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<h3>
Michael R. Crusoe 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/28b34300868629ea3017b70b2a8bef6427340f57">28b34300</a></strong>
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<span>by Michael R. Crusoe</span>
<i>at 2021-01-31T11:04:59+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix arch independent build issue
which cause the amd64 autopkgtests to fail.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/hyphy/-/commit/e3fb0dda2f749272d81c6c2ccc20400bffa6c2af">e3fb0dda</a></strong>
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<span>by Michael R. Crusoe</span>
<i>at 2021-01-31T11:41:32+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">On amd64, run the build-time tests the SIMD varients that are supported by the build-time CPU.
</pre>
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<strong><a href="https://salsa.debian.org/med-team/hyphy/-/commit/8cb707d2dbbd6ec462403f48887c838cf4fca2c3">8cb707d2</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-01-31T11:41:32+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">release 2.5.27+dfsg-4
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<h4>2 changed files:</h4>
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/hyphy/-/compare/0833938a0d724c8963adb0649722258eb6f731f0...8cb707d2dbbd6ec462403f48887c838cf4fca2c3#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">hyphy (2.5.27+dfsg-4) 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"> * Team upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Fix arch independent build issue which cause the amd64 autopkgtests to</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> fail.</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * On amd64, run the build-time tests the SIMD varients that are supported by</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> the build-time CPU.</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"> -- Michael R. Crusoe <crusoe@debian.org> Sun, 31 Jan 2021 11:05:20 +0100</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">hyphy (2.5.27+dfsg-3) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> * Team upload.</span>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/hyphy/-/compare/0833938a0d724c8963adb0649722258eb6f731f0...8cb707d2dbbd6ec462403f48887c838cf4fca2c3#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="20" 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="20" 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">@@ -20,8 +20,8 @@ override_dh_auto_clean:</td>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">override_dh_auto_configure:</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">ifeq (amd64,$(DEB_HOST_ARCH))</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> dh_auto_configure -- -DINSTALL_PREFIX=/usr -DNOAVX=ON -DNOSSE3=ON</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"> dh_auto_configure --builddirectory obj<span class="idiff left right">_</span>avx -- -DINSTALL_PREFIX=/usr -DNOAVX=OFF -DNOSSE3=OFF</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"> dh_auto_configure --builddirectory obj<span class="idiff left right">_</span>sse3 -- -DINSTALL_PREFIX=/usr -DNOAVX=ON -DNOSSE3=OFF</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> dh_auto_configure --builddirectory obj<span class="idiff left right">-</span>avx -- -DINSTALL_PREFIX=/usr -DNOAVX=OFF -DNOSSE3=OFF</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> dh_auto_configure --builddirectory obj<span class="idiff left right">-</span>sse3 -- -DINSTALL_PREFIX=/usr -DNOAVX=ON -DNOSSE3=OFF</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">else</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> dh_auto_configure -- -DINSTALL_PREFIX=/usr -DNOAVX=ON -DNOSSE3=ON</span>
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">endif</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">@@ -35,8 +35,8 @@ override_dh_auto_build:</td>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext"> ; done</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext">ifeq (amd64,$(DEB_HOST_ARCH))</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext"> dh_auto_build -- MP MPI</span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="plaintext"> dh_auto_build --builddirectory obj<span class="idiff left right">_</span>avx -- MP MPI</span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext"> dh_auto_build --builddirectory obj<span class="idiff left right">_</span>sse3 -- MP MPI</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> dh_auto_build --builddirectory obj<span class="idiff left right">-</span>avx -- MP MPI</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> dh_auto_build --builddirectory obj<span class="idiff left right">-</span>sse3 -- MP MPI</span>
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40
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext">else</span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext"> dh_auto_build -- MP MPI</span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext">endif</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="46" 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">@@ -46,11 +46,10 @@ override_dh_install-arch:</td>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext">ifeq (amd64,$(DEB_HOST_ARCH))</span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext"> mkdir -p debian/hyphy-mpi/usr/lib/$(DEB_SOURCE)/bin</span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext"> mkdir -p debian/hyphy-pt/usr/lib/$(DEB_SOURCE)/bin</span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="plaintext"> cp obj_avx/HYPHYMPI debian/hyphy-mpi/usr/lib/$(DEB_SOURCE)/bin/HYPHYMPI-avx</span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="plaintext"> cp obj_sse3/HYPHYMPI debian/hyphy-mpi/usr/lib/$(DEB_SOURCE)/bin/HYPHYMPI-sse3</span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="plaintext"> cp obj_avx/hyphy debian/hyphy-pt/usr/lib/$(DEB_SOURCE)/bin/hyphy-avx</span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="plaintext"> cp obj_sse3/hyphy debian/hyphy-pt/usr/lib/$(DEB_SOURCE)/bin/hyphy-sse3</span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="plaintext"> dh_install -phyphy-common debian/bin/simd-dispatch /usr/lib/$(DEB_SOURCE)/bin</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"> cp obj-avx/HYPHYMPI debian/hyphy-mpi/usr/lib/$(DEB_SOURCE)/bin/HYPHYMPI-avx</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> cp obj-sse3/HYPHYMPI debian/hyphy-mpi/usr/lib/$(DEB_SOURCE)/bin/HYPHYMPI-sse3</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"> cp obj-avx/hyphy debian/hyphy-pt/usr/lib/$(DEB_SOURCE)/bin/hyphy-avx</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"> cp obj-sse3/hyphy debian/hyphy-pt/usr/lib/$(DEB_SOURCE)/bin/hyphy-sse3</span>
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54
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="plaintext"> mv debian/hyphy-mpi/usr/bin/HYPHYMPI debian/hyphy-mpi/usr/lib/$(DEB_SOURCE)/bin/</span>
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55
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="plaintext"> mv debian/hyphy-pt/usr/bin/hyphy debian/hyphy-pt/usr/lib/$(DEB_SOURCE)/bin/</span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="plaintext"> cd $(CURDIR)/debian/hyphy-mpi/usr/bin && \</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -59,8 +58,26 @@ ifeq (amd64,$(DEB_HOST_ARCH))</td>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="plaintext"> ln -s ../lib/$(DEB_SOURCE)/bin/simd-dispatch hyphy</span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="plaintext">endif</span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">override_dh_install-indep:</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext"> dh_install -i</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">ifeq (amd64,$(DEB_HOST_ARCH))</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"> dh_install -phyphy-common debian/bin/simd-dispatch /usr/lib/$(DEB_SOURCE)/bin</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">endif</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="plaintext">override_dh_auto_test:</span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="plaintext">ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">ifeq (amd64,$(DEB_HOST_ARCH))</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext"> set -e ; for SIMD in avx sse3 ; do \</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext"> if lscpu | grep -q $${SIMD} ; then \</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext"> find "obj-$${SIMD}/" \</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext"> -not -path "*/CMakeFiles/*" \</span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext"> -type f,l \</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext"> -executable \</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext"> -exec cp -v '{}' . \; && \</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext"> ./run_unit_tests.sh ; \</span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext"> fi ; \</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="plaintext"> done</span>
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<td class="diff-line-num new old_line" data-linenumber="64" 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="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="plaintext">endif</span>
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64
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81
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="plaintext"> find "obj-$(DEB_HOST_GNU_TYPE)/" \</span>
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<td class="diff-line-num old_line" data-linenumber="65" 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">
65
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82
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="plaintext"> -not -path "*/CMakeFiles/*" \</span>
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<td class="diff-line-num old_line" data-linenumber="66" 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">
66
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83
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="plaintext"> -type f,l \</span>
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