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<h3>
Aaron M. Ucko pushed to branch master
at <a href="https://salsa.debian.org/med-team/sra-sdk">Debian Med / sra-sdk</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/sra-sdk/-/commit/c99f53c5f9f7dcfb0a74e2f0821fc6c8a807d3a3">c99f53c5</a></strong>
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<span>by Aaron M. Ucko</span>
<i>at 2021-10-18T21:31:06-04:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">allow_multi_help.patch (new): Tolerate extra --help in driver-tool.
</pre>
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<strong><a href="https://salsa.debian.org/med-team/sra-sdk/-/commit/a779f60e5e3aab5e1c15af9fe7b7231c4adadc28">a779f60e</a></strong>
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<span>by Aaron M. Ucko</span>
<i>at 2021-10-18T21:34:58-04:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">run_unversioned_tools.patch (new): Run tools by unversioned names
... per Debian's simplified installation arrangement.
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#7a04279dfa858a66c29dee9cd16387df40e4815c">
<span class="new-file">
+
debian/patches/allow_multi_help.patch
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<li class="file-stats">
<a href="#2aad1840c7a3048adafe52a8e758011861e55aa6">
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+
debian/patches/run_unversioned_tools.patch
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/sra-sdk/-/compare/8dac48d0b489b1f950ae805adc69f42f3642471a...a779f60e5e3aab5e1c15af9fe7b7231c4adadc28#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12,8 +12,12 @@ sra-sdk (2.11.2+dfsg-1) UNRELEASED; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> absent ngs library.</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> * debian/rules: Stop renaming kget (to avoid a file conflict, #851219)</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> now that it's retired altogether.</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> * d/p/allow_multi_help.patch (new): Tolerate redundant --help</span>
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<td class="new_line diff-line-num new" data-linenumber="16" 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="LC16" class="line" lang="plaintext"> declarations within tools/driver-tool.</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> * d/p/run_unversioned_tools.patch (new): Look for tools by their</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> unversioned names, per Debian's simplified installation arrangement.</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="LC16" class="line" lang="plaintext"> -- A<span class="idiff left">ndreas Tille <tille</span>@debian.org> <span class="idiff">Fri</span>, 1<span class="idiff">5</span> Oct 2021 <span class="idiff right">07:01:52 +02</span>00</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> -- A<span class="idiff left">aron M. Ucko <ucko</span>@debian.org> <span class="idiff">Mon</span>, 1<span class="idiff">8</span> Oct 2021 <span class="idiff right">21:34:57 -04</span>00</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">sra-sdk (2.10.9+dfsg-2) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"></span>
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<li id="7a04279dfa858a66c29dee9cd16387df40e4815c">
<a href="https://salsa.debian.org/med-team/sra-sdk/-/compare/8dac48d0b489b1f950ae805adc69f42f3642471a...a779f60e5e3aab5e1c15af9fe7b7231c4adadc28#7a04279dfa858a66c29dee9cd16387df40e4815c"><strong>debian/patches/allow_multi_help.patch</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">Last-Update: Mon, 18 Oct 2021 19:00:59 -0400</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Description: Tolerate redundant --help declarations within tools/driver-tool.</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/tools/driver-tool/cmdline.cpp</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/tools/driver-tool/cmdline.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -1622,7 +1622,7 @@</span> namespace ncbi</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> std :: pair < String, Option * > long_pair ( opt -> long_name, opt );</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> std :: pair < std :: map < String, Option * > :: iterator, bool > long_found</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> = mode -> long_opt_map . insert ( long_pair );</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if ( ! long_found . second )</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if ( ! long_found . second && opt -> long_name != "help" )</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> {</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> NULTerminatedString zlong_name ( opt -> long_name );</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> throw LogicException (</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="p">@@ -1640,7 +1640,7 @@</span> namespace ncbi</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> std :: pair < String, Option * > short_pair ( opt -> short_name, opt );</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> std :: pair < std :: map < String, Option * > :: iterator, bool > short_found</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> = mode -> short_opt_map . insert ( short_pair );</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if ( ! short_found . second )</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if ( ! short_found . second && opt -> long_name != "help" )</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> {</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> NULTerminatedString zshort_name ( opt -> short_name );</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> throw LogicException (</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="p">@@ -1678,7 +1678,8 @@</span> namespace ncbi</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> }</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> else</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> {</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if ( memcmp ( pshort . data (), oshort . data (), oshort . size () ) == 0 )</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if ( memcmp ( pshort . data (), oshort . data (), oshort . size () ) == 0</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ && opt -> long_name != "help" )</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> NULTerminatedString zoshort ( oshort );</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> NULTerminatedString zpshort ( pshort );</span></pre>
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<a href="https://salsa.debian.org/med-team/sra-sdk/-/compare/8dac48d0b489b1f950ae805adc69f42f3642471a...a779f60e5e3aab5e1c15af9fe7b7231c4adadc28#2aad1840c7a3048adafe52a8e758011861e55aa6"><strong>debian/patches/run_unversioned_tools.patch</strong></a>
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1
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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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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Mon, 18 Oct 2021 20:28:26 -0400</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Description: Look for tools by their unversioned names, per Debian's</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> simplified installation arrangement.</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">--- a/tools/driver-tool/tool-path.hpp</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tools/driver-tool/tool-path.hpp</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -72,7 +72,7 @@</span> public:</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> return path_ + ToolPath::seperator + basename_ + ".exe";</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> #else // POSIX</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> auto result = path_ + ToolPath::seperator + basename_;</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if (version_.size() > 0) result += '.' + version_;</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ // if (version_.size() > 0) result += '.' + version_;</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> return result;</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> #endif</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> }</span></pre>
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<a href="https://salsa.debian.org/med-team/sra-sdk/-/compare/8dac48d0b489b1f950ae805adc69f42f3642471a...a779f60e5e3aab5e1c15af9fe7b7231c4adadc28#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">@@ -22,3 +22,5 @@ use_exposed_headers.patch</td>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">skip_broken_loaders.patch</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">fix_libngs_linkage.patch</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">skip_test_using_lots_of_memory.patch</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">allow_multi_help.patch</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">run_unversioned_tools.patch</span></pre>
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