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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/gff2aplot">Debian Med / gff2aplot</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/gff2aplot/commit/749d6264bbcefd4bd59eb14a862740df0afea799">749d6264</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-30T12:27:09Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Spelling
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gff2aplot/commit/4254ea8b85a9300bad2c720b28e85a91999ff4ca">4254ea8b</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-30T12:43:06Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Less verbose logs to see what's happening
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gff2aplot/commit/3b5eaa35c7ac1c63b9469cb40efdfe27c71e8392">3b5eaa35</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-30T12:59:45Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix README used as shell script for testing
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gff2aplot/commit/334268a3c7d0a9e1f8e11053abed06407eab3953">334268a3</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-30T13:02:24Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">hardening=+all
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gff2aplot/commit/4fa961acde6b2da77bb110824520497fe9a42762">4fa961ac</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-30T13:10:57Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Silence test; Ignore issues we have no idea how to deal with. That's enough for testing compared to no testing at all as done before.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gff2aplot/commit/06891fb9ed8c8d86c2a2db0ca9738a8701cc9648">06891fb9</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-30T13:14:23Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#8f9f8bc7c27595c726971f9fc2bacb66f11758f5">
<span class="new-file">
+
debian/patches/fix_README_used_for_test.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#fe555f84509c564f4a0a350f51260621514b6cc2">
debian/patches/non_lexical_loop_iterator.patch
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/gff2aplot/compare/fff5d5ab38c06272b476e9a4620f4460eacb0c7a...06891fb9ed8c8d86c2a2db0ca9738a8701cc9648#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num new_line old" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">gff2aplot (2.0-11) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2" 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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<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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">gff2aplot (2.0-11) <span class="idiff left right">unstable</span>; urgency=medium</span>
</pre>
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<td class="diff-line-num new_line" data-linenumber="2" 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="LC2" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="3" 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="diff-line-num new_line" data-linenumber="3" 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="LC3" class="line" lang="plaintext"> * README files in examples are actually scripts - fix PATH to gff2aplot</span>
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<td class="diff-line-num old_line" data-linenumber="4" 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="diff-line-num new_line" data-linenumber="4" 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="LC4" class="line" lang="plaintext"> * Add autopkgtest</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 @@ gff2aplot (2.0-11) UNRELEASED; urgency=medium</td>
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<td class="diff-line-num 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">
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<td class="diff-line-num 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">
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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="LC7" class="line" lang="plaintext"> * Fix definition of CP in upstream makefile</span>
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<td class="diff-line-num old_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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<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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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> * Try hard to make sprint buffers have proper size</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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<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"> * Recommends: graphicsmagick | imagemagick, ghostscript (+ Test-Depends)</span>
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<td class="diff-line-num new old_line" data-linenumber="10" 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="LC10" class="line" lang="plaintext"> * Fix README used as shell script for testing</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"> * hardening=+all</span>
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<td class="diff-line-num new_line" data-linenumber="12" 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="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> <span class="idiff left right">Mon, 10 Dec 2018 07:36:57</span> +0100</span>
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<td class="diff-line-num new new_line" data-linenumber="13" 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="LC13" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> <span class="idiff left right">Wed, 30 Jan 2019 14:12:34</span> +0100</span>
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<td class="diff-line-num new_line" data-linenumber="14" 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="LC14" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="15" 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="LC15" class="line" lang="plaintext">gff2aplot (2.0-10) unstable; urgency=medium</span>
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<td class="diff-line-num new_line" data-linenumber="16" 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="LC16" class="line" lang="plaintext"></span>
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<li id="8f9f8bc7c27595c726971f9fc2bacb66f11758f5">
<a href="https://salsa.debian.org/med-team/gff2aplot/compare/fff5d5ab38c06272b476e9a4620f4460eacb0c7a...06891fb9ed8c8d86c2a2db0ca9738a8701cc9648#8f9f8bc7c27595c726971f9fc2bacb66f11758f5"><strong>debian/patches/fix_README_used_for_test.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Author: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Last-Update: Mon, 10 Dec 2018 07:36:57 +0100</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Description: The README file is used as shell script and one function</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> is broken. It should return basenames of *.ps files. This is fixed here</span>
