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<h3>
Michael R. Crusoe pushed to branch master
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/5746795e771ab3e7995f85a9b3e8bc134b169312">5746795e</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-01-13T11:47:23+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use #!/usr/bin/python3 (fixes autopkgtests)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/proteinortho/commit/49c17dfff9440aef1aa3d99985774409525e3dbd">49c17dff</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-01-13T11:51:32+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">make the build verbose
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/proteinortho/commit/04badf7b7a386cb4dab1517259e6e2c4c9c50ac7">04badf7b</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-01-13T12:38:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fix dependencies
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/proteinortho/commit/9e86b453a761871aa76e132b6d248bc25d12b9c3">9e86b453</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-01-13T12:38:53+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">patch: Find the packaged version of the Diamond aligner
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/proteinortho/commit/5a2b69a0d536e9d1b5503ff00bd18e2890c877d7">5a2b69a0</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-01-13T12:38:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">patch: Improve build hardening via CPPFLAGS & CFLAGS
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/proteinortho/commit/c5f545a501a4fe4aaa4bab4ce2be6ca8f0730dff">c5f545a5</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-01-13T12:38:55+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Expanded autopkgtests, following `make test`
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/proteinortho/commit/8bd53f4ec549644c227505d3cb010a7e6cd22ba9">8bd53f4e</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-01-13T12:38:55+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">patch: fix a spelling typo
</pre>
</li>
</ul>
<h4>9 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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</li>
<li class="file-stats">
<a href="#d7195c08d6c1cbdc57ce147094855c0ede6279ae">
<span class="new-file">
+
debian/patches/deb_diamond
</span>
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</li>
<li class="file-stats">
<a href="#d6c09299b1f914372840e8fd6fcc850f8a11b236">
<span class="new-file">
+
debian/patches/hardening
</span>
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<li class="file-stats">
<a href="#0a4e986b60a9240ca7d53abf5e2ed246987e8ffc">
<span class="new-file">
+
debian/patches/python3
</span>
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</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<span class="new-file">
+
debian/patches/series
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</li>
<li class="file-stats">
<a href="#e4c19aed51618bf0c7ebd03189c67e422f84d4eb">
<span class="new-file">
+
debian/patches/spelling
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<li class="file-stats">
<a href="#85ccdeeb03055211183e48520592d9a93592b330">
<span class="deleted-file">
−
debian/source/lintian-overrides
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</a>
</li>
<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/proteinortho/compare/13769eacc3e4da13660bc5ec7f5ea9010ee67fb8...8bd53f4ec549644c227505d3cb010a7e6cd22ba9#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">proteinortho (6.0.12+dfsg-2) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="3" 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="LC3" class="line" lang="plaintext"> * Team upload.</span>
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<td class="diff-line-num new new_line" data-linenumber="4" 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="LC4" class="line" lang="plaintext"> * patch: Use #!/usr/bin/python3 (fixes autopkgtests)</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * patch: Find the packaged version of the Diamond aligner</span>
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<td class="diff-line-num new new_line" data-linenumber="6" 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="LC6" class="line" lang="plaintext"> * patch: Improve build hardening via CPPFLAGS & CFLAGS</span>
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<td class="diff-line-num new new_line" data-linenumber="7" 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="LC7" class="line" lang="plaintext"> * Expanded autopkgtests, following `make test`</span>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * patch: fix a spelling typo</span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> -- Michael R. Crusoe <michael.crusoe@gmail.com> Mon, 13 Jan 2020 11:45:52 +0100</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">proteinortho (6.0.12+dfsg-1) unstable; urgency=medium</span>
