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<h3>
Sascha Steinbiss pushed to branch master
at <a href="https://salsa.debian.org/med-team/gffread">Debian Med / gffread</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/gffread/-/commit/393dcda1b32d83199ad144655608aaf038ce6144">393dcda1</a></strong>
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<span>by Sascha Steinbiss</span>
<i>at 2021-01-08T09:04:39+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">skip broken new AUGUSTUS examples in autopkgtest
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<h4>2 changed files:</h4>
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<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/-/commit/393dcda1b32d83199ad144655608aaf038ce6144#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">gffread (0.12.1-4) 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"> * Skip some new AUGUSTUS GTFs that are likely bad, causing autopkgtests to</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> fail.</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"> -- Sascha Steinbiss <satta@debian.org> Fri, 08 Jan 2021 08:52:52 +0100</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">gffread (0.12.1-3) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> * Team upload</span>
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<a href="https://salsa.debian.org/med-team/gffread/-/commit/393dcda1b32d83199ad144655608aaf038ce6144#aab2726ed6daf419caf178b1480b6d7da8a85af6"><strong>debian/tests/run-tests</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="113" 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">@@ -113,7 +113,7 @@ IFS=", " read -r -a pkgs <<< ${PACKAGES}</td>
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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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<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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<pre style="margin: 0;"> <span id="LC115" class="line" lang="shell"></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|/usr/share/doc/gff2aplot/examples/mhcregion/hs-mm.gff|/usr/share/doc/gff2aplot/examples/mhcregion/hs-mm.sim.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<span class="idiff left right">-cgp|/usr/share/doc/augustus/tutorial</span>/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|/usr/share/doc/gff2aplot/examples/mhcregion/hs-mm.gff|/usr/share/doc/gff2aplot/examples/mhcregion/hs-mm.sim.gff"</span></span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="shell"></span>
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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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<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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