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<h3>
Juhani Numminen pushed to branch master
at <a href="https://salsa.debian.org/med-team/spades">Debian Med / spades</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/spades/-/commit/aed48f25a67930a015248aa78e22d3b7275fa926">aed48f25</a></strong>
<div>
<span>by Juhani Numminen</span>
<i>at 2021-02-27T13:40:31+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Build-Deps: does not build python extensions; replace python3-dev with python3-all
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/spades/-/commit/ba3de0b208f87f9a0125226a669e1fce5b1f4dc4">ba3de0b2</a></strong>
<div>
<span>by Juhani Numminen</span>
<i>at 2021-02-27T13:42:33+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Depends: remove explicit shared lib packages which are handled as ${shlibs:Depends}
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</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/spades/-/commit/2ce1f0a2593da8233fd103ebfe80176d431ec1d0">2ce1f0a2</a></strong>
<div>
<span>by Juhani Numminen</span>
<i>at 2021-02-27T14:49:54+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update changelog
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<h4>2 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/spades/-/compare/16312b835188d25109564d1603f4e4d1e4150a45...2ce1f0a2593da8233fd103ebfe80176d431ec1d0#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="32" 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="32" 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">@@ -32,16 +32,17 @@ spades (3.15.1+dfsg-1) UNRELEASED; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"> * Simplify debian/rules: do not attempt to run as-installed tests before</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"> installation</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"> * Install scripts under FHS-compliant path /usr/libexec/spades/</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> - Adjust 0118_adjust_spades_home_again.patch</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext"> * Add patches to make the test suite runnable</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext"> * d/links: Add new binary coronaspades(.py)</span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="plaintext"> * Adjust 0118_adjust_spades_home_again.patch</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"> * Remove unused adapt_to_debian_pathes.patch</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"> * Add d/clean for test artifacts</span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext"> FIXME: Autopkgtests show that this way of frankenstein linking does not</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext"> produce working results</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext"> * Add disable_local_convertutf.patch: to cover for dfsg-removed ConvertUTF.o,</span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext"> link against system's LLVMSupport.a</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> * Build-Deps: does not build python extensions; s/python3-dev/python3-all/</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> * Depends: remove explicit shared libs (handled as ${shlibs:Depends})</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> * Use vendored boost which has local modifications to avoid include problems</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> during program use.</span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext"> [ Étienne Mollier ]</span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext"> * Add fix-sigill-on-non-popcnt-cpus.patch; fixes baseline violation.</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">@@ -9,7 +9,7 @@ Priority: optional</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 13),</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> dh-python,</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> cmake,</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> python3-<span class="idiff left right">dev</span>,</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> python3-<span class="idiff left right">all</span>,</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> zlib1g-dev,</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> libbz2-dev,</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> libbam-dev,</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">@@ -42,9 +42,7 @@ Depends: ${shlibs:Depends},</td>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext"> python3-yaml,</span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext"> bwa,</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext"> bamtools,</span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="plaintext"> samtools,</span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="plaintext"> libnlopt0,</span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="plaintext"> libssw0</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> samtools</span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext">Description: genome assembler for single-cell and isolates data sets</span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext"> The SPAdes – St. Petersburg genome assembler is intended for both</span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext"> standard isolates and single-cell MDA bacteria assemblies. It works</span>
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