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<h3>
Nilesh Patra pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/proteinortho">Debian Med / proteinortho</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/proteinortho/-/commit/3c35c1d73608e5ddc79f68abf3524b8a4d1e57ba">3c35c1d7</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-10-21T01:02:27+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 6.0.24+dfsg</pre>
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<h4>7 changed files:</h4>
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<li class="file-stats">
<a href="#1c497fbb3a46b78edf04cc2a2fa33f67e3ffbe2a">
CHANGELOG
</a>
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<li class="file-stats">
<a href="#ff6936350384213d6f693f4d604134188ce088c8">
CHANGEUID
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<li class="file-stats">
<a href="#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
Makefile
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#c9e37a96ac72f9ef076d7a41a57470524d63b36e">
proteinortho6.pl
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<li class="file-stats">
<a href="#ba368ee46e511166051985e745eaa37aea49d150">
src/proteinortho_clustering.cpp
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<li class="file-stats">
<a href="#62a037ff19b968a55076fe8ec1b004721c460a70">
src/proteinortho_clustering_nolapack.cpp
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<h4>Changes:</h4>
<li id="1c497fbb3a46b78edf04cc2a2fa33f67e3ffbe2a">
<a href="https://salsa.debian.org/med-team/proteinortho/-/commit/3c35c1d73608e5ddc79f68abf3524b8a4d1e57ba#1c497fbb3a46b78edf04cc2a2fa33f67e3ffbe2a"><strong>CHANGELOG</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="271" 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">@@ -271,3 +271,5 @@</td>
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271
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<td class="diff-line-num new_line" data-linenumber="271" 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">
271
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="plaintext"> 31. Aug (5110)</span>
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<td class="diff-line-num old_line" data-linenumber="272" 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="272" 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="LC272" class="line" lang="plaintext"> fixed a bug that the html version prints out ids encapsuled with parenthesis, while the proteinortho_grab_proteins.pl does not understand such queries.</span>
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<td class="diff-line-num old_line" data-linenumber="273" 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="273" 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="LC273" class="line" lang="plaintext"> refined the Makefile for proteinortho_clustering, now it additionally tests if the program is executable with the -test option </span>
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<td class="diff-line-num new old_line" data-linenumber="274" 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="274" 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="LC274" class="line" lang="plaintext"> 12. Oct (5122)</span>
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<td class="diff-line-num new old_line" data-linenumber="274" 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="275" 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="LC275" class="line" lang="plaintext"> enhancement of the Makefile (more verbose, added standard compiler flags, cleanup)</span></pre>
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<li id="ff6936350384213d6f693f4d604134188ce088c8">
<a href="https://salsa.debian.org/med-team/proteinortho/-/commit/3c35c1d73608e5ddc79f68abf3524b8a4d1e57ba#ff6936350384213d6f693f4d604134188ce088c8"><strong>CHANGEUID</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">51<span class="idiff left right">10</span></span></pre>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">51<span class="idiff left right">22</span></span></pre>
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<li id="836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
<a href="https://salsa.debian.org/med-team/proteinortho/-/commit/3c35c1d73608e5ddc79f68abf3524b8a4d1e57ba#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c"><strong>Makefile</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="148" 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="148" 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">@@ -148,71 +148,66 @@ echoENV:</td>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="make"></span>
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<td class="diff-line-num old_line" data-linenumber="149" 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="LC149" class="line" lang="make"><span class="nl">$(BUILDDIR)/proteinortho_clustering</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">src/proteinortho_clustering.cpp</span></span>
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<td class="diff-line-num old_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="make"> <span class="nv" style="color: #008080;">$(dir_guard)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="151" 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="LC151" class="line" lang="make"><span class="k" style="font-weight: 600;">ifeq</span> <span class="nv" style="color: #008080;">($(MTUNEARCH),TRUE)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="152" 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="151" 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="LC152" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"using the -mtune and -march compiler options. WARNING: this can lead to runtime errors (code 33792) on some machines."</span></span>
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<td class="diff-line-num old old_line" data-linenumber="153" 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">
153
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="make"><span class="k" style="font-weight: 600;">else</span></span>
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<td class="diff-line-num old old_line" data-linenumber="154" 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="LC154" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"the compiler options -mtune and -march are disabled. If you want to add these use MTUNEARCH=TRUE."</span></span>
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<td class="diff-line-num old old_line" data-linenumber="155" 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="LC155" class="line" lang="make"><span class="k" style="font-weight: 600;">endif</span></span>
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<td class="diff-line-num old_line" data-linenumber="156" 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="LC151" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"[ 10%] Prepare proteinortho_clustering ..."</span></span>
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<td class="diff-line-num old_line" data-linenumber="157" 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="LC152" class="line" lang="make"></span>
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<td class="diff-line-num old_line" data-linenumber="158" 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="LC153" class="line" lang="make"><span class="k" style="font-weight: 600;">ifeq</span> <span class="nv" style="color: #008080;">($(DEPLOY),TRUE)</span></span>
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<td class="diff-line-num old_line" data-linenumber="159" 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="LC154" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">@echo</span> <span class="s2" style="color: #d14;">"[ 20%] Building **proteinortho_clustering** with LAPACK (dynamic linking, no mtune,march , for gitlab)"</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">;</span></span>
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160
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<td class="diff-line-num new_line old" data-linenumber="155" 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="LC160" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">@<span class="idiff left">$(CXX)</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">-static</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">$(CXXFLAGS)</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff right">$(CXXFLAGS_PO</span>)</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-fopenmp</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-o</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$@</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$<</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(LDFLAGS)</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(LDLIBS)</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-Wl,--allow-multiple-definition</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-llapack</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-lblas</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-lgfortran</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-pthread</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-Wl,--whole-archive</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-lpthread</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-Wl,--no-whole-archive</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-lquadmath</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">&&</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">([</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$$?</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-eq</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">]</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">&&</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$@</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-test</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">&&</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">[</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$$?</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-eq</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">]</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">)</span> </span>
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<td class="diff-line-num new new_line" data-linenumber="155" 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">
155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">@<span class="idiff left">echo</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"$(CXX) -static $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -Wl,--allow-multiple-definition -llapack -lblas -lgfortran -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -lquadmath"</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">$(CXX)</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">-static</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">$(CPPFLAGS)</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff right">$(CXXFLAGS</span>)</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-fopenmp</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-o</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$@</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$<</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(LDFLAGS)</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(LDLIBS)</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-Wl,--allow-multiple-definition</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-llapack</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-lblas</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-lgfortran</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-pthread</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-Wl,--whole-archive</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-lpthread</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-Wl,--no-whole-archive</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-lquadmath</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">&&</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">([</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$$?</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-eq</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">]</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">&&</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$@</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-test</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">&&</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">[</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$$?</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-eq</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">]</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">)</span> </span>
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<td class="diff-line-num old_line" data-linenumber="161" 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">
161
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<td class="diff-line-num new_line" data-linenumber="156" 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">
156
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="make"><span class="k" style="font-weight: 600;">else</span></span>
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<td class="diff-line-num old_line" data-linenumber="162" 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">
162
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<td class="diff-line-num new_line" data-linenumber="157" 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">
157
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="make"><span class="k" style="font-weight: 600;">ifeq</span> <span class="nv" style="color: #008080;">($(USELAPACK),TRUE)</span></span>
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<td class="diff-line-num old_line" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
163
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<td class="diff-line-num new_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
158
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="make"><span class="k" style="font-weight: 600;">ifeq</span> <span class="nv" style="color: #008080;">($(USEPRECOMPILEDLAPACK),TRUE)</span></span>
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<td class="diff-line-num old_line" data-linenumber="164" 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">
164
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<td class="diff-line-num new_line" data-linenumber="159" 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">
159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="make"><span class="k" style="font-weight: 600;">ifeq</span> <span class="nv" style="color: #008080;">($(STATIC),TRUE)</span></span>
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<td class="diff-line-num old_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
165
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<td class="diff-line-num new_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">@echo</span> <span class="s2" style="color: #d14;">"[ 20%] Building **proteinortho_clustering** with LAPACK (static linking)"</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
166
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<td class="diff-line-num new_line old" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">@<span class="idiff left">$(CXX)</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">-static</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">$(CXXFLAGS)</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff right">$(CXXFLAGS_PO</span>)</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-fopenmp</span> <span class="nv" style="color: #008080;">-march</span><span class="o" style="font-weight: 600;">=</span>native <span class="nt" style="color: #000080;">-mtune</span><span class="o" style="font-weight: 600;">=</span>native <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nv" style="color: #008080;">$<</span> <span class="nv" style="color: #008080;">$(LDFLAGS)</span> <span class="nv" style="color: #008080;">$(LDLIBS)</span> <span class="nt" style="color: #000080;">-Wl</span>,--allow-multiple-definition <span class="nt" style="color: #000080;">-llapack</span> <span class="nt" style="color: #000080;">-lblas</span> <span class="nt" style="color: #000080;">-lgfortran</span> <span class="nt" style="color: #000080;">-pthread</span> <span class="nt" style="color: #000080;">-Wl</span>,--whole-archive <span class="nt" style="color: #000080;">-lpthread</span> <span class="nt" style="color: #000080;">-Wl</span>,--no-whole-archive <span class="nt" style="color: #000080;">-lquadmath</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">([</span> <span class="nv" style="color: #008080;">$$</span>? <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$@</span> <span class="nt" style="color: #000080;">-test</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$$</span>? <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">(</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="161" 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">
161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">@<span class="idiff left">echo</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"$(CXX) -O2 -static $(CPPFLAGS) $(CXXFLAGS) -fopenmp -march=native -mtune=native -o $@ $< $(LDFLAGS) $(LDLIBS) -Wl,--allow-multiple-definition -llapack -lblas -lgfortran -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -lquadmath"</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">$(CXX)</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">-O2</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">-static</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">$(CPPFLAGS)</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff right">$(CXXFLAGS</span>)</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-fopenmp</span> <span class="nv" style="color: #008080;">-march</span><span class="o" style="font-weight: 600;">=</span>native <span class="nt" style="color: #000080;">-mtune</span><span class="o" style="font-weight: 600;">=</span>native <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nv" style="color: #008080;">$<</span> <span class="nv" style="color: #008080;">$(LDFLAGS)</span> <span class="nv" style="color: #008080;">$(LDLIBS)</span> <span class="nt" style="color: #000080;">-Wl</span>,--allow-multiple-definition <span class="nt" style="color: #000080;">-llapack</span> <span class="nt" style="color: #000080;">-lblas</span> <span class="nt" style="color: #000080;">-lgfortran</span> <span class="nt" style="color: #000080;">-pthread</span> <span class="nt" style="color: #000080;">-Wl</span>,--whole-archive <span class="nt" style="color: #000080;">-lpthread</span> <span class="nt" style="color: #000080;">-Wl</span>,--no-whole-archive <span class="nt" style="color: #000080;">-lquadmath</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">([</span> <span class="nv" style="color: #008080;">$$</span>? <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$@</span> <span class="nt" style="color: #000080;">-test</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$$</span>? <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">(</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num old_line" data-linenumber="167" 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">
167
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<td class="diff-line-num new_line" data-linenumber="162" 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">
162
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="make"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"......</span><span class="nv" style="color: #008080;">$(ORANGE)</span><span class="s2" style="color: #d14;">dynamic linking failed too, now I try dynamic linking without -WL,-whole-archive... (this should now work for OSX).</span><span class="nv" style="color: #008080;">$(NC)</span><span class="s2" style="color: #d14;">"</span><span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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168
