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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/hyphy">Debian Med / hyphy</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/hyphy/commit/c81ecee53c7edc08c0e98290dfbf3be88a5e2247">c81ecee5</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-06T17:20:08Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Skip GTEST target for the moment since this is currently in flux
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/hyphy/commit/2102a5b95678a9c0fa267475d70c4c90c481c17d">2102a5b9</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-06T17:57:57Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">No need to rename executables any more since upstream is doing this now
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/hyphy/commit/7709ebf85d7ae0b9dd9448d4dfd0502c7ba87366">7709ebf8</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-06T19:43:26Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adapt to new executable names
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/hyphy/commit/df22bb6181beb43255a8a806f33c401f6df4d045">df22bb61</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-06T19:44:21Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix autopkgtest
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/hyphy/commit/6b85ea80f8d97e02e557162cf8d58f46ed618ae0">6b85ea80</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-06T21:40:18Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add NEWS.Debian to explain binary name change
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/hyphy/commit/ac1972b09eaa7e3a34ab73c8131f11727c835e2f">ac1972b0</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-06T21:47:39Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Autopkgtest exists since last release - so close bug
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/hyphy/commit/ea6108b09ab13f1a0027b8ef3d022975de518a0c">ea6108b0</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-06T21:54:33Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>7 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#08841a40e16345dc7a4307e37319e687cc49a53b">
<span class="new-file">
+
debian/NEWS.Debian.hyphy-mpi
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<li class="file-stats">
<a href="#87fb33d34686b7751b0fa7884634a159969f0bed">
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+
debian/NEWS.Debian.hyphy-pt
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#ed20f39540611f5cd66e6b51c7436454f703550a">
debian/hyphy-mpi.install
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<li class="file-stats">
<a href="#427789a3ec1530777c920a07f26044ee0498e0aa">
debian/hyphy-pt.install
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<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<li class="file-stats">
<a href="#b8880ead45e8d099a1552defb95ea70479f1572e">
debian/tests/run-unit-tests
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<h4>Changes:</h4>
<li id="08841a40e16345dc7a4307e37319e687cc49a53b">
<a href="https://salsa.debian.org/med-team/hyphy/compare/6176567316bb409c1d39967a98343e6d9b7c611d...ea6108b09ab13f1a0027b8ef3d022975de518a0c#08841a40e16345dc7a4307e37319e687cc49a53b"><strong>debian/NEWS.Debian.hyphy-mpi</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">hyphy (2.5.1+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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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"> Since version 2.5.1 the upstream names for the binaries have changed.</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"> In Debian we do not derive from upstream names any more. The executable</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> MPI executable is now</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> /usr/bin/HYPHYMPI</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Fri, 06 Dec 2019 13:30:30 +0100</span></pre>
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<li id="87fb33d34686b7751b0fa7884634a159969f0bed">
<a href="https://salsa.debian.org/med-team/hyphy/compare/6176567316bb409c1d39967a98343e6d9b7c611d...ea6108b09ab13f1a0027b8ef3d022975de518a0c#87fb33d34686b7751b0fa7884634a159969f0bed"><strong>debian/NEWS.Debian.hyphy-pt</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">hyphy (2.5.1+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> Since version 2.5.1 the upstream names for the binaries have changed.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> In Debian we do not derive from upstream names any more. The executable</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> is now</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> /usr/bin/hyphy</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Fri, 06 Dec 2019 13:30:30 +0100</span></pre>
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<a href="https://salsa.debian.org/med-team/hyphy/compare/6176567316bb409c1d39967a98343e6d9b7c611d...ea6108b09ab13f1a0027b8ef3d022975de518a0c#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">hyphy (2.5.1+dfsg-1) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">hyphy (2.5.1+dfsg-1) <span class="idiff left right">unstable</span>; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> [ Helmut Grohne ]</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * Add pkg-config to Build-Depends as FindMPI.cmake will need it for cross</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,9 +14,13 @@ hyphy (2.5.1+dfsg-1) UNRELEASED; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> * Use secure URI in Homepage field.</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> * Remove patches msse_option_only_if_available.patch that are missing</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> from debian/patches/series.