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<h3>
Aaron M. Ucko pushed to branch master
at <a href="https://salsa.debian.org/med-team/ncbi-blastplus">Debian Med / ncbi-blastplus</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-blastplus/-/commit/bdbae23d62335c45048673d73faf4d516411849d">bdbae23d</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2020-04-26T17:51:01-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">override_dh_clean: rm -rf fakehome c++/include/common/ncbi_revision.h
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-blastplus/-/commit/c3e321f11eb6c23c00d5ecd3ac989b8b60c86c4f">c3e321f1</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2020-04-26T17:58:16-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">+ d/patches/support_gcc10 for formal support of GCC 10+ (#957581).
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-blastplus/-/commit/3c25a8bc17ef634a05a67e20ba7a163c32787c0b">3c25a8bc</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2020-04-26T19:30:04-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">override_dh_install-arch: No .py for new cleanup-blastdb-volumes.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-blastplus/-/commit/75d69f12a1646f03ba36f8e5a9d59955b0b5ce12">75d69f12</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2020-04-26T19:30:51-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">+ d/patches/run_perl_directly for update_blastdb(.pl)'s #! line.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-blastplus/-/commit/501c028cc969c59b664e3ee50f960ec76bad0ddf">501c028c</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2020-04-26T19:30:51-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debian/rules: Half clean up -Wl,-as-needed.
Stop directly injecting -Wl,--as-needed into LDFLAGS, but keep
DEB_LDFLAGS_MAINT_APPEND for the sake of backports, along with a
comment that they can't rely on GCC 9+.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-blastplus/-/commit/36632f0fbb0c3a611416ebdc01e224271cdc4e38">36632f0f</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2020-04-26T19:32:56-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Add salsa-ci file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-blastplus/-/commit/77b9f02ee02e686bf8fe65aa458b5fcc9eeeb994">77b9f02e</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2020-04-26T19:35:09-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Wrap long lines in changelog entries: 2.2.25-6.
Fixes: lintian: debian-changelog-line-too-long
See-also: https://lintian.debian.org/tags/debian-changelog-line-too-long.html
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-blastplus/-/commit/ea0764c2e03c42daa0fc5fc7e78d5c31256f6b6f">ea0764c2</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2020-04-26T19:38:14-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Finalize ncbi-blast+ 2.10.0-1 for unstable.
</pre>
</li>
</ul>
<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#a30240106c3eb2b5f08a3bc6d86e3c40b3594d64">
<span class="new-file">
+
debian/patches/run_perl_directly
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#afd1c874c9aedc13558978d2279ce70823d34b5e">
<span class="new-file">
+
debian/patches/support_gcc10
</span>
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<li class="file-stats">
<a href="#b1dbf22e88351ec0d5d1d1a7f53295504b480e61">
<span class="new-file">
+
debian/salsa-ci.yml
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</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/ncbi-blastplus/-/compare/ef898b4071b9b52c91692c9a434937c1c73041ca...ea0764c2e03c42daa0fc5fc7e78d5c31256f6b6f#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">ncbi-blast+ (2.10.0-1) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">ncbi-blast+ (2.10.0-1) <span class="idiff left right">unstable</span>; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"> * New upstream release. (NOT RELEASED YET.)</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> * debian/patches: Formally refresh. (A few files needed straightforward</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> manual intervention.)</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> -- Aaron M. Ucko <ucko@debian.org> Sat, 25 Apr 2020 22:13:31 -0400</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * New upstream release.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * debian/patches:</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> - Formally refresh. (A few files needed straightforward manual</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> intervention.)</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> - support_gcc10: New, for formal support of GCC 10+. (Closes: #957581.)</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> - run_perl_directly: New, to streamline update_blastdb(.pl)'s #! line.</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> * debian/rules:</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> - override_dh_clean: Clean up new generated artifacts: fakehome/ and</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> c++/include/common/ncbi_revision.h.</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> - override_dh_install-arch: Install new cleanup-blastdb-volumes script</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> without its upstream .py suffix.</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> - Stop directly injecting -Wl,--as-needed into LDFLAGS, but keep</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> DEB_LDFLAGS_MAINT_APPEND for the sake of backports, along with a</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> comment that they can't rely on GCC 9+.</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> * Add salsa-ci file (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> * Wrap long lines in changelog entries: 2.2.25-6.</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> -- Aaron M. Ucko <ucko@debian.org> Sun, 26 Apr 2020 19:38:13 -0400</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">ncbi-blast+ (2.9.0-4) unstable; urgency=high</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="383" 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="396" 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">@@ -383,7 +396,8 @@ ncbi-blast+ (2.2.25-7) unstable; urgency=low</td>
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<pre style="margin: 0;"> <span id="LC396" class="line" lang="plaintext">ncbi-blast+ (2.2.25-6) unstable; urgency=low</span>
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<pre style="margin: 0;"> <span id="LC397" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC398" class="line" lang="plaintext"> * debian/control:</span>
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<pre style="margin: 0;">-<span id="LC386" class="line" lang="plaintext"> Luca Capello <luca@pca.it>, fix reference for legacy_blast (Closes: #642986).</span>
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="plaintext"> + Luca Capello <luca@pca.it>, fix reference for legacy_blast</span>
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="plaintext"> (Closes: #642986).</span>
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387
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<pre style="margin: 0;"> <span id="LC401" class="line" lang="plaintext"> + add a new line to separate the actual description from usage</span>
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388
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402
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<pre style="margin: 0;"> <span id="LC402" class="line" lang="plaintext"> instruction in the long Description:.</span>