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="make"> <span class="nv" style="color: #008080;"><span class="idiff left">$(CXX)</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-static</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CXXFLAGS)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$(CXXFLAGS_PO</span>)</span> <span class="nt" style="color: #000080;">-fopenmp</span> <span class="nt" style="color: #000080;">-march</span><span class="o" style="font-weight: 600;">=</span>native <span class="nt" style="color: #000080;">-mtune</span><span class="o" style="font-weight: 600;">=</span>native <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nv" style="color: #008080;">$<</span> <span class="nv" style="color: #008080;">$(LDFLAGS)</span> <span class="nv" style="color: #008080;">$(LDLIBS)</span> <span class="nt" style="color: #000080;">-llapack</span> <span class="nt" style="color: #000080;">-lblas</span> <span class="nt" style="color: #000080;">-pthread</span> <span class="nt" style="color: #000080;">-lpthread</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">([</span> <span class="nv" style="color: #008080;">$$</span>? <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$@</span> <span class="nt" style="color: #000080;">-test</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$$</span>? <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"......OK dynamic linking was successful for proteinortho_clustering!"</span><span class="p">;</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">(</span> <span class="se" style="color: #d14;">\</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="make"> <span class="nb" style="color: #0086b3;"><span class="idiff left">echo</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CXX)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -O2 -static </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CPPFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CXXFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -fopenmp -march=native -mtune=native -o </span></span><span class="nv" style="color: #008080;"><span class="idiff">$@</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$<</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(LDFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(LDLIBS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -llapack -lblas -pthread -lpthread"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CXX)</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-O2</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-static</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CPPFLAGS)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$(CXXFLAGS</span>)</span> <span class="nt" style="color: #000080;">-fopenmp</span> <span class="nt" style="color: #000080;">-march</span><span class="o" style="font-weight: 600;">=</span>native <span class="nt" style="color: #000080;">-mtune</span><span class="o" style="font-weight: 600;">=</span>native <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nv" style="color: #008080;">$<</span> <span class="nv" style="color: #008080;">$(LDFLAGS)</span> <span class="nv" style="color: #008080;">$(LDLIBS)</span> <span class="nt" style="color: #000080;">-llapack</span> <span class="nt" style="color: #000080;">-lblas</span> <span class="nt" style="color: #000080;">-pthread</span> <span class="nt" style="color: #000080;">-lpthread</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">([</span> <span class="nv" style="color: #008080;">$$</span>? <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$@</span> <span class="nt" style="color: #000080;">-test</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$$</span>? <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"......OK dynamic linking was successful for proteinortho_clustering!"</span><span class="p">;</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">(</span> <span class="se" style="color: #d14;">\</span></span>
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169
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164
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="make"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"......</span><span class="nv" style="color: #008080;">$(ORANGE)</span><span class="s2" style="color: #d14;">-march=native -mtune=native failed, I try without them again.</span><span class="nv" style="color: #008080;">$(NC)</span><span class="s2" style="color: #d14;">"</span><span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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170
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="make"> <span class="idiff left">@</span><span class="nv" style="color: #008080;"><span class="idiff">$(CXX)</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-static</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CXXFLAGS)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$(CXXFLAGS_PO</span>)</span> <span class="nt" style="color: #000080;">-fopenmp</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nv" style="color: #008080;">$<</span> <span class="nv" style="color: #008080;">$(LDFLAGS)</span> <span class="nv" style="color: #008080;">$(LDLIBS)</span> <span class="nt" style="color: #000080;">-Wl</span>,--allow-multiple-definition <span class="nt" style="color: #000080;">-llapack</span> <span class="nt" style="color: #000080;">-lblas</span> <span class="nt" style="color: #000080;">-lgfortran</span> <span class="nt" style="color: #000080;">-pthread</span> <span class="nt" style="color: #000080;">-Wl</span>,--whole-archive <span class="nt" style="color: #000080;">-lpthread</span> <span class="nt" style="color: #000080;">-Wl</span>,--no-whole-archive <span class="nt" style="color: #000080;">-lquadmath</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">([</span> <span class="nv" style="color: #008080;">$$</span>? <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$@</span> <span class="nt" style="color: #000080;">-test</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$$</span>? <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">(</span> <span class="se" style="color: #d14;">\</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="make"> <span class="nb" style="color: #0086b3;"><span class="idiff left">echo</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CXX)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -O2 -static </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CPPFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CXXFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -fopenmp -o </span></span><span class="nv" style="color: #008080;"><span class="idiff">$@</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$<</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(LDFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(LDLIBS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -Wl,--allow-multiple-definition -llapack -lblas -lgfortran -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -lquadmath"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CXX)</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-O2</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-static</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CPPFLAGS)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$(CXXFLAGS</span>)</span> <span class="nt" style="color: #000080;">-fopenmp</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nv" style="color: #008080;">$<</span> <span class="nv" style="color: #008080;">$(LDFLAGS)</span> <span class="nv" style="color: #008080;">$(LDLIBS)</span> <span class="nt" style="color: #000080;">-Wl</span>,--allow-multiple-definition <span class="nt" style="color: #000080;">-llapack</span> <span class="nt" style="color: #000080;">-lblas</span> <span class="nt" style="color: #000080;">-lgfortran</span> <span class="nt" style="color: #000080;">-pthread</span> <span class="nt" style="color: #000080;">-Wl</span>,--whole-archive <span class="nt" style="color: #000080;">-lpthread</span> <span class="nt" style="color: #000080;">-Wl</span>,--no-whole-archive <span class="nt" style="color: #000080;">-lquadmath</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">([</span> <span class="nv" style="color: #008080;">$$</span>? <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$@</span> <span class="nt" style="color: #000080;">-test</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$$</span>? <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">(</span> <span class="se" style="color: #d14;">\</span></span>
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171
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166
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="make"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"......</span><span class="nv" style="color: #008080;">$(ORANGE)</span><span class="s2" style="color: #d14;">static linking failed, now I try dynamic linking.</span><span class="nv" style="color: #008080;">$(NC)</span><span class="s2" style="color: #d14;">"</span><span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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172
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="make"> <span class="nv" style="color: #008080;"><span class="idiff left">$(CXX)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CXXFLAGS)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$(CXXFLAGS_PO</span>)</span> <span class="nt" style="color: #000080;">-fopenmp</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nv" style="color: #008080;">$<</span> <span class="nv" style="color: #008080;">$(LDFLAGS)</span> <span class="nv" style="color: #008080;">$(LDLIBS)</span> <span class="nt" style="color: #000080;">-llapack</span> <span class="nt" style="color: #000080;">-lblas</span> <span class="nt" style="color: #000080;">-pthread</span> <span class="nt" style="color: #000080;">-Wl</span>,--whole-archive <span class="nt" style="color: #000080;">-lpthread</span> <span class="nt" style="color: #000080;">-Wl</span>,--no-whole-archive <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">([</span> <span class="nv" style="color: #008080;">$$</span>? <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$@</span> <span class="nt" style="color: #000080;">-test</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$$</span>? <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"......OK dynamic linking was successful for proteinortho_clustering!"</span><span class="p">;</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">(</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="167" 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">
167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="make"> <span class="nb" style="color: #0086b3;"><span class="idiff left">echo</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CXX)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -O2 </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CPPFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CXXFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -fopenmp -o </span></span><span class="nv" style="color: #008080;"><span class="idiff">$@</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$<</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(LDFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(LDLIBS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -llapack -lblas -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CXX)</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-O2</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CPPFLAGS)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$(CXXFLAGS</span>)</span> <span class="nt" style="color: #000080;">-fopenmp</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nv" style="color: #008080;">$<</span> <span class="nv" style="color: #008080;">$(LDFLAGS)</span> <span class="nv" style="color: #008080;">$(LDLIBS)</span> <span class="nt" style="color: #000080;">-llapack</span> <span class="nt" style="color: #000080;">-lblas</span> <span class="nt" style="color: #000080;">-pthread</span> <span class="nt" style="color: #000080;">-Wl</span>,--whole-archive <span class="nt" style="color: #000080;">-lpthread</span> <span class="nt" style="color: #000080;">-Wl</span>,--no-whole-archive <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">([</span> <span class="nv" style="color: #008080;">$$</span>? <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$@</span> <span class="nt" style="color: #000080;">-test</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$$</span>? <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"......OK dynamic linking was successful for proteinortho_clustering!"</span><span class="p">;</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">(</span> <span class="se" style="color: #d14;">\</span></span>
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173
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<td class="diff-line-num new_line" data-linenumber="168" 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">
168
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="make"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"......</span><span class="nv" style="color: #008080;">$(ORANGE)</span><span class="s2" style="color: #d14;">dynamic linking failed too, now I try dynamic linking without -WL,-whole-archive (this should now work for OSX).</span><span class="nv" style="color: #008080;">$(NC)</span><span class="s2" style="color: #d14;">"</span><span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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174
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<td class="diff-line-num new_line old" data-linenumber="169" 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="LC174" class="line" lang="make"> <span class="nv" style="color: #008080;"><span class="idiff left">$(CXX)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CXXFLAGS)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$(CXXFLAGS_PO</span>)</span> <span class="nt" style="color: #000080;">-fopenmp</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nv" style="color: #008080;">$<</span> <span class="nv" style="color: #008080;">$(LDFLAGS)</span> <span class="nv" style="color: #008080;">$(LDLIBS)</span> <span class="nt" style="color: #000080;">-llapack</span> <span class="nt" style="color: #000080;">-lblas</span> <span class="nt" style="color: #000080;">-pthread</span> <span class="nt" style="color: #000080;">-lpthread</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">([</span> <span class="nv" style="color: #008080;">$$</span>? <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$@</span> <span class="nt" style="color: #000080;">-test</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$$</span>? <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"......OK dynamic linking was successful for proteinortho_clustering!"</span><span class="p">;</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">(</span> <span class="se" style="color: #d14;">\</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="make"> <span class="nb" style="color: #0086b3;"><span class="idiff left">echo</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CXX)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -O2 </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CPPFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CXXFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -fopenmp -o </span></span><span class="nv" style="color: #008080;"><span class="idiff">$@</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$<</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(LDFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(LDLIBS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -llapack -lblas -pthread -lpthread"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CXX)</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-O2</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CPPFLAGS)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$(CXXFLAGS</span>)</span> <span class="nt" style="color: #000080;">-fopenmp</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nv" style="color: #008080;">$<</span> <span class="nv" style="color: #008080;">$(LDFLAGS)</span> <span class="nv" style="color: #008080;">$(LDLIBS)</span> <span class="nt" style="color: #000080;">-llapack</span> <span class="nt" style="color: #000080;">-lblas</span> <span class="nt" style="color: #000080;">-pthread</span> <span class="nt" style="color: #000080;">-lpthread</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">([</span> <span class="nv" style="color: #008080;">$$</span>? <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$@</span> <span class="nt" style="color: #000080;">-test</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$$</span>? <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"......OK dynamic linking was successful for proteinortho_clustering!"</span><span class="p">;</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">(</span> <span class="se" style="color: #d14;">\</span></span>
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175
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<td class="diff-line-num new_line" data-linenumber="170" 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">
170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="make"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"......</span><span class="nv" style="color: #008080;">$(ORANGE)</span><span class="s2" style="color: #d14;">dynamic linking failed (without -WL,-whole-archive) too too, now I try to openblas.</span><span class="nv" style="color: #008080;">$(NC)</span><span class="s2" style="color: #d14;">"</span><span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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176
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<td class="diff-line-num new_line old" data-linenumber="171" 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="LC176" class="line" lang="make"> <span class="nv" style="color: #008080;"><span class="idiff left">$(CXX)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CXXFLAGS)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$(CXXFLAGS_PO</span>)</span> <span class="nt" style="color: #000080;">-fopenmp</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nv" style="color: #008080;">$<</span> <span class="nv" style="color: #008080;">$(LDFLAGS)</span> <span class="nv" style="color: #008080;">$(LDLIBS)</span> <span class="nt" style="color: #000080;">-lopenblas</span> <span class="nt" style="color: #000080;">-pthread</span> <span class="nt" style="color: #000080;">-lpthread</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">([</span> <span class="nv" style="color: #008080;">$$</span>? <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$@</span> <span class="nt" style="color: #000080;">-test</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$$</span>? <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"......OK dynamic linking was successful for proteinortho_clustering!"</span><span class="p">;</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">(</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="171" 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">
171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="make"> <span class="nb" style="color: #0086b3;"><span class="idiff left">echo</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CXX)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -O2 </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CPPFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CXXFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -fopenmp -o </span></span><span class="nv" style="color: #008080;"><span class="idiff">$@</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$<</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(LDFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(LDLIBS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -lopenblas -pthread -lpthread"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CXX)</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-O2</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CPPFLAGS)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$(CXXFLAGS</span>)</span> <span class="nt" style="color: #000080;">-fopenmp</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nv" style="color: #008080;">$<</span> <span class="nv" style="color: #008080;">$(LDFLAGS)</span> <span class="nv" style="color: #008080;">$(LDLIBS)</span> <span class="nt" style="color: #000080;">-lopenblas</span> <span class="nt" style="color: #000080;">-pthread</span> <span class="nt" style="color: #000080;">-lpthread</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">([</span> <span class="nv" style="color: #008080;">$$</span>? <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$@</span> <span class="nt" style="color: #000080;">-test</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$$</span>? <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"......OK dynamic linking was successful for proteinortho_clustering!"</span><span class="p">;</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">(</span> <span class="se" style="color: #d14;">\</span></span>
