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<h3>
Sascha Steinbiss pushed to branch debian/buster-backports
at <a href="https://salsa.debian.org/med-team/genometools">Debian Med / genometools</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/genometools/-/commit/b55f9502bfc9cf7ead96f126b2760f9d1d0a89d0">b55f9502</a></strong>
<div>
<span>by Sascha Steinbiss</span>
<i>at 2020-02-09T09:53:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">use static images for AnnotationSketch manual
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/genometools/-/commit/bb3bf8ab616752843b8cf4915e9998e3827198f4">bb3bf8ab</a></strong>
<div>
<span>by Sascha Steinbiss</span>
<i>at 2020-07-22T13:33:29+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add patch to fix build on GCC10
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/genometools/-/commit/b5308391dded5f707eafba10bebe4bddf5cf1b93">b5308391</a></strong>
<div>
<span>by Sascha Steinbiss</span>
<i>at 2020-07-29T13:01:41+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into debian/buster-backports
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/genometools/-/commit/cf1c416f6df665f670eaca5c6279a5c0c2a4f7b0">cf1c416f</a></strong>
<div>
<span>by Sascha Steinbiss</span>
<i>at 2020-07-29T13:13:47+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">rebuild for buster-backports
</pre>
</li>
</ul>
<h4>11 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#d57d4dd24058a0e307d81424b72c56c586776802">
<span class="new-file">
+
debian/doc-imgs/callbacks.png
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</li>
<li class="file-stats">
<a href="#30ae20fc6147f7148eaed1c948a287c19946663d">
<span class="new-file">
+
debian/doc-imgs/constructed.png
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<li class="file-stats">
<a href="#4005c525c5a1abb6cfdf3ecb7abcf4bfe88a4c72">
<span class="new-file">
+
debian/doc-imgs/parsed.png
</span>
</a>
</li>
<li class="file-stats">
<a href="#2b74f32a7f92773f8a255f183fe932e83d2ee910">
debian/patches/adding_soname
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</li>
<li class="file-stats">
<a href="#81a9a5b123fb5e9473f68e4733e9d389fa7872c9">
<span class="new-file">
+
debian/patches/gcc10.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#8eaf26dc9f7838a3ad588af945777ce6c949753c">
debian/patches/reproducible
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<li class="file-stats">
<a href="#d0b2adb0358f0eab7dd3bb1849dd4e795a81f242">
<span class="new-file">
+
debian/source/include-binaries
</span>
</a>
</li>
<li class="file-stats">
<a href="#881b2dcfcf99ecd827fefb40287e59f9307251ea">
<span class="deleted-file">
−
www/genometools.org/htdocs/libgenometools.html
</span>
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/genometools/-/compare/025c54c8736493aceb6cf2f726d75c09845c8241...cf1c416f6df665f670eaca5c6279a5c0c2a4f7b0#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">genometools (1.6.1+ds-3~bpo10+1) buster-backports; 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"> * Rebuild for buster-backports.</span>
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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"> -- Sascha Steinbiss <satta@debian.org> Wed, 29 Jul 2020 13:01:49 +0200</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="7" 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="LC7" class="line" lang="plaintext">genometools (1.6.1+ds-3) unstable; urgency=medium</span>
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<td class="diff-line-num new new_line" data-linenumber="8" 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="LC8" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="9" 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="LC9" class="line" lang="plaintext"> * Add patch to fix build on GCC 10.</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> Closes: #957268</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"> -- Sascha Steinbiss <satta@debian.org> Wed, 22 Jul 2020 13:00:06 +0200</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">genometools (1.6.1+ds-2) unstable; urgency=medium</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"> * Use static images for AnnotationSketch documentation.</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> This improves reproducibility in cases where (on some platforms)</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> different runs would create different images.</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"> -- Sascha Steinbiss <satta@debian.org> Sun, 09 Feb 2020 09:33:24 +0100</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">genometools (1.6.1+ds-1~bpo10+1) buster-backports; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> * Rebuild for buster-backports.</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">@@ -25,7 +25,7 @@ Author: Sascha Steinbiss <steinbiss@zbh.uni-hamburg.de></td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="diff"> define PROGRAM_template</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="diff"> $(1): $(2)</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"><span class="p">@@ -<span class="idiff left right">1003,7 +1005</span>,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="p">@@ -<span class="idiff left right">999,7 +1001</span>,8 @@</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="diff"> $(RANLIB) $(prefix)/lib/libgenometools.a</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="diff"> endif</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="diff"> ifneq ($(sharedlib),no)</span>
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<a href="https://salsa.debian.org/med-team/genometools/-/compare/025c54c8736493aceb6cf2f726d75c09845c8241...cf1c416f6df665f670eaca5c6279a5c0c2a4f7b0#81a9a5b123fb5e9473f68e4733e9d389fa7872c9"><strong>debian/patches/gcc10.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">From 51205942b1f41abdf841771deac4e0e35d7d5016 Mon Sep 17 00:00:00 2001</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">From: Sascha Steinbiss <satta@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Date: Wed, 22 Apr 2020 21:59:57 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Subject: [PATCH 1/2] make sure to not ignore snprintf output</span></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">GCC 10 will warn about the (here intended) silent string truncation</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">done by snprintf() unless the return value is handled.