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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/iitii">Debian Med / iitii</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/iitii/-/commit/b2e100e02659c2aa3058848c7edf1668588f13e9">b2e100e0</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-08T18:57:21+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Include Debian packaged version of ctpl
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/iitii/-/commit/77b8149aa51db32d8abff20497bc77a448c73219">77b8149a</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-08T19:47:04+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Configuration of tests works now - but there are build problems
</pre>
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<h4>2 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#a993d7a0b8757b07b4b547bf6fc0b00ff53c1e2e">
debian/patches/use_debian_packages_libs_in_test.patch
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/iitii/-/compare/544fee73310d478b6b1226a0f8783f6fed3a3f37...77b8149aa51db32d8abff20497bc77a448c73219#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">@@ -9,6 +9,8 @@ Build-Depends: debhelper-compat (= 13),</td>
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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"> libargs-dev,</span>
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<td class="diff-line-num old_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">
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<td class="diff-line-num 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">
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> libmmap-allocator-dev (>= 0.4.0+git20200122.adbfbe1),</span>
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<td class="diff-line-num old_line" 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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<td class="diff-line-num new_line" 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"> libopenmpi-dev,</span>
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<td class="diff-line-num new new_line" data-linenumber="12" 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="LC12" class="line" lang="plaintext"> catch2 <!nocheck>,</span>
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<td class="diff-line-num new old_line" data-linenumber="12" 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="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"> pkg-config <!nocheck>,</span>
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<td class="diff-line-num 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">
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<td class="diff-line-num new_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">
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> libhts-dev <!nocheck>,</span>
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<td class="diff-line-num old_line" 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="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"> libctpl-dev <!nocheck></span>
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<td class="diff-line-num 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">
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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">Standards-Version: 4.5.0</span>
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<li id="a993d7a0b8757b07b4b547bf6fc0b00ff53c1e2e">
<a href="https://salsa.debian.org/med-team/iitii/-/compare/544fee73310d478b6b1226a0f8783f6fed3a3f37...77b8149aa51db32d8abff20497bc77a448c73219#a993d7a0b8757b07b4b547bf6fc0b00ff53c1e2e"><strong>debian/patches/use_debian_packages_libs_in_test.patch</strong></a>
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<td class="diff-line-num unfold js-unfold old_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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -22,11 +22,16 @@ Description: Use Debian packaged libraries also in tests</td>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="diff"> ExternalProject_Add(catch</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="diff"> URL https://github.com/philsquared/Catch/archive/v2.9.1.zip</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"><span class="p">@@ -59,15 +63,<span class="idiff left right">15</span> @@</span> include_directories(${source_dir}/single</span>
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<td class="diff-line-num new old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="p">@@ -59,15 +63,<span class="idiff left right">20</span> @@</span> include_directories(${source_dir}/single</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="diff"> set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pthread -std=c++17 -Wall -Werror=return-type -Wno-reorder -fdiagnostics-color=auto")</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="diff"> add_executable(test_iitii util.h test_iitii.cc)</span>
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<td class="diff-line-num old_line" data-linenumber="29" 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="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-add_dependencies(test_iitii catch libhts)</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+find_package(PkgConfig REQUIRED)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="31" 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="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+pkg_search_module(GLIB REQUIRED glib-2.0)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="32" 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="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+include_directories(${GLIB_INCLUDE_DIRS})</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+include_directories("../src") ## FIXME: for autopkgtest this line has to be removed</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+## target_link_libraries(test_iitii ${GLIB_LDFLAGS})</span></span>
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30
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35
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#add_dependencies(test_iitii catch libhts)</span></span>
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31
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36
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="diff"> target_link_libraries(test_iitii libhts libz.a libbz2.a liblzma.a)</span>
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32
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37
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="diff"> </span>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="46" 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">@@ -41,3 +46,14 @@ Description: Use Debian packaged libraries also in tests</td>
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41
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46
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="diff"> target_link_libraries(gnomad_benchmark libhts libz.a libbz2.a liblzma.a)</span>
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42
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47
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="diff"> </span>
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43
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="diff"> include(CTest)</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/test/util.h</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/test/util.h</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="p">@@ -8,7 +8,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> #include <assert.h></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> #include "kstring.h"</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> #include "tbx.h"</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#include "ctpl_stl.h"</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include "ctpl/ctpl.h"</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> #include "iitii.h"</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"> using namespace std;</span></pre>
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