genomicfeatures, r-bioc-gviz, r-bioc-rhtslib, r-bioc-rtracklayer, seqan-apps, trinityrnaseq-examples"</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="nv" style="color: #008080;">PACKAGES</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"augustus-doc, bedtools-test, <span class="idiff left right">emboss-data, emboss-test, gbrowse, genometools-common, gff2aplot, gff2ps, htslib-test, libbio-graphics-perl, python3-gffuti</span>ls, r-bioc-genomicfeatures, r-bioc-gviz, r-bioc-rhtslib, r-bioc-rtracklayer, seqan-apps, trinityrnaseq-examples"</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC15" 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="si" style="color: #d14;">$(</span>dpkg-architecture <span class="nt" style="color: #000080;">-qDEB_BUILD_ARCH</span><span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">"amd64"</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>PACKAGES+<span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">", spades"</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>PACKAGES+<span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">", cnvkit, optimir, proteinortho, python3-pybedtools, spades"</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span>dpkg-architecture <span class="nt" style="color: #000080;">-qDEB_BUILD_ARCH</span><span class="si" style="color: #d14;">)</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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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>PACKAGES+<span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">", cnvkit, optimir, proteinortho, python3-pybedtools"</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"></span>
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23
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<pre style="margin: 0;">+<span id="LC23" 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="si" style="color: #d14;">$(</span>dpkg-architecture <span class="nt" style="color: #000080;">-qDEB_BUILD_ARCH</span><span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">"ppc64el"</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>PACKAGES+<span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">", cnvkit, optimir, proteinortho, python3-pybedtools"</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span>dpkg-architecture <span class="nt" style="color: #000080;">-qDEB_BUILD_ARCH</span><span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">"s390x"</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="LC28" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>PACKAGES+<span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">", proteinortho"</span></span>
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17
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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;">fi</span></span>
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18
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30
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="shell"></span>
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19
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="shell"><span class="nv" style="color: #008080;">IFS</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">", "</span> <span class="nb" style="color: #0086b3;">read</span> <span class="nt" style="color: #000080;">-r</span> <span class="nt" style="color: #000080;">-a</span> pkgs <span class="o" style="font-weight: 600;"><<<</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">PACKAGES</span><span class="k" style="font-weight: 600;">}</span></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">@@ -101,7 +113,7 @@ IFS=", " read -r -a pkgs <<< ${PACKAGES}</td>
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101
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113
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># gffread /usr/lib/python3/dist-packages/pybedtools/test/data/c.gff</span></span>
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102
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Error: discarding overlapping duplicate mRNA feature (496-576) with ID=AT1G01010.mRNA</span></span>
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103
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115
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="shell"></span>
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104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="shell"><span class="nv" style="color: #008080;">SKIPS</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"/usr/share/doc/augustus/tutorial/results/augustus.abinitio.gff|/usr/share/doc/augustus/tutorial/results/augustus.hints.gff|/usr/lib/R/site-library/Gviz/extdata/test.gff2|/usr/lib/R/site-library/rtracklayer/tests/genes.gff3|/usr/share/EMBOSS/test/data/featexample2.gff3|/usr/share/EMBOSS/test/data/gmod-quantitative.gff3|/usr/share/gbrowse/htdocs/tutorial/data_files/volvox.gff3|/usr/share/gbrowse/htdocs/tutorial/data_files/volvox_all.gff3|/usr/share/gbrowse/htdocs/tutorial/data_files/volvox_bacs.gff3|/var/lib/gbrowse/databases/ideograms/human_cytobands.gff|/var/lib/gbrowse/databases/ideograms/mouse_cytobands.gff|/var/lib/gbrowse/databases/ideograms/rat_cytobands.gff|/var/lib/gbrowse/databases/yeast_chr1</span><span class="se" style="color: #d14;">\+</span><span class="s2" style="color: #d14;">2/yeast_chr1</span><span class="se" style="color: #d14;">\+</span><span class="s2" style="color: #d14;">2.gff3|/usr/lib/python3/dist-packages/gffutils/test/data/F3-unique-3.v2.gff|/usr/lib/python3/dist-packages/gffutils/test/data/mouse_extra_comma.gff3|/usr/lib/R/site-library/GenomicFeatures/extdata/GFF3_files/TheCanonicalGene_v2.gff3|/usr/share/doc/seqan-apps/insegt/example/annoOutput.gff|/usr/lib/python3/dist-packages/optimir/resources/coordinates/hsa_miRCarta_v1.1.gff3|/usr/lib/python3/dist-packages/gffutils/test/data/dmel-all-no-analysis-r5.49_50k_lines.gff|/usr/lib/python3/dist-packages/gffutils/test/data/glimmer_nokeyval.gff3|/usr/lib/python3/dist-packages/gffutils/test/data/unsanitized.gff|/usr/lib/python3/dist-packages/pybedtools/test/data/c.gff|/usr/lib/R/site-library/rtracklayer/tests/v2.gff"</span></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="shell"><span class="nv" style="color: #008080;">SKIPS</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"/usr/share/doc/augustus/tutorial/results/augustus.abinitio.gff|/usr/share/doc/augustus/tutorial/results/augustus.hints.gff|/usr/lib/R/site-library/Gviz/extdata/test.gff2|/usr/lib/R/site-library/rtracklayer/tests/genes.gff3|/usr/share/EMBOSS/test/data/featexample2.gff3|/usr/share/EMBOSS/test/data/gmod-quantitative.gff3|/usr/share/gbrowse/htdocs/tutorial/data_files/volvox.gff3|/usr/share/gbrowse/htdocs/tutorial/data_files/volvox_all.gff3|/usr/share/gbrowse/htdocs/tutorial/data_files/volvox_bacs.gff3|/var/lib/gbrowse/databases/ideograms/human_cytobands.gff|/var/lib/gbrowse/databases/ideograms/mouse_cytobands.gff|/var/lib/gbrowse/databases/ideograms/rat_cytobands.gff|/var/lib/gbrowse/databases/yeast_chr1</span><span class="se" style="color: #d14;">\+</span><span class="s2" style="color: #d14;">2/yeast_chr1</span><span class="se" style="color: #d14;">\+</span><span class="s2" style="color: #d14;">2.gff3|/usr/lib/python3/dist-packages/gffutils/test/data/F3-unique-3.v2.gff|/usr/lib/python3/dist-packages/gffutils/test/data/mouse_extra_comma.gff3|/usr/lib/R/site-library/GenomicFeatures/extdata/GFF3_files/TheCanonicalGene_v2.gff3|/usr/share/doc/seqan-apps/insegt/example/annoOutput.gff|/usr/lib/python3/dist-packages/optimir/resources/coordinates/hsa_miRCarta_v1.1.gff3|/usr/lib/python3/dist-packages/gffutils/test/data/dmel-all-no-analysis-r5.49_50k_lines.gff|/usr/lib/python3/dist-packages/gffutils/test/data/glimmer_nokeyval.gff3|/usr/lib/python3/dist-packages/gffutils/test/data/unsanitized.gff|/usr/lib/python3/dist-packages/pybedtools/test/data/c.gff|/usr/lib/R/site-library/rtracklayer/tests/v2.gff<span class="idiff left right">|/usr/share/doc/gff2aplot/examples/mhcregion/hs-mm.gff|/usr/share/doc/gff2aplot/examples/mhcregion/hs-mm.sim.gff</span>"</span></span>
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105
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117
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="shell"></span>
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106
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118
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>package <span class="k" style="font-weight: 600;">in</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkgs</span><span class="p">[@]</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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107
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="shell"><span class="k" style="font-weight: 600;">do</span></span>
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