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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/strelka">Debian Med / strelka</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/strelka/-/commit/be91af1e1880a11cbd2f26fa375ed640be01bacf">be91af1e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-05-14T15:59:40+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Prevent build error
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/strelka/-/commit/749d3dd02c287e5030a4c868f841015ffdba73d0">749d3dd0</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-05-14T16:37:41+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix htslib linking
</pre>
</li>
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#71c77c717705108993cf64aa3b392547f752e7ba">
<span class="new-file">
+
debian/patches/gcc.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#eba50f83701826b6bc6990a2ecb07d5959ac1f6d">
debian/patches/use_debian_packaged_redist.patch
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/strelka/-/compare/d26f9031df084d6110ef1d9746cd31a3793ebcc2...749d3dd02c287e5030a4c868f841015ffdba73d0#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="18" 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="18" 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">@@ -18,6 +18,7 @@ Build-Depends: debhelper-compat (= 12),</td>
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<td class="diff-line-num new_line" data-linenumber="18" 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="LC18" class="line" lang="plaintext"> zlib1g-dev,</span>
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<td class="diff-line-num old_line" data-linenumber="19" 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="19" 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="LC19" class="line" lang="plaintext"> libhts-dev,</span>
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<td class="diff-line-num new_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">
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> rapidjson-dev,</span>
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<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> samtools</span>
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<td class="diff-line-num new_line" data-linenumber="22" 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="LC22" class="line" lang="plaintext">Standards-Version: 4.5.0</span>
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<td class="diff-line-num new_line" data-linenumber="23" 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="LC23" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/strelka</span>
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<td class="diff-line-num old_line" data-linenumber="23" 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="24" 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="LC24" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/strelka.git</span>
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</li>
<li id="71c77c717705108993cf64aa3b392547f752e7ba">
<a href="https://salsa.debian.org/med-team/strelka/-/compare/d26f9031df084d6110ef1d9746cd31a3793ebcc2...749d3dd02c287e5030a4c868f841015ffdba73d0#71c77c717705108993cf64aa3b392547f752e7ba"><strong>debian/patches/gcc.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: Wed, 13 May 2020 16:55:22 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Description: Prevent build error</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> error: moving a local object in a return statement prevents copy elision [-Werror=pessimizing-move]</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"> note: remove ‘std::move’ call</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff">--- a/src/c++/lib/blt_util/algo_util_impl.hh</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/src/c++/lib/blt_util/algo_util_impl.hh</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">@@ -46,5 +46,5 @@</span> getDuplicatesInSortedInput(</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> begin2++;</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>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return std::move(dups);</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;">+ return dups;</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> }</span></pre>
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<a href="https://salsa.debian.org/med-team/strelka/-/compare/d26f9031df084d6110ef1d9746cd31a3793ebcc2...749d3dd02c287e5030a4c868f841015ffdba73d0#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">2to3.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">use_debian_packaged_redist.patch</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">gcc.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/strelka/-/compare/d26f9031df084d6110ef1d9746cd31a3793ebcc2...749d3dd02c287e5030a4c868f841015ffdba73d0#eba50f83701826b6bc6990a2ecb07d5959ac1f6d"><strong>debian/patches/use_debian_packaged_redist.patch</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" 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">...</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">@@ -14,7 +14,41 @@ Description: Use Debian packaged libs</td>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"> #</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"> # htslib</span>
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"><span class="p">@@ -194,7 +194,7 @@</span> set (RAPIDJSON_FINAL_TASK ${RAPIDJSON_IN</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="p">@@ -108,13 +108,18 @@</span> endif ()</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> set(THIS_HTSLIB "${THIS_PROJECT_NAME}_htslib")</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> add_custom_target(${THIS_HTSLIB} DEPENDS "${HTSLIB_FINAL_TASK}")</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 class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> if (NOT WIN32)</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> install(PROGRAMS "${HTSLIB_DIR}/bgzip" DESTINATION "${THIS_LIBEXECDIR}")</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> install(PROGRAMS "${HTSLIB_DIR}/htsfile" DESTINATION "${THIS_LIBEXECDIR}")</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> install(PROGRAMS "${HTSLIB_DIR}/tabix" DESTINATION "${THIS_LIBEXECDIR}")</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> endif ()</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+else()</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+message("Use Debian packaged htslib")</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+message("================================")</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+superset(HTSLIB_LIBRARY "-lhts")</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+endif()</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> </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;">+if(!DEBIAN_BUILD)</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> # samtools</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> #</span>
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<td class="diff-line-num new new_line" data-linenumber="37" 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">
37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="p">@@ -175,7 +180,13 @@</span> if (NOT WIN32)</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> install(PROGRAMS "${BGCAT_PROG}" DESTINATION "${THIS_LIBEXECDIR}")</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> install(PROGRAMS "${BGZIP9_PROG}" DESTINATION "${THIS_LIBEXECDIR}")</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> endif ()</span>
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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;">+else()</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+message("Use Debian packaged samtools")</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+message("================================")</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+superset(SAMTOOLS_PROG "/usr/bin/samtools")</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+endif()</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> </span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if(!DEBIAN_BUILD)</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> #</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> # rapidjson</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> #</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="p">@@ -194,7 +205,7 @@</span> set (RAPIDJSON_FINAL_TASK ${RAPIDJSON_IN</span>
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18
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="diff"> </span>
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19
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="diff"> set(THIS_RAPIDJSON "${THIS_PROJECT_NAME}_rapidjson")</span>
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<td class="diff-line-num 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">
20
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<td class="diff-line-num new_line" data-linenumber="54" 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="LC54" class="line" lang="diff"> add_custom_target(${THIS_RAPIDJSON} DEPENDS "${RAPIDJSON_FINAL_TASK}")</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="23" 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="57" 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">@@ -23,7 +57,7 @@ Description: Use Debian packaged libs</td>
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23
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"><span class="p">@@ -213,6 +2<span class="idiff left right">13</span>,7 @@</span> add_custom_command(</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="p">@@ -213,6 +2<span class="idiff left right">24</span>,7 @@</span> add_custom_command(</span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="diff"> set(THIS_CODEMIN "${THIS_PROJECT_NAME}_codemin")</span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="diff"> add_custom_target(${THIS_CODEMIN} DEPENDS "${CODEMIN_MARK}")</span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="diff"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -31,7 +65,7 @@ Description: Use Debian packaged libs</td>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="diff"> #</span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="diff"> # pyflow</span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"><span class="p">@@ -242,13 +2<span class="idiff left right">43</span>,15 @@</span> install_python_lib_dir("${PYFLOW_DIR}/sr</span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="p">@@ -242,13 +2<span class="idiff left right">54</span>,15 @@</span> install_python_lib_dir("${PYFLOW_DIR}/sr</span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="diff"> set (THIS_PYFLOW "${THIS_PROJECT_NAME}_pyflow")</span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="diff"> add_custom_target(${THIS_PYFLOW} DEPENDS "${PYFLOW_DEPENDS}")</span>
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