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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> * Team upload.</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/proteinortho/compare/13769eacc3e4da13660bc5ec7f5ea9010ee67fb8...8bd53f4ec549644c227505d3cb010a7e6cd22ba9#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,7 +6,8 @@ Priority: optional</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 12),</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> ncbi-blast+,</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> liblapack-dev | libatlas-base-dev | liblapack.so,</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> diamond-aligner</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> diamond-aligner,</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> procps</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Standards-Version: 4.4.1</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/proteinortho</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/proteinortho.git</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -16,10 +17,12 @@ Package: proteinortho</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"> ${python3:Depends},</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> ${perl:Depends},</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> python3,</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> ncbi-blast+,</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> diamond-aligner,</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"> liblapack3</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> liblapack3,</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> procps</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">Description: Detection of (Co-)orthologs in large-scale protein analysis</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> Proteinortho is a stand-alone tool that is geared towards large datasets</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> and makes use of distributed computing techniques when run on multi-core</span>
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<li id="d7195c08d6c1cbdc57ce147094855c0ede6279ae">
<a href="https://salsa.debian.org/med-team/proteinortho/compare/13769eacc3e4da13660bc5ec7f5ea9010ee67fb8...8bd53f4ec549644c227505d3cb010a7e6cd22ba9#d7195c08d6c1cbdc57ce147094855c0ede6279ae"><strong>debian/patches/deb_diamond</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Michael R. Crusoe <michael.crusoe@gmail.com></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Description: Find some Debian packaged software under their original names</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- proteinortho.orig/proteinortho6.pl</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ proteinortho/proteinortho6.pl</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">@@ -535,6 +535,9 @@</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> $NC="";</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# Find some Debian packaged software under their original names</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+$ENV{PATH} = "$ENV{PATH}:/usr/lib/debian-med/bin";</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> ##########################################################################################</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> # Parameters</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> ##########################################################################################</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- proteinortho.orig/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ proteinortho/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="p">@@ -265,7 +265,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> fi</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> @echo -n " [3/12] -p=diamond test: "</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @if [ "$(shell which diamond)" = "" ]; then\</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ @if [ "$(shell which diamond-aligner)" = "" ]; then\</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> echo "$(ORANGE)diamond missing, skipping...$(NC)"; \</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> else \</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> ./proteinortho6.pl -silent -force -project=test_diamond -p=diamond test/*.faa; \</span></pre>
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<a href="https://salsa.debian.org/med-team/proteinortho/compare/13769eacc3e4da13660bc5ec7f5ea9010ee67fb8...8bd53f4ec549644c227505d3cb010a7e6cd22ba9#d6c09299b1f914372840e8fd6fcc850f8a11b236"><strong>debian/patches/hardening</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">From: Michael R. Crusoe <michael.crusoe@gmail.com></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Subject: Add CPPFLAGS & CFLAGS</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff">And make the build more verbose so we can confirm this.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- proteinortho.orig/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ proteinortho/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -152,13 +152,13 @@</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> ifeq ($(USEPRECOMPILEDLAPACK),TRUE)</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> ifeq ($(STATIC),TRUE)</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> @echo "[ 20%] Building **proteinortho_clustering** with LAPACK (static linking)";</span>
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @$(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -static -Wl,--allow-multiple-definition -llapack -lblas -lgfortran -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -lquadmath && ([ $$? -eq 0 ] ) || ( \</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -static -Wl,--allow-multiple-definition -llapack -lblas -lgfortran -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -lquadmath && ([ $$? -eq 0 ] ) || ( \</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> echo "......$(ORANGE)static linking failed, now I try dynamic linking.$(NC)"; \</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive && ([ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive && ([ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> echo "......$(ORANGE)dynamic linking failed too, now I try dynamic linking without -WL,-whole-archive (this should now work for OSX).