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177
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<td class="diff-line-num new_line" data-linenumber="172" 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">
172
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="make"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"......</span><span class="nv" style="color: #008080;">$(ORANGE)</span><span class="s2" style="color: #d14;">last linking failed too too too, now I try to recompile lapack (v.3.8.0) and then compile proteinortho_clustering with dynamic linking.</span><span class="nv" style="color: #008080;">$(NC)</span><span class="s2" style="color: #d14;">"</span><span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num old_line" data-linenumber="178" 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">
178
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<td class="diff-line-num new_line" data-linenumber="173" 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">
173
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="make"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"......[ 33%] Extracting the LAPACK library"</span><span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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179
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<td class="diff-line-num new_line old" data-linenumber="174" 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="LC179" class="line" lang="make"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-d</span> src/lapack-3.8.0 <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">cd </span>src<span class="p">;</span> <span class="nb" style="color: #0086b3;">tar</span> <span class="nt" style="color: #000080;">-xzvf</span> lapack-3.8.0.tar.gz <span class="o" style="font-weight: 600;">></span> /dev/null 2>&1<span class="p">;</span> <span class="nb" style="color: #0086b3;">cd</span> ..<span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span><span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="174" 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">
174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="make"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-d</span> src/lapack-3.8.0 <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;"><span class="idiff left">echo</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"cd src; tar -xzvf lapack-3.8.0.tar.gz"</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span><span class="nb" style="color: #0086b3;">cd </span>src<span class="p">;</span> <span class="nb" style="color: #0086b3;">tar</span> <span class="nt" style="color: #000080;">-xzvf</span> lapack-3.8.0.tar.gz <span class="o" style="font-weight: 600;">></span> /dev/null 2>&1<span class="p">;</span> <span class="nb" style="color: #0086b3;">cd</span> ..<span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span><span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num old_line" data-linenumber="180" 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">
180
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<td class="diff-line-num new_line" data-linenumber="175" 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">
175
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="make"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"......[ 66%] Compiling the LAPACK library (using cmake + make)"</span><span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num old old_line" data-linenumber="181" 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">
181
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<td class="diff-line-num new_line old" data-linenumber="176" 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="LC181" class="line" lang="make"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-f</span> src/lapack-3.8.0/build/lib/liblapack.a <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">mkdir </span>src/lapack-3.8.0/build 2> /dev/null<span class="p">;</span> <span class="nb" style="color: #0086b3;">cd </span>src/lapack-3.8.0/build<span class="p">;</span> cmake .. <span class="nt" style="color: #000080;">-DCMAKE_CXX_COMPILER</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$(CXX)</span> <span class="o" style="font-weight: 600;">></span> /dev/null<span class="p">;</span> make all <span class="nt" style="color: #000080;">-j4</span> <span class="o" style="font-weight: 600;">></span> /dev/null 2>&1<span class="p">;</span> <span class="nb" style="color: #0086b3;">cd</span> ../../.. <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span><span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="make"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-f</span> src/lapack-3.8.0/build/lib/liblapack.a <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;"><span class="idiff left">echo</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">" mkdir src/lapack-3.8.0/build; cd src/lapack-3.8.0/build; cmake .. -DCMAKE_CXX_COMPILER=</span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CXX)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> > /dev/null; make all -j4 "</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span><span class="nb" style="color: #0086b3;">mkdir </span>src/lapack-3.8.0/build 2> /dev/null<span class="p">;</span> <span class="nb" style="color: #0086b3;">cd </span>src/lapack-3.8.0/build<span class="p">;</span> cmake .. <span class="nt" style="color: #000080;">-DCMAKE_CXX_COMPILER</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$(CXX)</span> <span class="o" style="font-weight: 600;">></span> /dev/null<span class="p">;</span> make all <span class="nt" style="color: #000080;">-j4</span> <span class="o" style="font-weight: 600;">></span> /dev/null 2>&1<span class="p">;</span> <span class="nb" style="color: #0086b3;">cd</span> ../../.. <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span><span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num old_line" data-linenumber="182" 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">
182
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<td class="diff-line-num new_line" data-linenumber="177" 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">
177
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="make"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"......[ 99%] Building **proteinortho_clustering** with LAPACK (dynamic linking)"</span><span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num old old_line" data-linenumber="183" 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">
183
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<td class="diff-line-num new_line old" data-linenumber="178" 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="LC183" class="line" lang="make"> <span class="nv" style="color: #008080;"><span class="idiff left">$(CXX)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CXXFLAGS)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$(CXXFLAGS_PO</span>)</span> <span class="nt" style="color: #000080;">-fopenmp</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nv" style="color: #008080;">$<</span> <span class="nt" style="color: #000080;">-Isrc</span>/lapack-3.8.0/build/include/ <span class="nt" style="color: #000080;">-Lsrc</span>/lapack-3.8.0/build/lib/ <span class="nt" style="color: #000080;">-llapack</span> <span class="nt" style="color: #000080;">-lblas</span> <span class="nv" style="color: #008080;">$(LDFLAGS)</span> <span class="nv" style="color: #008080;">$(LDLIBS)</span> <span class="nt" style="color: #000080;">-lgfortran</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"......OK dynamic linking was successful for proteinortho_clustering!"</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">(</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">)</span> <span class="p">;</span> <span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="178" 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">
178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="make"> <span class="nb" style="color: #0086b3;"><span class="idiff left">echo</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CXX)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -O2 </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CPPFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CXXFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -fopenmp -o </span></span><span class="nv" style="color: #008080;"><span class="idiff">$@</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$<</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -Isrc/lapack-3.8.0/build/include/ -Lsrc/lapack-3.8.0/build/lib/ -llapack -lblas </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(LDFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(LDLIBS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -lgfortran"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CXX)</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-O2</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CPPFLAGS)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$(CXXFLAGS</span>)</span> <span class="nt" style="color: #000080;">-fopenmp</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nv" style="color: #008080;">$<</span> <span class="nt" style="color: #000080;">-Isrc</span>/lapack-3.8.0/build/include/ <span class="nt" style="color: #000080;">-Lsrc</span>/lapack-3.8.0/build/lib/ <span class="nt" style="color: #000080;">-llapack</span> <span class="nt" style="color: #000080;">-lblas</span> <span class="nv" style="color: #008080;">$(LDFLAGS)</span> <span class="nv" style="color: #008080;">$(LDLIBS)</span> <span class="nt" style="color: #000080;">-lgfortran</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"......OK dynamic linking was successful for proteinortho_clustering!"</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">(</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">)</span> <span class="p">;</span> <span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">)</span></span>
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184
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<td class="diff-line-num new_line" data-linenumber="179" 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">
179
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="make"><span class="k" style="font-weight: 600;">else</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="185" 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">
185
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<td class="diff-line-num new_line" data-linenumber="180" 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">
180
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">@echo</span> <span class="s2" style="color: #d14;">"[ 20%] Building **proteinortho_clustering** with LAPACK (dynamic linking)"</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">;</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="186" 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">
186
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<td class="diff-line-num new_line old" data-linenumber="181" 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="LC186" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">@<span class="idiff left">$(CXX)</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">$(CXXFLAGS)</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff right">$(CXXFLAGS_PO</span>)</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-fopenmp</span> <span class="nv" style="color: #008080;">-march</span><span class="o" style="font-weight: 600;">=</span>native <span class="nt" style="color: #000080;">-mtune</span><span class="o" style="font-weight: 600;">=</span>native <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nv" style="color: #008080;">$<</span> <span class="nv" style="color: #008080;">$(LDFLAGS)</span> <span class="nv" style="color: #008080;">$(LDLIBS)</span> <span class="nt" style="color: #000080;">-llapack</span> <span class="nt" style="color: #000080;">-lblas</span> <span class="nt" style="color: #000080;">-pthread</span> <span class="nt" style="color: #000080;">-Wl</span>,--whole-archive <span class="nt" style="color: #000080;">-lpthread</span> <span class="nt" style="color: #000080;">-Wl</span>,--no-whole-archive <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">([</span> <span class="nv" style="color: #008080;">$$</span>? <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$@</span> <span class="nt" style="color: #000080;">-test</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$$</span>? <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"......OK dynamic linking was successful for proteinortho_clustering!"</span><span class="p">;</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">(</span> <span class="se" style="color: #d14;">\</span></span>
</pre>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">@<span class="idiff left">echo</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"$(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) -fopenmp -march=native -mtune=native -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive"</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">$(CXX)</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">-O2</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">$(CPPFLAGS)</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff right">$(CXXFLAGS</span>)</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-fopenmp</span> <span class="nv" style="color: #008080;">-march</span><span class="o" style="font-weight: 600;">=</span>native <span class="nt" style="color: #000080;">-mtune</span><span class="o" style="font-weight: 600;">=</span>native <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nv" style="color: #008080;">$<</span> <span class="nv" style="color: #008080;">$(LDFLAGS)</span> <span class="nv" style="color: #008080;">$(LDLIBS)</span> <span class="nt" style="color: #000080;">-llapack</span> <span class="nt" style="color: #000080;">-lblas</span> <span class="nt" style="color: #000080;">-pthread</span> <span class="nt" style="color: #000080;">-Wl</span>,--whole-archive <span class="nt" style="color: #000080;">-lpthread</span> <span class="nt" style="color: #000080;">-Wl</span>,--no-whole-archive <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">([</span> <span class="nv" style="color: #008080;">$$</span>? <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$@</span> <span class="nt" style="color: #000080;">-test</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$$</span>? <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"......OK dynamic linking was successful for proteinortho_clustering!"</span><span class="p">;</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">(</span> <span class="se" style="color: #d14;">\</span></span>
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187
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<td class="diff-line-num new_line" data-linenumber="182" 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">
182
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="make"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"......</span><span class="nv" style="color: #008080;">$(ORANGE)</span><span class="s2" style="color: #d14;">-march=native -mtune=native failed, I try without them again.</span><span class="nv" style="color: #008080;">$(NC)</span><span class="s2" style="color: #d14;">"</span><span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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188
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<td class="diff-line-num new_line old" data-linenumber="183" 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="LC188" class="line" lang="make"> <span class="idiff left">@</span><span class="nv" style="color: #008080;"><span class="idiff">$(CXX)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CXXFLAGS)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$(CXXFLAGS_PO</span>)</span> <span class="nt" style="color: #000080;">-fopenmp</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nv" style="color: #008080;">$<</span> <span class="nv" style="color: #008080;">$(LDFLAGS)</span> <span class="nv" style="color: #008080;">$(LDLIBS)</span> <span class="nt" style="color: #000080;">-llapack</span> <span class="nt" style="color: #000080;">-lblas</span> <span class="nt" style="color: #000080;">-pthread</span> <span class="nt" style="color: #000080;">-Wl</span>,--whole-archive <span class="nt" style="color: #000080;">-lpthread</span> <span class="nt" style="color: #000080;">-Wl</span>,--no-whole-archive <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">([</span> <span class="nv" style="color: #008080;">$$</span>? <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$@</span> <span class="nt" style="color: #000080;">-test</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$$</span>? <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"......OK dynamic linking was successful for proteinortho_clustering!"</span><span class="p">;</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">(</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="183" 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">
183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="make"> <span class="nb" style="color: #0086b3;"><span class="idiff left">echo</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CXX)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -O2 </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CPPFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CXXFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -fopenmp -o </span></span><span class="nv" style="color: #008080;"><span class="idiff">$@</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$<</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(LDFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(LDLIBS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -llapack -lblas -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CXX)</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-O2</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CPPFLAGS)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$(CXXFLAGS</span>)</span> <span class="nt" style="color: #000080;">-fopenmp</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nv" style="color: #008080;">$<</span> <span class="nv" style="color: #008080;">$(LDFLAGS)</span> <span class="nv" style="color: #008080;">$(LDLIBS)</span> <span class="nt" style="color: #000080;">-llapack</span> <span class="nt" style="color: #000080;">-lblas</span> <span class="nt" style="color: #000080;">-pthread</span> <span class="nt" style="color: #000080;">-Wl</span>,--whole-archive <span class="nt" style="color: #000080;">-lpthread</span> <span class="nt" style="color: #000080;">-Wl</span>,--no-whole-archive <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">([</span> <span class="nv" style="color: #008080;">$$</span>? <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$@</span> <span class="nt" style="color: #000080;">-test</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$$</span>? <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"......OK dynamic linking was successful for proteinortho_clustering!"</span><span class="p">;</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">(</span> <span class="se" style="color: #d14;">\</span></span>
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189
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<td class="diff-line-num new_line" data-linenumber="184" 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">
184
