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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/b3639c90bbbae28778338fbe70b3a9babecc65e1">b3639c90</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2020-10-23T14:01:18-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.10.1+ds</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-blastplus/-/commit/d3605f7d996308a332f73ce3c0af7bf3d1c018d8">d3605f7d</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2020-10-23T14:09:47-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2.10.1+ds'
Update to upstream version '2.10.1+ds'.
Repack without c++/src/build-system/project_tree_builder_gui/bin.
Debian builds make no use of this (Java) GUI or supporting third-party
jars, and could do without prebuilt binaries even if they did use it.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-blastplus/-/commit/8f1185dd0cba27dfb51fca01fbbd2764010cd2a1">8f1185dd</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2020-10-23T14:12:32-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debian/{copyright,watch}: Update for repack without .../ptb_gui/bin.
* copyright: Set Files-Excluded accordingly.
* watch: Set dversionmangle and repacksuffix options accordingly.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-blastplus/-/commit/7fb935e7c71bb57d3475c8213595257bf095ca5b">7fb935e7</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2020-10-23T17:16:48-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debian/copyright: Correct typos for c++/src/html/ncbi_menu*.js.
* Replace duplicate .../ncbi_menu_dnd.js by .../ncbi_menu_dyn.js.
* Correct capitalization of Gary Smith's last name.
* Remove duplicate 1997-1999 for Netscape Communications Corp.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-blastplus/-/commit/e7f8b310e21ab9e0dd1d944c9044e4dbe20e6c0d">e7f8b310</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2020-10-23T17:21:31-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debian/source/lintian-overrides: Extend ncbi_menu*.js overrides.
Override source-contains-prebuilt-javascript-object in addition to
source-is-missing. (These files are editable despite long lines.)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-blastplus/-/commit/5a92988942401bcec4bb4b5212793f79eab09ee0">5a929889</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2020-10-23T17:23:47-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Finalize ncbi-blast+ 2.10.1+ds-1 for unstable.
</pre>
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<h4>7 changed files:</h4>
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<a href="#2b0ee4a743576af26ea1b9709e56670ed19b86d0">
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−
c++/src/build-system/project_tree_builder_gui/bin/lib/swing-layout-1.0.3.jar
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c++/src/build-system/project_tree_builder_gui/bin/lib/swing-layout-1.0.4.jar
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c++/src/build-system/project_tree_builder_gui/bin/ptbgui.jar
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
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debian/source/lintian-overrides
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<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">
debian/watch
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<h4>Changes:</h4>
<li id="2b0ee4a743576af26ea1b9709e56670ed19b86d0">
<a href="https://salsa.debian.org/med-team/ncbi-blastplus/-/compare/bcaf181b6d786ce85b77648643a5de52a23515ab...5a92988942401bcec4bb4b5212793f79eab09ee0#2b0ee4a743576af26ea1b9709e56670ed19b86d0"><strong>c++/src/build-system/project_tree_builder_gui/bin/lib/swing-layout-1.0.3.jar</strong>
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<li id="7c9524ba77e43a6e66ef567ed7d0518a266f03fc">
<a href="https://salsa.debian.org/med-team/ncbi-blastplus/-/compare/bcaf181b6d786ce85b77648643a5de52a23515ab...5a92988942401bcec4bb4b5212793f79eab09ee0#7c9524ba77e43a6e66ef567ed7d0518a266f03fc"><strong>c++/src/build-system/project_tree_builder_gui/bin/lib/swing-layout-1.0.4.jar</strong>
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<li id="e291591cd71249e650d4a78679e39bdf5fc66bd3">
<a href="https://salsa.debian.org/med-team/ncbi-blastplus/-/compare/bcaf181b6d786ce85b77648643a5de52a23515ab...5a92988942401bcec4bb4b5212793f79eab09ee0#e291591cd71249e650d4a78679e39bdf5fc66bd3"><strong>c++/src/build-system/project_tree_builder_gui/bin/ptbgui.jar</strong>
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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/ncbi-blastplus/-/compare/bcaf181b6d786ce85b77648643a5de52a23515ab...5a92988942401bcec4bb4b5212793f79eab09ee0#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">ncbi-blast+ (2.10.1+ds-1) unstable; 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"> * Repack without c++/src/build-system/project_tree_builder_gui/bin.</span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Debian builds make no use of this (Java) GUI or supporting third-party</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> jars, and could do without prebuilt binaries even if they did use it.</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * debian/copyright:</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> - Set Files-Excluded accordingly.</span>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> - Correct typos for c++/src/html/ncbi_menu*.js; in particular, replace</span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> duplicate .../ncbi_menu_dnd.js by .../ncbi_menu_dyn.js.</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> * debian/watch: Set dversionmangle and repacksuffix options accordingly.</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> * debian/source/lintian-overrides: For ncbi_menu*.js, which are editable</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> despite long lines, override source-contains-prebuilt-javascript-object</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> in addition to source-is-missing.</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> -- Aaron M. Ucko <ucko@debian.org> Fri, 23 Oct 2020 17:23:46 -0400</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">ncbi-blast+ (2.10.1-3) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> * debian/patches/tune_lmdb_defaults: Scale down slightly more on 32-bit</span>