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389
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403
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<pre style="margin: 0;"> <span id="LC403" class="line" lang="plaintext"> * debian/rules: add gene_info_reader binary in package</span>
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<a href="https://salsa.debian.org/med-team/ncbi-blastplus/-/compare/ef898b4071b9b52c91692c9a434937c1c73041ca...ea0764c2e03c42daa0fc5fc7e78d5c31256f6b6f#a30240106c3eb2b5f08a3bc6d86e3c40b3594d64"><strong>debian/patches/run_perl_directly</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Aaron M. Ucko <ucko@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Date: Sun Apr 26 11:28:03 2020 -0400</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Description: Bypass env in Perl script shebangs.</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">--- a/c++/src/app/blast/update_blastdb.pl</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/c++/src/app/blast/update_blastdb.pl</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</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;">-#!/usr/bin/env perl</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/perl</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> # $Id: update_blastdb.pl 597648 2019-11-25 18:31:12Z ivanov $</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></pre>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/ncbi-blastplus/-/compare/ef898b4071b9b52c91692c9a434937c1c73041ca...ea0764c2e03c42daa0fc5fc7e78d5c31256f6b6f#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,3 +13,5 @@ fix_unit_tests</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">system_mbedtls_only</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">reprobuild</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">spelling</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">support_gcc10</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">run_perl_directly</span></pre>
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<a href="https://salsa.debian.org/med-team/ncbi-blastplus/-/compare/ef898b4071b9b52c91692c9a434937c1c73041ca...ea0764c2e03c42daa0fc5fc7e78d5c31256f6b6f#afd1c874c9aedc13558978d2279ce70823d34b5e"><strong>debian/patches/support_gcc10</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Aaron M. Ucko <ucko@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Date: Sun Apr 26 11:20:45 2020 -0400</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Description: Support GCC 10+.</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Debian-Bug: 957581.</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">Formally recognize GCC 10 and up, even if (as in Debian) -dumpversion</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">reports only one or two components of the version number. Corresponds to</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff">https://www.ncbi.nlm.nih.gov/viewvc/v1?view=revision&revision=88985</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="p">https://www.ncbi.nlm.nih.gov/viewvc/v1?view=revision&revision=88988</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="p">https://www.ncbi.nlm.nih.gov/viewvc/v1?view=revision&revision=88989</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="p">https://www.ncbi.nlm.nih.gov/viewvc/v1?view=revision&revision=89711</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff">though the last of those doesn't apply cleanly without some</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="p">intervening changes for better Clang support.</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff">--- a/c++/src/build-system/config.h.in</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;">+++ b/c++/src/build-system/config.h.in</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="p">@@ -966,7 +966,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> /* Compiler name */</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> #undef NCBI_COMPILER_UNKNOWN</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-/* Compiler version as three-digit integer */</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+/* Compiler version as three- or four-digit integer */</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> #undef NCBI_COMPILER_VERSION</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> /* Compiler name */</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/c++/src/build-system/configure</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/c++/src/build-system/configure</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="p">@@ -8233,9 +8233,10 @@</span> fi</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> case "$compiler:$ncbi_compiler_ver" in</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> WorkShop*:?.?? ) ncbi_compiler_sed='s/\([0-9]\)\.\([0-9][0-9]\)/\1\20/' ;;</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> WorkShop*:[6-9].?) ncbi_compiler_sed='s/\([0-9]\)\.\([0-9\)/\10\20/' ;;</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ICC:??.? ) ncbi_compiler_sed='s/\([0-9][0-9]\)\.\([0-9]\)/\1\20/' ;;</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ICC:??.?.? | \</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ICC:??.?.?.* ) ncbi_compiler_sed='s/\([0-9][0-9]\)\.\([0-9]\)\.\([0-9]\).*/\1\2\3/' ;;</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ [GI]CC:??.? ) ncbi_compiler_sed='s/\([0-9][0-9]\)\.\([0-9]\)/\1\20/' ;;</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ GCC:??.?.? | ICC:??.?.? | ICC:??.?.?.* )</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ncbi_compiler_sed='s/\([0-9][0-9]\)\.\([0-9]\)\.\([0-9]\).*/\1\2\3/' ;;</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ GCC:?? ) ncbi_compiler_sed='s/\([0-9][0-9]\)/\100/' ;;</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> *:?.?.?) ncbi_compiler_sed='s/\([0-9]\)\.\([0-9]\)\.\([0-9]\)/\1\2\3/' ;;</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> *:?.??*) ncbi_compiler_sed='s/\([0-9]\)\.\([0-9][0-9]\).*/\1\2/' ;;</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> *:?.?) ncbi_compiler_sed='s/\([0-9]\).\([0-9]\)/\1\20/' ;;</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="p">@@ -8455,10 +8456,7 @@</span> if test "$with_mt" != "no" ; then</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> # Will allegedly support -openmp at some point, but as of 3.4,</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> # just parses it as specifying an output filename: -o penmp.</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> else</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- case "$compiler_version" in</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [123]?? | 4[01]? ) ;;</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- * ) : ${OPENMP_FLAGS=-fopenmp} ;;</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- esac</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ : ${OPENMP_FLAGS=-fopenmp}</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> fi</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> ;;</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> ICC )</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="p">@@ -8510,16 +8508,14 @@</span> case "$host_os:$compiler" in</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> # "incomplete type is not allowed" should be an error, not a warning!