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="make"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"......</span><span class="nv" style="color: #008080;">$(ORANGE)</span><span class="s2" style="color: #d14;">dynamic linking failed too, now I try dynamic linking without -WL,-whole-archive (this should now work for OSX).</span><span class="nv" style="color: #008080;">$(NC)</span><span class="s2" style="color: #d14;">"</span><span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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190
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<td class="diff-line-num new_line old" data-linenumber="185" 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="LC190" class="line" lang="make"> <span class="nv" style="color: #008080;"><span class="idiff left">$(CXX)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CXXFLAGS)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$(CXXFLAGS_PO</span>)</span> <span class="nt" style="color: #000080;">-fopenmp</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nv" style="color: #008080;">$<</span> <span class="nv" style="color: #008080;">$(LDFLAGS)</span> <span class="nv" style="color: #008080;">$(LDLIBS)</span> <span class="nt" style="color: #000080;">-llapack</span> <span class="nt" style="color: #000080;">-lblas</span> <span class="nt" style="color: #000080;">-pthread</span> <span class="nt" style="color: #000080;">-lpthread</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">([</span> <span class="nv" style="color: #008080;">$$</span>? <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$@</span> <span class="nt" style="color: #000080;">-test</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$$</span>? <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"......OK dynamic linking was successful for proteinortho_clustering!"</span><span class="p">;</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">(</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="185" 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">
185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="make"> <span class="nb" style="color: #0086b3;"><span class="idiff left">echo</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CXX)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -O2 </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CPPFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CXXFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -fopenmp -o </span></span><span class="nv" style="color: #008080;"><span class="idiff">$@</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$<</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(LDFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(LDLIBS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -llapack -lblas -pthread -lpthread"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CXX)</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-O2</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CPPFLAGS)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$(CXXFLAGS</span>)</span> <span class="nt" style="color: #000080;">-fopenmp</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nv" style="color: #008080;">$<</span> <span class="nv" style="color: #008080;">$(LDFLAGS)</span> <span class="nv" style="color: #008080;">$(LDLIBS)</span> <span class="nt" style="color: #000080;">-llapack</span> <span class="nt" style="color: #000080;">-lblas</span> <span class="nt" style="color: #000080;">-pthread</span> <span class="nt" style="color: #000080;">-lpthread</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">([</span> <span class="nv" style="color: #008080;">$$</span>? <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$@</span> <span class="nt" style="color: #000080;">-test</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$$</span>? <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"......OK dynamic linking was successful for proteinortho_clustering!"</span><span class="p">;</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">(</span> <span class="se" style="color: #d14;">\</span></span>
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191
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<td class="diff-line-num new_line" data-linenumber="186" 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">
186
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="make"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"......</span><span class="nv" style="color: #008080;">$(ORANGE)</span><span class="s2" style="color: #d14;">dynamic linking failed (without -WL,-whole-archive) too too, now I try to openblas.</span><span class="nv" style="color: #008080;">$(NC)</span><span class="s2" style="color: #d14;">"</span><span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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192
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="make"> <span class="nv" style="color: #008080;"><span class="idiff left">$(CXX)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CXXFLAGS)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$(CXXFLAGS_PO</span>)</span> <span class="nt" style="color: #000080;">-fopenmp</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nv" style="color: #008080;">$<</span> <span class="nv" style="color: #008080;">$(LDFLAGS)</span> <span class="nv" style="color: #008080;">$(LDLIBS)</span> <span class="nt" style="color: #000080;">-lopenblas</span> <span class="nt" style="color: #000080;">-pthread</span> <span class="nt" style="color: #000080;">-lpthread</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">([</span> <span class="nv" style="color: #008080;">$$</span>? <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$@</span> <span class="nt" style="color: #000080;">-test</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$$</span>? <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"......OK dynamic linking was successful for proteinortho_clustering!"</span><span class="p">;</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">(</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new old_line" data-linenumber="193" 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="187" 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">
187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="make"> <span class="nb" style="color: #0086b3;"><span class="idiff left">echo</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CXX)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -O2 </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CPPFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CXXFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -fopenmp -o </span></span><span class="nv" style="color: #008080;"><span class="idiff">$@</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$<</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(LDFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(LDLIBS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -lopenblas -pthread -lpthread"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CXX)</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-O2</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CPPFLAGS)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$(CXXFLAGS</span>)</span> <span class="nt" style="color: #000080;">-fopenmp</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nv" style="color: #008080;">$<</span> <span class="nv" style="color: #008080;">$(LDFLAGS)</span> <span class="nv" style="color: #008080;">$(LDLIBS)</span> <span class="nt" style="color: #000080;">-lopenblas</span> <span class="nt" style="color: #000080;">-pthread</span> <span class="nt" style="color: #000080;">-lpthread</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">([</span> <span class="nv" style="color: #008080;">$$</span>? <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$@</span> <span class="nt" style="color: #000080;">-test</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$$</span>? <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"......OK dynamic linking was successful for proteinortho_clustering!"</span><span class="p">;</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">(</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num old_line" data-linenumber="193" 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">
193
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<td class="diff-line-num new_line" data-linenumber="188" 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">
188
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="make"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"......</span><span class="nv" style="color: #008080;">$(ORANGE)</span><span class="s2" style="color: #d14;">last linking failed too too too, now I try to recompile lapack (v.3.8.0) and then compile proteinortho_clustering with dynamic linking.</span><span class="nv" style="color: #008080;">$(NC)</span><span class="s2" style="color: #d14;">"</span><span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num old_line" data-linenumber="194" 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">
194
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<td class="diff-line-num new_line" data-linenumber="189" 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">
189
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="make"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"......[ 33%] Extracting the LAPACK library"</span><span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num old old_line" data-linenumber="195" 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">
195
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<td class="diff-line-num new_line old" data-linenumber="190" 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="LC195" class="line" lang="make"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-d</span> src/lapack-3.8.0 <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">cd </span>src<span class="p">;</span> <span class="nb" style="color: #0086b3;">tar</span> <span class="nt" style="color: #000080;">-xzvf</span> lapack-3.8.0.tar.gz <span class="o" style="font-weight: 600;">></span> /dev/null 2>&1<span class="p">;</span> <span class="nb" style="color: #0086b3;">cd</span> ..<span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span><span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new old_line" data-linenumber="196" 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="190" 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">
190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="make"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-d</span> src/lapack-3.8.0 <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;"><span class="idiff left">echo</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"cd src; tar -xzvf lapack-3.8.0.tar.gz"</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span><span class="nb" style="color: #0086b3;">cd </span>src<span class="p">;</span> <span class="nb" style="color: #0086b3;">tar</span> <span class="nt" style="color: #000080;">-xzvf</span> lapack-3.8.0.tar.gz <span class="o" style="font-weight: 600;">></span> /dev/null 2>&1<span class="p">;</span> <span class="nb" style="color: #0086b3;">cd</span> ..<span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span><span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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196
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<td class="diff-line-num new_line" data-linenumber="191" 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">
191
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="make"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"......[ 66%] Compiling the LAPACK library (using cmake + make)"</span><span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num old old_line" data-linenumber="197" 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">
197
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<td class="diff-line-num new_line old" data-linenumber="192" 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="LC197" class="line" lang="make"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-f</span> src/lapack-3.8.0/build/lib/liblapack.a <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">mkdir </span>src/lapack-3.8.0/build 2> /dev/null<span class="p">;</span> <span class="nb" style="color: #0086b3;">cd </span>src/lapack-3.8.0/build<span class="p">;</span> cmake .. <span class="nt" style="color: #000080;">-DCMAKE_CXX_COMPILER</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$(CXX)</span> <span class="o" style="font-weight: 600;">></span> /dev/null<span class="p">;</span> make all <span class="nt" style="color: #000080;">-j4</span> <span class="o" style="font-weight: 600;">></span> /dev/null 2>&1<span class="p">;</span> <span class="nb" style="color: #0086b3;">cd</span> ../../.. <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span><span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new old_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="make"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-f</span> src/lapack-3.8.0/build/lib/liblapack.a <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;"><span class="idiff left">echo</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"mkdir src/lapack-3.8.0/build; cd src/lapack-3.8.0/build; cmake .. -DCMAKE_CXX_COMPILER=</span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CXX)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> > /dev/null; make all -j4"</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span><span class="nb" style="color: #0086b3;">mkdir </span>src/lapack-3.8.0/build 2> /dev/null<span class="p">;</span> <span class="nb" style="color: #0086b3;">cd </span>src/lapack-3.8.0/build<span class="p">;</span> cmake .. <span class="nt" style="color: #000080;">-DCMAKE_CXX_COMPILER</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$(CXX)</span> <span class="o" style="font-weight: 600;">></span> /dev/null<span class="p">;</span> make all <span class="nt" style="color: #000080;">-j4</span> <span class="o" style="font-weight: 600;">></span> /dev/null 2>&1<span class="p">;</span> <span class="nb" style="color: #0086b3;">cd</span> ../../.. <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span><span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="198" 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">
198
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<td class="diff-line-num new_line" data-linenumber="193" 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">
193
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="make"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"......[ 99%] Building **proteinortho_clustering** with LAPACK (dynamic linking)"</span><span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="199" 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">
199
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<td class="diff-line-num new_line old" data-linenumber="194" 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="LC199" class="line" lang="make"> <span class="nv" style="color: #008080;"><span class="idiff left">$(CXX)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CXXFLAGS)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$(CXXFLAGS_PO</span>)</span> <span class="nt" style="color: #000080;">-fopenmp</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nv" style="color: #008080;">$<</span> <span class="nt" style="color: #000080;">-Isrc</span>/lapack-3.8.0/build/include/ <span class="nt" style="color: #000080;">-Lsrc</span>/lapack-3.8.0/build/lib/ <span class="nt" style="color: #000080;">-llapack</span> <span class="nt" style="color: #000080;">-lblas</span> <span class="nv" style="color: #008080;">$(LDFLAGS)</span> <span class="nv" style="color: #008080;">$(LDLIBS)</span> <span class="nt" style="color: #000080;">-lgfortran</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"......OK dynamic linking was successful for proteinortho_clustering!"</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">(</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">)</span> <span class="p">;</span> <span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="194" 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">
194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="make"> <span class="nb" style="color: #0086b3;"><span class="idiff left">echo</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CXX)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -O2 </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CPPFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CXXFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -fopenmp -o </span></span><span class="nv" style="color: #008080;"><span class="idiff">$@</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$<</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -Isrc/lapack-3.8.0/build/include/ -Lsrc/lapack-3.8.0/build/lib/ -llapack -lblas </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(LDFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(LDLIBS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -lgfortran"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CXX)</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-O2</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CPPFLAGS)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$(CXXFLAGS</span>)</span> <span class="nt" style="color: #000080;">-fopenmp</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nv" style="color: #008080;">$<</span> <span class="nt" style="color: #000080;">-Isrc</span>/lapack-3.8.0/build/include/ <span class="nt" style="color: #000080;">-Lsrc</span>/lapack-3.8.0/build/lib/ <span class="nt" style="color: #000080;">-llapack</span> <span class="nt" style="color: #000080;">-lblas</span> <span class="nv" style="color: #008080;">$(LDFLAGS)</span> <span class="nv" style="color: #008080;">$(LDLIBS)</span> <span class="nt" style="color: #000080;">-lgfortran</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"......OK dynamic linking was successful for proteinortho_clustering!"</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">(</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">)</span> <span class="p">;</span> <span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">)</span></span>
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200
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<td class="diff-line-num new_line" data-linenumber="195" 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">
195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="make"><span class="k" style="font-weight: 600;">endif</span></span>
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201
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<td class="diff-line-num new_line" data-linenumber="196" 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">
196
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="make"> <span class="nl">@if [ ! -e $(BUILDDIR)/proteinortho_clustering ]; then echo "proteinortho_clustering compilation failed. Please visit https</span><span class="o" style="font-weight: 600;">:</span><span class="nf" style="color: #900; font-weight: 600;">//gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Codes"; false; fi</span></span>
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202
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<td class="diff-line-num new_line" data-linenumber="197" 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">
197
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="make"><span class="k" style="font-weight: 600;">else</span></span>
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203
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<td class="diff-line-num new_line" data-linenumber="198" 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">
198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"[ 15%] Extracting the LAPACK library"</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="204" 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">
204
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<td class="diff-line-num new_line old" data-linenumber="199" 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="LC204" class="line" lang="make"> <span class="p">@</span><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-d</span> src/lapack-3.8.0 <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">cd </span>src<span class="p">;</span> <span class="nb" style="color: #0086b3;">tar</span> <span class="nt" style="color: #000080;">-xzvf</span> lapack-3.8.0.tar.gz <span class="o" style="font-weight: 600;">></span> /dev/null 2>&1<span class="p">;</span> <span class="nb" style="color: #0086b3;">cd</span> ..<span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="199" 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">
