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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/iqtree">Debian Med / iqtree</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/iqtree/-/commit/8c143aad10b4898555bcea903b00a33ba0d576e4">8c143aad</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-01-20T15:42:28+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Drop invalid option `-omp` from build time test
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/iqtree/-/commit/d1c4466dfb61696a17ee0781a7431df5fe1abbe5">d1c4466d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-01-21T11:39:26+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Deal with renamed omp version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/iqtree/-/commit/3260ddf24df063faddab191c2615bedf0c898381">3260ddf2</a></strong>
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<span>by Andreas Tille</span>
<i>at 2022-01-21T12:04:58+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove -omp option from autopkgtest
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/iqtree/-/commit/c24cf02087cce83aa517d1d1ce3004fa1524411e">c24cf020</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-01-21T12:30:51+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
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<li class="file-stats">
<a href="#68d8c5c6babbf5cf109b2584c454449dbff75772">
debian/install
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/iqtree/-/compare/92ab7cbe976b8a8a83757664d5c4150dbae2113e...c24cf02087cce83aa517d1d1ce3004fa1524411e#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">iqtree (2.0.7+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">iqtree (2.0.7+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"> [ Andreas Tille ]</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * New upstream version</span>
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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>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,17 +9,13 @@ iqtree (2.0.7+dfsg-1) UNRELEASED; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> Repository-Browse.</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> * Build-Depends: libboost-dev</span>
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<td class="old_line diff-line-num" 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"> * Executables are now named iqtree2</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> * Drop invalid option `-omp` from build time test</span>
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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"> [ Steffen Moeller ]</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> * Fix watchfile to detect new versions on github (routine-update)</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> * Standards-Version: 4.6.0</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"> TODO: Wait for upstream for answer to rename from iqtree to iqtree2</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> + time /build/iqtree-2.0.7+dfsg/build.omp/iqtree2-omp -s example.phy -omp 2 -redo</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"> Invalid "-omp" option.</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> Command exited with non-zero status 2</span>
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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"> -- Andreas Tille <tille@debian.org> Wed, 14 Oct 2020 09:15:22 +0200</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Fri, 21 Jan 2022 12:05:21 +0100</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">iqtree (1.6.12+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/iqtree/-/compare/92ab7cbe976b8a8a83757664d5c4150dbae2113e...c24cf02087cce83aa517d1d1ce3004fa1524411e#68d8c5c6babbf5cf109b2584c454449dbff75772"><strong>debian/install</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">build.omp/iqtree-omp usr/bin</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">build.omp/iqtree<span class="idiff left right">2</span>-omp usr/bin</span></pre>
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<a href="https://salsa.debian.org/med-team/iqtree/-/compare/92ab7cbe976b8a8a83757664d5c4150dbae2113e...c24cf02087cce83aa517d1d1ce3004fa1524411e#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">@@ -33,7 +33,7 @@ dh_auto_build_%:</td>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"> if [ -x build.omp/iqtree2 ] ; then mv build.omp/iqtree2 build.omp/iqtree2-omp ; fi</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext">dh_auto_install_%:</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext"> dh_auto_install -Bbuild.$(subst dh_auto_install_,,$@)</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> <span class="idiff left">if [ "$(subst dh_auto_install_,,$@)" != "omp" ] ; then </span>dh_auto_install -Bbuild.$(subst dh_auto_install_,,$@)<span class="idiff right">; fi</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext">override_dh_install:</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"> dh_install</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">@@ -72,7 +72,7 @@ ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</td>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="plaintext"># fi</span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="plaintext">ifneq ($(shell nproc), 1)</span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="plaintext"> sed '/ myprefix/,$$d' debian/Documents_source/example.sh > example.short</span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="plaintext"> echo 'time $(CURDIR)/build.omp/iqtree2-omp -s example.phy <span class="idiff left right">-omp 2 </span>-redo' >> example.short</span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext"> echo 'time $(CURDIR)/build.omp/iqtree2-omp -s example.phy -redo' >> example.short</span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="plaintext"> time sh example.short</span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="plaintext"> rm example.short</span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="plaintext">endif</span>
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<a href="https://salsa.debian.org/med-team/iqtree/-/compare/92ab7cbe976b8a8a83757664d5c4150dbae2113e...c24cf02087cce83aa517d1d1ce3004fa1524411e#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">@@ -43,10 +43,7 @@ time $PATHTOEXE -redo -s example.phy -m TIM+I+G -lbp 1000</td>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="shell"><span class="nb" style="color: #0086b3;">time</span> <span class="nv" style="color: #008080;">$PATHTOEXE</span> <span class="nt" style="color: #000080;">-redo</span> <span class="nt" style="color: #000080;">-s</span> example.phy <span class="nt" style="color: #000080;">-m</span> TIM+I+G <span class="nt" style="color: #000080;">-alrt</span> 1000 <span class="nt" style="color: #000080;">-lbp</span> 1000</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="shell"><span class="nb" style="color: #0086b3;">time</span> <span class="nv" style="color: #008080;">$PATHTOEXE</span> <span class="nt" style="color: #000080;">-redo</span> <span class="nt" style="color: #000080;">-s</span> example.phy <span class="nt" style="color: #000080;">-m</span> TIM+I+G <span class="nt" style="color: #000080;">-bb</span> 1000 <span class="nt" style="color: #000080;">-alrt</span> 1000 <span class="nt" style="color: #000080;">-lbp</span> 1000</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="shell"><span class="nb" style="color: #0086b3;">time</span> <span class="nv" style="color: #008080;">$PATHTOEXE</span> <span class="nt" style="color: #000080;">-redo</span> <span class="nt" style="color: #000080;">-s</span> example.phy <span class="nt" style="color: #000080;">-sp</span> example.nex</span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="shell"><span class="nb" style="color: #0086b3;">time</span> <span class="nv" style="color: #008080;">$PATHTOEXEOMP</span> <span class="nt" style="color: #000080;">-redo</span> <span class="nt" style="color: #000080;">-s</span> example.phy <span class="nt" style="color: #000080;">-omp</span> 2</span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">nproc</span><span class="si" style="color: #d14;">)</span> <span class="nt" style="color: #000080;">-ge</span> 3 <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">time</span> <span class="nv" style="color: #008080;">$PATHTOEXEOMP</span> <span class="nt" style="color: #000080;">-redo</span> <span class="nt" style="color: #000080;">-s</span> example.phy <span class="nt" style="color: #000080;">-omp</span> 3</span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="shell"><span class="nb" style="color: #0086b3;">time</span> <span class="nv" style="color: #008080;">$PATHTOEXEOMP</span> <span class="nt" style="color: #000080;">-redo</span> <span class="nt" style="color: #000080;">-s</span> example.phy</span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-e</span> example.treels <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">time</span> <span class="nv" style="color: #008080;">$PATHTOEXE</span> <span class="nt" style="color: #000080;">-redo</span> <span class="nt" style="color: #000080;">-s</span> example.phy <span class="nt" style="color: #000080;">-z</span> example.treels</span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">time</span> <span class="nv" style="color: #008080;">$PATHTOEXE</span> <span class="nt" style="color: #000080;">-redo</span> <span class="nt" style="color: #000080;">-s</span> example.phy <span class="nt" style="color: #000080;">-z</span> example.treels <span class="nt" style="color: #000080;">-n</span> 1</span>
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