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<h3>
Steffen Möller pushed to branch master
at <a href="https://salsa.debian.org/med-team/seqwish">Debian Med / seqwish</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/seqwish/-/commit/d566dc0d67b8cadf33b597fb124d6d2d97581b46">d566dc0d</a></strong>
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<span>by Steffen Möller</span>
<i>at 2021-06-20T23:45:04+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adjusted changelog
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<h4>2 changed files:</h4>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#ee54dc79014b3def963898e50c98877d46c6b27e">
debian/patches/use_debian_packaged_libs.patch
</a>
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/seqwish/-/commit/d566dc0d67b8cadf33b597fb124d6d2d97581b46#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</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">@@ -7,12 +7,12 @@ seqwish (0.7-1) UNRELEASED; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> path = deps/gzip_reader</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> url = https://github.com/gatoravi/gzip_reader.git</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> [ <span class="idiff left right">Steffen Möller</span> ]</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> * Standards-Version: 4.5.1<span class="idiff left right"> (routine-update)</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> * debhelper-compat 13<span class="idiff left right"> (routine-update)</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> * Remove trailing whitespace in debian/rules<span class="idiff left right"> (routine-update)</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> * Rules-Requires-Root: no<span class="idiff left right"> (routine-update)</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> [ <span class="idiff left right">routine-update</span> ]</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> * Standards-Version: 4.5.1</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> * debhelper-compat 13</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> * Remove trailing whitespace in debian/rules</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> * Rules-Requires-Root: no</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> Repository-Browse.</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> -- <span class="idiff left">Andreas Ti</span>lle <<span class="idiff">ti</span>lle@debian.org> Sun, 2<span class="idiff">4 May 2020 16:17</span>:0<span class="idiff right">7</span> +0200</span></pre>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> -- <span class="idiff left">Steffen Mö</span>lle<span class="idiff">r</span> <<span class="idiff">moe</span>lle<span class="idiff">r</span>@debian.org> Sun, 2<span class="idiff">0 Jun 2021 23:28</span>:0<span class="idiff right">6</span> +0200</span></pre>
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<li id="ee54dc79014b3def963898e50c98877d46c6b27e">
<a href="https://salsa.debian.org/med-team/seqwish/-/commit/d566dc0d67b8cadf33b597fb124d6d2d97581b46#ee54dc79014b3def963898e50c98877d46c6b27e"><strong>debian/patches/use_debian_packaged_libs.patch</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/CMakeLists.txt</span></span>
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<pre style="margin: 0;">-<span id="LC2" 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="LC3" class="line" lang="diff"><span class="p">@@ -25,6 +25,7 @@</span> include_directories("${PROJECT_SOURCE_DI</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">Index: seqwish/CMakeLists.txt</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- seqwish.orig/CMakeLists.txt</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ seqwish/CMakeLists.txt</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">@@ -27,6 +27,7 @@</span> include_directories("${PROJECT_SOURCE_DI</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"> # Add external projects</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"> include(${CMAKE_ROOT}/Modules/ExternalProject.cmake)</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"> </span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,7 +10,7 @@</td>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> # sdsl-lite (full build using its cmake config)</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"> ExternalProject_Add(sdsl-lite</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"> SOURCE_DIR "${CMAKE_SOURCE_DIR}/deps/sdsl-lite"</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="p">@@ -3<span class="idiff left">6</span>,7 +3<span class="idiff right">7</span>,14 @@</span> set(sdsl-lite_INCLUDE "${INSTALL_DIR}/sr</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="p">@@ -3<span class="idiff left">8</span>,7 +3<span class="idiff right">9</span>,14 @@</span> set(sdsl-lite_INCLUDE "${INSTALL_DIR}/sr</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"> set(sdsl-lite-divsufsort_INCLUDE "${INSTALL_DIR}/src/sdsl-lite-build/external/libdivsufsort/include")</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"> set(sdsl-lite_LIB "${INSTALL_DIR}/src/sdsl-lite-build/lib")</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="diff"> set(sdsl-lite-divsufsort_LIB "${INSTALL_DIR}/src/sdsl-lite-build/external/libdivsufsort/lib")</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -23,8 +25,8 @@</td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="diff"> # taywee's C++ args library, header only</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="diff"> ExternalProject_Add(tayweeargs</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="diff"> SOURCE_DIR "${CMAKE_SOURCE_DIR}/deps/args"</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"><span class="p">@@ -4<span class="idiff left">4</span>,7 +5<span class="idiff right">2</span>,14 @@</span> ExternalProject_Add(tayweeargs</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"> <span class="idiff left right">INSTALL</span>_COMMAND "")</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="p">@@ -4<span class="idiff left">8</span>,7 +5<span class="idiff right">6</span>,14 @@</span> ExternalProject_Add(tayweeargs</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> <span class="idiff left right">CONFIGURE</span>_COMMAND "")</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="diff"> ExternalProject_Get_property(tayweeargs SOURCE_DIR)</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="diff"> set(tayweeargs_INCLUDE "${SOURCE_DIR}")</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+else()</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -38,7 +40,7 @@</td>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="diff"> # gzip file reader, header