199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="make"> <span class="p">@</span><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-d</span> src/lapack-3.8.0 <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;"><span class="idiff left">echo</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"cd src; tar -xzvf lapack-3.8.0.tar.gz"</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span><span class="nb" style="color: #0086b3;">cd </span>src<span class="p">;</span> <span class="nb" style="color: #0086b3;">tar</span> <span class="nt" style="color: #000080;">-xzvf</span> lapack-3.8.0.tar.gz <span class="o" style="font-weight: 600;">></span> /dev/null 2>&1<span class="p">;</span> <span class="nb" style="color: #0086b3;">cd</span> ..<span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="205" 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">
205
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<td class="diff-line-num new_line" data-linenumber="200" 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">
200
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"[ 18%] Compiling the LAPACK library (using cmake + make)"</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="206" 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">
206
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<td class="diff-line-num new_line old" data-linenumber="201" 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="LC206" class="line" lang="make"> <span class="p">@</span><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-f</span> src/lapack-3.8.0/build/lib/liblapack.a <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">mkdir </span>src/lapack-3.8.0/build<span class="p">;</span> <span class="nb" style="color: #0086b3;">cd </span>src/lapack-3.8.0/build<span class="p">;</span> cmake .. <span class="nt" style="color: #000080;">-DCMAKE_CXX_COMPILER</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$(CXX)</span> <span class="o" style="font-weight: 600;">></span> /dev/null 2>&1<span class="p">;</span> make all <span class="nt" style="color: #000080;">-j4</span> <span class="o" style="font-weight: 600;">></span> /dev/null 2>&1<span class="p">;</span> <span class="nb" style="color: #0086b3;">cd</span> ../../.. <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="207" 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="201" 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">
201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="make"> <span class="p">@</span><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-f</span> src/lapack-3.8.0/build/lib/liblapack.a <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;"><span class="idiff left">echo</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"mkdir src/lapack-3.8.0/build; cd src/lapack-3.8.0/build; cmake .. -DCMAKE_CXX_COMPILER=</span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CXX)</span></span><span class="s2" style="color: #d14;"><span class="idiff">; make all -j4"</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span><span class="nb" style="color: #0086b3;">mkdir </span>src/lapack-3.8.0/build<span class="p">;</span> <span class="nb" style="color: #0086b3;">cd </span>src/lapack-3.8.0/build<span class="p">;</span> cmake .. <span class="nt" style="color: #000080;">-DCMAKE_CXX_COMPILER</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$(CXX)</span> <span class="o" style="font-weight: 600;">></span> /dev/null 2>&1<span class="p">;</span> make all <span class="nt" style="color: #000080;">-j4</span> <span class="o" style="font-weight: 600;">></span> /dev/null 2>&1<span class="p">;</span> <span class="nb" style="color: #0086b3;">cd</span> ../../.. <span class="p">;</span> <span class="k" style="font-weight: 600;">fi</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="207" 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">
207
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<td class="diff-line-num new_line" data-linenumber="202" 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">
202
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"[ 20%] Building **proteinortho_clustering** with LAPACK (dynamic linking)"</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="208" 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">
208
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<td class="diff-line-num new_line old" data-linenumber="203" 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="LC208" class="line" lang="make"> <span class="p">@</span><span class="nv" style="color: #008080;"><span class="idiff left">$(CXX)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CXXFLAGS)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$(CXXFLAGS_PO</span>)</span> <span class="nt" style="color: #000080;">-fopenmp</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nv" style="color: #008080;">$<</span> <span class="nt" style="color: #000080;">-Isrc</span>/lapack-3.8.0/build/include/ <span class="nt" style="color: #000080;">-Lsrc</span>/lapack-3.8.0/build/lib/ <span class="nt" style="color: #000080;">-llapack</span> <span class="nt" style="color: #000080;">-lblas</span> <span class="nv" style="color: #008080;">$(LDFLAGS)</span> <span class="nv" style="color: #008080;">$(LDLIBS)</span> <span class="nt" style="color: #000080;">-lgfortran</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;"><span class="idiff left">echo</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CXX)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -O2 </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CPPFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CXXFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -fopenmp -o </span></span><span class="nv" style="color: #008080;"><span class="idiff">$@</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$<</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -Isrc/lapack-3.8.0/build/include/ -Lsrc/lapack-3.8.0/build/lib/ -llapack -lblas </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(LDFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(LDLIBS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -lgfortran"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CXX)</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-O2</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CPPFLAGS)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$(CXXFLAGS</span>)</span> <span class="nt" style="color: #000080;">-fopenmp</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nv" style="color: #008080;">$<</span> <span class="nt" style="color: #000080;">-Isrc</span>/lapack-3.8.0/build/include/ <span class="nt" style="color: #000080;">-Lsrc</span>/lapack-3.8.0/build/lib/ <span class="nt" style="color: #000080;">-llapack</span> <span class="nt" style="color: #000080;">-lblas</span> <span class="nv" style="color: #008080;">$(LDFLAGS)</span> <span class="nv" style="color: #008080;">$(LDLIBS)</span> <span class="nt" style="color: #000080;">-lgfortran</span><span class="p">;</span></span>
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209
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204
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="make"><span class="k" style="font-weight: 600;">endif</span></span>
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210
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205
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="make"><span class="k" style="font-weight: 600;">endif</span></span>
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211
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206
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="make"><span class="k" style="font-weight: 600;">ifeq</span> <span class="nv" style="color: #008080;">($(USELAPACK),FALSE)</span></span>
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212
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207
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"[ 20%] Building **proteinortho_clustering** WITHOUT(!) LAPACK"</span><span class="p">;</span></span>
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213
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="make"> <span class="p">@</span><span class="nv" style="color: #008080;"><span class="idiff left">$(CXX)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CXXFLAGS)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$(CXXFLAGS_PO</span>)</span> <span class="nt" style="color: #000080;">-fopenmp</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> src/proteinortho_clustering_nolapack.cpp <span class="nv" style="color: #008080;">$(LDFLAGS)</span> <span class="nv" style="color: #008080;">$(LDLIBS)</span> <span class="nt" style="color: #000080;">-static</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">([</span> <span class="nv" style="color: #008080;">$$</span>? <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">(</span> <span class="se" style="color: #d14;">\</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;"><span class="idiff left">echo</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CXX)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -O2 </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CPPFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CXXFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -fopenmp -o </span></span><span class="nv" style="color: #008080;"><span class="idiff">$@</span></span><span class="s2" style="color: #d14;"><span class="idiff"> src/proteinortho_clustering_nolapack.cpp </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(LDFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(LDLIBS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -static"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CXX)</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-O2</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CPPFLAGS)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$(CXXFLAGS</span>)</span> <span class="nt" style="color: #000080;">-fopenmp</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> src/proteinortho_clustering_nolapack.cpp <span class="nv" style="color: #008080;">$(LDFLAGS)</span> <span class="nv" style="color: #008080;">$(LDLIBS)</span> <span class="nt" style="color: #000080;">-static</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">([</span> <span class="nv" style="color: #008080;">$$</span>? <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">(</span> <span class="se" style="color: #d14;">\</span></span>
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214
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209
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="make"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"......</span><span class="nv" style="color: #008080;">$(ORANGE)</span><span class="s2" style="color: #d14;">static linking failed of proteinortho_clustering_nolapack, now i switch to dynamic linking.</span><span class="nv" style="color: #008080;">$(NC)</span><span class="s2" style="color: #d14;">"</span><span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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215
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="make"> <span class="nv" style="color: #008080;"><span class="idiff left">$(CXX)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CXXFLAGS)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$(CXXFLAGS_PO</span>)</span> <span class="nt" style="color: #000080;">-fopenmp</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> src/proteinortho_clustering_nolapack.cpp <span class="nv" style="color: #008080;">$(LDFLAGS)</span> <span class="nv" style="color: #008080;">$(LDLIBS)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"......OK dynamic linking was successful for proteinortho_clustering_nolapack!"</span><span class="p">;</span> <span class="o" style="font-weight: 600;">)</span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="make"> <span class="nb" style="color: #0086b3;"><span class="idiff left">echo</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CXX)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -O2 </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CPPFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CXXFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -fopenmp -o </span></span><span class="nv" style="color: #008080;"><span class="idiff">$@</span></span><span class="s2" style="color: #d14;"><span class="idiff"> src/proteinortho_clustering_nolapack.cpp </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(LDFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(LDLIBS)</span></span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CXX)</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-O2</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CPPFLAGS)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$(CXXFLAGS</span>)</span> <span class="nt" style="color: #000080;">-fopenmp</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> src/proteinortho_clustering_nolapack.cpp <span class="nv" style="color: #008080;">$(LDFLAGS)</span> <span class="nv" style="color: #008080;">$(LDLIBS)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"......OK dynamic linking was successful for proteinortho_clustering_nolapack!"</span><span class="p">;</span> <span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="make"><span class="k" style="font-weight: 600;">endif</span></span>
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212
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="make"><span class="k" style="font-weight: 600;">endif</span></span>
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213
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="make"></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">@@ -220,33 +215,33 @@ $(BUILDDIR)/proteinortho_cleanupblastgraph: src/cleanupblastgraph.cpp</td>
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220
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215
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="make"> <span class="nv" style="color: #008080;">$(dir_guard)</span></span>
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221
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"[ 50%] Building **cleanupblastgraph**"</span></span>
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222
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217
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="make"><span class="k" style="font-weight: 600;">ifeq</span> <span class="nv" style="color: #008080;">($(STATIC),TRUE)</span></span>
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="make"> <span class="p">@</span><span class="nv" style="color: #008080;"><span class="idiff left">$(CXX)</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff">c++11 </span><span class="nv" style="color: #008080;"><span class="idiff">$(CXXFLAGS)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$(CXXFLAGS_PO</span>)</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nv" style="color: #008080;">$<</span> <span class="nv" style="color: #008080;">$(LDFLAGS)</span> <span class="nv" style="color: #008080;">$(LDLIBS)</span> <span class="nt" style="color: #000080;">-static</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">([</span> <span class="nv" style="color: #008080;">$$</span>? <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">(</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;"><span class="idiff left">echo</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CXX)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -std=c++11 </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CPPFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CXXFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -o </span></span><span class="nv" style="color: #008080;"><span class="idiff">$@</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$<</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(LDFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(LDLIBS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -static"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CXX)</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff">c++11 </span><span class="nv" style="color: #008080;"><span class="idiff">$(CPPFLAGS)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$(CXXFLAGS</span>)</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nv" style="color: #008080;">$<</span> <span class="nv" style="color: #008080;">$(LDFLAGS)</span> <span class="nv" style="color: #008080;">$(LDLIBS)</span> <span class="nt" style="color: #000080;">-static</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">([</span> <span class="nv" style="color: #008080;">$$</span>? <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">(</span> <span class="se" style="color: #d14;">\</span></span>
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224
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219
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="make"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"......</span><span class="nv" style="color: #008080;">$(ORANGE)</span><span class="s2" style="color: #d14;">static linking failed of cleanupblastgraph, now i switch to dynamic linking.</span><span class="nv" style="color: #008080;">$(NC)</span><span class="s2" style="color: #d14;">"</span><span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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225
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="make"> <span class="nv" style="color: #008080;"><span class="idiff left">$(CXX)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CXXFLAGS)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CXXFLAGS_PO)</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-o</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$@</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$<</span></span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"......OK dynamic linking was successful of cleanupblastgraph!"</span><span class="p">;</span> <span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="make"> <span class="nb" style="color: #0086b3;"><span class="idiff left">echo</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CXX)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CPPFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CXXFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -o </span></span><span class="nv" style="color: #008080;"><span class="idiff">$@</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$<</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(LDFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(LDLIBS)</span></span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CXX)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CPPFLAGS)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CXXFLAGS)</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-o</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$@</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$<</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(LDFLAGS)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$(LDLIBS)</span></span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"......OK dynamic linking was successful of cleanupblastgraph!"</span><span class="p">;</span> <span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="make"><span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">-<span id="LC227" class="line" lang="make"> <span class="p">@</span><span class="nv" style="color: #008080;"><span class="idiff left">$(CXX)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CXXFLAGS)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$(CXXFLAGS_PO</span>)</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nv" style="color: #008080;">$<</span> <span class="nv" style="color: #008080;">$(LDFLAGS)</span> <span class="nv" style="color: #008080;">$(LDLIBS)</span></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;"><span class="idiff left">echo</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CXX)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CPPFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CXXFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -o </span></span><span class="nv" style="color: #008080;"><span class="idiff">$@</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$<</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(LDFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(LDLIBS)</span></span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CXX)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CPPFLAGS)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$(CXXFLAGS</span>)</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nv" style="color: #008080;">$<</span> <span class="nv" style="color: #008080;">$(LDFLAGS)</span> <span class="nv" style="color: #008080;">$(LDLIBS)</span></span>
