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<h3>
Étienne Mollier pushed to branch master
at <a href="https://salsa.debian.org/med-team/ivar">Debian Med / ivar</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/ivar/-/commit/4c24e1b4651891b8cb65eb5b60ceca6cf6c38121">4c24e1b4</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-08-28T10:55:34+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add forward-build-options.patch
This addresses ivar not being built with Debian default build options.
</pre>
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<strong><a href="https://salsa.debian.org/med-team/ivar/-/commit/860546294995decce64e143f4a4a4d94274f6f2e">86054629</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-08-28T10:56:37+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add gcc-11.patch
This fixes a failure to build from source with Gcc 11.
Closes: #984067
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/ivar/-/commit/58108eb3724c1a09776bc6f7ed59c82ce0f5f4c3">58108eb3</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-08-28T10:59:07+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">update changelog
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<li>
<strong><a href="https://salsa.debian.org/med-team/ivar/-/commit/66cbbce4f6bfda7d9e0f2b5b334f22b55a80a2ba">66cbbce4</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-08-28T11:14:39+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/salsa-ci.yml: allow reprotest to fail, for now
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<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#5c6a8c0b89136d4e8d64c7ad29b75e9187bb5469">
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+
debian/patches/forward-build-options.patch
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<li class="file-stats">
<a href="#c380dd360f216fd789904f2794009be1ce992d4b">
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+
debian/patches/gcc-11.patch
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#b1dbf22e88351ec0d5d1d1a7f53295504b480e61">
debian/salsa-ci.yml
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/ivar/-/compare/f7462dcad6edb5c5b6c206c8e19a9e5bd7a5df63...66cbbce4f6bfda7d9e0f2b5b334f22b55a80a2ba#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">ivar (1.3.1+dfsg-2) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * add forward-build-options.patch; build ivar with Debian build options</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * add gcc-11.patch; fixes ftbfs with Gcc 11 (Closes: #984067)</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"> -- Étienne Mollier <emollier@debian.org> Sat, 28 Aug 2021 10:57:25 +0200</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">ivar (1.3.1+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> [ Étienne Mollier ]</span>
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<li id="5c6a8c0b89136d4e8d64c7ad29b75e9187bb5469">
<a href="https://salsa.debian.org/med-team/ivar/-/compare/f7462dcad6edb5c5b6c206c8e19a9e5bd7a5df63...66cbbce4f6bfda7d9e0f2b5b334f22b55a80a2ba#5c6a8c0b89136d4e8d64c7ad29b75e9187bb5469"><strong>debian/patches/forward-build-options.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: inject Debian build options</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Author: Étienne Mollier <emollier@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: 2021-08-28</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">---</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">This patch header follows DEP-3: http://dep.debian.net/deps/dep3/</span></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;">--- ivar.orig/src/Makefile.am</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ivar/src/Makefile.am</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">@@ -1,6 +1,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> LIBS = -lhts -lz -lpthread</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-CXXFLAGS = -v -g -std=c++11 -Wall -Wextra -Werror</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;">+CXXFLAGS += -v -g -std=c++11 -Wall -Wextra -Werror</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> # this lists the binaries to produce, the (non-PHONY, binary) targets in</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> # the previous manual Makefile</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ivar.orig/tests/Makefile.am</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ivar/tests/Makefile.am</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="p">@@ -1,6 +1,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> LIBS = -lhts -lz -lpthread</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"><span class="gd" style="color: #000; background-color: #fdd;">-CXXFLAGS = -g -std=c++11 -Wall -Wextra -Werror</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+CXXFLAGS += -g -std=c++11 -Wall -Wextra -Werror</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> TESTS = check_primer_trim check_trim check_quality_trim check_consensus check_allele_depth check_consensus_threshold check_consensus_min_depth check_consensus_seq_id check_primer_bed check_getmasked check_removereads check_variants check_common_variants check_unpaired_trim check_primer_trim_edge_cases check_isize_trim check_interval_tree check_amplicon_search</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> check_PROGRAMS = check_primer_trim check_trim check_quality_trim check_consensus check_allele_depth check_consensus_threshold check_consensus_min_depth check_consensus_seq_id check_primer_bed check_getmasked check_removereads check_variants check_common_variants check_unpaired_trim check_primer_trim_edge_cases check_isize_trim check_interval_tree check_amplicon_search</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="p">@@ -21,4 +21,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> check_primer_trim_edge_cases_SOURCES = test_primer_trim_edge_cases.cpp ../src/trim_primer_quality.cpp ../src/primer_bed.cpp ../src/interval_tree.cpp</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> check_isize_trim_SOURCES = test_isize_trim.cpp ../src/trim_primer_quality.cpp ../src/primer_bed.cpp ../src/interval_tree.cpp</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> check_interval_tree_SOURCES = test_interval_tree.cpp ../src/primer_bed.cpp ../src/interval_tree.cpp</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-check_amplicon_search_SOURCES = test_amplicon_search.cpp ../src/trim_primer_quality.cpp ../src/primer_bed.cpp ../src/interval_tree.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span> No newline at end of file</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+check_amplicon_search_SOURCES = test_amplicon_search.cpp ../src/trim_primer_quality.cpp ../src/primer_bed.cpp ../src/interval_tree.cpp</span></span></pre>
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<a href="https://salsa.debian.org/med-team/ivar/-/compare/f7462dcad6edb5c5b6c206c8e19a9e5bd7a5df63...66cbbce4f6bfda7d9e0f2b5b334f22b55a80a2ba#c380dd360f216fd789904f2794009be1ce992d4b"><strong>debian/patches/gcc-11.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: fix ftbfs with gcc-11</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> Failure is caused by a mismatch between an instance allocation via "new"</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"> operator, and it's freeing via free(3) instead of "delete". The failure to</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> build from source is caused by the warning -Wno-mismatched-new-delete, which</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"> is treated as an error.</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">Author: Étienne Mollier <emollier@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=984067</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">Forwarded: no</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">Last-Update: 2021-08-28</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="p">---</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="p">This patch header follows DEP-3: http://dep.debian.net/deps/dep3/</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ivar.orig/src/ivar.cpp</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;">+++ ivar/src/ivar.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="p">@@ -484,7 +484,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> for (int i = 0; i < nfiles; ++i) {</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> free(files[i]);</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 class="gd" style="color: #000; background-color: #fdd;">- free(files);</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ delete files;</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> } else {</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> res = common_variants(g_args.prefix, g_args.min_threshold, argv + optind, argc - optind);</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> }</span></pre>
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<a href="https://salsa.debian.org/med-team/ivar/-/compare/f7462dcad6edb5c5b6c206c8e19a9e5bd7a5df63...66cbbce4f6bfda7d9e0f2b5b334f22b55a80a2ba#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Fix-warning.patch</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">forward-build-options.patch</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">gcc-11.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/ivar/-/compare/f7462dcad6edb5c5b6c206c8e19a9e5bd7a5df63...66cbbce4f6bfda7d9e0f2b5b334f22b55a80a2ba#b1dbf22e88351ec0d5d1d1a7f53295504b480e61"><strong>debian/salsa-ci.yml</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 +2,6 @@</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">include</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="yaml"><span class="na" style="color: #008080;">variables</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="yaml"> <span class="na" style="color: #008080;">SALSA_CI_DISABLE_REPROTEST</span><span class="pi">:</span> <span class="m" style="color: #099;">1</span></span></pre>
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