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GitLab

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<h3>

Andreas Tille pushed to branch master

at <a href="https://salsa.debian.org/med-team/staden">Debian Med / staden</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/staden/commit/546cf0a9b64796141a4c57252b7b810bfa863025">546cf0a9</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-07-15T07:01:11+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Enable autoreconf finding all macros and suppress warnings

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/staden/commit/0e17cf42b31e2ddfb618f5a2d93bf88a4577efbc">0e17cf42</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-07-15T07:10:41+02:00</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/staden/commit/e18a6c3a81d0eff5ee2510056d4a8f0dd5389037">e18a6c3a</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-07-15T07:14:10+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix spelling

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/staden/commit/2ce5810c7b40b74c712f3afafb0227535b80742f">2ce5810c</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-07-15T07:17:15+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable

</pre>

</li>

</ul>

<h4>7 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

</a>

</li>

<li class="file-stats">

<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

debian/control

</a>

</li>

<li class="file-stats">

<a href="#5aaa63e54b6a2a7c72c0ad5576a8b70fe7709582">

<span class="new-file">

+

debian/patches/autoconfig.patch

</span>

</a>

</li>

<li class="file-stats">

<a href="#a67dc3026669feda5dcd6b08d6f31cc2920054fa">

debian/patches/fix_implicit_declaration.patch

</a>

</li>

<li class="file-stats">

<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

debian/patches/series

</a>

</li>

<li class="file-stats">

<a href="#45ae034d1d71b2d961abb7c91cf3d2f1a02a59c6">

<span class="new-file">

+

debian/patches/spelling.patch

</span>

</a>

</li>

<li class="file-stats">

<a href="#8756c63497c8dc39f7773438edf53b220c773f67">

debian/rules

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/staden/compare/9e2d13c25894edf228805a0f18b4efedbdbe87c9...2ce5810c7b40b74c712f3afafb0227535b80742f#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

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1

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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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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">staden (2.0.0+b11-3) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>

</pre>

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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">

1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">staden (2.0.0+b11-3) <span class="idiff left right">unstable</span>; urgency=medium</span>

</pre>

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2

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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">

2

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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>

</pre>

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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">

3

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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">

3

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">  * Fix homepage</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">

4

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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">

4

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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">  * debhelper 11</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="5" 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">

5

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5

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">  * Point Vcs fields to salsa.debian.org</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="6" 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">

6

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6

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">  * Standards-Version: 4.1.5</span>

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<td class="diff-line-num old old_line" data-linenumber="7" 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">

7

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<td class="diff-line-num new_line old" data-linenumber="7" 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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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">  * Build-Depends: autoconf-archive, pkg-config</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="8" 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">

8

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<td class="diff-line-num new_line old" data-linenumber="7" 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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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">  TODO: This does not help to fix</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="9" 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">

9

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<td class="diff-line-num new_line old" data-linenumber="7" 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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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">     error: possibly undefined macro: AC_MSG_ERROR</span>

</pre>

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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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<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">

7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">  * Enable autoreconf finding all macros and suppress warnings (thanks to</span>

</pre>

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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">

8

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">    Yavor Doganov for the patch)</span>

</pre>

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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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<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">

9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">  * hardening=+all</span>

</pre>

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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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<td class="diff-line-num new new_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">

10

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">  * Fix spelling</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="10" 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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11

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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="LC11" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="12" 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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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org>  S<span class="idiff left right">at, 14 Jul 2018 17:31:37</span> +0200</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="12" 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="12" 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">

12

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org>  S<span class="idiff left right">un, 15 Jul 2018 07:14:23</span> +0200</span>

</pre>

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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">staden (2.0.0+b11-2) unstable; urgency=medium</span>

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>

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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

<a href="https://salsa.debian.org/med-team/staden/compare/9e2d13c25894edf228805a0f18b4efedbdbe87c9...2ce5810c7b40b74c712f3afafb0227535b80742f#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5" 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">@@ -5,8 +5,6 @@ Uploaders: Tim Booth <tbooth@ceh.ac.uk>,</td>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Section: science</span>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Priority: optional</span>

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper (>= 11~),</span>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">               autoconf-archive,</span>

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">               pkg-config,</span>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">               libstaden-read-dev (>= 1.14.6),</span>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">               itcl3-dev,</span>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">               itk3-dev,</span>