</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> CFLAGS="-we70 $CFLAGS"</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> CXXFLAGS="-we70 $CXXFLAGS"</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- case "$compiler_version" in</span></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;">- 1[1-9]?? ) MATH_LIBS=-Wl,-lm ;; # avoid static libimf in shared libs</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- esac</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ MATH_LIBS=-Wl,-lm # avoid static libimf in shared libs</span></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"> linux*:GCC )</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> if test -r $srcdir/src/build-system/config.site.ncbi && test -d "$NCBI"</span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> then</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> case "$compiler_version" in</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 5* ) CPPFLAGS="-D_GLIBCXX_USE_CXX11_ABI=0 $CPPFLAGS" ;;</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ 5?? ) CPPFLAGS="-D_GLIBCXX_USE_CXX11_ABI=0 $CPPFLAGS" ;;</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> esac</span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"> fi</span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> ;;</span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="p">@@ -9888,7 +9884,7 @@</span> esac</span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> ### large file support (switch to AC_SYS_LARGEFILE?)</span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"> case "$host_os:$compiler:$compiler_version" in</span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> cygwin* ) with_lfs=no ;;</span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- *:GCC:3[4-9]* | *:GCC:[4-9]* | *:ICC:[91]* ) : ${with_lfs=yes} ;;</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ *:GCC:* | *:ICC:* ) : ${with_lfs=yes} ;;</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"> esac</span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"> if test "$with_lfs" = "yes" ; then</span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"><span class="p">@@ -9910,17 +9906,9 @@</span> wsrx="[$wschars]"</span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> #### Flags to enable (potentially unsafe) extra optimization.</span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"> if test "$skip_fast_flags" = no -a -z "$DEF_FAST_FLAGS" ; then</span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> case "$compiler:$compiler_version" in</span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- GCC:2* | GCC:344 )</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # GCC 2.9x sometimes experiences internal errors at high optimization;</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # GCC 3.4.4 (at least on FreeBSD) meanwhile generates crashprone code.</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- DEF_FAST_FLAGS="-O2"</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ;;</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> GCC:* )</span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"> DEF_FAST_FLAGS="-O3 -finline-functions -fstrict-aliasing"</span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- case "$host_os:$host_cpu:$compiler_version" in</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- freebsd* | solaris*:*86*:* | *:4[5-9]? | *:[5-9]?? ) ;;</span></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;">- * ) DEF_FAST_FLAGS="$DEF_FAST_FLAGS -ffast-math" ;;</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- esac</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # DEF_FAST_FLAGS="$DEF_FAST_FLAGS -ffast-math" ;;</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"> if test "$with_profiling" != "yes"; then</span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"> # incompatible with -pg</span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"> DEF_FAST_FLAGS="$DEF_FAST_FLAGS -fomit-frame-pointer"</span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="p">@@ -9958,15 +9946,6 @@</span> if test "$skip_fast_flags" = no -a -z "$</span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"> solaris* ) DEF_FAST_FLAGS="$DEF_FAST_FLAGS -fast $ARCH_CFLAGS" ;;</span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"> esac</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"><span class="gd" style="color: #000; background-color: #fdd;">- ICC:[1-8]?? )</span></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;">- DEF_FAST_FLAGS="-O2"</span></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ;;</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ICC:9?? )</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- DEF_FAST_FLAGS="-O3 -axP -ip" # optimized for Core or P4 w/SSE3 (max)</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ;;</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ICC:10?? )</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- DEF_FAST_FLAGS="-O3 -axT -ip" # Core 2 w/SSSE3; axS would cover SSE 4.1</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ;;</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"> ICC:* )</span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"> # Core 2; ICC 11 goes up to SSE4.2 (i7), ICC 12 up to CORE-AVX-I</span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"> DEF_FAST_FLAGS="-O3 -axSSSE3 -ip"</span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"><span class="p">@@ -10108,12 +10087,7 @@</span> echo "$as_me: error: Unable to find stat</span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"> ;;</span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"> GCC:* )</span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"> # Need to specify runpath for compiler-provided libraries</span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- case $compiler_version in</span></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 30* ) major=3 ;;</span></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 31* ) major=4 ;;</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 3[23]*) major=5 ;;</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- * ) major=6 ;;</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- esac</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ major=6 # true for all supported versions at present</span></span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"> found=false</span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"> for f in libstdc++.so.$major libgcc_s.so.1 libstdc++.a; do</span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"> path=`$CXX $LDFLAGS -print-file-name=$f`</span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"><span class="p">@@ -10294,9 +10268,6 @@</span> esac</span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"> if test "$compiler" = "GCC" ; then</span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"> CFLAGS="-Wall -Wno-format-y2k $CFLAGS"</span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"> CXXFLAGS="-Wall -Wno-format-y2k $CXXFLAGS"</span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- case "$compiler_version" in</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 2* ) CXXFLAGS="-ftemplate-depth-32 $CXXFLAGS" ;;</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- esac</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"> case "$host_os" in</span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"> solaris* ) CPPFLAGS="-D__EXTENSIONS__ $CPPFLAGS" ;;</span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"> irix* ) CXXFLAGS="$CXXFLAGS -D_LANGUAGE_C_PLUS_PLUS" ;;</span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"><span class="p">@@ -13214,13 +13185,11 @@</span> _ACEOF</span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"> ;;</span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"> linux* | *gnu* ) # | *bsd*</span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"> case "$compiler:$compiler_version" in</span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ICC:9* | ICC:1??? )</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ICC:* )</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"> ncbi_cv_prog_cc_wl_no_asu=no</span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"> LIBS="$LIBS -lc"</span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"> C_LIBS="$C_LIBS -lc"</span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"> ;;</span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ICC:* )</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" 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="LC155" class="line" lang="diff"> * )</span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"> FORBID_UNDEF='-Wl,--no-undefined'</span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"> ;;</span>