$(NC)"; \</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -lpthread && ([ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -lpthread && ([ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> echo "......$(ORANGE)dynamic linking failed (without -WL,-whole-archive) too too, now I try to openblas.$(NC)"; \</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -lopenblas -pthread -lpthread && ([ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -lopenblas -pthread -lpthread && ([ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> echo "......$(ORANGE)last linking failed too too too, now I try to recompile lapack (v.3.8.0) and then compile proteinortho_clustering with dynamic linking.$(NC)"; \</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> echo "......[ 33%] Extracting the LAPACK library"; \</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> if [ ! -d src/lapack-3.8.0 ]; then cd src; tar -xzvf lapack-3.8.0.tar.gz > /dev/null 2>&1; cd ..; fi; \</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="p">@@ -168,18 +168,18 @@</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> $(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp -o $@ $< -Isrc/lapack-3.8.0/build/include/ -Lsrc/lapack-3.8.0/build/lib/ -llapack -lblas $(LDFLAGS) $(LDLIBS) -lgfortran && echo "......OK dynamic linking was successful for proteinortho_clustering!" || ( echo "" ) ; ) ) ) )</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> else</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> @echo "[ 20%] Building **proteinortho_clustering** with LAPACK (dynamic linking)";</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @$(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive && ([ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive && ([ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> echo "......$(ORANGE)dynamic linking failed too, now I try dynamic linking without -WL,-whole-archive (this should now work for OSX).$(NC)"; \</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -lpthread && ([ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -lpthread && ([ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> echo "......$(ORANGE)dynamic linking failed (without -WL,-whole-archive) too too, now I try to openblas.$(NC)"; \</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -lopenblas -pthread -lpthread && ([ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -lopenblas -pthread -lpthread && ([ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> echo "......$(ORANGE)last linking failed too too too, now I try to recompile lapack (v.3.8.0) and then compile proteinortho_clustering with dynamic linking.$(NC)"; \</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> echo "......[ 33%] Extracting the LAPACK library"; \</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> if [ ! -d src/lapack-3.8.0 ]; then cd src; tar -xzvf lapack-3.8.0.tar.gz > /dev/null 2>&1; cd ..; fi; \</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> echo "......[ 66%] Compiling the LAPACK library (using cmake + make)"; \</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> if [ ! -f src/lapack-3.8.0/build/lib/liblapack.a ]; then mkdir src/lapack-3.8.0/build 2> /dev/null; cd src/lapack-3.8.0/build; cmake .. -DCMAKE_CXX_COMPILER=$(CXX) > /dev/null; make all -j4 > /dev/null 2>&1; cd ../../.. ; fi; \</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> echo "......[ 99%] Building **proteinortho_clustering** with LAPACK (dynamic linking)"; \</span>
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<td class="diff-line-num new new_line" data-linenumber="43" 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="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp -o $@ $< -Isrc/lapack-3.8.0/build/include/ -Lsrc/lapack-3.8.0/build/lib/ -llapack -lblas $(LDFLAGS) $(LDLIBS) -lgfortran && echo "......OK dynamic linking was successful for proteinortho_clustering!" || ( echo "" ) ; ) ) )</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp -o $@ $< -Isrc/lapack-3.8.0/build/include/ -Lsrc/lapack-3.8.0/build/lib/ -llapack -lblas $(LDFLAGS) $(LDLIBS) -lgfortran && echo "......OK dynamic linking was successful for proteinortho_clustering!" || ( echo "" ) ; ) ) )</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> endif</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> @if [ ! -e $(BUILDDIR)/proteinortho_clustering ]; then echo "proteinortho_clustering compilation failed. Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Codes"; false; fi</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> else</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="p">@@ -188,47 +188,47 @@</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> @echo "[ 18%] Compiling the LAPACK library (using cmake + make)";</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> @if [ ! -f src/lapack-3.8.0/build/lib/liblapack.a ]; then mkdir src/lapack-3.8.0/build; cd src/lapack-3.8.0/build; cmake .. -DCMAKE_CXX_COMPILER=$(CXX) > /dev/null 2>&1; make all -j4 > /dev/null 2>&1; cd ../../.. ; fi;</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> @echo "[ 20%] Building **proteinortho_clustering** with LAPACK (dynamic linking)";</span>
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<td class="diff-line-num new new_line" data-linenumber="52" 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">
52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @$(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp -o $@ $< -Isrc/lapack-3.8.0/build/include/ -Lsrc/lapack-3.8.0/build/lib/ -llapack -lblas $(LDFLAGS) $(LDLIBS) -lgfortran;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="53" 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">
