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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/phyx">Debian Med / phyx</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/phyx/commit/2171679eced012e59677fcc6d251ac021aedaf59">2171679e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-09-08T20:20:49Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix linking
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/phyx/commit/db665cb41e8002a35f33edd6338f1d23955f7136">db665cb4</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-09-08T20:22:01Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Respect DEB_BUILD_OPTIONS in override_dh_auto_test
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/phyx/commit/61cf7af73fbd1714b7c60e36d8b0565f90dd3b9b">61cf7af7</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-09-08T20:22:33Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/phyx/commit/33487a469ff5d53c3dd8754124aabdaa266c5b0c">33487a46</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-09-08T20:26:11Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.2.1
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/phyx/commit/09ddc84098b1894368f5cc12673bc21be001799a">09ddc840</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-09-08T20:26:52Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add myself to Uploaders
</pre>
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<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#0e851bd9762dc8b6b479bde9cdff0e089eb7d986">
<span class="new-file">
+
debian/patches/link_lnlopt.patch
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<span class="new-file">
+
debian/patches/series
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</a>
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/phyx/compare/08d24ff6d2a69cc83c8237562f5834935c3ddfc4...09ddc84098b1894368f5cc12673bc21be001799a#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2" 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">@@ -2,4 +2,4 @@ phyx (0.99+ds-1) unstable; urgency=medium</td>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> * Initial release (Closes: #855597)</span>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> -- A<span class="idiff left right">fif Elghraoui <afif@debian.org> Fri, 01 Jun 2018 11:30:27</span> +0200</span></pre>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- A<span class="idiff left right">ndreas Tille <tille@debian.org> Sat, 08 Sep 2018 22:16:39</span> +0200</span></pre>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/phyx/compare/08d24ff6d2a69cc83c8237562f5834935c3ddfc4...09ddc84098b1894368f5cc12673bc21be001799a#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Source: phyx</span>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Uploaders: Afif Elghraoui <afif@debian.org></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Uploaders: Afif Elghraoui <afif@debian.org>,</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Section: science</span>
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<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Priority: optional</span>
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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper (>= 11~),</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -10,7 +11,7 @@ Build-Depends: debhelper (>= 11~),</td>
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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> libnlopt-dev,</span>
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<td class="diff-line-num new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> libatlas-cpp-0.6-dev,</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> libarmadillo-dev</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">1.4</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">2.1</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/phyx</span>
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15
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/phyx.git</span>
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<td class="diff-line-num 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">
16
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<td class="diff-line-num new_line" data-linenumber="17" 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">
17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Homepage: https://github.com/FePhyFoFum/phyx</span>
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<li id="0e851bd9762dc8b6b479bde9cdff0e089eb7d986">
<a href="https://salsa.debian.org/med-team/phyx/compare/08d24ff6d2a69cc83c8237562f5834935c3ddfc4...09ddc84098b1894368f5cc12673bc21be001799a#0e851bd9762dc8b6b479bde9cdff0e089eb7d986"><strong>debian/patches/link_lnlopt.patch</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Author: Andreas Tille <tille@debian.org></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Last-Update: Sat, 08 Sep 2018 22:16:39 +0200</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Description: Somehow nlopt library needs to be added</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/Makefile.in</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/Makefile.in</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -317,7 +317,7 @@ all: pxmrca pxmrcacut pxmrcaname pxconsq</span></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="diff"> </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="diff"> pxstrec: $(CPP_OBJS) $(RATE_OBJS) $(STREC_OBJ) #$(FORT_OBJS)</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> @echo 'building pxstrec'</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) -o "pxstrec" $(OPT_FLAGS) $(STREC_OBJ) $(CPP_OBJS) $(RATE_OBJS) $(CPP_LIBS) #$(FORT_OBJS) -lgfortran</span></span>
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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CXX) -o "pxstrec" $(OPT_FLAGS) $(STREC_OBJ) $(CPP_OBJS) $(RATE_OBJS) $(CPP_LIBS) -lnlopt_cxx -lnlopt #$(FORT_OBJS) -lgfortran</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"> pxmrca: $(CPP_OBJS) $(MRCA_OBJ)</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> @echo 'building pxmrca'</span>
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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -417,7 +417,7 @@ pxboot: $(CPP_OBJS) $(SEQSAMP_OBJ)</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> pxseqgen: $(CPP_OBJS) $(RATE_OBJS) $(SEQGEN_OBJ) $(FORT_OBJS)</span>
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<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> @echo 'building pxseqgen'</span>
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<td class="diff-line-num new new_line" data-linenumber="20" 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="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(CXX) -o "pxseqgen" $(OPT_FLAGS) $(SEQGEN_OBJ) $(CPP_OBJS) $(RATE_OBJS) $(CPP_LIBS) #$(FORT_OBJS) -lgfortran</span></span>
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<td class="diff-line-num new new_line" data-linenumber="21" 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="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CXX) -o "pxseqgen" $(OPT_FLAGS) $(SEQGEN_OBJ) $(CPP_OBJS) $(RATE_OBJS) $(CPP_LIBS) -lnlopt_cxx -lnlopt #$(FORT_OBJS) -lgfortran</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> </span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> pxcat: $(CPP_OBJS) $(CONCAT_OBJ)</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> @echo 'building pxcat'</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -433,7 +433,7 @@ pxvcf2fa: $(CPP_OBJS) $(VCF2FA_OBJ)</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="27" 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">
27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> pxcontrates: $(CPP_OBJS) $(CONTRATES_OBJ) $(RATE_OBJS) $(FORT_OBJS)</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> @echo 'building pxcontrates'</span>
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<td class="diff-line-num new new_line" data-linenumber="29" 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">
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) -o "pxcontrates" $(OPT_FLAGS) $(CONTRATES_OBJ) $(RATE_OBJS) $(CPP_OBJS) $(CPP_LIBS) #$(FORT_OBJS) -lgfortran</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) -o "pxcontrates" $(OPT_FLAGS) $(CONTRATES_OBJ) $(RATE_OBJS) $(CPP_OBJS) $(CPP_LIBS) -lnlopt_cxx -lnlopt #$(FORT_OBJS) -lgfortran</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> </span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> pxrecode: $(CPP_OBJS) $(SEQRECODE_OBJ)</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> @echo 'building pxrecode'</span></pre>
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<a href="https://salsa.debian.org/med-team/phyx/compare/08d24ff6d2a69cc83c8237562f5834935c3ddfc4...09ddc84098b1894368f5cc12673bc21be001799a#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">link_lnlopt.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/phyx/compare/08d24ff6d2a69cc83c8237562f5834935c3ddfc4...09ddc84098b1894368f5cc12673bc21be001799a#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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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">@@ -9,7 +9,9 @@ include /usr/share/dpkg/default.mk</td>
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9
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> dh $@ --sourcedirectory=src</span>
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10
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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11
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">override_dh_auto_test:</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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12
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> cd src && python run_tests.py</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">endif</span>
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13
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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14
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">override_dh_auto_install:</span>
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15
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> mkdir -p $(CURDIR)/debian/$(DEB_SOURCE)/usr/bin</span>
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