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<h3>
Michael R. Crusoe pushed to branch debian/experimental
at <a href="https://salsa.debian.org/med-team/htslib">Debian Med / htslib</a>
</h3>
<h4>
Commits:
</h4>
<ul>
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<strong><a href="https://salsa.debian.org/med-team/htslib/commit/c6579182471e49b2877cd575738661e7ca075743">c6579182</a></strong>
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<span>by Michael R. Crusoe</span>
<i>at 2018-12-18T08:38:50Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">try suggestion from https://github.com/samtools/htslib/issues/565#issuecomment-448028771
</pre>
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<h4>4 changed files:</h4>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<a href="#9dc5408ee6e19d2c1f6475ed46a0bf87988c2cc1">
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+
debian/htslib-test.lintian-overrides
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</a>
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/htslib/commit/c6579182471e49b2877cd575738661e7ca075743#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="mosel"><span class="n" style="color: #333;">htslib</span> <span class="p">(</span><span class="m" style="color: #099;">1.9</span><span class="p">-</span><span class="m" style="color: #099;">7</span><span class="p">~</span><span class="m" style="color: #099;">1</span><span class="p">~</span><span class="n" style="color: #333;">i386</span><span class="p">~</span><span class="m" style="color: #099;">1</span><span class="p">)</span> <span class="n" style="color: #333;">experimental</span><span class="p">;</span> <span class="n" style="color: #333;">urgency</span><span class="p">=</span><span class="n" style="color: #333;">medium</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="mosel"></span>
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<td class="diff-line-num new new_line" 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="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Turn</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">SSE</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">i386</span><span class="p">,</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">suggested</span> <span class="n" style="color: #333;">at</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4" 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">
4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">github</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">samtools</span><span class="p">/</span><span class="n" style="color: #333;">htslib</span><span class="p">/</span><span class="n" style="color: #333;">issues</span><span class="p">/</span><span class="m" style="color: #099;">565</span><span class="p">#</span><span class="n" style="color: #333;">issuecomment</span><span class="p">-</span><span class="m" style="color: #099;">448028771</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="mosel"> <span class="p">--</span> <span class="n" style="color: #333;">Michael</span> <span class="n" style="color: #333;">R</span><span class="p">.</span> <span class="n" style="color: #333;">Crusoe</span> <span class="p"><</span><span class="n" style="color: #333;">michael</span><span class="p">.</span><span class="n" style="color: #333;">crusoe</span><span class="p">@</span><span class="n" style="color: #333;">gmail</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">></span> <span class="n" style="color: #333;">Tue</span><span class="p">,</span> <span class="m" style="color: #099;">18</span> <span class="n" style="color: #333;">Dec</span> <span class="m" style="color: #099;">2018</span> <span class="m" style="color: #099;">00</span><span class="p">:</span><span class="m" style="color: #099;">27</span><span class="p">:</span><span class="m" style="color: #099;">40</span> <span class="p">-</span><span class="m" style="color: #099;">0800</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="mosel"></span>
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1
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<td class="diff-line-num new_line" data-linenumber="8" 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">
8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="mosel"><span class="n" style="color: #333;">htslib</span> <span class="p">(</span><span class="m" style="color: #099;">1.9</span><span class="p">-</span><span class="m" style="color: #099;">7</span><span class="p">~</span><span class="m" style="color: #099;">0</span><span class="p">~</span><span class="n" style="color: #333;">i386</span><span class="p">~</span><span class="n" style="color: #333;">gcc7</span><span class="p">~</span><span class="m" style="color: #099;">1</span><span class="p">)</span> <span class="n" style="color: #333;">experimental</span><span class="p">;</span> <span class="n" style="color: #333;">urgency</span><span class="p">=</span><span class="n" style="color: #333;">medium</span></span>
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2
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<td class="diff-line-num 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">
9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="mosel"></span>
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<td class="diff-line-num new_line" data-linenumber="10" 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="LC10" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Try</span> <span class="n" style="color: #333;">dropping</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">gcc</span><span class="p">-</span><span class="m" style="color: #099;">7</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">i386</span><span class="p">*</span></span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/htslib/commit/c6579182471e49b2877cd575738661e7ca075743#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6" 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="6" 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">@@ -6,7 +6,6 @@ Uploaders: Charles Plessy <plessy@debian.org>,</td>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">Build-Depends: debhelper (>= 11~),</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> gcc-7 [i386 kfreebsd-i386 hurd-i386],</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> dh-exec,</span>
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<td class="diff-line-num old_line" 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="LC10" class="line" lang="plaintext"> libbz2-dev,</span>
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<td class="diff-line-num old_line" data-linenumber="12" 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"> libcurl4-gnutls-dev,</span>
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<li id="9dc5408ee6e19d2c1f6475ed46a0bf87988c2cc1">
<a href="https://salsa.debian.org/med-team/htslib/commit/c6579182471e49b2877cd575738661e7ca075743#9dc5408ee6e19d2c1f6475ed46a0bf87988c2cc1"><strong>debian/htslib-test.lintian-overrides</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># As needed for testing</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">duplicated-compressed-file usr/share/htslib-test/test/bgziptest.txt.gz</span></pre>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/htslib/commit/c6579182471e49b2877cd575738661e7ca075743#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">@@ -8,12 +8,9 @@ export DH_VERBOSE=1</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">include /usr/share/dpkg/default.mk</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">ifneq (,$(filter $(DEB_HOST_ARCH),i386 kfreebsd-i386 hurd-i386))</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> export DEB_CFLAGS_MAINT_APPEND=-fno-strict-aliasing -fno-code-hoisting</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> export CC=gcc-7</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">else</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> export CC=gcc</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> DEB_CFLAGS_MAINT_APPEND=-msse -mfpmath=sse</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">endif</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">DEB_CFLAGS_MAINT_APPEND+=-flto</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"><span class="idiff left right">export </span>DEB_CFLAGS_MAINT_APPEND+=-flto</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">export DEB_LDFLAGS_MAINT_APPEND+=-Wl,-flto</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">%:</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">@@ -26,7 +23,7 @@ override_dh_auto_configure:</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> dh_auto_configure -- --enable-libcurl</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">override_dh_auto_build:</span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext"> dh_auto_build -- <span class="idiff left right">CC=$(CC)</span>\</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> dh_auto_build -- \</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> CFLAGS="$$(dpkg-buildflags --get CFLAGS)" \</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> CPPFLAGS="-I. -DSAMTOOLS=1 $$(dpkg-buildflags --get CPPFLAGS)" \</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"> LDFLAGS="$$(dpkg-buildflags --get LDFLAGS)" \</span>
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