53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp -o $@ $< -Isrc/lapack-3.8.0/build/include/ -Lsrc/lapack-3.8.0/build/lib/ -llapack -lblas $(LDFLAGS) $(LDLIBS) -lgfortran;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> endif</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> endif</span>
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<td class="diff-line-num new new_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> ifeq ($(USELAPACK),FALSE)</span>
</pre>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> @echo "[ 20%] Building **proteinortho_clustering** WITHOUT(!) LAPACK";</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="58" 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">
58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @$(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp -o $@ src/proteinortho_clustering_nolapack.cpp $(LDFLAGS) $(LDLIBS) -static && ([ $$? -eq 0 ] ) || ( \</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp -o $@ src/proteinortho_clustering_nolapack.cpp $(LDFLAGS) $(LDLIBS) -static && ([ $$? -eq 0 ] ) || ( \</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> echo "......$(ORANGE)static linking failed of proteinortho_clustering_nolapack, now i switch to dynamic linking.$(NC)"; \</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="61" 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">
61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp -o $@ src/proteinortho_clustering_nolapack.cpp $(LDFLAGS) $(LDLIBS) && echo "......OK dynamic linking was successful for proteinortho_clustering_nolapack!"; )</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="62" 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">
62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp -o $@ src/proteinortho_clustering_nolapack.cpp $(LDFLAGS) $(LDLIBS) && echo "......OK dynamic linking was successful for proteinortho_clustering_nolapack!"; )</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> endif</span>
</pre>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> </span>
</pre>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> $(BUILDDIR)/proteinortho_cleanupblastgraph: src/cleanupblastgraph.cpp</span>
</pre>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> $(dir_guard)</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> @echo "[ 50%] Building **cleanupblastgraph**"</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> ifeq ($(STATIC),TRUE)</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="69" 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">
69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @$(CXX) -std=c++11 $(CXXFLAGS) $(CXXFLAGS_PO) -o $@ $< $(LDFLAGS) $(LDLIBS) -static && ([ $$? -eq 0 ] ) || ( \</span></span>
</pre>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CXX) -std=c++11 $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -o $@ $< $(LDFLAGS) $(LDLIBS) -static && ([ $$? -eq 0 ] ) || ( \</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="71" 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">
71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> echo "......$(ORANGE)static linking failed of cleanupblastgraph, now i switch to dynamic linking.$(NC)"; \</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="72" 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">
72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -o $@ $< && echo "......OK dynamic linking was successful of cleanupblastgraph!"; )</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="73" 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">
73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -o $@ $< && echo "......OK dynamic linking was successful of cleanupblastgraph!"; )</span></span>
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<td class="diff-line-num new new_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> else</span>
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<td class="diff-line-num new new_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @$(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -o $@ $< $(LDFLAGS) $(LDLIBS)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="76" 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">
76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -o $@ $< $(LDFLAGS) $(LDLIBS)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="77" 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">
77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"> endif</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="79" 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">
79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"> $(BUILDDIR)/proteinortho_graphMinusRemovegraph: src/graphMinusRemovegraph.cpp</span>
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<td class="diff-line-num new new_line" data-linenumber="80" 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">
80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> $(dir_guard)</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"> @echo "[ 25%] Building **graphMinusRemovegraph**"</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"> ifeq ($(STATIC),TRUE)</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="83" 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">
83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @$(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -o $@ $< $(LDFLAGS) $(LDLIBS) -static && ([ $$? -eq 0 ] ) || ( \</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -o $@ $< $(LDFLAGS) $(LDLIBS) -static && ([ $$? -eq 0 ] ) || ( \</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="85" 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">