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<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">
<a href="https://salsa.debian.org/med-team/ncbi-blastplus/-/compare/bcaf181b6d786ce85b77648643a5de52a23515ab...5a92988942401bcec4bb4b5212793f79eab09ee0#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/</span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Upstream-Name: ncbi-blast+</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Upstream-Contact: blastsoft@ncbi.nlm.nih.gov</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Files-Excluded: c++/src/build-system/project_tree_builder_gui/bin</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Files: c++/*</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Copyright: NCBI</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">@@ -42,9 +43,9 @@ License: Apache-2.0</td>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext">Files: c++/src/html/ncbi_menu.js</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext"> c++/src/html/ncbi_menu_dnd.js</span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="plaintext"> c++/src/html/ncbi_menu_d<span class="idiff left right">nd</span>.js</span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="plaintext">Copyright: 1997 Gary S<span class="idiff left right">M</span>ith</span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="plaintext"> 1997-1999 <span class="idiff left right">1997-1999 </span>Netscape Communications Corp.</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> c++/src/html/ncbi_menu_d<span class="idiff left right">yn</span>.js</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">Copyright: 1997 Gary S<span class="idiff left right">m</span>ith</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> 1997-1999 Netscape Communications Corp.</span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext">License: Netscape</span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext"> Netscape grants you a royalty free license to use or modify this</span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext"> software provided that this copyright notice appears on all copies.</span>
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<li id="85ccdeeb03055211183e48520592d9a93592b330">
<a href="https://salsa.debian.org/med-team/ncbi-blastplus/-/compare/bcaf181b6d786ce85b77648643a5de52a23515ab...5a92988942401bcec4bb4b5212793f79eab09ee0#85ccdeeb03055211183e48520592d9a93592b330"><strong>debian/source/lintian-overrides</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,6 +2,9 @@</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">ncbi-blast+ source: source-is-missing c++/src/html/ncbi_menu.js line length is 357 characters (>256)</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">ncbi-blast+ source: source-is-missing c++/src/html/ncbi_menu_dnd.js line length is 333 characters (>256)</span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">ncbi-blast+ source: source-is-missing c++/src/html/ncbi_menu_dyn.js line length is 333 characters (>256)</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">ncbi-blast+ source: source-contains-prebuilt-javascript-object c++/src/html/ncbi_menu.js line length is 357 characters (>256)</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">ncbi-blast+ source: source-contains-prebuilt-javascript-object c++/src/html/ncbi_menu_dnd.js line length is 333 characters (>256)</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">ncbi-blast+ source: source-contains-prebuilt-javascript-object c++/src/html/ncbi_menu_dyn.js line length is 333 characters (>256)</span>
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5
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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"># JSON not evil license, related code is not present</span>
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6
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">ncbi-blast+ source: license-problem-json-evil c++/include/misc/jsonwrapp/rapidjson10/license.txt</span>
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7
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">ncbi-blast+ source: license-problem-json-evil c++/include/misc/jsonwrapp/rapidjson11/license.txt</span></pre>
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<a href="https://salsa.debian.org/med-team/ncbi-blastplus/-/compare/bcaf181b6d786ce85b77648643a5de52a23515ab...5a92988942401bcec4bb4b5212793f79eab09ee0#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">version=3</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">opts=filenamemangle=s/\+-src/-orig/,filenamemangle=s/blast/blast+/ \</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">opts=filenamemangle=s/\+-src/-orig/,filenamemangle=s/blast/blast+/<span class="idiff left right">,dversionmangle=s/\+ds//,repacksuffix=+ds</span> \</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-(.*)\+-src\.tar\.gz debian uupdate</span></pre>
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