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"><span class="p">@@ -13963,7 +13932,7 @@</span> echo "$as_me: error: --with-max-debug=$w</span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"> echo " $LDFLAGS " | $EGREP_Q "$dbgrx1|$dbgrx2" || LDFLAGS="$LDFLAGS -g"</span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"> STRIP="@:"</span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"> case "$compiler:$compiler_version" in</span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- GCC:4[89]? | GCC:[5-9]? | GCC:???? )</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ GCC:* )</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"> # GCC 4.8 defaults to DWARF 4, which Totalview for one</span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"> # can't handle; roll back to version 3 by default.</span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"> echo " $USER_CFLAGS " | $EGREP_Q "$dbgrx1|$dbgrx2" || \</span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"><span class="p">@@ -25344,10 +25313,6 @@</span> ac_compiler_gnu=$ac_cv_cxx_compiler_gnu</span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"> </span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"> # Avoid using unsupported (and noisily ignored) attributes.</span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff"> case "$compiler:$compiler_version" in</span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- GCC:2* | GCC:3[01]* )</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ncbi_cv_c_deprecation_syntax=none</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ncbi_cv_c_forceinline=inline</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ;;</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"> VisualAge:* )</span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff"> ncbi_cv_c_forceinline=inline</span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="diff"> ;;</span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"><span class="p">@@ -25585,7 +25550,7 @@</span> _ACEOF</span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="diff"> fi</span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="diff"> </span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="diff"> case "$compiler:$compiler_version $CFLAGS $CXXFLAGS" in</span>
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<td class="diff-line-num new new_line" data-linenumber="182" 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">
182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- GCC:[4-9]??\ *\ -fvisibility*|ICC:*\ -fvisibility* ) ;;</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ GCC:*\ *\ -fvisibility* | ICC:*\ -fvisibility* ) ;;</span></span>
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="diff"> * ) ncbi_cv_c_attribute_visibility_default=unnecessary ;;</span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="diff"> esac</span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="diff"><span class="p">@@ -37178,7 +37143,7 @@</span> _ACEOF</span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="diff"> # when using Boost at all.</span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="diff"> BOOST_INCLUDE="$BOOST_INCLUDE -erroff=reftotemp"</span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="diff"> ;;</span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- GCC*:4[7-9]* | GCC*:5*)</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ GCC*)</span></span>
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="diff"> # Some portions of Boost also have a lot of "unused" typedefs</span>
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="diff"> # from concept checking.</span>
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="diff"> BOOST_INCLUDE="$BOOST_INCLUDE -Wno-unused-local-typedefs"</span>
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="diff"><span class="p">@@ -37221,6 +37186,7 @@</span> echo $ECHO_N "checking for Boost library</span>
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="diff"> *:MSVC) BOOST_TAG="-vc" ;;</span>
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="diff"> esac</span>
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="diff"> case "$BOOST_TAG" in</span>
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # Still valid for version 10.x and up?</span></span>
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="diff"> -*gcc|-il ) boost_comp_vers=`echo $compiler_version | cut -c1-2` ;;</span>
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="diff"> * ) boost_comp_vers='' ;;</span>
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="diff"> esac</span>
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/c++/src/build-system/configure.ac</span></span>
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/c++/src/build-system/configure.ac</span></span>
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="diff"><span class="p">@@ -1257,9 +1257,10 @@</span> changequote(, )dnl</span>
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="diff"> case "$compiler:$ncbi_compiler_ver" in</span>
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="diff"> WorkShop*:?.?? ) ncbi_compiler_sed='s/\([0-9]\)\.\([0-9][0-9]\)/\1\20/' ;;</span>
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="diff"> WorkShop*:[6-9].?) ncbi_compiler_sed='s/\([0-9]\)\.\([0-9\)/\10\20/' ;;</span>
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ICC:??.? ) ncbi_compiler_sed='s/\([0-9][0-9]\)\.\([0-9]\)/\1\20/' ;;</span></span>
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ICC:??.?.? | \</span></span>
