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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/infernal">Debian Med / infernal</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/infernal/commit/c763413aa1604000be7331d53c272514e46812c0">c763413a</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-11-30T11:45:27Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Enable a verbose build log
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/infernal/commit/f80d3b0e82e7edd03275127bca0d01fe95065ec3">f80d3b0e</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-11-30T11:47:10Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">infernal-doc: mark Multi-Arch: foreign
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/infernal/commit/aca65ff937b1cd5d961ba8f56e787444525ad5b4">aca65ff9</a></strong>
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<span>by Michael R. Crusoe</span>
<i>at 2019-11-30T12:31:00Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">CPPFLAGS for easel
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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="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#d6c09299b1f914372840e8fd6fcc850f8a11b236">
<span class="new-file">
+
debian/patches/hardening
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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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/infernal/compare/21c20708447abd0b24921c624af953f4983e555a...aca65ff937b1cd5d961ba8f56e787444525ad5b4#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<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">@@ -6,6 +6,9 @@ infernal (1.1.3-2) UNRELEASED; urgency=medium</td>
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<td class="diff-line-num 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">
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> * Remove trailing whitespace in debian/changelog</span>
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<td class="diff-line-num new_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">
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> * Trim trailing whitespace.</span>
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<td class="diff-line-num old_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">
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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">
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> * Set upstream metadata fields: Bug-Submit.</span>
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<td class="diff-line-num new new_line" data-linenumber="9" 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="LC9" class="line" lang="plaintext"> * Enable a verbose build log</span>
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<td class="diff-line-num new old_line" data-linenumber="9" 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="10" 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="LC10" class="line" lang="plaintext"> * infernal-doc: mark Multi-Arch: foreign (thanks Multiarch hinter!)</span>
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<td class="diff-line-num new old_line" data-linenumber="9" 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="11" 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="LC11" class="line" lang="plaintext"> * debian/patches/hardening: added CPPFLAGS to easel, rmark, and hmmer/profmark</span>
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<td class="diff-line-num new_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="LC12" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="13" 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="LC13" class="line" lang="plaintext"> -- Michael R. Crusoe <michael.crusoe@gmail.com> Sat, 30 Nov 2019 11:00:30 +0100</span>
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<td class="diff-line-num new_line" data-linenumber="14" 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="LC14" class="line" lang="plaintext"></span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/infernal/compare/21c20708447abd0b24921c624af953f4983e555a...aca65ff937b1cd5d961ba8f56e787444525ad5b4#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="31" 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="31" 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">@@ -31,6 +31,7 @@ Description: inference of RNA secondary structural alignments</td>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext">Package: infernal-doc</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext">Section: doc</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">Multi-Arch: foreign</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext"> ${misc:Depends}</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext">Description: inference of RNA secondary structural alignments – documentation</span>
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<li id="d6c09299b1f914372840e8fd6fcc850f8a11b236">
<a href="https://salsa.debian.org/med-team/infernal/compare/21c20708447abd0b24921c624af953f4983e555a...aca65ff937b1cd5d961ba8f56e787444525ad5b4#d6c09299b1f914372840e8fd6fcc850f8a11b236"><strong>debian/patches/hardening</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">From: Michael R. Crusoe <michael.crusoe@gmail.com></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Subject: insert CPPFLAGS in easel</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- infernal.orig/easel/Makefile.in</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ infernal/easel/Makefile.in</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">@@ -549,7 +549,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> @${RANLIB} libeasel.a</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> ${ALL_OBJS}: %.o : %.c ${HDRS} esl_config.h</span>
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<td class="diff-line-num new new_line" data-linenumber="9" 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="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ${QUIET_CC}${CC} -I. -I${srcdir} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} -c $<</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ${QUIET_CC}${CC} -I. -I${srcdir} ${CPPFLAGS} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} -c $<</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> # Driver compilation:</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="p">@@ -573,10 +573,10 @@</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> else DFILE=${srcdir}/esl_$${BASENAME}.c ;\</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> fi;\</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> if test ${V} ;\</span>