</pre>

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</li>

<li id="5aaa63e54b6a2a7c72c0ad5576a8b70fe7709582">

<a href="https://salsa.debian.org/med-team/staden/compare/9e2d13c25894edf228805a0f18b4efedbdbe87c9...2ce5810c7b40b74c712f3afafb0227535b80742f#5aaa63e54b6a2a7c72c0ad5576a8b70fe7709582"><strong>debian/patches/autoconfig.patch</strong></a>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Author: Yavor Doganov <yavor@gnu.org></span>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Last-Update: Sun, 15 Jul 2018 07:06:40 +0300</span>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Description: Enable autoreconf finding all macros and suppress warnings</span>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/ac_stubs/libcurl_check_config.m4 b/ac_stubs/libcurl_check_config.m4</span></span>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gh" style="color: #999;">index 9b41a73..0c17884 100644</span></span>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/ac_stubs/libcurl_check_config.m4</span></span>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/ac_stubs/libcurl_check_config.m4</span></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">

9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -116,7 +116,7 @@ AC_DEFUN([LIBCURL_CHECK_CONFIG],</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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">

10

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff">                  _libcurl_save_libs=$LIBS</span>

</pre>

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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">

11

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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="LC11" class="line" lang="diff">                  LIBS="$LIBCURL $LIBS"</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="12" 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">

12

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff">          </span>

</pre>

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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">

13

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         AC_LINK_IFELSE(AC_LANG_PROGRAM([#include <curl/curl.h>],[</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="14" 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">

14

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+         AC_LINK_IFELSE([AC_LANG_PROGRAM([[#include <curl/curl.h>]],[[</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="15" 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">

15

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> /* Try and use a few common options to force a failure if we are</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="16" 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">

16

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff">    missing symbols or can't link. */</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="17" 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">

17

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> int x;</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="18" 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="LC18" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -127,7 +127,7 @@ x=CURLOPT_FILE;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="19" 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="LC19" class="line" lang="diff"> x=CURLOPT_ERRORBUFFER;</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="20" 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="LC20" class="line" lang="diff"> x=CURLOPT_STDERR;</span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> x=CURLOPT_VERBOSE;</span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-]),libcurl_cv_lib_curl_only_needs_minus_l_curl=yes,libcurl_cv_lib_curl_only_needs_minus_l_curl=no)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="23" 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="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+]])],libcurl_cv_lib_curl_only_needs_minus_l_curl=yes,libcurl_cv_lib_curl_only_needs_minus_l_curl=no)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="24" 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="LC24" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="25" 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="LC25" class="line" lang="diff">                  CPPFLAGS=$_libcurl_save_cppflags</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="26" 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="LC26" class="line" lang="diff">                  LIBS=$_libcurl_save_libs</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="27" 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="LC27" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -178,7 +178,7 @@ x=CURLOPT_VERBOSE;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="28" 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="LC28" class="line" lang="diff">            _libcurl_save_libs=$LIBS</span>

</pre>

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff">            LIBS="$LIBCURL $LIBS"</span>

</pre>

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-           AC_LINK_IFELSE(AC_LANG_PROGRAM([#include <curl/curl.h>],[</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+           AC_LINK_IFELSE([AC_LANG_PROGRAM([[#include <curl/curl.h>]],[[</span></span>

</pre>

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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"> /* Try and use a few common options to force a failure if we are</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="34" 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="LC34" class="line" lang="diff">    missing symbols or can't link. */</span>

</pre>

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> int x;</span>

</pre>

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -189,7 +189,7 @@ x=CURLOPT_FILE;</span></span>

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> x=CURLOPT_ERRORBUFFER;</span>

</pre>

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> x=CURLOPT_STDERR;</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="39" 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="LC39" class="line" lang="diff"> x=CURLOPT_VERBOSE;</span>

</pre>

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-]),libcurl_cv_lib_curl_usable=yes,libcurl_cv_lib_curl_usable=no)</span></span>

</pre>

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41

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+]])],libcurl_cv_lib_curl_usable=yes,libcurl_cv_lib_curl_usable=no)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="42" 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="LC42" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="43" 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="LC43" class="line" lang="diff">            CPPFLAGS=$_libcurl_save_cppflags</span>

</pre>

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff">            LIBS=$_libcurl_save_libs</span>

</pre>

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/configure.in b/configure.in</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gh" style="color: #999;">index a3ee01b..ddf3f5e 100644</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/configure.in</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/configure.in</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -8,6 +8,7 @@ AC_INIT([staden],[2.0.0b11-2016])</span></span>

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> AC_CONFIG_HEADERS(staden_config.h)</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;">+AC_CONFIG_MACRO_DIR([ac_stubs])</span></span>

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> #-----------------------------------------------------------------------------</span>

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> # Checks for compiler programs.</span></pre>