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ICC:??.?.?.* ) ncbi_compiler_sed='s/\([0-9][0-9]\)\.\([0-9]\)\.\([0-9]\).*/\1\2\3/' ;;</span></span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ [GI]CC:??.? ) ncbi_compiler_sed='s/\([0-9][0-9]\)\.\([0-9]\)/\1\20/' ;;</span></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ GCC:??.?.? | ICC:??.?.? | ICC:??.?.?.* )</span></span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ncbi_compiler_sed='s/\([0-9][0-9]\)\.\([0-9]\)\.\([0-9]\).*/\1\2\3/' ;;</span></span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ GCC:?? ) ncbi_compiler_sed='s/\([0-9][0-9]\)/\100/' ;;</span></span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="diff"> *:?.?.?) ncbi_compiler_sed='s/\([0-9]\)\.\([0-9]\)\.\([0-9]\)/\1\2\3/' ;;</span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="diff"> *:?.??*) ncbi_compiler_sed='s/\([0-9]\)\.\([0-9][0-9]\).*/\1\2/' ;;</span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="diff"> *:?.?) ncbi_compiler_sed='s/\([0-9]\).\([0-9]\)/\1\20/' ;;</span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="diff"><span class="p">@@ -1287,7 +1288,7 @@</span> fi</span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="diff"> AC_DEFINE_UNQUOTED(NCBI_COMPILER, "$ncbi_compiler", [Compiler name])</span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="diff"> AC_DEFINE_UNQUOTED(NCBI_COMPILER_$ncbi_compiler, 1, [Compiler name])</span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="diff"> AC_DEFINE_UNQUOTED(NCBI_COMPILER_VERSION, $ncbi_compiler_ver,</span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [Compiler version as three-digit integer])</span></span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ [Compiler version as three- or four-digit integer])</span></span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="diff"> #### Additional check for pre-defined compilers</span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="diff"><span class="p">@@ -1407,10 +1408,7 @@</span> if test "$with_mt" != "no" ; then</span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="diff"> # Will allegedly support -openmp at some point, but as of 3.4,</span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="diff"> # just parses it as specifying an output filename: -o penmp.</span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="diff"> else</span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- case "$compiler_version" in</span></span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [[123]]?? | 4[[01]]? ) ;;</span></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- * ) : ${OPENMP_FLAGS=-fopenmp} ;;</span></span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- esac</span></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ : ${OPENMP_FLAGS=-fopenmp}</span></span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="diff"> fi</span>
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239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="diff"> ;;</span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="diff"> ICC )</span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="diff"><span class="p">@@ -1462,16 +1460,14 @@</span> case "$host_os:$compiler" in</span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="diff"> # "incomplete type is not allowed" should be an error, not a warning!</span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="diff"> CFLAGS="-we70 $CFLAGS"</span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="diff"> CXXFLAGS="-we70 $CXXFLAGS"</span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- case "$compiler_version" in</span></span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 1[[1-9]]?? ) MATH_LIBS=-Wl,-lm ;; # avoid static libimf in shared libs</span></span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- esac</span></span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ MATH_LIBS=-Wl,-lm # avoid static libimf in shared libs</span></span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="diff"> ;;</span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="diff"> linux*:GCC )</span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="diff"> if test -r $srcdir/src/build-system/config.site.ncbi && test -d "$NCBI"</span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="diff"> then</span>
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="diff"> case "$compiler_version" in</span>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 5* ) CPPFLAGS="-D_GLIBCXX_USE_CXX11_ABI=0 $CPPFLAGS" ;;</span></span>
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ 5?? ) CPPFLAGS="-D_GLIBCXX_USE_CXX11_ABI=0 $CPPFLAGS" ;;</span></span>
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="diff"> esac</span>
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="diff"> fi</span>
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="diff"> ;;</span>
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="diff"><span class="p">@@ -2046,7 +2042,7 @@</span> esac</span>
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="diff"> ### large file support (switch to AC_SYS_LARGEFILE?)</span>
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="diff"> case "$host_os:$compiler:$compiler_version" in</span>
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="diff"> cygwin* ) with_lfs=no ;;</span>
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- *:GCC:3[[4-9]]* | *:GCC:[[4-9]]* | *:ICC:[[91]]* ) : ${with_lfs=yes} ;;</span></span>
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ *:GCC:* | *:ICC:* ) : ${with_lfs=yes} ;;</span></span>
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="diff"> esac</span>
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="diff"> if test "$with_lfs" = "yes" ; then</span>
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="diff"><span class="p">@@ -2068,17 +2064,9 @@</span> wsrx="[[$wschars]]"</span>
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="diff"> #### Flags to enable (potentially unsafe) extra optimization.</span>
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="diff"> if test "$skip_fast_flags" = no -a -z "$DEF_FAST_FLAGS" ; then</span>
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="diff"> case "$compiler:$compiler_version" in</span>
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- GCC:2* | GCC:344 )</span></span>
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # GCC 2.9x sometimes experiences internal errors at high optimization;</span></span>
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # GCC 3.4.4 (at least on FreeBSD) meanwhile generates crashprone code.</span></span>
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- DEF_FAST_FLAGS="-O2"</span></span>
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ;;</span></span>
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="diff"> GCC:* )</span>
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="diff"> DEF_FAST_FLAGS="-O3 -finline-functions -fstrict-aliasing"</span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- case "$host_os:$host_cpu:$compiler_version" in</span></span>
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- freebsd* | solaris*:*86*:* | *:4[[5-9]]? | *:[[5-9]]?? ) ;;</span></span>
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- * ) DEF_FAST_FLAGS="$DEF_FAST_FLAGS -ffast-math" ;;</span></span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- esac</span></span>
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # DEF_FAST_FLAGS="$DEF_FAST_FLAGS -ffast-math" ;;</span></span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="diff"> if test "$with_profiling" != "yes"; then</span>
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="diff"> # incompatible with -pg</span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="diff"> DEF_FAST_FLAGS="$DEF_FAST_FLAGS -fomit-frame-pointer"</span>
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="diff"><span class="p">@@ -2116,15 +2104,6 @@</span> if test "$skip_fast_flags" = no -a -z "$</span>
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="diff"> solaris* ) DEF_FAST_FLAGS="$DEF_FAST_FLAGS -fast $ARCH_CFLAGS" ;;</span>
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="diff"> esac</span>
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="diff"> ;;</span>
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ICC:[[1-8]]?? )</span></span>
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- DEF_FAST_FLAGS="-O2"</span></span>
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294
