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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/kallisto">Debian Med / kallisto</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/kallisto/commit/663dd0bb6d300661c9d9ddd4972198f35440e10d">663dd0bb</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-03-21T16:57:21Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adapt build system to Debian packaged libhts
</pre>
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<h4>4 changed files:</h4>
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<span class="new-file">
+
debian/patches/series
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<li class="file-stats">
<a href="#e9ffd79035f20df75689c726e3780374ee2ad4f4">
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+
debian/patches/use_debian_packaged_htslib.patch
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</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/kallisto/commit/663dd0bb6d300661c9d9ddd4972198f35440e10d#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5" 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="5" 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">@@ -5,7 +5,8 @@ Section: science</td>
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<td class="diff-line-num new_line" data-linenumber="5" 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">Priority: optional</span>
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<td class="diff-line-num old_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="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">Build-Depends: debhelper (>= 12~),</span>
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<td class="diff-line-num old_line" data-linenumber="7" 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="7" 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="LC7" class="line" lang="plaintext"> cmake,</span>
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<td class="diff-line-num old old_line" data-linenumber="8" 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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<td class="diff-line-num new_line old" data-linenumber="8" 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="LC8" class="line" lang="plaintext"> libhdf5-dev</span>
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<td class="diff-line-num new old_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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<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"> libhdf5-dev,</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"> libhts-dev</span>
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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="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="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Standards-Version: 4.3.0</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/kallisto</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/kallisto.git</span>
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</li>
<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/kallisto/commit/663dd0bb6d300661c9d9ddd4972198f35440e10d#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">use_debian_packaged_htslib.patch</span></pre>
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<li id="e9ffd79035f20df75689c726e3780374ee2ad4f4">
<a href="https://salsa.debian.org/med-team/kallisto/commit/663dd0bb6d300661c9d9ddd4972198f35440e10d#e9ffd79035f20df75689c726e3780374ee2ad4f4"><strong>debian/patches/use_debian_packaged_htslib.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: Thu, 21 Mar 2019 15:53:04 +0100</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Description: Adapt build system to Debian packaged libhts</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/CMakeLists.txt</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/CMakeLists.txt</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;">@@ -34,7 +34,7 @@ ELSE(LINK MATCHES shared)</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> message("shared build")</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> ENDIF(LINK MATCHES static)</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> </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;">-</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if(!DEBIAN_BUILD)</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> include(ExternalProject)</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> ExternalProject_Add(htslib</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> PREFIX ${PROJECT_SOURCE_DIR}/ext/htslib</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -47,7 +47,7 @@ ExternalProject_Add(htslib</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> )</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> </span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> include_directories(${htslib_PREFIX}/src/htslib)</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" 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="LC22" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> # add_compile_options(-Wdeprecated-register)</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/CMakeLists.txt</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/CMakeLists.txt</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -3,7 +3,9 @@ file(GLOB headers *.h *.hpp)</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> </span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> list(REMOVE_ITEM sources main.cpp)</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC31" 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="LC32" class="line" lang="diff"> include_directories(../ext/htslib)</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;">+endif()</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"> add_library(kallisto_core ${sources} ${headers})</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> target_include_directories(kallisto_core PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -11,7 +13,11 @@ target_include_directories(kallisto_core</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> add_executable(kallisto main.cpp)</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> </span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> find_package( Threads REQUIRED )</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;">+if(DEBIAN_BUILD)</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;">+target_link_libraries(kallisto kallisto_core pthread hts)</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;">+else()</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> target_link_libraries(kallisto kallisto_core pthread ${CMAKE_CURRENT_SOURCE_DIR}/../ext/htslib/libhts.a)</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+endif()</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> if(LINK MATCHES static)</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> set(BUILD_SHARED_LIBS OFF)</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -56,4 +62,4 @@ else()</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> endif(LINK MATCHES static)</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> </span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-install(TARGETS kallisto DESTINATION "${CMAKE_INSTALL_BINDIR}")</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff">\ No newline at end of file</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+install(TARGETS kallisto DESTINATION "${CMAKE_INSTALL_BINDIR}")</span></span></pre>
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</li>
<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/kallisto/commit/663dd0bb6d300661c9d9ddd4972198f35440e10d#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>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -20,12 +20,11 @@ include /usr/share/dpkg/default.mk</td>
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">%:</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> dh $@</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">override_dh_auto_configure:</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> dh_auto_configure -- -DDEBIAN_BUILD=1</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">### When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">#override_dh_auto_test:</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">#ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"># do_stuff_for_testing</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext">#endif</span></pre>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext">### If you **really** can not use uscan (even not with mode=git) use a debian/get-orig-script</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext">#get-orig-source:</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext"># . debian/get-orig-source</span></pre>
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