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<h3>
Sascha Steinbiss pushed to branch master
at <a href="https://salsa.debian.org/med-team/roary">Debian Med / roary</a>
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<h4>
Commits:
</h4>
<ul>
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<strong><a href="https://salsa.debian.org/med-team/roary/commit/5c5a8b4ad7085f4574a183fdb2f66aef0f2027bb">5c5a8b4a</a></strong>
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<span>by Sascha Steinbiss</span>
<i>at 2019-06-08T10:21:39Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">support Bioperl >= 1.7.4
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<h4>4 changed files:</h4>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#823dd570b05916ec9a98762f4d0f85bbcf2e9809">
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+
debian/patches/new-bioperl-require.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/roary/commit/5c5a8b4ad7085f4574a183fdb2f66aef0f2027bb#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">roary (3.12.0+dfsg-3) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="3" 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="LC3" class="line" lang="plaintext"> * Fix support for BioPerl 1.7.4 package currently in unstable.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Sascha Steinbiss <satta@debian.org> Sat, 08 Jun 2019 11:52:37 +0200</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">roary (3.12.0+dfsg-2) unstable; urgency=medium</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" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> * Team upload.</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/roary/commit/5c5a8b4ad7085f4574a183fdb2f66aef0f2027bb#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6" 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="6" 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">@@ -6,7 +6,7 @@ Priority: optional</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper (>= 11~),</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> dh-dist-zilla,</span>
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<td class="diff-line-num old_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"> libdist-zilla-plugin-podweaver-perl,</span>
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<td class="diff-line-num old old_line" data-linenumber="9" 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="LC9" class="line" lang="plaintext"> bioperl,</span>
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<td class="diff-line-num new old_line" data-linenumber="10" 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="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"> bioperl<span class="idiff left right"> (>= 1.7.4)</span>,</span>
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<td class="diff-line-num new_line" data-linenumber="10" 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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> libarray-utils-perl,</span>
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<td class="diff-line-num old_line" data-linenumber="11" 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">
11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> libenv-path-perl,</span>
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<td class="diff-line-num old_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">
12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> libexception-class-perl,</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="44" 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="44" 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">@@ -44,7 +44,7 @@ Package: roary</td>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext">Depends: ${perl:Depends},</span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="plaintext"> bioperl,</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> bioperl<span class="idiff left right"> (>= 1.7.4)</span>,</span>
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48
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48
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext"> libarray-utils-perl,</span>
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49
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext"> libdigest-md5-file-perl,</span>
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50
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext"> libenv-path-perl,</span>
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<li id="823dd570b05916ec9a98762f4d0f85bbcf2e9809">
<a href="https://salsa.debian.org/med-team/roary/commit/5c5a8b4ad7085f4574a183fdb2f66aef0f2027bb#823dd570b05916ec9a98762f4d0f85bbcf2e9809"><strong>debian/patches/new-bioperl-require.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Description: use new-style BioPerl include</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Author: Sascha Steinbiss <satta@debian.org></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Last-Update: 2019-06-08</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/lib/Bio/Roary.pm</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/lib/Bio/Roary.pm</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -10,7 +10,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> use Moose;</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> use File::Copy;</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-use Bio::Perl;</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+use BioPerl;</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> use Bio::Roary::ParallelAllAgainstAllBlast;</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> use Bio::Roary::CombinedProteome;</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> use Bio::Roary::External::Cdhit;</span></pre>
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<a href="https://salsa.debian.org/med-team/roary/commit/5c5a8b4ad7085f4574a183fdb2f66aef0f2027bb#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">rename_R_script.patch</span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">use-dz-starter.patch</span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">use-debian-perl-path.patch</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">new-bioperl-require.patch</span></pre>
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