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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- then echo "${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${UTEST_CFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}" ;\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ then echo "${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${CPPFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}" ;\</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> else echo ' ' GEN $@ ;\</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> fi ;\</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${CPPFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> ${ALL_BENCHMARKS}: libeasel.a</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> @BASENAME=`echo $@ | sed -e 's/_benchmark//'| sed -e 's/^esl_//'` ;\</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="p">@@ -587,10 +587,10 @@</span></span>
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<td class="diff-line-num new new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> else DFILE=${srcdir}/esl_$${BASENAME}.c ;\</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> fi;\</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> if test ${V} ;\</span>
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<td class="diff-line-num new new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- then echo "${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMDFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}" ;\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ then echo "${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${CPPFLAGS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}" ;\</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> else echo ' ' GEN $@ ;\</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> fi ;\</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${CPPFLAGS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> </span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> ${ALL_EXPERIMENTS}: libeasel.a</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> @BASENAME=`echo $@ | sed -e 's/_experiment//'| sed -e 's/^esl_//'` ;\</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="p">@@ -601,10 +601,10 @@</span></span>
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<td class="diff-line-num new new_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> else DFILE=${srcdir}/esl_$${BASENAME}.c ;\</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> fi;\</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> if test ${V} ;\</span>
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<td class="diff-line-num new new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- then echo "${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMDFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}" ;\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ then echo "${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${CPPFLAGS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}" ;\</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> else echo ' ' GEN $@ ;\</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> fi ;\</span>
</pre>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${CPPFLAGS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> ${ALL_EXAMPLES}: libeasel.a</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> @BASENAME=`echo $@ | sed -e 's/_example[0-9]*//'| sed -e 's/^esl_//'` ;\</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="p">@@ -614,10 +614,10 @@</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> else DFILE=${srcdir}/esl_$${BASENAME}.c ;\</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> fi ;\</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> if test ${V}; \</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- then echo "${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMDFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}" ;\</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ then echo "${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${CPPFLAGS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}" ;\</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> else echo ' ' GEN $@ ;\</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> fi ;\</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${CPPFLAGS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- infernal.orig/easel/miniapps/Makefile.in</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ infernal/easel/miniapps/Makefile.in</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="p">@@ -94,13 +94,13 @@</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> check: ${PROGS} easel</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> easel: % : %.c ../libeasel.a ${SUBCMDOBJS}</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ${QUIET_GEN}${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${DEFS} ${LDFLAGS} -L.. -I. -I.. -I${srcdir} -I${srcdir}/.. -o $@ $< ${SUBCMDOBJS} ${LIBS}</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ${QUIET_GEN}${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${DEFS} ${LDFLAGS} ${CPPFLAGS} -L.. -I. -I.. -I${srcdir} -I${srcdir}/.. -o $@ $< ${SUBCMDOBJS} ${LIBS}</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> ${PROGS}: % : %.c ../libeasel.a </span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ${QUIET_GEN}${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${DEFS} ${LDFLAGS} -L.. -I. -I.. -I${srcdir} -I${srcdir}/.. -o $@ $< ${LIBS}</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ${QUIET_GEN}${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${DEFS} ${LDFLAGS} ${CPPFLAGS} -L.. -I. -I.. -I${srcdir} -I${srcdir}/.. -o $@ $< ${LIBS}</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"> ${SUBCMDOBJS}: %.o : %.c ../libeasel.a</span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ${QUIET_CC}${CC} -I. -I.. -I${srcdir} -I${srcdir}/.. ${CFLAGS} ${PTHREAD_CFLAGS} ${SIMD_CFLAGS} ${DEFS} -c $<</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ${QUIET_CC}${CC} ${CPPFLAGS} -I. -I.. -I${srcdir} -I${srcdir}/.. ${CFLAGS} ${PTHREAD_CFLAGS} ${SIMD_CFLAGS} ${DEFS} -c $<</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"> install: ${PROGS} </span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> ${INSTALL} -m 0755 easel ${DESTDIR}${bindir}/</span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- infernal.orig/hmmer/profmark/Makefile.in</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ infernal/hmmer/profmark/Makefile.in</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="p">@@ -43,12 +43,12 @@</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> dev: ${PROGS}</span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"> ${PROGS}: % : %.o ../${ESLDIR}/libeasel.a ../src/libhmmer.a </span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ${QUIET_GEN}${CC} ${CFLAGS} ${SSE_CFLAGS} ${VMX_CFLAGS} ${PTHREAD_CFLAGS} ${DEFS} ${LDFLAGS} -L../${ESLDIR} -L../src -o $@ $@.o ${LIBS}</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ${QUIET_GEN}${CC} ${CPPFLAGS} ${CFLAGS} ${SSE_CFLAGS} ${VMX_CFLAGS} ${PTHREAD_CFLAGS} ${DEFS} ${LDFLAGS} -L../${ESLDIR} -L../src -o $@ $@.o ${LIBS}</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"> ${PROGOBJS}: ../src/hmmer.h ../src/p7_config.h</span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"> .c.o: </span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ${QUIET_CC}${CC} ${ESLINC} ${SRCINC} ${CFLAGS} ${SSE_CFLAGS} ${VMX_CFLAGS} ${PTHREAD_CFLAGS} ${DEFS} -o $@ -c $< </span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ${QUIET_CC}${CC} ${CPPFLAGS} ${ESLINC} ${SRCINC} ${CFLAGS} ${SSE_CFLAGS} ${VMX_CFLAGS} ${PTHREAD_CFLAGS} ${DEFS} -o $@ -c $< </span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"> clean:</span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"> -rm -f *.o *~ ${PROGS} </span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- infernal.orig/rmark/Makefile.in</span></span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ infernal/rmark/Makefile.in</span></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"><span class="p">@@ -43,12 +43,12 @@</span></span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"> dev: ${PROGS}</span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"> ${PROGS}: % : %.o ../${HMMERDIR}/src/libhmmer.a ../${ESLDIR}/libeasel.a </span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ${QUIET_GEN}${CC} ${CFLAGS} ${DEFS} ${LDFLAGS} -L../${HMMERDIR}/src -L../${ESLDIR} -L${SRCDIR} -o $@ $@.o ${LIBS}</span></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ${QUIET_GEN}${CC} ${CPPFLAGS} ${CFLAGS} ${DEFS} ${LDFLAGS} -L../${HMMERDIR}/src -L../${ESLDIR} -L${SRCDIR} -o $@ $@.o ${LIBS}</span></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"> ${PROGOBJS}: ../${HMMERDIR}/src/hmmer.h ../${HMMERDIR}/src/p7_config.h ../src/infernal.h ../src/config.h</span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"> .c.o: </span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ${QUIET_CC}${CC} ${ESLINC} ${SRCINC} ${CFLAGS} ${DEFS} -o $@ -c $< </span></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ${QUIET_CC}${CC} ${CPPFLAGS} ${ESLINC} ${SRCINC} ${CFLAGS} ${DEFS} -o $@ -c $< </span></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"> distclean: clean</span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"> -rm -f Makefile</span></pre>
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<a href="https://salsa.debian.org/med-team/infernal/compare/21c20708447abd0b24921c624af953f4983e555a...aca65ff937b1cd5d961ba8f56e787444525ad5b4#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">#format_security.patch</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">#autoreconf.patch</span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">spelling.patch</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">hardening</span></pre>
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<a href="https://salsa.debian.org/med-team/infernal/compare/21c20708447abd0b24921c624af953f4983e555a...aca65ff937b1cd5d961ba8f56e787444525ad5b4#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">@@ -20,8 +20,11 @@ override_dh_auto_clean:</td>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="make"><span class="nl">override_dh_compress </span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="make"> dh_compress <span class="nt" style="color: #000080;">-X</span>.pdf</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="make"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="make"><span class="nl">override_dh_auto_build</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="make"> dh_auto_build <span class="nt" style="color: #000080;">--</span> <span class="nv" style="color: #008080;">V</span><span class="o" style="font-weight: 600;">=</span>1</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="make"><span class="nl">override_dh_auto_install</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="make"> <span class="nv" style="color: #008080;">$(MAKE)</span> <span class="nb" style="color: #0086b3;">install </span><span class="nv" style="color: #008080;">prefix</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$(CURDIR)</span>/debian/tmp</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="make"> <span class="nv" style="color: #008080;">$(MAKE)</span> <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;"><span class="idiff left">-j</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">$(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">shell</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">nproc</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">AM_UPDATE_INFO_DIR</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff">no </span><span class="nv" style="color: #008080;"><span class="idiff">V</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right">1 </span><span class="nv" style="color: #008080;">prefix</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$(CURDIR)</span>/debian/tmp</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="make"><span class="nl">override_dh_install</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="make"> dh_install</span>
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