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<h3>
Maarten L. Hekkelman pushed to branch master
at <a href="https://salsa.debian.org/med-team/dssp">Debian Med / dssp</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/dssp/-/commit/86a9daa529d18d66f116f4de47f86e9e0dba771b">86a9daa5</a></strong>
<div>
<span>by Maarten L. Hekkelman</span>
<i>at 2020-11-24T14:30:07+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">last minute changes
</pre>
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<h4>7 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#a7207dd0e26a3c71e9f893a4cc2edd40811dd590">
GNUmakefile.in
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#7c6c40862992239970f348432411f67e95cb5583">
<span class="new-file">
+
debian/patches/configure-patch
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</a>
</li>
<li class="file-stats">
<a href="#c6d79ce365cd63d6af97be49d4427aed34caf4c0">
debian/patches/man-patch
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<li class="file-stats">
<a href="#17d8869115f55e024a85a6d17443302815985358">
debian/tests/installation-test
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</li>
</ul>
<h4>Changes:</h4>
<li id="a7207dd0e26a3c71e9f893a4cc2edd40811dd590">
<a href="https://salsa.debian.org/med-team/dssp/-/commit/86a9daa529d18d66f116f4de47f86e9e0dba771b#a7207dd0e26a3c71e9f893a4cc2edd40811dd590"><strong>GNUmakefile.in</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="35" 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">@@ -35,7 +35,7 @@ LIBS = @LIBS@ \</td>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext"> @BOOST_PROGRAM_OPTIONS_LIB@ \</span>
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<td class="diff-line-num old_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext"> @BOOST_DATE_TIME_LIB@</span>
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<td class="diff-line-num old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext"></span>
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<td class="diff-line-num old old_line" data-linenumber="38" 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="LC38" class="line" lang="plaintext">prefix = <span class="idiff left right">$(DESTDIR)</span>@prefix@</span>
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<td class="diff-line-num new old_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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<td class="diff-line-num new new_line" data-linenumber="38" 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="LC38" class="line" lang="plaintext">prefix = @prefix@</span>
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<td class="diff-line-num old_line" data-linenumber="39" 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">
39
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext">exec_prefix = @exec_prefix@</span>
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<td class="diff-line-num old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext">bindir = @bindir@</span>
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<td class="diff-line-num old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext">datarootdir = @datarootdir@</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/dssp/-/commit/86a9daa529d18d66f116f4de47f86e9e0dba771b#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Uploaders: Maarten L. Hekkelman <maarten@hekkelman.com></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">2</span>),</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">3</span>),</span>
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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> libboost-iostreams-dev,</span>
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<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> libboost-program-options-dev,</span>
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<td class="diff-line-num old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> libboost-system-dev,</span>
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<li id="7c6c40862992239970f348432411f67e95cb5583">
<a href="https://salsa.debian.org/med-team/dssp/-/commit/86a9daa529d18d66f116f4de47f86e9e0dba771b#7c6c40862992239970f348432411f67e95cb5583"><strong>debian/patches/configure-patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Fix man page for mkdssp</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Author: Maarten L. Hekkelman <maarten@hekkelman.com></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Last-Update: Tue, 24 Nov 2020 14:17:09 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Forwarded: yes</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">--- a/configure.ac</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/configure.ac</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -23,15 +23,28 @@</span></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"> AC_ARG_VAR([MRC], [Specify a location for the mrc executable])</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-dnl We would like to use mrc</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+USE_RSRC=0</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> if test "x$MRC" = "x"; then</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> AC_PATH_PROG([MRC], [mrc])</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> fi</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> if test "x$MRC" = "x"; then</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- AC_MSG_ERROR([mrc not found, the application will be built without resources])</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ AC_MSG_WARN([The mrc application was not found, not using resources.])</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+else</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ AC_ARG_ENABLE(</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ resources,</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ [AS_HELP_STRING([--disable-resources], [Do not use mrc to store data in resources])])</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ AS_IF([test "x$enable_resources" != "xno" ], [</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;">+ USE_RSRC=1</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;">+ ])</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> fi</span>
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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_SUBST([USE_RSRC], [$USE_RSRC])</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+AC_DEFINE_UNQUOTED([USE_RSRC], [$USE_RSRC], [Use mrc to store resources])</span></span>
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<pre style="margin: 0;">+<span id="LC35" 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="LC36" class="line" lang="diff"> dnl revision numbering is something used internally at the NKI</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> AC_ARG_ENABLE(</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> revision,</span></pre>
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<li id="c6d79ce365cd63d6af97be49d4427aed34caf4c0">
<a href="https://salsa.debian.org/med-team/dssp/-/commit/86a9daa529d18d66f116f4de47f86e9e0dba771b#c6d79ce365cd63d6af97be49d4427aed34caf4c0"><strong>debian/patches/man-patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Fix man page for mkdssp</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Author: Maarten L. Hekkelman <maarten@hekkelman.com></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Last-Update: Tue, 24 Nov 2020 11:29:28 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Forwarded: yes</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"></span>
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1
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff">--- a/mkdssp.1</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/mkdssp.1</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"><span class="p">@@ -21,7 +21,7 @@</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -15,7 +20,7 @@</td>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="diff"> S BEND Bend</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-' ' OTHER Loop</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+T{</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+\<span class="idiff left right">' \'</span> (space)</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+\<span class="idiff left right">(aq \(aq</span> (space)</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+T} OTHER Loop</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="diff"> .TE</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="diff"> .SH BUGS</span>
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<a href="https://salsa.debian.org/med-team/dssp/-/commit/86a9daa529d18d66f116f4de47f86e9e0dba771b#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">man-patch</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">makefile</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">configure-patch</span></pre>
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<a href="https://salsa.debian.org/med-team/dssp/-/commit/86a9daa529d18d66f116f4de47f86e9e0dba771b#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">@@ -15,4 +15,4 @@ export LDOPTS:=$(LDFLAGS)</td>
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> dh $@</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">override_dh_auto_configure:</span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> dh_auto_configure -- --disable-revision</span></pre>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> dh_auto_configure -- --disable-re<span class="idiff left right">sources --disable-re</span>vision</span></pre>
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<a href="https://salsa.debian.org/med-team/dssp/-/commit/86a9daa529d18d66f116f4de47f86e9e0dba771b#17d8869115f55e024a85a6d17443302815985358"><strong>debian/tests/installation-test</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,13 +9,13 @@ if [ "$AUTOPKGTEST_TMP" = "" ] ; then</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp </span>debian/tests/1cbs.cif<span class="idiff left right">.gz</span> <span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp </span>debian/tests/1cbs.cif <span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># simply run mkdssp on 1cbs, should produce an output file</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="shell">mkdssp 1cbs.cif<span class="idiff left right">.gz</span> 1cbs-dssp.cif</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell">mkdssp 1cbs.cif 1cbs-dssp.cif</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-s</span> 1cbs-dssp.cif <span class="o" style="font-weight: 600;">]</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="shell">mkdssp 1cbs.cif<span class="idiff left right">.gz</span> 1cbs-dssp.dssp</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell">mkdssp 1cbs.cif 1cbs-dssp.dssp</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-s</span> 1cbs-dssp.dssp <span class="o" style="font-weight: 600;">]</span></span></pre>
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