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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/hmmer">Debian Med / hmmer</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/hmmer/commit/27ce1de6ced1e5d9a97919729b0b74759494c47d">27ce1de6</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-09-30T13:49:48Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">move hmmc2 out of /usr/bin/
</pre>
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<h4>6 changed files:</h4>
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<a href="#f5f51601866c86e59a004bd93fa415f5675be8c5">
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+
debian/clean
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<li class="file-stats">
<a href="#8b697339f0888bc255b08a38509737ba42c05e4f">
debian/hmmer.install
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#7178252f78db79374b0895987b902b9a83c26258">
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+
debian/patches/skip_threads_check
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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="f5f51601866c86e59a004bd93fa415f5675be8c5">
<a href="https://salsa.debian.org/med-team/hmmer/commit/27ce1de6ced1e5d9a97919729b0b74759494c47d#f5f51601866c86e59a004bd93fa415f5675be8c5"><strong>debian/clean</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/test_log</span></pre>
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<li id="8b697339f0888bc255b08a38509737ba42c05e4f">
<a href="https://salsa.debian.org/med-team/hmmer/commit/27ce1de6ced1e5d9a97919729b0b74759494c47d#8b697339f0888bc255b08a38509737ba42c05e4f"><strong>debian/hmmer.install</strong></a>
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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>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="php"><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">man</span></span></pre>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="php"><span class="nx">src</span><span class="o" style="font-weight: 600;">/</span><span class="nx">hmmc2</span> <span class="o" style="font-weight: 600;">/</span><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></pre>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/hmmer/commit/27ce1de6ced1e5d9a97919729b0b74759494c47d#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3" 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">@@ -3,3 +3,4 @@ use_debian_packaged_libdivsufsort.patch</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">verbose-easel</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">hardening</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">spelling</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">skip_threads_check</span></pre>
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<li id="7178252f78db79374b0895987b902b9a83c26258">
<a href="https://salsa.debian.org/med-team/hmmer/commit/27ce1de6ced1e5d9a97919729b0b74759494c47d#7178252f78db79374b0895987b902b9a83c26258"><strong>debian/patches/skip_threads_check</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- hmmer.orig/testsuite/i19-hmmpgmd-ga.pl</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ hmmer/testsuite/i19-hmmpgmd-ga.pl</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">@@ -53,11 +53,11 @@</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> # if not found, threads are not enabled and this</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"> # test would fail, but we return ok status 0 because</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> # we don't want the full testsuite to fail.</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-$have_threads = `cat $builddir/src/p7_config.h | grep "^#define HMMER_THREADS"`;</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-if($have_threads eq "") { </span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- printf("HMMER_THREADS not defined in p7_config.h\n"); </span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- exit 0;</span></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;">-}</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;">+#$have_threads = `cat $builddir/src/p7_config.h | grep "^#define HMMER_THREADS"`;</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#if($have_threads eq "") { </span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# printf("HMMER_THREADS not defined in p7_config.h\n"); </span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# exit 0;</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#}</span></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"> </span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> # Verify that the wport and cport are CLOSED - we don't want to</span></pre>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/hmmer/commit/27ce1de6ced1e5d9a97919729b0b74759494c47d#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">@@ -37,7 +37,8 @@ override_dh_auto_configure:</td>
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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_auto_test:</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext">ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext"> export V=VERBOSE ; make check -j$(shell nproc)</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> export V=VERBOSE ; make check -j$(shell nproc) | tee debian/test_log</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> if tail -n 6 debian/test_log | head -n 1 | grep -q FAILED ; then false ; fi</span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext">endif</span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext">override_dh_auto_build:</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">@@ -54,6 +55,11 @@ override_dh_auto_clean:</td>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="plaintext">override_dh_compress:</span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="plaintext"> dh_compress -Xtutorial/</span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">override_dh_auto_install:</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"> dh_auto_install</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"> mkdir -p $(CURDIR)/debian/$(DEB_SOURCE)/usr/lib/${DEB_HOST_MULTIARCH}/hmmer/</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"> cp src/hmmc2 $(CURDIR)/debian/$(DEB_SOURCE)/usr/lib/${DEB_HOST_MULTIARCH}/hmmer/</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext"></span>
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57
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="plaintext">override_dh_installexamples:</span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="plaintext"> dh_installexamples</span>
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59
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="plaintext"> mkdir -p $(sampledir)/src/impl</span>
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<a href="https://salsa.debian.org/med-team/hmmer/commit/27ce1de6ced1e5d9a97919729b0b74759494c47d#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">@@ -21,6 +21,7 @@ $AUTOPKGTEST_TMP/easel/devkit/sqc -v 2 ./easel/testsuite/testsuite.sqc ./easel .</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span>hmmer testsuite</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="shell">find /usr/bin <span class="nt" style="color: #000080;">-name</span> <span class="s2" style="color: #d14;">"*hmm*"</span> <span class="nt" style="color: #000080;">-exec</span> <span class="nb" style="color: #0086b3;">ln</span> <span class="nt" style="color: #000080;">-s</span> <span class="se" style="color: #d14;">\{\}</span> src <span class="se" style="color: #d14;">\;</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell">find /usr/lib/<span class="k" style="font-weight: 600;">*</span>/hmmer <span class="nt" style="color: #000080;">-type</span> f <span class="nt" style="color: #000080;">-exec</span> <span class="nb" style="color: #0086b3;">ln</span> <span class="nt" style="color: #000080;">-s</span> <span class="se" style="color: #d14;">\{\}</span> src <span class="se" style="color: #d14;">\;</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="shell">./testsuite/../easel/devkit/sqc <span class="nt" style="color: #000080;">-v</span> 2 ./testsuite/testsuite.sqc <span class="nb" style="color: #0086b3;">.</span> ./testsuite/.. <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="shell"> | <span class="nb" style="color: #0086b3;">tee</span> <span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span>/hmmer.log</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$top_builddir</span></span>
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