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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>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/sra-sdk/-/commit/94b390d077a614d371d2c5727498f89b979e6333">94b390d0</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2020-05-22T09:25:14-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">sra-sdk 2.10.6+dfsg-4: Account for new sratools setup (#961256).
* debian/rules: Rework deversioning logic to account for sratools and
*-orig.* while still keeping hardcoding to a minimum; formally
supply a hardcoded but originally random standard installation ID in
a new /etc/ncbi/debian.kfg.
* debian/patches/use_unversioned_tools.patch (new): Have sratools look
for executable names without version extensions.
</pre>
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<h4>4 changed files:</h4>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#54a86f2fa1d3565fa9b7afd9ff8705afbae67d62">
<span class="new-file">
+
debian/patches/use_unversioned_tools.patch
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/sra-sdk/-/commit/94b390d077a614d371d2c5727498f89b979e6333#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">sra-sdk (2.10.6+dfsg-4) 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"> * Account for new sratools setup. (Closes: #961256.)</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> - debian/rules: Rework deversioning logic to account for sratools and</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> *-orig.* while still keeping hardcoding to a minimum; formally</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> supply a hardcoded but originally random standard installation ID in</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> a new /etc/ncbi/debian.kfg.</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> - debian/patches/use_unversioned_tools.patch (new): Have sratools look</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> for executable names without version extensions.</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> -- Aaron M. Ucko <ucko@debian.org> Fri, 22 May 2020 09:25:13 -0400</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">sra-sdk (2.10.6+dfsg-3) unstable; urgency=medium</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"> * Also exclude sra-pileup check_skiplist test per network access.</span>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/sra-sdk/-/commit/94b390d077a614d371d2c5727498f89b979e6333#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="18" 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="18" 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">@@ -18,3 +18,4 @@ drop_tests.patch</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">ignore_failing_test_for_the_moment_FIXME.patch</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">python3</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">use_exposed_headers.patch</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">use_unversioned_tools.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/sra-sdk/-/commit/94b390d077a614d371d2c5727498f89b979e6333#54a86f2fa1d3565fa9b7afd9ff8705afbae67d62"><strong>debian/patches/use_unversioned_tools.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="gh" style="color: #999;">Index: b/tools/driver-tool/tool-path.hpp</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tools/driver-tool/tool-path.hpp</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tools/driver-tool/tool-path.hpp</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">@@ -71,7 +71,7 @@</span> public:</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> #if WINDOWS</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> return path_ + ToolPath::seperator + basename_ + ".exe";</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> #else // POSIX</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return path_ + ToolPath::seperator + basename_ + '.' + version_;</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return path_ + ToolPath::seperator + basename_ /* + '.' + version_ */;</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> #endif</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> bool executable() const {</span></pre>
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<a href="https://salsa.debian.org/med-team/sra-sdk/-/commit/94b390d077a614d371d2c5727498f89b979e6333#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">#!/usr/bin/make -f</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"># Pregenerated with uuidgen -r</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">DEBIAN_GUID = 806b5c3b-0088-4732-8359-51630950d723</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"># +pie breaks the build</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">export DEB_BUILD_MAINT_OPTIONS = hardening=+all</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -46,15 +49,29 @@ override_dh_auto_install:</td>
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49
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext">override_dh_install:</span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext"> # upstream installs versioned *.a libs - we only want a single version</span>
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49
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="plaintext"> for bin in debian/tmp/usr/bin/*[a-z] ; do \</span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="plaintext"> mv debian/tmp/usr/bin/`readlink $$bin` $$bin ; \</span>
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51
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="plaintext"> mv debian/tmp/usr/bin/`readlink $$bin` $$bin ; \</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"> ls -l debian/tmp/usr/bin</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"> cd debian/tmp/usr/bin && \</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"> for bin in *-orig.* ; do \</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"> base=$${bin%-orig.*} && \</span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"> vbase=$$(readlink "$$(readlink $$base)") && \</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"> vdriver=$$(readlink "$$vbase") && \</span>
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<td class="diff-line-num new new_line" data-linenumber="58" 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">
58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"> mv -v $$bin $$base-orig && \</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"> ln -snfv $${vdriver%%.[0-9]*} $$vbase || exit $$? ; \</span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"> done && \</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"> for bin in *[a-z] ; do \</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext"> bin2=$$(readlink $$bin) ; \</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"> bin3=$$(readlink "$$bin2") ; \</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"> case $$bin2 in \</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext"> $$bin.* ) rm -v $$bin2 && mv -v $$bin3 $$bin || exit $$? ;; \</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext"> esac ; \</span>
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52
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67
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="plaintext"> done</span>
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53
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68
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="plaintext"> dh_install</span>
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54
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="plaintext"> # remove susipcious file which is not executable and conflicts with package magic</span>
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55
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="plaintext"> rm -f debian/*/usr/bin/magic</span>
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56
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="plaintext"> # rename kget which conflicts with kget download manager (see #851219)</span>
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57
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="plaintext"> mv debian/$(pkg)/usr/bin/kget debian/$(pkg)/usr/bin/vdb-get</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext"> # Formally supply a standard installation ID to satisfy sratools</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext"> echo '/LIBS/GUID = "$(DEBIAN_GUID)"' >debian/$(pkg)/etc/ncbi/debian.kfg</span>
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58
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="plaintext"></span>
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59
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76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="plaintext">override_dh_auto_test:</span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="plaintext">ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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