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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/examples/splice_sites/README</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/examples/splice_sites/README</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;">@@ -140,8 +140,7 @@ $BIN/gff2aplot.pl -v -t "DONOR + ACCEPTO</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> # Preparing web images</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> filenames () {</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;">- cat << 'EOF';</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-EOF</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;">+ ls *.ps | sed 's/\.ps//'</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> };</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> # echo "# Using \"ghostscript\" to obtain JPEG images from PS files" ;</span></pre>
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<li id="fe555f84509c564f4a0a350f51260621514b6cc2">
<a href="https://salsa.debian.org/med-team/gff2aplot/compare/fff5d5ab38c06272b476e9a4620f4460eacb0c7a...06891fb9ed8c8d86c2a2db0ca9738a8701cc9648#fe555f84509c564f4a0a350f51260621514b6cc2"><strong>debian/patches/non_lexical_loop_iterator.patch</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff">Description: Make sure that iterator variable is explicit<span class="idiff left right">e</span>ly decalred as</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Description: Make sure that iterator variable is explicitly decalred as</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"> a lexcical using my keyword. See PBP, page 108. Add perl shebang.</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff">From: Alex Mestiashvili <amestia@rsh2.donotuse.de></span>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- gff2aplot.orig/src/gff2aplot.pl</span></span>
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<a href="https://salsa.debian.org/med-team/gff2aplot/compare/fff5d5ab38c06272b476e9a4620f4460eacb0c7a...06891fb9ed8c8d86c2a2db0ca9738a8701cc9648#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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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>
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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">@@ -7,3 +7,4 @@ fis-privacy-breach.patch</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">perl_5.28.patch</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">fix_install_ali2gff.patch</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">enhance_sprintf_buffer.patch</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">fix_README_used_for_test.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/gff2aplot/compare/fff5d5ab38c06272b476e9a4620f4460eacb0c7a...06891fb9ed8c8d86c2a2db0ca9738a8701cc9648#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</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">@@ -3,6 +3,8 @@</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"># Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"># GPL</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">export DEB_BUILD_MAINT_OPTIONS=hardening=+all</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">%:</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> dh $@</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/gff2aplot/compare/fff5d5ab38c06272b476e9a4620f4460eacb0c7a...06891fb9ed8c8d86c2a2db0ca9738a8701cc9648#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -19,9 +19,19 @@ ERR=0</td>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>script <span class="k" style="font-weight: 600;">in</span> <span class="sb" style="color: #d14;">`</span>find <span class="nb" style="color: #0086b3;">.</span> <span class="nt" style="color: navy;">-name</span> README<span class="sb" style="color: #d14;">`</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">cd</span> <span class="k" style="font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">dirname</span> <span class="nv" style="color: teal;">$script</span><span class="k" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># Suppress verbose output for testing</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: navy;">-i</span> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'/^[[:space:]]\+--verbose[[:space:]]\+\\$/d'</span> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'s/--verbose//'</span> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'s/MG *-verbose/MG -quiet/'</span> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'s?$BIN/\([a-z0-9]\+\).pl?\1?'</span> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'s?^$BIN/??'</span> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'1i set -x'</span> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'1i set -e'</span> README</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: navy;">-i</span> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'/^[[:space:]]\+--verbose[[:space:]]\+\\$/d'</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'s/--verbose//'</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'s/gff2aplot \+-v/gff2aplot /'</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'s/MG *-verbose/MG -quiet/'</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'s?$BIN/\([a-z0-9]\+\).pl?\1?'</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'s?^$BIN/??'</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'1i set -e'</span> <span class="se" style="color: #d14;">\</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"> README</span>
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23
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="shell"> sh README | <span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: navy;">-v</span> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'^KCRB.GT.hs-mm.log'</span> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'^#'</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;">if </span><span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: navy;">-q</span> <span class="nt" style="color: navy;">-v</span> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'^#'</span> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'^|'</span> <span class="k" style="font-weight: 600;">*</span>.log <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if </span><span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: navy;">-q</span> <span class="nt" style="color: navy;">-v</span> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'^#'</span> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'^|'</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'^Redundant argument in sprintf at /usr/bin/gff2aplot line 3676.'</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"> <span class="nt" style="color: navy;">-e</span> <span class="s2" style="color: #d14;">"Can't open taf6.mmhs.genomic.tblastx: No such file or directory at /usr/bin/parseblast line 889."</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell"> <span class="k" style="font-weight: 600;">*</span>.log <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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25
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">ERR</span><span class="o" style="font-weight: 600;">=</span>1</span>
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26
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Some errors were found in logfiles"</span></span>
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27
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: navy;">-H</span> <span class="nt" style="color: navy;">-v</span> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'^#'</span> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'^|'</span> <span class="k" style="font-weight: 600;">*</span>.log</span>
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