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<pre style="margin: 0;">+<span id="LC294" 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="LC295" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ICC:9?? )</span></span>
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- DEF_FAST_FLAGS="-O3 -axP -ip" # optimized for Core or P4 w/SSE3 (max)</span></span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ;;</span></span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ICC:10?? )</span></span>
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- DEF_FAST_FLAGS="-O3 -axT -ip" # Core 2 w/SSSE3; axS would cover SSE 4.1</span></span>
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300
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<pre style="margin: 0;">+<span id="LC300" 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="LC301" class="line" lang="diff"> ICC:* )</span>
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="diff"> # Core 2; ICC 11 goes up to SSE4.2 (i7), ICC 12 up to CORE-AVX-I</span>
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="diff"> DEF_FAST_FLAGS="-O3 -axSSSE3 -ip"</span>
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="diff"><span class="p">@@ -2225,12 +2204,7 @@</span> case "$compiler:$compiler_version:$with_</span>
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="diff"> ;;</span>
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="diff"> GCC:* )</span>
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="diff"> # Need to specify runpath for compiler-provided libraries</span>
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- case $compiler_version in</span></span>
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 30* ) major=3 ;;</span></span>
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 31* ) major=4 ;;</span></span>
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 3[[23]]*) major=5 ;;</span></span>
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- * ) major=6 ;;</span></span>
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- esac</span></span>
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ major=6 # true for all supported versions at present</span></span>
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="diff"> found=false</span>
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="diff"> for f in libstdc++.so.$major libgcc_s.so.1 libstdc++.a; do</span>
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="diff"> path=`$CXX $LDFLAGS -print-file-name=$f`</span>
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="diff"><span class="p">@@ -2388,9 +2362,6 @@</span> AC_SUBST(USUAL_AND_LIB)</span>
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="diff"> if test "$compiler" = "GCC" ; then</span>
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="diff"> CFLAGS="-Wall -Wno-format-y2k $CFLAGS"</span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="diff"> CXXFLAGS="-Wall -Wno-format-y2k $CXXFLAGS"</span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- case "$compiler_version" in</span></span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 2* ) CXXFLAGS="-ftemplate-depth-32 $CXXFLAGS" ;;</span></span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- esac</span></span>
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="diff"> case "$host_os" in</span>
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="diff"> solaris* ) CPPFLAGS="-D__EXTENSIONS__ $CPPFLAGS" ;;</span>
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="diff"> irix* ) CXXFLAGS="$CXXFLAGS -D_LANGUAGE_C_PLUS_PLUS" ;;</span>
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="diff"><span class="p">@@ -3029,13 +3000,11 @@</span> case "$compiler" in</span>
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="diff"> ;;</span>
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="diff"> linux* | *gnu* ) # | *bsd*</span>
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="diff"> case "$compiler:$compiler_version" in</span>
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ICC:9* | ICC:1??? )</span></span>
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ICC:* )</span></span>
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="diff"> ncbi_cv_prog_cc_wl_no_asu=no</span>
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="diff"> LIBS="$LIBS -lc"</span>
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336
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="diff"> C_LIBS="$C_LIBS -lc"</span>
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337
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="diff"> ;;</span>
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ICC:* )</span></span>
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ;;</span></span>
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340
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="diff"> * )</span>
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="diff"> FORBID_UNDEF='-Wl,--no-undefined'</span>
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342
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="diff"> ;;</span>
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="diff"><span class="p">@@ -3319,7 +3288,7 @@</span> changequote(, )dnl</span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="diff"> echo " $LDFLAGS " | $EGREP_Q "$dbgrx1|$dbgrx2" || LDFLAGS="$LDFLAGS -g"</span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="diff"> STRIP="@:"</span>
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="diff"> case "$compiler:$compiler_version" in</span>
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- GCC:4[89]? | GCC:[5-9]? | GCC:???? )</span></span>
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ GCC:* )</span></span>
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="diff"> # GCC 4.8 defaults to DWARF 4, which Totalview for one</span>
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="diff"> # can't handle; roll back to version 3 by default.</span>
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351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="diff"> echo " $USER_CFLAGS " | $EGREP_Q "$dbgrx1|$dbgrx2" || \</span>
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="diff"><span class="p">@@ -3929,10 +3898,6 @@</span> AC_LANG_POP(C)</span>
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353
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="diff"> # Avoid using unsupported (and noisily ignored) attributes.</span>
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="diff"> case "$compiler:$compiler_version" in</span>
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356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- GCC:2* | GCC:3[[01]]* )</span></span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ncbi_cv_c_deprecation_syntax=none</span></span>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ncbi_cv_c_forceinline=inline</span></span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ;;</span></span>
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360
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="diff"> VisualAge:* )</span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="diff"> ncbi_cv_c_forceinline=inline</span>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="diff"> ;;</span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="diff"><span class="p">@@ -3985,7 +3950,7 @@</span> if test $ncbi_cv_c_attribute_destructor</span>
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364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="diff"> fi</span>
