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<h3>
Shayan Doust pushed to branch master
at <a href="https://salsa.debian.org/med-team/raxml-ng">Debian Med / raxml-ng</a>
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<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/raxml-ng/-/commit/29831099eba5795479f5b994f9644bbf66584bd1">29831099</a></strong>
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<span>by Shayan Doust</span>
<i>at 2020-05-29T18:00:06+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Append cmake as a build dependency
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<strong><a href="https://salsa.debian.org/med-team/raxml-ng/-/commit/c2c893b3abbe3d3a29d2b3fec4cf07bcda2693c5">c2c893b3</a></strong>
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<span>by Shayan Doust</span>
<i>at 2020-05-29T18:07:58+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add patch to modify some options within CMakeLists
libp11-dev is available on debian as a package, but terraphast needs packaging (not necessary?)
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<h4>3 changed files:</h4>
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<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<a href="#84abfa9f60b6a4a53f7a9138ad11f167acf03eb2">
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+
debian/patches/modify_cmake_options.patch
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<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
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+
debian/patches/series
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<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/raxml-ng/-/compare/bf4084b52894fbd4d27e41341176c4fa12009834...c2c893b3abbe3d3a29d2b3fec4cf07bcda2693c5#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="8" 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="8" 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 +8,8 @@ Build-Depends: debhelper (>= 10),</td>
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<td class="diff-line-num new_line" data-linenumber="8" 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="LC8" class="line" lang="plaintext"> flex,</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="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"> bison,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> libgmp3-dev,</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> libpll-dev</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> libpll-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"> cmake</span>
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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Standards-Version: 3.9.8</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/raxml-ng.git</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Vcs-Git: https://anonscm.debian.org/git/debian-med/raxml-ng.git</span>
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<li id="84abfa9f60b6a4a53f7a9138ad11f167acf03eb2">
<a href="https://salsa.debian.org/med-team/raxml-ng/-/compare/bf4084b52894fbd4d27e41341176c4fa12009834...c2c893b3abbe3d3a29d2b3fec4cf07bcda2693c5#84abfa9f60b6a4a53f7a9138ad11f167acf03eb2"><strong>debian/patches/modify_cmake_options.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Set options within CMakeLists for libs</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> Ensure we do not cause cmake to build the "supplied" libraries, instead rely on the already-packaged libraries</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Author: Shayan Doust <hello@shayandoust.me></span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: 2020-05-29</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">---</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- raxml-ng.orig/CMakeLists.txt</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ raxml-ng/CMakeLists.txt</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -4,7 +4,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> set(CMAKE_DISABLE_SOURCE_CHANGES ON)</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"> set(RAXML_BINARY_NAME "" CACHE STRING "Custom RAxML-NG binary name")</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-set(USE_LIBPLL_CMAKE ON CACHE BOOL "Use CMake to build libpll and pll-modules")</span></span>
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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">
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;">+set(USE_LIBPLL_CMAKE OFF CACHE BOOL "Use CMake to build libpll and pll-modules")</span></span>
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<td class="diff-line-num new new_line" data-linenumber="14" 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">
14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> set(BUILD_AS_LIBRARY OFF CACHE BOOL "Build RAxML-NG as shared library (instead of stand-alone executable)")</span>
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<td class="diff-line-num new new_line" 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">
15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> set(PLLMOD_DEBUG OFF CACHE BOOL "Debug pll-modules (tons of console output!)")</span>
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<td class="diff-line-num new new_line" data-linenumber="16" 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">
16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" 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">
17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="p">@@ -20,7 +20,7 @@</span></span>
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<td class="diff-line-num new new_line" data-linenumber="18" 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">
18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> # build a static binary</span>
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<td class="diff-line-num new new_line" data-linenumber="19" 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="LC19" class="line" lang="diff"> set(STATIC_BUILD OFF CACHE BOOL "Build static binary")</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;">-set(USE_TERRAPHAST ON CACHE BOOL "Use phylogentic terraces library (terraphast) ")</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+set(USE_TERRAPHAST OFF CACHE BOOL "Use phylogentic terraces library (terraphast) ")</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> set(USE_GMP OFF CACHE BOOL "Use Gnu Muliple precision (GMP) library ")</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> set(ENABLE_PTHREADS ${USE_PTHREADS})</span></pre>
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<a href="https://salsa.debian.org/med-team/raxml-ng/-/compare/bf4084b52894fbd4d27e41341176c4fa12009834...c2c893b3abbe3d3a29d2b3fec4cf07bcda2693c5#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">modify_cmake_options.patch</span></pre>
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