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</li>

<li id="a67dc3026669feda5dcd6b08d6f31cc2920054fa">

<a href="https://salsa.debian.org/med-team/staden/compare/9e2d13c25894edf228805a0f18b4efedbdbe87c9...2ce5810c7b40b74c712f3afafb0227535b80742f#a67dc3026669feda5dcd6b08d6f31cc2920054fa"><strong>debian/patches/fix_implicit_declaration.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: Fri, 27 May 2016 08:58:49 +0200</span>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff">Description: Implicite declarations are now breaking the build.</span>

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"> This patch adds explicit<span class="idiff left right">e</span> declarations</span>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> This patch adds explicit declarations</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/eba/conf.c</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/eba/conf.c</span></span>

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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

<a href="https://salsa.debian.org/med-team/staden/compare/9e2d13c25894edf228805a0f18b4efedbdbe87c9...2ce5810c7b40b74c712f3afafb0227535b80742f#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5" 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">@@ -5,3 +5,5 @@ enable_setting_stadenroot.patch</td>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">include_xalloc.patch</span>

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6

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">use_mkstemp_instead_of_tmpnam.patch</span>

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7

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">fix_implicit_declaration.patch</span>

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8

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">autoconfig.patch</span>

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9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">spelling.patch</span></pre>

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<br>

</li>

<li id="45ae034d1d71b2d961abb7c91cf3d2f1a02a59c6">

<a href="https://salsa.debian.org/med-team/staden/compare/9e2d13c25894edf228805a0f18b4efedbdbe87c9...2ce5810c7b40b74c712f3afafb0227535b80742f#45ae034d1d71b2d961abb7c91cf3d2f1a02a59c6"><strong>debian/patches/spelling.patch</strong></a>

<hr>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Description: Fix spelling</span>

</pre>

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2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Author: Andreas Tille <tille@debian.org></span>

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3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Last-Update: Sat, 14 Jul 2018 17:31:37 +0200</span>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/gap5/export_contigs.c</span></span>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/gap5/export_contigs.c</span></span>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -864,7 +864,7 @@ static void sam_export_cons_tag(GapIO *i</span></span>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> /*</span>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff">  * Exports a single sam sequence, marrying up annotations to the appropriate</span>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- * sequences and adding these in auxillary tags.</span></span>

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ * sequences and adding these in auxiliary tags.</span></span>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff">  *</span>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff">  * We use the new format PT:Z:<tag_list> for these.</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 class="gd" style="color: #000; background-color: #fdd;">--- a/gap5/sam_index.c</span></span>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/gap5/sam_index.c</span></span>

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -19,7 +19,7 @@</span></span>

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> #include "consensus.h"</span>

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> /*</span>

</pre>

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- * Uncomment this if you want sam auxillary tags to be added as tag in</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ * Uncomment this if you want sam auxiliary tags to be added as tag in</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff">  * gap5.</span>

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff">  */</span>

</pre>

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> //#define SAM_AUX_AS_TAG</span>

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1114,7 +1114,7 @@ int bio_add_unmapped(bam_io_t *bio, bam_</span></span>

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff">     /*</span>

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff">      * Uncomment one of the two sections below if you wish to allow storing</span>

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-     * sam auxillary records in gap5.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+     * sam auxiliary records in gap5.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff">      * This is experimental and the format for these hasn't been finalised</span>

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff">      * yet.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff">      */</span>

</pre>

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1237,7 +1237,7 @@ int bio_add_unmapped(bam_io_t *bio, bam_</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff">     }</span>

</pre>

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> #ifdef SAM_AUX_AS_TAG</span>

</pre>

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    /* Make an annotation out of the sam auxillary data */</span></span>

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    /* Make an annotation out of the sam auxiliary data */</span></span>

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff">     aux = bam_aux_stringify(b, 1);</span>

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff">     if (aux && *aux) {</span>

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff">  anno_ele_t *e;</span>

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1533,7 +1533,7 @@ int bio_del_seq(bam_io_t *bio, pileup_t</span></span>

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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>

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff">      * Uncomment one of the two sections below if you wish to allow storing</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;">-     * sam auxillary records in gap5.</span></span>

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+     * sam auxiliary records in gap5.</span></span>

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff">      * This is experimental and the format for these hasn't been finalised</span>

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff">      * yet.</span>

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff">      */</span>

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1651,7 +1651,7 @@ int bio_del_seq(bam_io_t *bio, pileup_t</span></span>

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff">     }</span>

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> #ifdef SAM_AUX_AS_TAG</span>

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    /* Make an annotation out of the sam auxillary data */</span></span>

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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    /* Make an annotation out of the sam auxiliary data */</span></span>

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff">     aux = bam_aux_stringify(b, 1);</span>

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff">     if (aux && *aux) {</span>