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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="diff"> </span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="diff"> case "$compiler:$compiler_version $CFLAGS $CXXFLAGS" in</span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- GCC:[[4-9]]??\ *\ -fvisibility*|ICC:*\ -fvisibility* ) ;;</span></span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ GCC:*\ *\ -fvisibility* | ICC:*\ -fvisibility* ) ;;</span></span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="diff"> * ) ncbi_cv_c_attribute_visibility_default=unnecessary ;;</span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="diff"> esac</span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="diff"><span class="p">@@ -5632,7 +5597,7 @@</span> ncbi_cv_lib_boost_version=\`get_BOOST_LI</span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="diff"> # when using Boost at all.</span>
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="diff"> BOOST_INCLUDE="$BOOST_INCLUDE -erroff=reftotemp"</span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="diff"> ;;</span>
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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- GCC*:4[[7-9]]* | GCC*:5*)</span></span>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ GCC*)</span></span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="diff"> # Some portions of Boost also have a lot of "unused" typedefs</span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="diff"> # from concept checking.</span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="diff"> BOOST_INCLUDE="$BOOST_INCLUDE -Wno-unused-local-typedefs"</span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="diff"><span class="p">@@ -5672,6 +5637,7 @@</span> ncbi_cv_lib_boost_version=\`get_BOOST_LI</span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="diff"> *:MSVC) BOOST_TAG="-vc" ;;</span>
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="diff"> esac</span>
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="diff"> case "$BOOST_TAG" in</span>
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # Still valid for version 10.x and up?</span></span>
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="diff"> -*gcc|-il ) boost_comp_vers=`echo $compiler_version | cut -c1-2` ;;</span>
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="diff"> * ) boost_comp_vers='' ;;</span>
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="diff"> esac</span></pre>
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<a href="https://salsa.debian.org/med-team/ncbi-blastplus/-/compare/ef898b4071b9b52c91692c9a434937c1c73041ca...ea0764c2e03c42daa0fc5fc7e78d5c31256f6b6f#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">@@ -26,13 +26,12 @@ DEB_CONFIGURE_EXTRA_FLAGS += --with-symbols</td>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#export DEB_BUILD_MAINT_OPTIONS=hardening=+all,-pie</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="make"><span class="k" style="font-weight: 600;">export </span><span class="nv" style="color: #008080;">DEB_BUILD_MAINT_OPTIONS</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">hardening</span><span class="o" style="font-weight: 600;">=</span>+all,-pie</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="make"><span class="k" style="font-weight: 600;">export </span><span class="nv" style="color: #008080;">DEB_CFLAGS_MAINT_APPEND</span><span class="o" style="font-weight: 600;">=</span><span class="nt" style="color: #000080;">-Wall</span> <span class="nt" style="color: #000080;">-pedantic</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Kept for the sake of backports, which can't rely on GCC 9+.</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="make"><span class="k" style="font-weight: 600;">export </span><span class="nv" style="color: #008080;">DEB_LDFLAGS_MAINT_APPEND</span><span class="o" style="font-weight: 600;">=</span><span class="nt" style="color: #000080;">-Wl</span>,--as-needed</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="make"><span class="k" style="font-weight: 600;">include</span><span class="sx" style="color: #d14;"> /usr/share/dpkg/architecture.mk</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="make"><span class="k" style="font-weight: 600;">include</span><span class="sx" style="color: #d14;"> /usr/share/dpkg/buildflags.mk</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="make"><span class="nv" style="color: #008080;">LDFLAGS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nt" style="color: #000080;">-Wl</span>,--as-needed</span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="make"><span class="k" style="font-weight: 600;">ifneq</span> <span class="nv" style="color: #008080;">(,$(findstring mips,$(DEB_HOST_ARCH)))</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="make"><span class="nv" style="color: #008080;">CXXFLAGS</span> <span class="o" style="font-weight: 600;">:=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>CXXFLAGS:-O%<span class="o" style="font-weight: 600;">=</span><span class="nt" style="color: #000080;">-O</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="make"><span class="nv" style="color: #008080;">DEB_CONFIGURE_EXTRA_FLAGS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nv" style="color: #008080;">FAST_CXXFLAGS</span><span class="o" style="font-weight: 600;">=</span><span class="nt" style="color: #000080;">-O</span></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">@@ -99,6 +98,8 @@ override_dh_install-arch:</td>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="make"> <span class="nb" style="color: #0086b3;">mv</span> <span class="nv" style="color: #008080;">$(instroot)</span>/bin/seedtop <span class="nv" style="color: #008080;">$(instroot)</span>/bin/seedtop+</span>
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<td class="diff-line-num new_line" data-linenumber="99" 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">
99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="make"> <span class="nb" style="color: #0086b3;">mv</span> <span class="nv" style="color: #008080;">$(instroot)</span>/bin/get_species_taxids.sh <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num old_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
101
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<td class="diff-line-num new_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="make"> <span class="nv" style="color: #008080;">$(instroot)</span>/bin/get_species_taxids</span>
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<td class="diff-line-num new old_line" data-linenumber="102" 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="101" 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">
101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="make"> <span class="nb" style="color: #0086b3;">mv</span> <span class="nv" style="color: #008080;">$(instroot)</span>/bin/cleanup-blastdb-volumes.py <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new old_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="make"> <span class="nv" style="color: #008080;">$(instroot)</span>/bin/cleanup-blastdb-volumes</span>
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<td class="diff-line-num old_line" data-linenumber="102" 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">
102
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<td class="diff-line-num new_line" data-linenumber="103" 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">
103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="make"> <span class="nb" style="color: #0086b3;">mv</span> <span class="nv" style="color: #008080;">$(instroot)</span>/bin/legacy_blast.pl <span class="nv" style="color: #008080;">$(instroot)</span>/bin/legacy_blast</span>
