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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/bio-tradis">Debian Med / bio-tradis</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/bio-tradis/commit/714927b9eacd32ecaa7e84531929af456b2e5fff">714927b9</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-02-12T15:06:21+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.1.3
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bio-tradis/commit/d61c6f2add2bf01d75b1663da47f041dfba0e1bc">d61c6f2a</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-02-12T15:12:55+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Downgrade r-bioc-edger from Depends to Suggests
</pre>
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<strong><a href="https://salsa.debian.org/med-team/bio-tradis/commit/5dd0f74d2dc7324fd79b83e59120a3222fc5d9fc">5dd0f74d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-02-12T15:13:49+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debhelper 11
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/bio-tradis/commit/abfc0e4324456e9233dc85b4a15748c064893816">abfc0e43</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-03-16T15:01:37+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
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<h4>5 changed files:</h4>
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<a href="#cd17ac7b86c178cbc1654c388dec4bb7b211db49">
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debian/NEWS.Debian
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<li class="file-stats">
<a href="#f168b81935360ddcf2dd0f2d4b98b8603829060f">
debian/README.Debian
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
debian/compat
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<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<h4>Changes:</h4>
<li id="cd17ac7b86c178cbc1654c388dec4bb7b211db49">
<a href="https://salsa.debian.org/med-team/bio-tradis/compare/df1c09beb81afdc813cf79d7bf2d1176749beabd...abfc0e4324456e9233dc85b4a15748c064893816#cd17ac7b86c178cbc1654c388dec4bb7b211db49"><strong>debian/NEWS.Debian</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">bio-tradis (1.3.3+dfsg-3) unstable; urgency=medium</span>
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<td class="diff-line-num new new_line" data-linenumber="2" 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="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">The package r-bioc-edger was removed from Debian since it was severely</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">outdated. An upgrade is not possible since recent version of BioConductor</span>
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<td class="diff-line-num new new_line" data-linenumber="5" 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="LC5" class="line" lang="plaintext">Edger can not be distributed by Debian since it is using non-distributable</span>
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<td class="diff-line-num new new_line" data-linenumber="6" 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="LC6" class="line" lang="plaintext">code locfit.</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="8" 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="LC8" class="line" lang="plaintext">Thus you need to manually install Edger in your R environment.</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"> -- Andreas Tille <tille@debian.org> Mon, 12 Feb 2018 15:05:27 +0100</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"></span></pre>
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<li id="f168b81935360ddcf2dd0f2d4b98b8603829060f">
<a href="https://salsa.debian.org/med-team/bio-tradis/compare/df1c09beb81afdc813cf79d7bf2d1176749beabd...abfc0e4324456e9233dc85b4a15748c064893816#f168b81935360ddcf2dd0f2d4b98b8603829060f"><strong>debian/README.Debian</strong></a>
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<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">@@ -6,3 +6,11 @@ it has to be excluded from the package source. You can find the</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">documentation here:</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"> https://github.com/sanger-pathogens/Bio-Tradis/blob/master/BioTraDISTutorial.pdf</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"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">Please note: You need to manually install BioConductor Edger which can</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">not be distributed by Debian in recent version since it is using</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">non-distributable code locfit. So the way outdated r-bioc-edger package</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">was removed from Debian.</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Mon, 12 Feb 2018 15:05:27 +0100</span></pre>
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<a href="https://salsa.debian.org/med-team/bio-tradis/compare/df1c09beb81afdc813cf79d7bf2d1176749beabd...abfc0e4324456e9233dc85b4a15748c064893816#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">bio-tradis (1.3.3+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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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Standards-Version: 4.1.3</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Downgrade r-bioc-edger from Depends to Suggests since the package</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> was removed from Debian but people might consider local installations</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> Closes: #890096</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * debhelper 11</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> Mon, 12 Feb 2018 15:13:51 +0100</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">bio-tradis (1.3.3+dfsg-2) 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"> * Team upload.</span>
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<a href="https://salsa.debian.org/med-team/bio-tradis/compare/df1c09beb81afdc813cf79d7bf2d1176749beabd...abfc0e4324456e9233dc85b4a15748c064893816#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">1<span class="idiff left right">0</span></span></pre>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">1<span class="idiff left right">1</span></span></pre>
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<a href="https://salsa.debian.org/med-team/bio-tradis/compare/df1c09beb81afdc813cf79d7bf2d1176749beabd...abfc0e4324456e9233dc85b4a15748c064893816#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -4,12 +4,12 @@ Uploaders: Andreas Tille <tille@debian.org></td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: perl</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Testsuite: autopkgtest-pkg-perl</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper (>= 1<span class="idiff left right">0</span>),</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper (>= 1<span class="idiff left right">1~</span>),</span>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> libtrycatch-perl,</span>
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9
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9
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> libtest-most-perl,</span>
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10
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10
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> libtest-files-perl,</span>
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11
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> libbio-perl-perl</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">0.0</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">1.3</span></span>
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/bio-tradis.git</span>
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<td class="diff-line-num old_line" data-linenumber="14" 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">
14
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Vcs-Git: https://anonscm.debian.org/git/debian-med/bio-tradis.git</span>
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<td class="diff-line-num old_line" data-linenumber="15" 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">
15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Homepage: https://github.com/sanger-pathogens/Bio-Tradis</span>
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<td class="diff-line-num unfold js-unfold old_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="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">@@ -22,10 +22,10 @@ Depends: ${perl:Depends},</td>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> samtools,</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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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> tabix,</span>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> r-base-core,</span>
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<td class="diff-line-num old old_line" data-linenumber="25" 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="LC25" class="line" lang="plaintext"> r-bioc-edger,</span>
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<td class="diff-line-num old_line" data-linenumber="26" 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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25
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> r-cran-getopt,</span>
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<td class="diff-line-num old_line" data-linenumber="27" 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">
27
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<td class="diff-line-num new_line" data-linenumber="26" 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 noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> r-cran-mass</span>
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<td class="diff-line-num old old_line" data-linenumber="28" 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">
28
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext">Suggests: artemis</span>
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<td class="diff-line-num new old_line" data-linenumber="29" 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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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">Suggests: artemis,</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> r-bioc-edger,</span>
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29
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29
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">Description: analyse the output from TraDIS analyses of genomic sequences</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="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"> Bio-Tradis contains a set of tools to analyse the output from</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"> TraDIS analyses.</span>
</pre>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold new_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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -33,3 +33,7 @@ Description: analyse the output from TraDIS analyses of genomic sequences</td>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"> The Bio-Tradis analysis pipeline is implemented as an extensible Perl</span>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"> library which can either be used as is, or as a basis for the</span>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext"> development of more advanced analysis tools.</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> Please note: You need to manually install BioConductor Edger which can</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> not be distributed by Debian in recent version since it is using</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> non-distributable code locfit.</span></pre>
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