</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">Obviously this will break the build as we use -Werror. We</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">circumvent the problem by checking the output value and printing a</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="p">warning if we notice a truncation.</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="p">---</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> src/ltr/ltrdigest_file_out_stream.c | 17 ++++++++++++-----</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> 1 file changed, 12 insertions(+), 5 deletions(-)</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff">diff --git a/src/ltr/ltrdigest_file_out_stream.c b/src/ltr/ltrdigest_file_out_stream.c</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gh" style="color: #999;">index 723b8cf9a..61325b693 100644</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/ltr/ltrdigest_file_out_stream.c</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/ltr/ltrdigest_file_out_stream.c</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="p">@@ -1,5 +1,5 @@</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> /*</span>
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<td class="diff-line-num new new_line" data-linenumber="21" 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">
21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Copyright (c) 2008-2015 Sascha Steinbiss <sascha@steinbiss.name></span></span>
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<td class="diff-line-num new new_line" data-linenumber="22" 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">
22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Copyright (c) 2008-2020 Sascha Steinbiss <sascha@steinbiss.name></span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> Copyright (c) 2008-2013 Center for Bioinformatics, University of Hamburg</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> Permission to use, copy, modify, and distribute this software for any</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="p">@@ -33,6 +33,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> #include "core/symbol.h"</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> #include "core/undef_api.h"</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> #include "core/unused_api.h"</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include "core/warning_api.h"</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> #include "extended/extract_feature_sequence.h"</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> #include "extended/feature_node.h"</span>
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<td class="diff-line-num new new_line" data-linenumber="33" 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="LC33" class="line" lang="diff"> #include "extended/feature_node_iterator_api.h"</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="p">@@ -416,6 +417,8 @@</span> int gt_ltrfileout_stream_next(GtNodeStream *ns, GtGenomeNode **gn, GtError *err)</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> if (!had_err) {</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> GtRange rng;</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ int ret = 0;</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> ls->element.seqid = gt_calloc((size_t) ls->seqnamelen+1, sizeof (char));</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> (void) snprintf(ls->element.seqid,</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> GT_MIN((size_t) gt_str_length(sdesc),</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="p">@@ -425,12 +428,16 @@</span> int gt_ltrfileout_stream_next(GtNodeStream *ns, GtGenomeNode **gn, GtError *err)</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> if (gt_str_length(sdesc) > (GtUword) ls->seqnamelen)</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> ls->element.seqid[ls->seqnamelen] = '\0';</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- (void) gt_ltrelement_format_description(&ls->element,</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ls->seqnamelen,</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- desc,</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- (size_t) (GT_MAXFASTAHEADER-1));</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ret = gt_ltrelement_format_description(&ls->element,</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ls->seqnamelen,</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ desc,</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ (size_t) (GT_MAXFASTAHEADER-1));</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (ret < 0) {</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ gt_warning("FASTA header truncated: %s", desc);</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> gt_str_delete(sdesc);</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> /* output basic retrotransposon data */</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> lltr_rng = gt_genome_node_get_range((GtGenomeNode*) ls->element.leftLTR);</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> rltr_rng = gt_genome_node_get_range((GtGenomeNode*) ls->element.rightLTR);</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff">From 30ae36037228dc4ed174e8462f3489638e6f5e76 Mon Sep 17 00:00:00 2001</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="p">From: Sascha Steinbiss <satta@debian.org></span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="p">Date: Wed, 22 Apr 2020 22:01:00 +0200</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="p">Subject: [PATCH 2/2] declare hashmap type as extern</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff">This fixes a build issue with GCC 10.</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="p">Closes #941.</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="p">---</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"> src/mgth/metagenomethreader.h | 2 +-</span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> 1 file changed, 1 insertion(+), 1 deletion(-)</span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff">diff --git a/src/mgth/metagenomethreader.h b/src/mgth/metagenomethreader.h</span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="gh" style="color: #999;">index 92f16d498..7f76fffb9 100644</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/mgth/metagenomethreader.h</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/mgth/metagenomethreader.h</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="p">@@ -221,7 +221,7 @@</span> typedef struct</span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"> } ParseStruct;</span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"> /* specific access mode of queryhash */</span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-DECLARE_HASHMAP(char *, gt_cstr_nofree, GtUword *, ulp,,)</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+DECLARE_HASHMAP(char *, gt_cstr_nofree, GtUword *, ulp, extern,)</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"> DECLARE_SAFE_DEREF(GtUword *, ulp)</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> /* Funktion, mit der der Metagenomethreader gestartet wird</span></pre>
