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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/sortmerna">Debian Med / sortmerna</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/sortmerna/-/commit/86e8e1ef4c54765ca371cd7ea742cdbeb0798c1f">86e8e1ef</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-01-31T17:40:50+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove old hacks
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sortmerna/-/commit/583ebbff6c9eb136abe99f11127533f63fe6bab7">583ebbff</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-01-31T17:41:30+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Build-Depends: libconcurrentqueue-dev
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sortmerna/-/commit/b86324c41e36f23e84553b77231994a5d36e9cb6">b86324c4</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-02-01T09:04:58+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Try hard to prevent static linking but its not fully working.
</pre>
</li>
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<h4>6 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="#97c0d95066f17e57c78e44c66636eadb7c62df71">
<span class="new-file">
+
debian/patches/concurrentqueue.h.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#64ba99e9bb0134dddef8cfc9c8ee3b0d0199daae">
<span class="new-file">
+
debian/patches/no_static_linking.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/sortmerna/-/compare/7cbe41c0d788a9f188f841553bb54cf0e2be55cd...b86324c41e36f23e84553b77231994a5d36e9cb6#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12,8 +12,7 @@ sortmerna (4.3.4-1) UNRELEASED; urgency=medium</td>
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<td class="old_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> * Versioned Build-Depends: librocksdb-dev (>= 6.25.3)</span>
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<td class="old_line diff-line-num" data-linenumber="13" 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="new_line diff-line-num" data-linenumber="13" 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="LC13" class="line" lang="plaintext"> * Build-Depends: libgflags-dev, libsnappy-dev, libzstd-dev</span>
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<td class="old_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> (needed by librocksdb-dev (>= 6.25.3) - see #1004665)</span>
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<td class="old_line diff-line-num old" data-linenumber="15" 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="LC15" class="line" lang="plaintext"> * Build-Depends: rapidjson-dev</span>
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<td class="old_line diff-line-num old" data-linenumber="16" 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="LC16" class="line" lang="plaintext"> TODO: cmake issues </span>
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<td class="old_line diff-line-num new" 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">
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<td class="new_line diff-line-num new" 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">
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> * Build-Depends: rapidjson-dev, libconcurrentqueue-dev</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Mon, 31 Jan 2022 13:37:04 +0100</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"></span>
</pre>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/sortmerna/-/compare/7cbe41c0d788a9f188f841553bb54cf0e2be55cd...b86324c41e36f23e84553b77231994a5d36e9cb6#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,7 +9,8 @@ Build-Depends: debhelper-compat (= 13),</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> libgflags-dev,</span>
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<td class="old_line diff-line-num" 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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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> libsnappy-dev,</span>
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<td class="old_line diff-line-num" 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">
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> libzstd-dev,</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> rapidjson-dev</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> rapidjson-dev,</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> libconcurrentqueue-dev</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"># python3 <!nocheck>,</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"># python3-skbio <!nocheck>,</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Standards-Version: 4.6.0</span>
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<li id="97c0d95066f17e57c78e44c66636eadb7c62df71">
<a href="https://salsa.debian.org/med-team/sortmerna/-/compare/7cbe41c0d788a9f188f841553bb54cf0e2be55cd...b86324c41e36f23e84553b77231994a5d36e9cb6#97c0d95066f17e57c78e44c66636eadb7c62df71"><strong>debian/patches/concurrentqueue.h.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Mon, 31 Jan 2022 13:37:04 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Description: Fix include statement for Debian packaged concurrentqueue</span></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">--- a/include/readsqueue.hpp</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/include/readsqueue.hpp</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -46,7 +46,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> #include "read.hpp"</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"> #if defined(CONCURRENTQUEUE)</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;">-# include "concurrentqueue.h"</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;">+# include <concurrentqueue/concurrentqueue.h></span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> #elif defined(LOCKQUEUE)</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> # include <queue></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> #endif</span></pre>
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<li id="64ba99e9bb0134dddef8cfc9c8ee3b0d0199daae">
<a href="https://salsa.debian.org/med-team/sortmerna/-/compare/7cbe41c0d788a9f188f841553bb54cf0e2be55cd...b86324c41e36f23e84553b77231994a5d36e9cb6#64ba99e9bb0134dddef8cfc9c8ee3b0d0199daae"><strong>debian/patches/no_static_linking.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Mon, 31 Jan 2022 13:37:04 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Description: Prevent static linking</span></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">--- a/CMakeLists.txt</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/CMakeLists.txt</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -69,8 +69,8 @@</span> set(CONCURRENTQUEUE_URL https://github.c</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> set(CONCURRENTQUEUE_HOME ${EXTERNAL_DEPS}/concurrentqueue CACHE PATH "Concurrent queue library installation directory")</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> #set(gflags_DIR ${EXTERNAL_DEPS}/gflags/dist/lib/cmake/gflags CACHE PATH "GFlags library configuration")</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> </span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-option(ROCKSDB_STATIC "Use static RocksDB library" ON)</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-option(ZLIB_STATIC "Use static ZLib library" ON)</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#option(ROCKSDB_STATIC "Use static RocksDB library" ON)</span></span>
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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;">+#option(ZLIB_STATIC "Use static ZLib library" ON)</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> </span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> option(PORTABLE "Build portable/statically linked executable" ON)</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> </span></pre>
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<a href="https://salsa.debian.org/med-team/sortmerna/-/compare/7cbe41c0d788a9f188f841553bb54cf0e2be55cd...b86324c41e36f23e84553b77231994a5d36e9cb6#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">cmake_RocksDB.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">rapidjson.patch</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">concurrentqueue.h.patch</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">no_static_linking.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/sortmerna/-/compare/7cbe41c0d788a9f188f841553bb54cf0e2be55cd...b86324c41e36f23e84553b77231994a5d36e9cb6#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">@@ -15,12 +15,10 @@ export CMAKE_PREFIX_PATH=/usr/lib/$(DEB_HOST_MULTIARCH)/cmake/</td>
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15
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">override_dh_clean:</span>
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> dh_clean</span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> rm -f index/.tobuild</span>
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19
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> rm -f include/memcheck.h</span>
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20
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> rm -rf tmp</span>
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21
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"></span>
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22
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">override_dh_auto_build:</span>
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23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"> touch index/.tobuild</span>
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24
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> dh_auto_build</span>
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25
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> mkdir -p tmp</span>
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> cat debian/README_scripts.txt rRNA_databases/README.txt > tmp/README.txt</span>
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