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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/pique">Debian Med / pique</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/pique/-/commit/8a0c2b348ee07aeb4be670b6cc1d59cd64729dbe">8a0c2b34</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-07-20T12:05:03+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">typo
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pique/-/commit/31046b15f939ecf1232f9aa612c4dc43c899311c">31046b15</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-07-20T12:08:58+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix copyright
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pique/-/commit/701abe3a36c77e2a9b513b5817cb33f360f01f8d">701abe3a</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-07-20T12:10:05+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix permissions
</pre>
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<h4>3 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
</a>
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/pique/-/compare/35f20be9ac31f0a9f1fed03916fc627315610eee...701abe3a36c77e2a9b513b5817cb33f360f01f8d#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="29" 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="29" 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">@@ -29,7 +29,7 @@ Description: software pipeline for performing genome wide association studies</td>
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<td class="diff-line-num new_line" data-linenumber="29" 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="LC29" class="line" lang="plaintext"> wrappers that allow users to perform GWAS using the popular program</span>
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<td class="diff-line-num old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="30" 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="LC30" class="line" lang="plaintext"> EMMAX (Kang et al., 2010) without the need to be familiar with all of</span>
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<td class="diff-line-num old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"> the software tools used to generate the required EMMAX input files.</span>
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<td class="diff-line-num old old_line" data-linenumber="32" 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="LC32" class="line" lang="plaintext"> PIQUE will also perform a number of <span class="idiff left right">of </span>quality control steps prior to</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> PIQUE will also perform a number of quality control steps prior to</span>
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<td class="diff-line-num old_line" data-linenumber="33" 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="LC33" class="line" lang="plaintext"> running EMMAX, ensuring that the various input data files are in the</span>
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<td class="diff-line-num old_line" data-linenumber="34" 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="LC34" class="line" lang="plaintext"> correct format. PIQUE proceeds in two main stages although there are</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext"> multiple entry and exit points from which the pipeline can be run. The</span>
</pre>
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<br>
</li>
<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">
<a href="https://salsa.debian.org/med-team/pique/-/compare/35f20be9ac31f0a9f1fed03916fc627315610eee...701abe3a36c77e2a9b513b5817cb33f360f01f8d#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4" 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">@@ -4,9 +4,25 @@ Upstream-Contact: Tony Travis <tony.travis@minke-informatics.co.uk></td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Source: https://github.com/tony-travis/PIQUE/releases</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: *</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">Copyright: 20<span class="idiff left right">xx-20yy <upstream></span></span>
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<td class="diff-line-num old old_line" data-linenumber="8" 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="LC8" class="line" lang="plaintext">License: <span class="idiff left right"><license></span></span>
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<td class="diff-line-num new old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="7" 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="LC7" class="line" lang="plaintext">Copyright: 20<span class="idiff left right">16-2018 A. J. Travis and A. Douglas</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">License: <span class="idiff left right">GPL-3.0</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Files: debian/*</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">Copyright: 2019 Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">License: <license></span></pre>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">Copyright: 2019-2020 Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">License: GPL-3.0</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">License: GPL-3.0</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> This program is free software: you can redistribute it and/or modify</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> it under the terms of the GNU General Public License as published by</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> the Free Software Foundation, either version 3 of the License.</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> .</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> This package is distributed in the hope that it will be useful,</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> GNU General Public License for more details.</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> .</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> You should have received a copy of the GNU General Public License</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> along with this program. If not, see <https://www.gnu.org/licenses/>.</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> .</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> On Debian systems, the complete text of the GNU General Public</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> License version 3 can be found in "/usr/share/common-licenses/GPL-3".</span></pre>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/pique/-/compare/35f20be9ac31f0a9f1fed03916fc627315610eee...701abe3a36c77e2a9b513b5817cb33f360f01f8d#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">@@ -4,15 +4,6 @@</td>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">export LC_ALL=C.UTF-8</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">include /usr/share/dpkg/default.mk</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"># this provides:</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"># DEB_SOURCE: the source package name</span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"># DEB_VERSION: the full version of the package (epoch + upstream vers. + revision)</span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"># DEB_VERSION_EPOCH_UPSTREAM: the package's version without the Debian revision</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"># DEB_VERSION_UPSTREAM_REVISION: the package's version without the Debian epoch</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"># DEB_VERSION_UPSTREAM: the package's upstream version</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"># DEB_DISTRIBUTION: the distribution(s) listed in the current entry of debian/changelog</span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"># SOURCE_DATE_EPOCH: the source release date as seconds since the epoch, as</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"># specified by <https://reproducible-builds.org/specs/source-date-epoch/></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"># for hardening you might like to uncomment this:</span>
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<td class="diff-line-num 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">
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"># export DEB_BUILD_MAINT_OPTIONS=hardening=+all</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -31,3 +22,7 @@ override_dh_auto_install:</td>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">#ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"># do_stuff_for_testing</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">#endif</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">override_dh_fixperms:</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> dh_fixperms</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> find debian -name "*.R" -exec chmod -x \{\} \;</span></pre>
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