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="make"><span class="k" style="font-weight: 600;">endif</span></span>
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224
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="make"></span>
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230
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="make"><span class="nl">$(BUILDDIR)/proteinortho_graphMinusRemovegraph</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">src/graphMinusRemovegraph.cpp</span></span>
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226
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="make"> <span class="nv" style="color: #008080;">$(dir_guard)</span></span>
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232
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"[ 25%] Building **graphMinusRemovegraph**"</span></span>
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="make"><span class="k" style="font-weight: 600;">ifeq</span> <span class="nv" style="color: #008080;">($(STATIC),TRUE)</span></span>
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234
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<pre style="margin: 0;">-<span id="LC234" class="line" lang="make"> <span class="p">@</span><span class="nv" style="color: #008080;"><span class="idiff left">$(CXX)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CXXFLAGS)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$(CXXFLAGS_PO</span>)</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nv" style="color: #008080;">$<</span> <span class="nv" style="color: #008080;">$(LDFLAGS)</span> <span class="nv" style="color: #008080;">$(LDLIBS)</span> <span class="nt" style="color: #000080;">-static</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">([</span> <span class="nv" style="color: #008080;">$$</span>? <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">(</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;"><span class="idiff left">echo</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CXX)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CPPFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CXXFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -o </span></span><span class="nv" style="color: #008080;"><span class="idiff">$@</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$<</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(LDFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(LDLIBS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -static"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CXX)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CPPFLAGS)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$(CXXFLAGS</span>)</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nv" style="color: #008080;">$<</span> <span class="nv" style="color: #008080;">$(LDFLAGS)</span> <span class="nv" style="color: #008080;">$(LDLIBS)</span> <span class="nt" style="color: #000080;">-static</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">([</span> <span class="nv" style="color: #008080;">$$</span>? <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">(</span> <span class="se" style="color: #d14;">\</span></span>
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235
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230
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="make"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"......</span><span class="nv" style="color: #008080;">$(ORANGE)</span><span class="s2" style="color: #d14;">static linking failed of graphMinusRemovegraph, now i switch to dynamic linking.</span><span class="nv" style="color: #008080;">$(NC)</span><span class="s2" style="color: #d14;">"</span><span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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236
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="make"> <span class="nv" style="color: #008080;"><span class="idiff left">$(CXX)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CXXFLAGS)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$(CXXFLAGS_PO</span>)</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nv" style="color: #008080;">$<</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"......OK dynamic linking was successful of graphMinusRemovegraph!"</span><span class="p">;</span> <span class="o" style="font-weight: 600;">)</span></span>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="make"> <span class="nb" style="color: #0086b3;"><span class="idiff left">echo</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CXX)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CPPFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CXXFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -o </span></span><span class="nv" style="color: #008080;"><span class="idiff">$@</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$<</span></span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CXX)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CPPFLAGS)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$(CXXFLAGS</span>)</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nv" style="color: #008080;">$<</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"......OK dynamic linking was successful of graphMinusRemovegraph!"</span><span class="p">;</span> <span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="make"><span class="k" style="font-weight: 600;">else</span></span>
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238
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<pre style="margin: 0;">-<span id="LC238" class="line" lang="make"> <span class="p">@</span><span class="nv" style="color: #008080;"><span class="idiff left">$(CXX)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CXXFLAGS)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$(CXXFLAGS_PO</span>)</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nv" style="color: #008080;">$<</span> <span class="nv" style="color: #008080;">$(LDFLAGS)</span> <span class="nv" style="color: #008080;">$(LDLIBS)</span></span>
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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;"><span class="idiff left">echo</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CXX)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CPPFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CXXFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -o </span></span><span class="nv" style="color: #008080;"><span class="idiff">$@</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$<</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(LDFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(LDLIBS)</span></span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CXX)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CPPFLAGS)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$(CXXFLAGS</span>)</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nv" style="color: #008080;">$<</span> <span class="nv" style="color: #008080;">$(LDFLAGS)</span> <span class="nv" style="color: #008080;">$(LDLIBS)</span></span>
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234
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="make"><span class="k" style="font-weight: 600;">endif</span></span>
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240
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235
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="make"></span>
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241
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="make"><span class="nl">$(BUILDDIR)/proteinortho_treeBuilderCore</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">src/po_tree.c</span></span>
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242
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237
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="make"> <span class="nv" style="color: #008080;">$(dir_guard)</span></span>
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243
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238
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"[ 75%] Building **po_tree**"</span></span>
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244
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239
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="make"><span class="k" style="font-weight: 600;">ifeq</span> <span class="nv" style="color: #008080;">($(STATIC),TRUE)</span></span>
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245
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="make"> <span class="p">@</span><span class="nv" style="color: #008080;"><span class="idiff left">$(CC)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$(C</span>CFLAGS)</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nv" style="color: #008080;">$<</span> <span class="nv" style="color: #008080;">$(LDFLAGS)</span> <span class="nv" style="color: #008080;">$(LDLIBS)</span> <span class="nt" style="color: #000080;">-static</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">([</span> <span class="nv" style="color: #008080;">$$</span>? <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">(</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;"><span class="idiff left">echo</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CC)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CPPFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CCFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -o </span></span><span class="nv" style="color: #008080;"><span class="idiff">$@</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$<</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(LDFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(LDLIBS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -static"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CC)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CPPFLAGS)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CCFLAGS)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$(</span>CFLAGS)</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nv" style="color: #008080;">$<</span> <span class="nv" style="color: #008080;">$(LDFLAGS)</span> <span class="nv" style="color: #008080;">$(LDLIBS)</span> <span class="nt" style="color: #000080;">-static</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">([</span> <span class="nv" style="color: #008080;">$$</span>? <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">(</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="make"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"......</span><span class="nv" style="color: #008080;">$(ORANGE)</span><span class="s2" style="color: #d14;">static linking failed of po_tree, now i switch to dynamic linking.</span><span class="nv" style="color: #008080;">$(NC)</span><span class="s2" style="color: #d14;">"</span><span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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247
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="make"> <span class="nv" style="color: #008080;"><span class="idiff left">$(CC)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CCFLAGS)</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-o</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$@</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$<</span></span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"......OK dynamic linking was successful of po_tree!"</span><span class="p">;</span> <span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="make"> <span class="nb" style="color: #0086b3;"><span class="idiff left">echo</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CC)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CPPFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CCFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -o </span></span><span class="nv" style="color: #008080;"><span class="idiff">$@</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$<</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(LDFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(LDLIBS)</span></span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CC)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CPPFLAGS)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CCFLAGS)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CFLAGS)</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-o</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$@</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$<</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(LDFLAGS)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$(LDLIBS)</span></span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"......OK dynamic linking was successful of po_tree!"</span><span class="p">;</span> <span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC243" class="line" lang="make"><span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">-<span id="LC249" class="line" lang="make"> <span class="p"><span class="idiff left">@</span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CC)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$(C</span>CFLAGS)</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nv" style="color: #008080;">$<</span> <span class="nv" style="color: #008080;">$(LDFLAGS)</span> <span class="nv" style="color: #008080;">$(LDLIBS)</span></span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="make"> <span class="nv" style="color: #008080;"><span class="idiff left">$(CC)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CPPFLAGS)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$(CCFLAGS)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$(</span>CFLAGS)</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nv" style="color: #008080;">$<</span> <span class="nv" style="color: #008080;">$(LDFLAGS)</span> <span class="nv" style="color: #008080;">$(LDLIBS)</span></span>
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="make"><span class="k" style="font-weight: 600;">endif</span></span>
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC247" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">install</span></span>
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<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/proteinortho/-/commit/3c35c1d73608e5ddc79f68abf3524b8a4d1e57ba#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="77" 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">@@ -77,31 +77,29 @@ If you cannot execute the src/BUILD/Linux_x86_64/proteinortho_clustering, then y</td>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="markdown"><span class="nt" style="color: #000080;"><br></span></span>
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79
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### Easy installation with (bio)conda (for Linux + OSX)</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### Easy installation with (bio)conda (for Linux + OSX)<span class="idiff left right"> [](http://bioconda.github.io/recipes/proteinortho/README.html) [](https://bioconda.github.io/recipes/proteinortho/README.html)</span></span></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="markdown"><span class="sb" style="color: #d14;"> conda install proteinortho</span></span>
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83
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="markdown"></span>
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="markdown">If you need conda (see <span class="p">[</span><span class="nv" style="color: #008080;">here</span><span class="p">](</span><span class="sx" style="color: #d14;">https://docs.anaconda.com/anaconda/install/</span><span class="p">)</span>) and the bioconda channel: <span class="sb" style="color: #d14;">`conda config --add channels defaults && conda config --add channels bioconda && conda config --add channels conda-forge`</span>.</span>
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85
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85
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![install with bioconda</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat</span><span class="p">)</span>](http://bioconda.github.io/recipes/proteinortho/README.html) <span class="p">[</span><span class="nv" style="color: #008080;">![alt</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/conda/dn/bioconda/proteinortho.svg?style=flat</span><span class="p">)</span>](https://bioconda.github.io/recipes/proteinortho/README.html)</span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="markdown"></span>
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86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="markdown"><span class="nt" style="color: #000080;"><br></span></span>
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87
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### Easy installation with brew (for OSX)</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### Easy installation with brew (for OSX)<span class="idiff left right"> [](https://formulae.brew.sh/formula/proteinortho) [](https://formulae.brew.sh/formula/proteinortho)</span></span></span>
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89
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="markdown"><span class="sb" style="color: #d14;"> brew install proteinortho</span></span>
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93
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91
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="94" 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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92
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="markdown">If you need brew (see <span class="p">[</span><span class="nv" style="color: #008080;">here</span><span class="p">](</span><span class="sx" style="color: #d14;">https://brew.sh/index_de</span><span class="p">)</span>)</span>
</pre>
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95
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93
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![install with brew</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/install%20with-brew-brightgreen.svg?style=flat</span><span class="p">)</span>](https://formulae.brew.sh/formula/proteinortho) <span class="p">[</span><span class="nv" style="color: #008080;">![dl</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/dynamic/json.svg?label=downloads&query=$[%27analytics%27][%27install%27][%27365d%27][%27proteinortho%27]&url=https%3A%2F%2Fformulae.brew.sh%2Fapi%2Fformula%2Fproteinortho.json&color=green</span><span class="p">)</span>](https://formulae.brew.sh/formula/proteinortho)</span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="markdown"></span>
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94
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="markdown"><span class="nt" style="color: #000080;"><br></span></span>
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99
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95
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### Easy installation with docker</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### Easy installation with docker [](https://quay.io/repository/biocontainers/proteinortho)</span></span>
