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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/kraken">Debian Med / kraken</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/kraken/commit/556316d3ac5c9b62876fd45e9866949b4b65d3af">556316d3</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-07T12:06:08Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Point Vcs fields to salsa.debian.org
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kraken/commit/280fe4d4866cef07c21a8f2e90ba388c7e83b51d">280fe4d4</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-07T12:06:08Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.3.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kraken/commit/863875d32eeaeb48a2a67d2284b7e6fd7b28890e">863875d3</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-07T12:12:07Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix Perl interpreter path
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kraken/commit/4146dec379b172f9a07b9dba3619db7500d9be83">4146dec3</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-07T12:15:26Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">propagate build options
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kraken/commit/f0e9bb633f414e07079591e9d3a633e047a3e1cd">f0e9bb63</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-07T12:17:21Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>5 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="#4d4a394ff4174f20019a8af4d8b6185efe92c21f">
<span class="new-file">
+
debian/patches/hardening.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/kraken/compare/1a4a832b8e7add54b28f8e3ff6d24cc2d58e6e9c...f0e9bb633f414e07079591e9d3a633e047a3e1cd#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">kraken (1.1-3) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">kraken (1.1-3) <span class="idiff left right">unstable</span>; urgency=medium</span>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<td class="diff-line-num 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">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> [ Jelmer Vernooij ]</span>
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<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * Trim trailing whitespace.</span>
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<td class="diff-line-num old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> * Use secure copyright file specification URI.</span>
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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">
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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="LC6" class="line" lang="plaintext"></span>
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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="LC6" class="line" lang="plaintext"> -- Jelmer Vernooij <jelmer@debian.org> Wed, 24 Oct 2018 21:58:35 +0000</span>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> [ Andreas Tille ]</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">
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * Point Vcs fields to salsa.debian.org</span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> * Standards-Version: 4.3.0</span>
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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">
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> * Fix Perl interpreter path</span>
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> * propagate build options</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Mon, 07 Jan 2019 13:15:32 +0100</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">kraken (1.1-2) unstable; urgency=medium</span>
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<td class="diff-line-num new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/kraken/compare/1a4a832b8e7add54b28f8e3ff6d24cc2d58e6e9c...f0e9bb633f414e07079591e9d3a633e047a3e1cd#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">@@ -5,9 +5,9 @@ Section: science</td>
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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 (>= 11~),</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> jellyfish1</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">1.3</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">Vcs-Browser: https://<span class="idiff left right">anonscm.debian.org/cgit/debian-med/kraken.git</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">Vcs-Git: https://<span class="idiff left right">anonscm.debian.org/git/debian-med</span>/kraken.git</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">3.0</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Vcs-Browser: https://<span class="idiff left right">salsa.debian.org/med-team/kraken</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Vcs-Git: https://<span class="idiff left right">salsa.debian.org/med-team</span>/kraken.git</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Homepage: http://ccb.jhu.edu/software/kraken/</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Package: kraken</span>
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<li id="4d4a394ff4174f20019a8af4d8b6185efe92c21f">
<a href="https://salsa.debian.org/med-team/kraken/compare/1a4a832b8e7add54b28f8e3ff6d24cc2d58e6e9c...f0e9bb633f414e07079591e9d3a633e047a3e1cd#4d4a394ff4174f20019a8af4d8b6185efe92c21f"><strong>debian/patches/hardening.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Author: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Last-Update: Mon, 07 Jan 2019 13:14:41 +0100</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Description: propagate build options</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/src/Makefile</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/src/Makefile</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;">@@ -1,5 +1,5 @@</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> CXX = g++</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-CXXFLAGS = -Wall -fopenmp -O3</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+CXXFLAGS += -Wall -fopenmp -O3</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> PROGS = db_sort set_lcas classify make_seqid_to_taxid_map db_shrink kmer_estimator</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> .PHONY: all install clean</span></pre>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/kraken/compare/1a4a832b8e7add54b28f8e3ff6d24cc2d58e6e9c...f0e9bb633f414e07079591e9d3a633e047a3e1cd#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">use_jellyfish1.patch</span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">kraken_tmp_dir.patch</span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">fix_reading_fasta.patch</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">hardening.patch</span></pre>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/kraken/compare/1a4a832b8e7add54b28f8e3ff6d24cc2d58e6e9c...f0e9bb633f414e07079591e9d3a633e047a3e1cd#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -20,3 +20,9 @@ override_dh_link:</td>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">override_dh_auto_install:</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> dh_auto_install -- KRAKEN_DIR=$(CURDIR)/debian/$(DEB_SOURCE)/usr/lib/$(DEB_SOURCE)</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> ./install_kraken.sh /usr/lib/$(DEB_SOURCE) $(DEB_SOURCE)</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">override_dh_install:</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> dh_install</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> for pl in `grep -Rl '#![[:space:]]*/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> sed -i '1s?^#![[:space:]]*/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' $${pl} ; \</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> done</span></pre>
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