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff">  anno_ele_t *e;</span>

</pre>

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/gap5/tg_iface_g.c</span></span>

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/gap5/tg_iface_g.c</span></span>

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -4681,7 +4681,7 @@ static cached_item *io_seq_block_read(vo</span></span>

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff">  }</span>

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff">     }</span>

</pre>

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    /* Sam auxillary records */</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    /* Sam auxiliary records */</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff">     if (sam_aux) {</span>

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff">  for (i = 0; i < SEQ_BLOCK_SZ; i++) {</span>

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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff">      if (!b->seq[i]) continue;</span>

</pre>

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -4855,7 +4855,7 @@ static int io_seq_block_write(void *dbh,</span></span>

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff">  memcpy(out[14], s->alignment, s->alignment_len);</span>

</pre>

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff">  out[14] += s->alignment_len;</span>

</pre>

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- /* Sam auxillary records */</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ /* Sam auxiliary records */</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff">  out[17] += int2u7(s->aux_len, out[17]);</span>

</pre>

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff">  if (s->aux_len) {</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="82" 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">

82

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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff">      memcpy(out[18], s->sam_aux, s->aux_len);</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="83" 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">

83

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/gap5/tg_index.c</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="84" 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">

84

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/gap5/tg_index.c</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="85" 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">

85

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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="LC85" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -64,7 +64,7 @@ void usage(void) {</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="86" 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">

86

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"> /*    fprintf(stderr, "      -V                   Input is AFG (Velvet)format\n"); */</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="87" 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">

87

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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="LC87" class="line" lang="diff">     fprintf(stderr, "\n");</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="88" 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">

88

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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff">     fprintf(stderr, "      -u                   Also store unmapped reads           ({S,B,CR}AM only)\n");</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="89" 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">

89

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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    fprintf(stderr, "      -x                   Also store auxillary records        ({S,B,CR}AM only)\n");</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="90" 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">

90

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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    fprintf(stderr, "      -x                   Also store auxiliary records        ({S,B,CR}AM only)\n");</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="91" 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">

91

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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff">     fprintf(stderr, "      -r                   Store reference-position data (on)  ({S,B,CR}AM only)\n");</span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="92" 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">

92

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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="LC92" class="line" lang="diff">     fprintf(stderr, "      -R                   Don't store reference-position data ({S,B,CR}AM only)\n");</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="93" 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">

93

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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff">     fprintf(stderr, "      -D                   Do not remove duplicates ({S,B,CR}AM only)\n");</span></pre>

</td>

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</table>

<br>

</li>

<li id="8756c63497c8dc39f7773438edf53b220c773f67">

<a href="https://salsa.debian.org/med-team/staden/compare/9e2d13c25894edf228805a0f18b4efedbdbe87c9...2ce5810c7b40b74c712f3afafb0227535b80742f#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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1

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<td class="diff-line-num new_line" data-linenumber="1" 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">

1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">#!/usr/bin/make -f</span>

</pre>

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<td class="diff-line-num old_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">

2

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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">

2

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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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="3" 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">

3

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<td class="diff-line-num new_line old" data-linenumber="3" 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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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"># all does not work due to build error with -fpie</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="4" 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">

4

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<td class="diff-line-num new_line old" data-linenumber="3" 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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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"># export DEB_BUILD_MAINT_OPTIONS = hardening=+all</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="5" 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">

5

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<td class="diff-line-num new_line old" data-linenumber="3" 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="LC5" class="line" lang="plaintext">export DEB_BUILD_MAINT_OPTIONS = hardening=+bindnow</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="6" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="3" 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">

3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">export DEB_BUILD_MAINT_OPTIONS = hardening=+all</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="6" 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">

6

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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">

4

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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"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<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">

7

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<td class="diff-line-num new_line" data-linenumber="5" 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">

5

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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="LC5" class="line" lang="plaintext">## DEB_BUILD_ARCH or DEB_BUILD_ARCH_BITS ??</span>

</pre>

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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">

8

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<td class="diff-line-num new_line" data-linenumber="6" 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">

6

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">BITARCH := $(shell dpkg-architecture -qDEB_BUILD_ARCH)</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="9" 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">

9

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<td class="diff-line-num new_line old" data-linenumber="7" 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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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">DEB_HOST_MULTIARCH := $(shell dpkg-architecture -qDEB_HOST_MULTIARCH)</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="10" 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">

10

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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">

7

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">ifeq ($(BITARCH),64)</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="11" 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">

11

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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">

8

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">    enable64bit:=--enable-64bit</span>

</pre>

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<td class="diff-line-num old_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">

12

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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">

9

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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">else</span>

</pre>

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