</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"> TODO: Fix build failure</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> * Skip GTEST target for the moment since this is currently in flux</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> see https://github.com/veg/hyphy/issues/1058</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> * No need to rename executables any more since upstream is doing this now</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> * Autopkgtest exists since last release - so close bug</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> Closes: #909707</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Fri, 06 Dec 2019 <span class="idiff left right">13:30:30</span> +0100</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Fri, 06 Dec 2019 <span class="idiff left right">22:47:47</span> +0100</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">hyphy (2.3.14+dfsg-2) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/hyphy/compare/6176567316bb409c1d39967a98343e6d9b7c611d...ea6108b09ab13f1a0027b8ef3d022975de518a0c#ed20f39540611f5cd66e6b51c7436454f703550a"><strong>debian/hyphy-mpi.install</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="php"><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span><span class="o" style="font-weight: 600;">/<span class="idiff left">*</span></span><span class="nx"><span class="idiff right">mpi</span></span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span><span class="o" style="font-weight: 600;">/</span><span class="nx"><span class="idiff left right">HYPHYMPI</span></span></span></pre>
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<a href="https://salsa.debian.org/med-team/hyphy/compare/6176567316bb409c1d39967a98343e6d9b7c611d...ea6108b09ab13f1a0027b8ef3d022975de518a0c#427789a3ec1530777c920a07f26044ee0498e0aa"><strong>debian/hyphy-pt.install</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="php"><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span><span class="o" style="font-weight: 600;">/<span class="idiff left">*</span></span><span class="nx"><span class="idiff right">mp</span></span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span><span class="o" style="font-weight: 600;">/</span><span class="nx"><span class="idiff left right">hyphy</span></span></span></pre>
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<a href="https://salsa.debian.org/med-team/hyphy/compare/6176567316bb409c1d39967a98343e6d9b7c611d...ea6108b09ab13f1a0027b8ef3d022975de518a0c#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</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">@@ -21,19 +21,20 @@ override_dh_auto_configure:</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">override_dh_auto_build:</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> # no idea about the purpose of the dynamic library - executables are not simply linked against it</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"> dh_auto_build -- MP MPI GTEST # LIB</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> dh_auto_build -- MP MPI</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> # GTEST</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> echo "Skip GTEST target for the moment - see https://github.com/veg/hyphy/issues/1058"</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> # LIB</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">override_dh_auto_test:</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext">ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"> find obj-* -name HYPHYGTEST -exec \{\} \;</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext">endif</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext">override_dh_install:</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext"> # smallcaps for executables</span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext"> for bindir in `find . -type d -name bin` ; do \</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext"> for bin in $${bindir}/* ; do \</span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext"> # ln -s `basename $${bin}` $${bindir}/`basename $${bin} | tr [A-Z] [a-z]` ; \</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext"> mv $${bindir}/`basename $${bin}` $${bindir}/`basename $${bin} | tr [A-Z] [a-z]` ; \</span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="plaintext"> done ; \</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">override_dh_installdocs:</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> dh_installdocs</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> for news in debian/NEWS.Debian.* ; do \</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> pkg=`echo $${news} | sed 's/.*NEWS.Debian.//'` ; \</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> cp -a $${news} debian/$${pkg}/usr/share/doc/$${pkg}/NEWS.Debian ; \</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"> done</span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext"><span class="idiff left right"> dh_install</span></span></pre>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"></span></pre>
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<li id="b8880ead45e8d099a1552defb95ea70479f1572e">
<a href="https://salsa.debian.org/med-team/hyphy/compare/6176567316bb409c1d39967a98343e6d9b7c611d...ea6108b09ab13f1a0027b8ef3d022975de518a0c#b8880ead45e8d099a1552defb95ea70479f1572e"><strong>debian/tests/run-unit-tests</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">@@ -28,7 +28,7 @@ rm -f MolecularClockHKY85.bf MolecularClockF81.bf RelativeRatePBS.bf ParametricB</td>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>i <span class="k" style="font-weight: 600;">in</span> <span class="k" style="font-weight: 600;">*</span>.bf<span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="shell"> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-f</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$i</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">break</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="shell"><span class="nb" style="color: #0086b3;"> </span>hyphy<span class="idiff left right">mp</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$i</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell"><span class="nb" style="color: #0086b3;"> </span>hyphy <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$i</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Clean up</span></span>
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