only</span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="diff"> ExternalProject_Add(gzipreader</span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="diff"> SOURCE_DIR "${CMAKE_SOURCE_DIR}/deps/gzip_reader"</span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="diff"><span class="p">@@ -5<span class="idiff left">2</span>,7 +<span class="idiff right">6</span>7,14 @@</span> ExternalProject_Add(gzipreader</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="p">@@ -5<span class="idiff left">6</span>,7 +7<span class="idiff right">1</span>,14 @@</span> ExternalProject_Add(gzipreader</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="diff"> INSTALL_COMMAND "")</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="diff"> ExternalProject_Get_property(gzipreader SOURCE_DIR)</span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="diff"> set(gzipreader_INCLUDE "${SOURCE_DIR}")</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -53,7 +55,7 @@</td>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="diff"> # mmmulti (memory mapped multimap, multiset, and interval tree)</span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="diff"> ExternalProject_Add(mmmulti</span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="diff"> SOURCE_DIR "${CMAKE_SOURCE_DIR}/deps/mmmulti"</span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="diff"><span class="p">@@ -6<span class="idiff left">2</span>,7 +8<span class="idiff right">4</span>,14 @@</span> ExternalProject_Add(mmmulti</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="p">@@ -6<span class="idiff left">6</span>,7 +8<span class="idiff right">8</span>,14 @@</span> ExternalProject_Add(mmmulti</span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="diff"> CONFIGURE_COMMAND "")</span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="diff"> ExternalProject_Get_property(mmmulti SOURCE_DIR)</span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="diff"> set(mmmulti_INCLUDE "${SOURCE_DIR}/src")</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -68,7 +70,7 @@</td>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="diff"> # iitii, like cgranges but with interpolation and memory mapping</span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="diff"> ExternalProject_Add(iitii</span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="diff"> SOURCE_DIR "${CMAKE_SOURCE_DIR}/deps/iitii"</span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="diff"><span class="p">@@ -8<span class="idiff left">0</span>,7 +1<span class="idiff right">09</span>,14 @@</span> ExternalProject_Add(mmap_allocator</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="p">@@ -8<span class="idiff left">4</span>,7 +1<span class="idiff right">13</span>,14 @@</span> ExternalProject_Add(mmap_allocator</span>
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="diff"> ExternalProject_Get_property(mmap_allocator INSTALL_DIR)</span>
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="diff"> set(mmap_allocator_INCLUDE "${INSTALL_DIR}/include/mmap_allocator")</span>
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74
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76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="diff"> set(mmap_allocator_LIB "${INSTALL_DIR}/lib")</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">@@ -83,7 +85,7 @@</td>
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83
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85
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="diff"> # In-place Parallel Super Scalar Samplesort (IPS⁴o), header only</span>
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84
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86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="diff"> ExternalProject_Add(ips4o</span>
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85
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87
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="diff"> SOURCE_DIR "${CMAKE_SOURCE_DIR}/deps/ips4o"</span>
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86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="diff"><span class="p">@@ -1<span class="idiff left">09</span>,7 +14<span class="idiff right">5</span>,9 @@</span> ExternalProject_Add(atomicbitvector</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"><span class="p">@@ -1<span class="idiff left">13</span>,7 +14<span class="idiff right">9</span>,9 @@</span> ExternalProject_Add(atomicbitvector</span>
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87
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89
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="diff"> CONFIGURE_COMMAND "")</span>
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88
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90
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="diff"> ExternalProject_Get_property(atomicbitvector SOURCE_DIR)</span>
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89
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91
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="diff"> set(atomicbitvector_INCLUDE "${SOURCE_DIR}/include")</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">@@ -93,7 +95,7 @@</td>
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93
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95
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="diff"> # atomic queue library</span>
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94
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96
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="diff"> ExternalProject_Add(atomicqueue</span>
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95
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97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="diff"> SOURCE_DIR "${CMAKE_SOURCE_DIR}/deps/atomic_queue"</span>
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96
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="diff"><span class="p">@@ -1<span class="idiff left">19</span>,6 +1<span class="idiff right">57</span>,12 @@</span> ExternalProject_Add(atomicqueue</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="p">@@ -1<span class="idiff left">23</span>,6 +1<span class="idiff right">61</span>,12 @@</span> ExternalProject_Add(atomicqueue</span>
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97
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99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="diff"> CONFIGURE_COMMAND "")</span>
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98
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="diff"> ExternalProject_Get_property(atomicqueue SOURCE_DIR)</span>
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99
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="diff"> set(atomicqueue_INCLUDE "${SOURCE_DIR}")</span>
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