85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> echo "......$(ORANGE)static linking failed of graphMinusRemovegraph, now i switch to dynamic linking.$(NC)"; \</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="86" 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">
86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -o $@ $< && echo "......OK dynamic linking was successful of graphMinusRemovegraph!"; )</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="87" 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">
87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -o $@ $< && echo "......OK dynamic linking was successful of graphMinusRemovegraph!"; )</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> else</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
89
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @$(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -o $@ $< $(LDFLAGS) $(LDLIBS)</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="90" 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">
90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -o $@ $< $(LDFLAGS) $(LDLIBS)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="91" 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">
91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"> endif</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="92" 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">
92
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="93" 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">
93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> $(BUILDDIR)/proteinortho_treeBuilderCore: src/po_tree.c</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="94" 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">
94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"> $(dir_guard)</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
95
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"> @echo "[ 75%] Building **po_tree**"</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"> ifeq ($(STATIC),TRUE)</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="97" 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">
97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @$(CC) $(CCFLAGS) -o $@ $< $(LDFLAGS) $(LDLIBS) -static && ([ $$? -eq 0 ] ) || ( \</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CC) $(CPPFLAGS) $(CCFLAGS) $(CFLAGS) -o $@ $< $(LDFLAGS) $(LDLIBS) -static && ([ $$? -eq 0 ] ) || ( \</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"> echo "......$(ORANGE)static linking failed of po_tree, now i switch to dynamic linking.$(NC)"; \</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(CC) $(CCFLAGS) -o $@ $< && echo "......OK dynamic linking was successful of po_tree!"; )</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CC) $(CPPFLAGS) $(CCFLAGS) $(CFLAGS) -o $@ $< && echo "......OK dynamic linking was successful of po_tree!"; )</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"> else</span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @$(CC) $(CCFLAGS) -o $@ $< $(LDFLAGS) $(LDLIBS)</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CC) $(CPPFLAGS) $(CCFLAGS) $(CFLAGS) -o $@ $< $(LDFLAGS) $(LDLIBS)</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"> endif</span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"> </span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"> .PHONY: install</span></pre>
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<a href="https://salsa.debian.org/med-team/proteinortho/compare/13769eacc3e4da13660bc5ec7f5ea9010ee67fb8...8bd53f4ec549644c227505d3cb010a7e6cd22ba9#0a4e986b60a9240ca7d53abf5e2ed246987e8ffc"><strong>debian/patches/python3</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">From: Michael R. Crusoe <michael.crusoe@gmail.com></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Description: For Debian, we are only supporting Python version 3</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- proteinortho.orig/src/proteinortho_ffadj_mcs.py</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ proteinortho/src/proteinortho_ffadj_mcs.py</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> from sys import stderr, exit, argv, maxsize</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> from copy import deepcopy</span></pre>
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<a href="https://salsa.debian.org/med-team/proteinortho/compare/13769eacc3e4da13660bc5ec7f5ea9010ee67fb8...8bd53f4ec549644c227505d3cb010a7e6cd22ba9#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">python3</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">hardening</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">deb_diamond</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">spelling</span></pre>
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<a href="https://salsa.debian.org/med-team/proteinortho/compare/13769eacc3e4da13660bc5ec7f5ea9010ee67fb8...8bd53f4ec549644c227505d3cb010a7e6cd22ba9#e4c19aed51618bf0c7ebd03189c67e422f84d4eb"><strong>debian/patches/spelling</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">From: Michael R. Crusoe <michael.crusoe@gmail.com></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Subject: Fix a typo</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff">Found via Debian's "lintian"</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- proteinortho.orig/src/proteinortho_clustering.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ proteinortho/src/proteinortho_clustering.