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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/bioperl-run">Debian Med / bioperl-run</a>
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<h4>
Commits:
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<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/bioperl-run/commit/c2700f24859587984aff91d93ea9af77522ec550">c2700f24</a></strong>
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<span>by Andreas Tille</span>
<i>at 2018-09-14T12:11:12Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">do not run tests parallel to get sensibly sorted output
</pre>
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<strong><a href="https://salsa.debian.org/med-team/bioperl-run/commit/407c1747df94cc8c46493f40a6d5ab792b936635">407c1747</a></strong>
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<span>by Andreas Tille</span>
<i>at 2018-09-14T12:46:28Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Allow MPI oversubscription (as in phyml build since phyml caused problems inside build time tests)
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<h4>3 changed files:</h4>
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/bioperl-run/compare/c559c463e55181ab8c31814dc9aa160dae439013...407c1747df94cc8c46493f40a6d5ab792b936635#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">bioperl-run (1.7.2-4) UNRELEASED; 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"> * (Build-)Depends: ncoils</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * do not run tests parallel to get sensibly sorted output</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Allow MPI oversubscription (as in phyml build since phyml caused</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> problems inside build time tests)</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> Closes: #906337</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Fri, 14 Sep 2018 13:22:55 +0200</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">bioperl-run (1.7.2-3) unstable; urgency=medium</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"> * Drop adjust_bowtie_tests.patch, Closes: #887578</span>
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<a href="https://salsa.debian.org/med-team/bioperl-run/compare/c559c463e55181ab8c31814dc9aa160dae439013...407c1747df94cc8c46493f40a6d5ab792b936635#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="35" 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">@@ -35,6 +35,7 @@ Build-Depends-Indep: perl,</td>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext"> maq,</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext"> mafft,</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext"> muscle,</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> ncoils,</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"> phylip,</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext"> phyml,</span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext"> primer3,</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="74" 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">@@ -73,6 +74,7 @@ Recommends: amap-align,</td>
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="plaintext"> maq,</span>
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74
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="plaintext"> mafft,</span>
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75
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76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="plaintext"> muscle,</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext"> ncoils,</span>
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76
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78
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="plaintext"> phylip,</span>
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77
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79
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="plaintext"> phyml,</span>
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78
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80
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="plaintext"> primer3,</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="92" 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="94" 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">@@ -92,7 +94,6 @@ Suggests: gmap,</td>
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92
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94
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="plaintext"># The following list of packages is not available in Debian:</span>
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93
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95
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="plaintext"># blat,</span>
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94
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96
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="plaintext"># cap3,</span>
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95
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="plaintext"># coils,</span>
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96
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97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="plaintext"># condense,</span>
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97
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="plaintext"># drawgram,</span>
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98
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99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="plaintext"># drawtree,</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="136" 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="137" 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">@@ -136,7 +137,7 @@ Suggests: gmap,</td>
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136
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137
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="plaintext"># tigr-assembler,</span>
</pre>
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137
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138
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="plaintext"># tmhmm,</span>
</pre>
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138
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139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="plaintext"># tribe,</span>
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139
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="plaintext"># trnascan<span class="idiff left right">,</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="plaintext"># trnascan<span class="idiff left right">-se, # non-free</span></span>
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140
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<td class="diff-line-num new_line" data-linenumber="141" 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">
141
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="plaintext"># vista-align</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="141" 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">
141
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142
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="plaintext">Description: BioPerl wrappers: scripts</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="142" 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">
142
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143
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="plaintext"> Contains scripts from the BioPerl-Run package. This package will also install</span>
</pre>
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<br>
</li>
<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/bioperl-run/compare/c559c463e55181ab8c31814dc9aa160dae439013...407c1747df94cc8c46493f40a6d5ab792b936635#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="21" 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="21" 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">@@ -21,6 +21,7 @@ FAILING_TESTS_FOR_DUE_TO_MISSING_MODULES=BWA \</td>
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"># Important for hyphympi</span>
</pre>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"># See https://lists.debian.org/debian-science/2012/03/msg00005.html</span>
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<td class="diff-line-num old_line" data-linenumber="23" 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="LC23" class="line" lang="plaintext">export OMPI_MCA_plm_rsh_agent=/bin/false</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">export OMPI_MCA_rmaps_base_oversubscribe=1</span>
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24
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"></span>
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25
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">%:</span>
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26
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> dh $@</span>
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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="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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -29,10 +30,12 @@ override_dh_auto_configure:</td>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"> dh_auto_configure -- --install_scripts $(NETWORK)</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext">override_dh_auto_test:</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"> mkdir t.skip</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="LC35" class="line" lang="plaintext"> for t in $(NOT_SUPPORTED_TESTS) $(FAILING_TESTS_FOR_DUE_TO_MISSING_MODULES) ; do mv t/$${t}.t t.skip ; done</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext"> PATH=$$PATH:/usr/lib/emboss:/usr/lib/phylip/bin/:/usr/lib/tigr-glimmer:debian/test_hack_bin \</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext"> HOME_4_TCOFFEE=/tmp \</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext"> dh_auto_test</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> dh_auto_test<span class="idiff left right"> --no-parallel</span></span>
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37
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"> mv t.skip/* t</span>
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<td class="diff-line-num old_line" data-linenumber="38" 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">
38
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext"> rm -rf t.skip</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">endif</span></pre>
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