</pre>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="markdown"><span class="sb" style="color: #d14;"> docker pull quay.io/biocontainers/proteinortho:TAG</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="markdown">with TAG specified <span class="p">[</span><span class="nv" style="color: #008080;">here</span><span class="p">](</span><span class="sx" style="color: #d14;">https://quay.io/repository/biocontainers/proteinortho?tab=tags</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">e.g.</span> 6.0.23--hfd40d39_0).</span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="markdown"><span class="sb" style="color: #d14;"> docker pull quay.io/biocontainers/proteinortho</span></span>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![install with docker</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/install%20with-docker-brightgreen.svg?style=flat</span><span class="p">)</span>](https://quay.io/repository/biocontainers/proteinortho)</span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="markdown"><span class="nt" style="color: #000080;"><details></span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="111" 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="109" 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">@@ -111,7 +109,7 @@ If you need brew (see [here](https://brew.sh/index_de))</td>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="markdown"> To start a bash shell </span>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="markdown"> <span class="p">```</span><span class="nl"><span class="idiff left right">sudo </span>docker run --rm -it quay.io/biocontainers/proteinortho:6.0.22--hfd40d39_0 bash ```</span></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="markdown"> <span class="p">```</span><span class="nl">docker run --rm -it quay.io/biocontainers/proteinortho:6.0.22--hfd40d39_0 bash ```</span></span>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="markdown"><span class="sb" style="color: #d14;"> Here you can start/use proteinortho.</span></span>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="markdown"><span class="sb" style="color: #d14;"> You can change "6.0.22--hfd40d39_0" with any tag/version that is available [here](https://quay.io/repository/biocontainers/proteinortho?tab=tags). Sadly there is no ":latest" tag available ...</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="120" 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="118" 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">@@ -120,9 +118,9 @@ If you need brew (see [here](https://brew.sh/index_de))</td>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="markdown"><span class="sb" style="color: #d14;"> This is neccessary if you want to access your local files:</span></span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="markdown"> <span class="p">```</span><span class="idiff left right">sudo </span>docker run --rm --mount "type=bind,src=/home/$(id -un),dst=/home/$(id -un)" -u $(id -u):$(id -g) -it quay.io/biocontainers/proteinortho:6.0.22--hfd40d39_0 bash<span class="sb" style="color: #d14;">```</span></span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="markdown"> <span class="p">```</span>docker run --rm --mount "type=bind,src=/home/$(id -un),dst=/home/$(id -un)" -u $(id -u):$(id -g) -it quay.io/biocontainers/proteinortho:6.0.22--hfd40d39_0 bash<span class="sb" style="color: #d14;">```</span></span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="markdown"><span class="sb" style="color: #d14;"> now you have your home directory mounted to /home/YOURNAME. (load your bashrc with<span class="idiff left"> ```</span></span><span class="idiff right">source ~</span>/.bashrc<span class="sb" style="color: #d14;">```)</span></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="markdown"><span class="sb" style="color: #d14;"> now you have your home directory mounted to /home/YOURNAME. (load your bashrc with<span class="idiff left">in docker : ```</span></span><span class="idiff right">source /home/YOURNAME</span>/.bashrc<span class="sb" style="color: #d14;">```)</span></span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="markdown"><span class="sb" style="color: #d14;"></details></span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="149" 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="147" 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">@@ -149,13 +147,13 @@ Afterwards the deb package can be installed with `sudo dpkg -i proteinortho*deb`</td>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="markdown"><span class="sb" style="color: #d14;">#### *(Easy installation with apt-get)*</span></span>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="markdown"><span class="sb" style="color: #d14;">**! Disclamer: Work in progress !**</span></span>
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="markdown"><span class="sb" style="color: #d14;">*proteinortho will be released to stable with Debian 11 (~2021), then proteinortho can be installed with `<span class="idiff left right">sudo </span>apt-get install proteinortho` (currently this installes the outdated version v5.16b)*</span></span>
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="markdown"><span class="sb" style="color: #d14;">*proteinortho will be released to stable with Debian 11 (~2021), then proteinortho can be installed with `apt-get install proteinortho` (currently this installes the outdated version v5.16b)*</span></span>
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="markdown"><span class="sb" style="color: #d14;"><br></span></span>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="markdown"><span class="sb" style="color: #d14;">#### Prerequisites for compiling proteinortho from source</span></span>
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="markdown"><span class="sb" style="color: #d14;">Proteinortho uses standard software which is often installed already or is part of then package repositories and can thus easily be installed. The sources come with a precompiled version of Proteinortho for 64bit Linux.</span></span>
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="markdown"><span class="sb" style="color: #d14;">Proteinortho uses standard software which is often installed already or is part of then package repositories and can thus easily be installed. The sources come with a precompiled version of Proteinortho for 64bit Linux<span class="idiff left right"> x86</span>.</span></span>
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="markdown"><span class="sb" style="color: #d14;"><details></span></span>
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="markdown"><span class="sb" style="color: #d14;"> <summary>To <b>run</b> Proteinortho, you need: (Click to expand)</summary></span></span>
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<a href="https://salsa.debian.org/med-team/proteinortho/-/commit/3c35c1d73608e5ddc79f68abf3524b8a4d1e57ba#c9e37a96ac72f9ef076d7a41a57470524d63b36e"><strong>proteinortho6.pl</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">@@ -464,7 +464,7 @@ use POSIX;</td>
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<pre style="margin: 0;"> <span id="LC464" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">##########################################################################################</span></span>
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<pre style="margin: 0;"> <span id="LC465" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Variables</span></span>
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<pre style="margin: 0;"> <span id="LC466" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">##########################################################################################</span></span>
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<pre style="margin: 0;">-<span id="LC467" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$version</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="s2" style="color: #d14;">6.0.2<span class="idiff left right">3</span></span><span class="p">";</span></span>
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$version</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="s2" style="color: #d14;">6.0.2<span class="idiff left right">4</span></span><span class="p">";</span></span>
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468
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<pre style="margin: 0;"> <span id="LC468" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$step</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;"># 0/1/2/3 -> do all / only apply step 1 / only apply step 2 / only apply step 3</span></span>
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469
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<pre style="margin: 0;"> <span id="LC469" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$verbose</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;"># 0/1 -> don't / be verbose</span></span>
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<pre style="margin: 0;"> <span id="LC470" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$debug</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;"># 0/1 -> don't / show debug data</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="698" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -698,7 +698,6 @@ if ($jobnumber != -1) {</td>
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<pre style="margin: 0;"> <span id="LC698" class="line" lang="perl"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC699" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC700" class="line" lang="perl"></span>
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<pre style="margin: 0;">-<span id="LC701" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC701" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$gccversionstr</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">`</span><span class="sb" style="color: #d14;">gcc --version 2>/dev/null</span><span class="p">`;</span></span>
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<pre style="margin: 0;"> <span id="LC702" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$gccversion_main</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"";</span></span>
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<pre style="margin: 0;"> <span id="LC703" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="841" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -842,6 +841,28 @@ if ($step == 0 || $step == 1) {</td>
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<pre style="margin: 0;"> <span id="LC841" class="line" lang="perl"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC842" class="line" lang="perl"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC843" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC844" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># start the daemon</span></span>
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<pre style="margin: 0;">+<span id="LC845" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="p">){</span></span>
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846
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<pre style="margin: 0;">+<span id="LC846" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$updateIntervalInSeconds</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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847
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<pre style="margin: 0;">+<span id="LC847" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="s2" style="color: #d14;">pstree >/dev/null 2>&1</span><span class="p">");</span></span>
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848
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<pre style="margin: 0;">+<span id="LC848" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$masterpid</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">getppid</span><span class="p">;</span></span>
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849
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<pre style="margin: 0;">+<span id="LC849" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">){</span></span>
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850
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<pre style="margin: 0;">+<span id="LC850" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$pid</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">fork</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;"># make a fork of the current process </span></span>
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<td class="diff-line-num new new_line" data-linenumber="851" 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">
851
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<pre style="margin: 0;">+<span id="LC851" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># this is now executed in parallel !</span></span>
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852
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<pre style="margin: 0;">+<span id="LC852" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$ppid</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">getppid</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;"># parent pid </span></span>
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853
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<pre style="margin: 0;">+<span id="LC853" class="line" lang="perl"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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854
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<pre style="margin: 0;">+<span id="LC854" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">sleep</span> <span class="nv" style="color: #008080;">$updateIntervalInSeconds</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="855" 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">
855
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<pre style="margin: 0;">+<span id="LC855" class="line" lang="perl"> <span class="k" style="font-weight: 600;">unless</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">kill</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nv" style="color: #008080;">$ppid</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;"># check if parent is still alive (kill 0 = no kill is send but checked for errors) </span></span>
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856
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<pre style="margin: 0;">+<span id="LC856" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">exit</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="857" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
857
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<pre style="margin: 0;">+<span id="LC857" class="line" lang="perl"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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858
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<pre style="margin: 0;">+<span id="LC858" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">ps --forest -o pid,tty,stat,time,cmd -g </span><span class="si" style="color: #d14;">$masterpid</span><span class="se" style="color: #d14;">\n</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">`</span><span class="sb" style="color: #d14;">ps --forest -o pid,tty,stat,time,cmd -g </span><span class="si" style="color: #d14;">$masterpid</span><span class="p">`</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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859
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<pre style="margin: 0;">+<span id="LC859" class="line" lang="perl"> <span class="p">}</span></span>
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860
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<pre style="margin: 0;">+<span id="LC860" class="line" lang="perl"> <span class="p">}</span></span>
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861
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<pre style="margin: 0;">+<span id="LC861" class="line" lang="perl"> <span class="p">}</span></span>
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862
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<pre style="margin: 0;">+<span id="LC862" class="line" lang="perl"> <span class="p">}</span></span>
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863
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<pre style="margin: 0;">+<span id="LC863" class="line" lang="perl"><span class="p">}</span></span>
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864
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<pre style="margin: 0;">+<span id="LC864" class="line" lang="perl"></span>
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865
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<pre style="margin: 0;">+<span id="LC865" class="line" lang="perl"></span>
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845
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866
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<pre style="margin: 0;"> <span id="LC866" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Step 2, run blast and synteny algorithm</span></span>
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846
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867
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<pre style="margin: 0;"> <span id="LC867" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$step</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$step</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>
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847
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868
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<pre style="margin: 0;"> <span id="LC868" class="line" lang="perl"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2144" 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="2165" 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">@@ -2144,6 +2165,7 @@ sub blast {</td>
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2144
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2165
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<pre style="margin: 0;"> <span id="LC2165" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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2145
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2166
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<pre style="margin: 0;"> <span id="LC2166" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># note: e.g. diamond can directly pass the output to @data</span></span>
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<td class="diff-line-num old_line" data-linenumber="2146" 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">
2146
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<td class="diff-line-num new_line" data-linenumber="2167" 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">
2167
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<pre style="margin: 0;"> <span id="LC2167" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># </span></span>
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<td class="diff-line-num new old_line" data-linenumber="2147" 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="2168" 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">
2168
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<pre style="margin: 0;">+<span id="LC2168" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># sh -ic '{ cat 1>&3; kill 0; } | { sleep 2; kill 0; }' 3>&1</span></span>
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2147
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<td class="diff-line-num new_line" data-linenumber="2169" 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">
2169
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<pre style="margin: 0;"> <span id="LC2169" class="line" lang="perl"></span>
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<td class="diff-line-num old_line" data-linenumber="2148" 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">
2148
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<td class="diff-line-num new_line" data-linenumber="2170" 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">
2170