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -1851,7 +1851,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> }else{</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> do_normalPartitionAlgorithm:</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if (debug_level > 0) cerr << getTime() << " [DEBUG] perfoming a normal split of " << nodes.size()<< " nodes" << endl;</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (debug_level > 0) cerr << getTime() << " [DEBUG] performing a normal split of " << nodes.size()<< " nodes" << endl;</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> // Store data about two groups (Zero cannot be assigned with certainty)</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> map<unsigned int,bool> groupA, groupB, groupZero;</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- proteinortho.orig/src/proteinortho_clustering_nolapack.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ proteinortho/src/proteinortho_clustering_nolapack.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="p">@@ -1611,7 +1611,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> }else{</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> do_normalPartitionAlgorithm:</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if (debug_level > 0) cerr << getTime() << " [DEBUG] perfoming a normal split of " << nodes.size()<< " nodes" << endl;</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (debug_level > 0) cerr << getTime() << " [DEBUG] performing a normal split of " << nodes.size()<< " nodes" << endl;</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> // Store data about two groups (Zero cannot be assigned with certainty)</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> map<unsigned int,bool> groupA, groupB, groupZero;</span></pre>
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<a href="https://salsa.debian.org/med-team/proteinortho/compare/13769eacc3e4da13660bc5ec7f5ea9010ee67fb8...8bd53f4ec549644c227505d3cb010a7e6cd22ba9#85ccdeeb03055211183e48520592d9a93592b330"><strong>debian/source/lintian-overrides</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">proteinortho source: python3-depends-but-no-python3-helper proteinortho</span></pre>
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<a href="https://salsa.debian.org/med-team/proteinortho/compare/13769eacc3e4da13660bc5ec7f5ea9010ee67fb8...8bd53f4ec549644c227505d3cb010a7e6cd22ba9#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</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">@@ -13,7 +13,57 @@ mkdir test</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/examples/<span class="k" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">test</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">gunzip</span> <span class="nt" style="color: #000080;">-r</span> <span class="k" style="font-weight: 600;">*</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="shell">proteinortho <span class="nt" style="color: #000080;">-project</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">test</span> <span class="nt" style="color: #000080;">-synteny</span> <span class="nt" style="color: #000080;">-singles</span> <span class="nb" style="color: #0086b3;">test</span>/<span class="k" style="font-weight: 600;">*</span>.faa</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="shell">./test/chk_test.pl test.proteinortho.tsv</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="shell">./test/chk_test.pl test.poff.tsv</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell">proteinortho <span class="nt" style="color: #000080;">-force</span> <span class="nt" style="color: #000080;">-project</span><span class="o" style="font-weight: 600;">=</span>test_blastp <span class="nt" style="color: #000080;">-p</span><span class="o" style="font-weight: 600;">=</span>blastp+ <span class="nb" style="color: #0086b3;">test</span>/<span class="k" style="font-weight: 600;">*</span>.faa</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell">./test/chk_test.pl test_blastp.proteinortho.tsv</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell">proteinortho <span class="nt" style="color: #000080;">-force</span> <span class="nt" style="color: #000080;">-project</span><span class="o" style="font-weight: 600;">=</span>test_synteny <span class="nt" style="color: #000080;">-synteny</span> <span class="nt" style="color: #000080;">-singles</span> <span class="nt" style="color: #000080;">-p</span><span class="o" style="font-weight: 600;">=</span>blastp+ <span class="nb" style="color: #0086b3;">test</span>/<span class="k" style="font-weight: 600;">*</span>.faa</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell">./test/chk_test.pl test_synteny.proteinortho.tsv</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell">./test/chk_test.pl test_synteny.poff.tsv</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell">proteinortho <span class="nt" style="color: #000080;">-force</span> <span class="nt" style="color: #000080;">-project</span><span class="o" style="font-weight: 600;">=</span>test_diamond <span class="nt" style="color: #000080;">-p</span><span class="o" style="font-weight: 600;">=</span>diamond <span class="nb" style="color: #0086b3;">test</span>/<span class="k" style="font-weight: 600;">*</span>.faa</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell">./test/chk_test.pl test_diamond.proteinortho.tsv</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell">proteinortho <span class="nt" style="color: #000080;">-force</span> <span class="nt" style="color: #000080;">-project</span><span class="o" style="font-weight: 600;">=</span>test_diamondmoresensitive <span class="nt" style="color: #000080;">-p</span><span class="o" style="font-weight: 600;">=</span>diamond <span class="nt" style="color: #000080;">-subparaBlast</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"--more-sensitive"</span> <span class="nb" style="color: #0086b3;">test</span>/<span class="k" style="font-weight: 600;">*</span>.faa</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell">./test/chk_test.pl test_diamondmoresensitive.proteinortho.tsv</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Not yet packaged?</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#proteinortho -force -project=test_lastp -p=lastp test/*.faa</span></span>
