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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/gemma">Debian Med / gemma</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/gemma/-/commit/779930063759d287263a03ccf7d0434576c8f487">77993006</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-07-31T07:19:24+02:00</i>
</div>
<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/gemma/-/commit/2f6560256f587aa660c526f9073be62ef43513db">2f656025</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-07-31T07:26:55+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Enable hardening
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gemma/-/commit/08e185663601aed00e23dd8de2de19110083e6f7">08e18566</a></strong>
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<span>by Andreas Tille</span>
<i>at 2021-07-31T07:28:49+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Rename autopkgtest script to use a unique name for all our packages
</pre>
</li>
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<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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</li>
<li class="file-stats">
<a href="#4d4a394ff4174f20019a8af4d8b6185efe92c21f">
<span class="new-file">
+
debian/patches/hardening.patch
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</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
debian/tests/control
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</li>
<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-sample-analysis
→
debian/tests/run-unit-test
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</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/gemma/-/compare/7daa7b267b1bc18516dc776461633e00c4487629...08e185663601aed00e23dd8de2de19110083e6f7#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">gemma (0.98.4+dfsg-4) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">gemma (0.98.4+dfsg-5) UNRELEASED; 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="new_line diff-line-num new" 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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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Enable hardening</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Rename autopkgtest script to use a unique name for all our packages</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Sat, 31 Jul 2021 07:26:49 +0200</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">gemma (0.98.4+dfsg-4) unstable; urgency=medium</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"> * Team upload.</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> * Apply patch from upstream who explained:</span>
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<td class="diff-line-num unfold js-unfold old_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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="15" 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">@@ -7,7 +15,7 @@ gemma (0.98.4+dfsg-4) UNRELEASED; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> results (mostly SIMD differences).</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> Closes: #991652</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="LC10" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Fri, 30 Jul 2021 21:5<span class="idiff left right">2:30</span> +0200</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Fri, 30 Jul 2021 21:5<span class="idiff left right">3:57</span> +0200</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">gemma (0.98.4+dfsg-3) 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/gemma/-/compare/7daa7b267b1bc18516dc776461633e00c4487629...08e185663601aed00e23dd8de2de19110083e6f7#4d4a394ff4174f20019a8af4d8b6185efe92c21f"><strong>debian/patches/hardening.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Propagate LDFLAGS to enable hardening</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Last-Update: Mon, 22 Mar 2021 14:38:26 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">--- a/Makefile</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;">+++ b/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -219,14 +219,14 @@</span> debug: $(OUTPUT)</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> $(shell bash $(VGEN) $(GUIX_PROFILE) > src/version.h)</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> $(OUTPUT): $(OBJS)</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;">- $(CPP) $(CPPFLAGS) $(OBJS) $(LIBS) -o $(OUTPUT)</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;">+ $(CPP) $(CPPFLAGS) $(OBJS) $(LIBS) -o $(OUTPUT) $(LDFLAGS)</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"> $(OBJS): $(HDR)</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> .SUFFIXES : .cpp .c .o $(SUFFIXES)</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> ./bin/unittests-gemma: $(TEST_SRC_DIR)/unittests-main.o $(TEST_SRC_DIR)/unittests-math.o $(OBJS)</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(CPP) $(CPPFLAGS) $(TEST_SRC_DIR)/unittests-main.o $(TEST_SRC_DIR)/unittests-math.o $(filter-out src/main.o, $(OBJS)) $(LIBS) -o ./bin/unittests-gemma</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CPP) $(CPPFLAGS) $(TEST_SRC_DIR)/unittests-main.o $(TEST_SRC_DIR)/unittests-math.o $(filter-out src/main.o, $(OBJS)) $(LIBS) -o ./bin/unittests-gemma $(LDFLAGS)</span></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"> unittests: all ./bin/unittests-gemma</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> ./bin/unittests-gemma</span></pre>
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<a href="https://salsa.debian.org/med-team/gemma/-/compare/7daa7b267b1bc18516dc776461633e00c4487629...08e185663601aed00e23dd8de2de19110083e6f7#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</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">@@ -2,3 +2,4 @@ exclude_assertions_failing_under_some_circumstances.patch</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Reproducible_builds.patch</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">no-lquadmath.patch</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Makefile.patch</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">hardening.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/gemma/-/compare/7daa7b267b1bc18516dc776461633e00c4487629...08e185663601aed00e23dd8de2de19110083e6f7#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">#!/usr/bin/make -f</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">export DH_VERBOSE = 1</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"><span class="idiff left right">#</span>export DEB_BUILD_MAINT_OPTIONS = hardening=+all</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">export DEB_BUILD_MAINT_OPTIONS = hardening=+all</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">export DEB_CFLAGS_MAINT_APPEND = -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">export DEB_CXXFLAGS_MAINT_APPEND = -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen</span>
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<a href="https://salsa.debian.org/med-team/gemma/-/compare/7daa7b267b1bc18516dc776461633e00c4487629...08e185663601aed00e23dd8de2de19110083e6f7#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Tests: run-<span class="idiff left right">sample-analysis</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Tests: run-<span class="idiff left right">unit-test</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Depends: @</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Restrictions: allow-stderr</span></pre>
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<a href="https://salsa.debian.org/med-team/gemma/-/compare/7daa7b267b1bc18516dc776461633e00c4487629...08e185663601aed00e23dd8de2de19110083e6f7#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-sample-analysis</strong>
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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">@@ -4,6 +4,7 @@ pkg=gemma</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <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="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC10" 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;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/example/<span class="k" style="font-weight: 600;">*</span> <span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="18" 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">@@ -18,7 +19,7 @@ gemma -g mouse_hs1940.geno.txt.gz -p mouse_hs1940.pheno.txt \</td>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="shell"><span class="nv" style="color: #008080;">hostarch</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span>dpkg-architecture <span class="nt" style="color: #000080;">-qDEB_HOST_ARCH</span><span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Ignore single test on armhf <span class="idiff left right">and i386 </span>(see bug #972553)</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Ignore single test on armhf (see bug #972553)</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$hostarch</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">"armhf"</span> <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="LC24" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Do only one test for </span><span class="nv" style="color: #008080;">$hostarch</span><span class="s2" style="color: #d14;"> to reduce test time (see bug #985004)"</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>0</span>
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