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<li id="8eaf26dc9f7838a3ad588af945777ce6c949753c">
<a href="https://salsa.debian.org/med-team/genometools/-/compare/025c54c8736493aceb6cf2f726d75c09845c8241...cf1c416f6df665f670eaca5c6279a5c0c2a4f7b0#8eaf26dc9f7838a3ad588af945777ce6c949753c"><strong>debian/patches/reproducible</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">@@ -19,17 +19,15 @@ Author: Sascha Steinbiss <satta@debian.org></td>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="diff"> echo '$(EXP_CPPFLAGS) $(GT_CPPFLAGS)' | \</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="diff"> sed -e 's/\([^\]\)"/\1\\"/g' -e 's/^"/\\"/g' -e 's/$$/"/' \</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="diff"> -e 's/^/#define GT_CPPFLAGS "/'; \</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"><span class="p">@@ -922,6 +923,10 @@</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"> bin/examples/sketch_constructed gtdata/sketch/default.style \</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"> www/genometools.org/htdocs/images/constructed.png</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"> endif</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ mogrify -format jpg +set date:create +set date:modify \</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ -define png:exclude-chunk=time \</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ www/genometools.org/htdocs/images/*.png && \</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ rm -rf www/genometools.org/htdocs/images/*.png</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"> sed -nf scripts/incl.sed \</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"> www/genometools.org/htdocs/examples_tmpl.html | \</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"> sed 'N;N;s/\n//' > /tmp/tmp.sed.$$$$ && \</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="p">@@ -911,7 +912,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> > www/genometools.org/htdocs/libgenometools.html</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> bin/gt gtscripts/gtdoc.lua -lua -html $(CURDIR) \</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> > www/genometools.org/htdocs/docs.html</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-ifdef SKETCH_EXTRA_BINARIES</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ifdef ___SKETCH_EXTRA_BINARIES</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> bin/examples/sketch_parsed gtdata/sketch/default.style \</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> www/genometools.org/htdocs/images/parsed.png \</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> testdata/eden.gff3</span>
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33
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/doc/manuals/annotationsketch.tex</span></span>
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34
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32
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/doc/manuals/annotationsketch.tex</span></span>
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35
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="diff"><span class="p">@@ -51,6 +51,7 @@</span></span>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/genometools/-/compare/025c54c8736493aceb6cf2f726d75c09845c8241...cf1c416f6df665f670eaca5c6279a5c0c2a4f7b0#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<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">@@ -7,3 +7,4 @@ split-manuals</td>
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7
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">use-mx32</span>
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8
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">gtdoc-traverse-sorted</span>
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9
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">ignore-m32-m64.patch</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">gcc10.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/genometools/-/compare/025c54c8736493aceb6cf2f726d75c09845c8241...cf1c416f6df665f670eaca5c6279a5c0c2a4f7b0#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">@@ -55,6 +55,7 @@ override_dh_auto_clean:</td>
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55
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-rf</span> obj</span>
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56
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="make"></span>
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57
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="make"><span class="nl">override_dh_auto_build</span><span class="o" style="font-weight: 600;">:</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="make"> <span class="nb" style="color: #0086b3;">cp </span>debian/doc-imgs/<span class="k" style="font-weight: 600;">*</span>png www/genometools.org/htdocs/images</span>
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58
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="make"> <span class="nv" style="color: #008080;">$(FAKETIME)</span> dh_auto_build <span class="nt" style="color: #000080;">--</span> <span class="nv" style="color: #008080;">verbose</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">yes </span><span class="nv" style="color: #008080;">useshared</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">yes </span><span class="nv" style="color: #008080;">x32</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$(X32)</span> <span class="nv" style="color: #008080;">64bit</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$(64BIT)</span> <span class="nv" style="color: #008080;">errorcheck</span><span class="o" style="font-weight: 600;">=</span>no all docs manuals</span>
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59
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="make"><span class="nl">override_dh_auto_test</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/doc-imgs/constructed.png</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">debian/doc-imgs/parsed.png</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">debian/doc-imgs/callbacks.png</span></pre>
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