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<td class="diff-line-num new new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#./test/chk_test.pl test_lastp.proteinortho.tsv</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Not yet packaged?</span></span>
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<td class="diff-line-num new new_line" data-linenumber="34" 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">
34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#proteinortho -force -project=test_topaz -p=topaz test/*.faa</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#./test/chk_test.pl test_topaz.proteinortho.tsv</span></span>
</pre>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Not yet packaged</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#proteinortho -force -project=test_usearch -p=usearch test/*.faa</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#./test/chk_test.pl test_usearch.proteinortho.tsv</span></span>
</pre>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="shell"></span>
</pre>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Not yet packaged?</span></span>
</pre>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#proteinortho -force -project=test_ublast -p=ublast test/*.faa</span></span>
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<td class="diff-line-num new new_line" data-linenumber="43" 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">
43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#./test/chk_test.pl test_ublast.proteinortho.tsv</span></span>
</pre>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="shell"></span>
</pre>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Not yet packaged?</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="46" 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">
46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#proteinortho -force -project=test_rapsearch -p=rapsearch test/*.faa</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="47" 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">
47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#./test/chk_test.pl test_rapsearch.proteinortho.tsv</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="48" 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">
48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="shell"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="49" 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">
49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Not yet packaged?</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="50" 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">
50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#proteinortho -force -project=test_blatp -p=blatp test/*.faa</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="51" 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="LC51" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#./test/chk_test.pl test_blatp.proteinortho.tsv</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="shell"></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Not yet packaged?</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#proteinortho -force -project=test_mmseqsp -p=mmseqsp test/*.faa</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#./test/chk_test.pl test_blatp.proteinortho.tsv</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="shell">proteinortho <span class="nt" style="color: #000080;">-force</span> <span class="nt" style="color: #000080;">-project</span><span class="o" style="font-weight: 600;">=</span>test_blastall <span class="nt" style="color: #000080;">-p</span><span class="o" style="font-weight: 600;">=</span>blastp <span class="nb" style="color: #0086b3;">test</span>/<span class="k" style="font-weight: 600;">*</span>.faa</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="shell">./test/chk_test.pl test_blastall.proteinortho.tsv</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="shell">/usr/lib/proteinortho/proteinortho_clustering <span class="nt" style="color: #000080;">-test</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Compare results of 'with lapack' and 'without lapack'</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="shell">/usr/lib/proteinortho/proteinortho_clustering <span class="nt" style="color: #000080;">-epsilon</span> 0 test_blastp.blast-graph</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="shell"><span class="nb" style="color: #0086b3;">sort </span>remove.graph <span class="nt" style="color: #000080;">-o</span> test.A</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="shell">/usr/lib/proteinortho/proteinortho_clustering <span class="nt" style="color: #000080;">-epsilon</span> 0 <span class="nt" style="color: #000080;">-lapack</span> 0 test_blastp.blast-graph</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="shell"><span class="nb" style="color: #0086b3;">sort </span>remove.graph <span class="nt" style="color: #000080;">-o</span> test.B</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="shell">diff test.A test.B</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="shell"></span>
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19
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Test okay"</span></span></pre>
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