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<td class="diff-line-num old_line" data-linenumber="103" 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">
103
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<td class="diff-line-num new_line" data-linenumber="104" 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">
104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="make"> <span class="nb" style="color: #0086b3;">mv</span> <span class="nv" style="color: #008080;">$(instroot)</span>/bin/update_blastdb.pl <span class="nv" style="color: #008080;">$(instroot)</span>/bin/update_blastdb</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="104" 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">
104
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<td class="diff-line-num new_line" data-linenumber="105" 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">
105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="make"> <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'1s/$$/3/'</span> <span class="nv" style="color: #008080;">$(instroot)</span>/bin/windowmasker_2.2.22_adapter.py <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="157" 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="158" 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">@@ -157,8 +158,9 @@ override_dh_clean:</td>
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157
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<td class="diff-line-num new_line" data-linenumber="158" 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">
158
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="make"> <span class="k" style="font-weight: 600;">done</span></span>
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<td class="diff-line-num old_line" data-linenumber="158" 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">
158
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<td class="diff-line-num new_line" data-linenumber="159" 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">
159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">rm</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-rf</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">c++/compilers/dll</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">c++/config.log</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">c++/Makefile</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="159" 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">
159
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<td class="diff-line-num new_line" data-linenumber="160" 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">
160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">rm</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-f</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">c++/configure.lineno</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">c++/src/objects/blastxml/blastxml.module</span></span>
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<td class="diff-line-num new old_line" data-linenumber="160" 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="161" 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">
161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">rm</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-f</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">c++/include/common/ncbi_revision.h</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="160" 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">
160
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<td class="diff-line-num new_line" data-linenumber="162" 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">
162
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">find</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-name</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">check_exec.pid</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-delete</span></span>
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<td class="diff-line-num old old_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
161
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<td class="diff-line-num new_line old" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">rm</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-rf</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">c++/BUILD</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">c++/BUILD.native</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="162" 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="163" 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">
163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">rm</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-rf</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">c++/BUILD</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">c++/BUILD.native</span><span class="idiff left"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff right">fakehome</span></span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="162" 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">
162
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<td class="diff-line-num new_line" data-linenumber="164" 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">
164
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">mv</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">configure.orig.save</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">c++/configure.orig</span></span>
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<td class="diff-line-num old_line" data-linenumber="163" 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">
163
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<td class="diff-line-num new_line" data-linenumber="165" 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">
165
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">mv</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">c++/src/util/lmdb/Makefile.orig.save</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">c++/src/util/lmdb/Makefile.orig</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="164" 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">
164
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<td class="diff-line-num new_line" data-linenumber="166" 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">
166
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC166" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">mv</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">c++/src/util/lmdbxx/Makefile.orig.save</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">c++/src/util/lmdbxx/Makefile.orig</span></span>
</pre>
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<a href="https://salsa.debian.org/med-team/ncbi-blastplus/-/compare/ef898b4071b9b52c91692c9a434937c1c73041ca...ea0764c2e03c42daa0fc5fc7e78d5c31256f6b6f#b1dbf22e88351ec0d5d1d1a7f53295504b480e61"><strong>debian/salsa-ci.yml</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="nn" style="color: #555;">---</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2" 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">
2
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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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<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">
3
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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></pre>
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