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<h3>
Pierre Gruet pushed to branch master
at <a href="https://salsa.debian.org/med-team/libgoby-java">Debian Med / libgoby-java</a>
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<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/libgoby-java/-/commit/1f0226ab043686355a13f957d4060a95c7529140">1f0226ab</a></strong>
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<span>by Pierre Gruet</span>
<i>at 2021-08-04T14:44:20+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adding dep3 headers in patches when missing
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<h4>3 changed files:</h4>
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<li class="file-stats">
<a href="#729a4cacc53b031da47f89f5aee04741ec835694">
debian/patches/adapting_to_old_fastutil.patch
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<li class="file-stats">
<a href="#1f91261da06177ad9a3b396ac07d0c383bbf8b1a">
debian/patches/using_GeneratedMessageV3.patch
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<li class="file-stats">
<a href="#cf3fc76fed161bccf82d0e694add0230b157ccc7">
debian/patches/using_jbzip2.patch
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<h4>Changes:</h4>
<li id="729a4cacc53b031da47f89f5aee04741ec835694">
<a href="https://salsa.debian.org/med-team/libgoby-java/-/commit/1f0226ab043686355a13f957d4060a95c7529140#729a4cacc53b031da47f89f5aee04741ec835694"><strong>debian/patches/adapting_to_old_fastutil.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: changing some imports linked to fastutil classes</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> Goby 3.3.1 was written for an old fastutil library.</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Author: Pierre Gruet <pgt@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">Last-Update: 2021-08-04</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff">--- a/goby-distribution/src/main/java/org/campagnelab/goby/alignments/ConcatSortedAlignmentReader.java</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/goby-distribution/src/main/java/org/campagnelab/goby/alignments/ConcatSortedAlignmentReader.java</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"><span class="p">@@ -20,7 +20,7 @@</span></span>
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<li id="1f91261da06177ad9a3b396ac07d0c383bbf8b1a">
<a href="https://salsa.debian.org/med-team/libgoby-java/-/commit/1f0226ab043686355a13f957d4060a95c7529140#1f91261da06177ad9a3b396ac07d0c383bbf8b1a"><strong>debian/patches/using_GeneratedMessageV3.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: using GeneratedMessageV3 from protobuf to replace GeneratedMessage</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> The protobuf package has changed quite a bit since the version goby 3.3.1</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"> relies on was edited.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Author: Pierre Gruet <pgt@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">Last-Update: 2021-08-04</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">--- a/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentCollectionHandler.java</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentCollectionHandler.java</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"><span class="p">@@ -20,7 +20,7 @@</span></span>
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<li id="cf3fc76fed161bccf82d0e694add0230b157ccc7">
<a href="https://salsa.debian.org/med-team/libgoby-java/-/commit/1f0226ab043686355a13f957d4060a95c7529140#cf3fc76fed161bccf82d0e694add0230b157ccc7"><strong>debian/patches/using_jbzip2.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: using the classes of libjbzip2-java as a replacement for Bzip2*</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Author: Pierre Gruet <pgt@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: 2021-08-04</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff">--- a/goby-distribution/src/main/java/org/campagnelab/goby/compression/BZip2ChunkCodec.java</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/goby-distribution/src/main/java/org/campagnelab/goby/compression/BZip2ChunkCodec.java</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"><span class="p">@@ -19,8 +19,8 @@</span></span>
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