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<pre style="margin: 0;"> <span id="LC2170" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">blastp_legacy</span><span class="p">"</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$blastmode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">blastn_legacy</span><span class="p">"</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$blastmode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">tblastx_legacy</span><span class="p">")</span> <span class="p">{</span><span class="nv" style="color: #008080;">lock</span><span class="p">(</span><span class="nv" style="color: #008080;">$threads_per_process</span><span class="p">);</span> <span class="nv" style="color: #008080;">$command</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$binpath</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">blastall -a </span><span class="si" style="color: #d14;">$threads_per_process</span><span class="s2" style="color: #d14;"> -d '</span><span class="si" style="color: #d14;">$a</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' -i '</span><span class="si" style="color: #d14;">$b</span><span class="s2" style="color: #d14;">' -p </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;"> -m8 -e </span><span class="si" style="color: #d14;">$evalue</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">$blastOptions</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">$printSTDERR</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="nv" style="color: #008080;">$keep</span> <span class="p">?</span> <span class="p">"</span><span class="s2" style="color: #d14;"> | tee '</span><span class="si" style="color: #d14;">$bla</span><span class="s2" style="color: #d14;">.tmp'</span><span class="p">"</span> <span class="p">:</span> <span class="p">"");}</span></span>
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<td class="diff-line-num old_line" data-linenumber="2149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2149
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<td class="diff-line-num new_line" data-linenumber="2171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2171
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<pre style="margin: 0;"> <span id="LC2171" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">autoblast</span><span class="p">"</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$autoblast_fileis</span><span class="p">{</span><span class="nv" style="color: #008080;">$a</span><span class="p">}</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">prot</span><span class="p">"</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$autoblast_fileis</span><span class="p">{</span><span class="nv" style="color: #008080;">$b</span><span class="p">}</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">prot</span><span class="p">")</span> <span class="p">{</span><span class="nv" style="color: #008080;">lock</span><span class="p">(</span><span class="nv" style="color: #008080;">$threads_per_process</span><span class="p">);</span> <span class="nv" style="color: #008080;">$command</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$binpath</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">blastp -num_threads </span><span class="si" style="color: #d14;">$threads_per_process</span><span class="s2" style="color: #d14;"> -db '</span><span class="si" style="color: #d14;">$a</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' -query '</span><span class="si" style="color: #d14;">$b</span><span class="s2" style="color: #d14;">' -evalue </span><span class="si" style="color: #d14;">$evalue</span><span class="s2" style="color: #d14;"> -outfmt 6 </span><span class="si" style="color: #d14;">$blastOptions</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">$printSTDERR</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="nv" style="color: #008080;">$keep</span> <span class="p">?</span> <span class="p">"</span><span class="s2" style="color: #d14;"> | tee '</span><span class="si" style="color: #d14;">$bla</span><span class="s2" style="color: #d14;">.tmp'</span><span class="p">"</span> <span class="p">:</span> <span class="p">"");}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2178" 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="2200" 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">@@ -2178,7 +2200,6 @@ sub blast {</td>
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<td class="diff-line-num old_line" data-linenumber="2178" 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">
2178
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<td class="diff-line-num new_line" data-linenumber="2200" 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">
2200
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<pre style="margin: 0;"> <span id="LC2200" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$debug</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$verbose</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$command</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span> <span class="c1" style="color: #998; font-style: italic;"># 5.16</span></span>
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<td class="diff-line-num old_line" data-linenumber="2179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2179
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<td class="diff-line-num new_line" data-linenumber="2201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2201
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<pre style="margin: 0;"> <span id="LC2201" class="line" lang="perl"></span>
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<td class="diff-line-num old_line" data-linenumber="2180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2180
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<td class="diff-line-num new_line" data-linenumber="2202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2202
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<pre style="margin: 0;"> <span id="LC2202" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">diamond</span><span class="p">")</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2181" 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">
2181
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<td class="diff-line-num new_line old" data-linenumber="2203" 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="LC2181" class="line" lang="perl"></span>
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<td class="diff-line-num old_line" data-linenumber="2182" 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">
2182
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<td class="diff-line-num new_line" data-linenumber="2203" 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">
2203
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<pre style="margin: 0;"> <span id="LC2203" class="line" lang="perl"> <span class="nv" style="color: #008080;">@data</span><span class="o" style="font-weight: 600;">=</span><span class="p">`</span><span class="si" style="color: #d14;">$command</span><span class="p">`;</span> <span class="c1" style="color: #998; font-style: italic;"># run diamond</span></span>
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<td class="diff-line-num old_line" data-linenumber="2183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2183
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<td class="diff-line-num new_line" data-linenumber="2204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2204
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<pre style="margin: 0;"> <span id="LC2204" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span><span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">Error</span><span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> failed with code $?.</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> (Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Code)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">The most common sources of this error are:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- no space left on device error.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- outdated </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">, please update </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;"> or consider another -p algorithm.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- the databases are missing. Maybe you ran --step=1 and removed the databases afterwards? Please rerun 'proteinortho --step=1 --force /path/to/fastas'</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- maybe the fasta files are mixed nucleotide and aminoacid sequences or just not suited for </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">? (For example diamond only processes protein sequences) Try 'proteinortho --step=1 --check --force /path/to/fastas'.</span><span class="p">");}</span></span>
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<td class="diff-line-num old_line" data-linenumber="2184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2184
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<td class="diff-line-num new_line" data-linenumber="2205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2205
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<pre style="margin: 0;"> <span id="LC2205" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$debug</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">test_sort</span><span class="p">"){</span><span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="o" style="font-weight: 600;"><</span><span class="p">"</span><span class="si" style="color: #d14;">$bla</span><span class="s2" style="color: #d14;">.tmp</span><span class="p">"</span><span class="o" style="font-weight: 600;">></span><span class="p">){</span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$_</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/[^\t]+([,])[^\t]+[eE]/</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="s2" style="color: #d14;">found forbidden symbol '$1' at </span><span class="si" style="color: #d14;">$_</span><span class="s2" style="color: #d14;"> in </span><span class="si" style="color: #d14;">$bla</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span><span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">reset_locale</span><span class="p">();</span><span class="nb" style="color: #0086b3;">die</span><span class="p">;}}}</span></span>
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<li id="ba368ee46e511166051985e745eaa37aea49d150">
<a href="https://salsa.debian.org/med-team/proteinortho/-/commit/3c35c1d73608e5ddc79f68abf3524b8a4d1e57ba#ba368ee46e511166051985e745eaa37aea49d150"><strong>src/proteinortho_clustering.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="276" 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="276" 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">@@ -276,7 +276,7 @@ size_t getCurrentRSS( )</td>
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Main</span></span>
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">///////////////////////////////////////////////////////////</span></span>
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278
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">printHelp</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC279" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"proteinortho_clustering - Spectral partitioning algorithm (v6.0.6)"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"proteinortho_clustering - Spectral partitioning algorithm (<span class="idiff left right">last updated with proteinortho </span>v6.0.6)"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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280
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<pre style="margin: 0;"> <span id="LC280" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"-----------------------------------------------------"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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281
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"This tool is part of Proteinortho"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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282
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1851" 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="1851" 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">@@ -1851,7 +1851,7 @@ void splitGroups(vector<floattype>& y, vector<unsigned int>& nodes , bool useLap</td>
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1851
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1851
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<pre style="margin: 0;"> <span id="LC1851" class="line" lang="cpp"> <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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1852
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<pre style="margin: 0;"> <span id="LC1852" class="line" lang="cpp"> <span class="nl">do_normalPartitionAlgorithm:</span></span>
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1853
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1853
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<pre style="margin: 0;"> <span id="LC1853" class="line" lang="cpp"></span>
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1854
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<pre style="margin: 0;">-<span id="LC1854" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">debug_level</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">getTime</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" [DEBUG] perfoming a normal split of "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">nodes</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" nodes"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1854" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">debug_level</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">getTime</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" [DEBUG] perfo<span class="idiff left right">r</span>ming a normal split of "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">nodes</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" nodes"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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1855
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<pre style="margin: 0;"> <span id="LC1855" class="line" lang="cpp"></span>
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1856
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1856
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<pre style="margin: 0;"> <span id="LC1856" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Store data about two groups (Zero cannot be assigned with certainty)</span></span>
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1857
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1857
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<pre style="margin: 0;"> <span id="LC1857" class="line" lang="cpp"> <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">bool</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">groupA</span><span class="p">,</span> <span class="n" style="color: #333;">groupB</span><span class="p">,</span> <span class="n" style="color: #333;">groupZero</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1869" 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="1869" 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">@@ -1869,7 +1869,7 @@ void splitGroups(vector<floattype>& y, vector<unsigned int>& nodes , bool useLap</td>
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1869
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1869
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<pre style="margin: 0;"> <span id="LC1869" class="line" lang="cpp"> <span class="p">}</span></span>
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1870
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1870
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<pre style="margin: 0;"> <span id="LC1870" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="p">(</span><span class="n" style="color: #333;">groupA</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">groupB</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">){</span></span>
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<pre style="margin: 0;"> <span id="LC1871" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">-<span id="LC1872" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" [WARNING] All nodes are below the purty threshold. Continue without purity."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1872" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" [WARNING] All nodes are below the pur<span class="idiff left right">i</span>ty threshold. Continue without purity."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1873" class="line" lang="cpp"></span>
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1874
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<pre style="margin: 0;"> <span id="LC1874" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">y</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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1875
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<pre style="margin: 0;"> <span id="LC1875" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<a href="https://salsa.debian.org/med-team/proteinortho/-/commit/3c35c1d73608e5ddc79f68abf3524b8a4d1e57ba#62a037ff19b968a55076fe8ec1b004721c460a70"><strong>src/proteinortho_clustering_nolapack.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1611" 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">@@ -1611,7 +1611,7 @@ void splitGroups(vector<floattype>& y, vector<unsigned int>& nodes , bool useLap</td>
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1611
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1611
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<pre style="margin: 0;"> <span id="LC1611" class="line" lang="cpp"> <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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1612
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1612
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<pre style="margin: 0;"> <span id="LC1612" class="line" lang="cpp"> <span class="nl">do_normalPartitionAlgorithm:</span></span>
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1613
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1613
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<pre style="margin: 0;"> <span id="LC1613" class="line" lang="cpp"></span>
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1614
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<pre style="margin: 0;">-<span id="LC1614" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">debug_level</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">getTime</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" [DEBUG] perfoming a normal split of "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">nodes</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" nodes"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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1614
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<pre style="margin: 0;">+<span id="LC1614" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">debug_level</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">getTime</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" [DEBUG] perfo<span class="idiff left right">r</span>ming a normal split of "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">nodes</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" nodes"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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1615
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1615
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<pre style="margin: 0;"> <span id="LC1615" class="line" lang="cpp"></span>
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1616
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1616
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<pre style="margin: 0;"> <span id="LC1616" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Store data about two groups (Zero cannot be assigned with certainty)</span></span>
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1617
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1617
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<pre style="margin: 0;"> <span id="LC1617" class="line" lang="cpp"> <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">bool</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">groupA</span><span class="p">,</span> <span class="n" style="color: #333;">groupB</span><span class="p">,</span> <span class="n" style="color: #333;">groupZero</span><span class="p">;</span></span>
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