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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/picard-tools">Debian Med / picard-tools</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/037e04a93ea341f62a51d3e415cd45eb6e06ca3b">037e04a9</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-10-08T18:22:18+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">adjustments to avoid testing on non-amd64
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/cec5373c70806f93fb9e87ef6220315d84a72799">cec5373c</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-10-08T18:22:23+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Mark the remaining patches as not needing forwarding to upstream.
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/d03515e4af88a91efb4c911bc65cef479b3d3814">d03515e4</a></strong>
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<span>by Michael R. Crusoe</span>
<i>at 2020-10-08T18:42:08+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">release 2.23.4+dfsg-3
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<h4>9 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#4851dcaa1d5c2005435e71f102230da1daac1df0">
debian/patches/20-shadowjar.patch
</a>
</li>
<li class="file-stats">
<a href="#2112a29d6b2dc089fd18634ad82cb140e99b56c6">
debian/patches/40-tests-fix-testng.patch
</a>
</li>
<li class="file-stats">
<a href="#4c28a8ec31f904862c75ca6cdb725c2cba7bae50">
debian/patches/50-tests-exclude-Barclay.patch
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<li class="file-stats">
<a href="#9126f334daf6ad90527cca2c80f2dc88b472204a">
debian/patches/fix_javadoc_ascii.patch
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<li class="file-stats">
<a href="#2338e60d4382624824f4ac493301417b621e0a9d">
debian/patches/fix_unreadabletests.patch
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<li class="file-stats">
<a href="#a19ab181f42f2952911fb425a841f9a77adf945f">
debian/patches/remove_google_nio.patch
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
debian/tests/control
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/picard-tools/-/compare/5e179c294f3840f5f9c2edc282332af3f4aecfbe...d03515e4af88a91efb4c911bc65cef479b3d3814#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">picard-tools (2.23.4+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"> * Team upload.</span>
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<td class="diff-line-num new new_line" data-linenumber="4" 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="LC4" class="line" lang="plaintext"> * debian/tests/control: adjustments to avoid testing on non-amd64</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> Closes: #970502</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Mark the remaining patches as not needing forwarding to upstream.</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"> -- Michael R. Crusoe <crusoe@debian.org> Thu, 08 Oct 2020 18:41:58 +0200</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">picard-tools (2.23.4+dfsg-2) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_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">
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> * Fixed classpath in picard.jar Manifest (s/:/ /g)</span>
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<li id="4851dcaa1d5c2005435e71f102230da1daac1df0">
<a href="https://salsa.debian.org/med-team/picard-tools/-/compare/5e179c294f3840f5f9c2edc282332af3f4aecfbe...d03515e4af88a91efb4c911bc65cef479b3d3814#4851dcaa1d5c2005435e71f102230da1daac1df0"><strong>debian/patches/20-shadowjar.patch</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff"><span class="p">Description: do not use shadowjar</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Author: Sascha Steinbiss <satta@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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<td class="diff-line-num new_line" data-linenumber="4" 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="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- picard-tools.orig/build.gradle</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;">+++ picard-tools/build.gradle</span></span>
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<td class="diff-line-num 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">
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="p">@@ -126,7 +126,7 @@</span></span>
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<li id="2112a29d6b2dc089fd18634ad82cb140e99b56c6">
<a href="https://salsa.debian.org/med-team/picard-tools/-/compare/5e179c294f3840f5f9c2edc282332af3f4aecfbe...d03515e4af88a91efb4c911bc65cef479b3d3814#2112a29d6b2dc089fd18634ad82cb140e99b56c6"><strong>debian/patches/40-tests-fix-testng.patch</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5" 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">@@ -5,6 +5,7 @@ Description: Fix testng version and disable some tests.</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"> long and Integers. This leads to test issues when provider [0,9] values</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"> and methods expects a long (testng sends an Integer).</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"> This patch disable some tests around this</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- picard-tools.orig/build.gradle</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ picard-tools/build.gradle</span></span>
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<td class="diff-line-num new_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">
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"><span class="p">@@ -69,9 +69,6 @@</span></span>
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<li id="4c28a8ec31f904862c75ca6cdb725c2cba7bae50">
<a href="https://salsa.debian.org/med-team/picard-tools/-/compare/5e179c294f3840f5f9c2edc282332af3f4aecfbe...d03515e4af88a91efb4c911bc65cef479b3d3814#4c28a8ec31f904862c75ca6cdb725c2cba7bae50"><strong>debian/patches/50-tests-exclude-Barclay.patch</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">@@ -6,7 +6,7 @@ Description: There used to be a tes suite error with BarclayParser</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"> deleted.</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"> FIXME: Try next release without this patch</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></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;">--- a/src/test/java/picard/cmdline/PicardCommandLineTest.java</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;">+++ b/src/test/java/picard/cmdline/PicardCommandLineTest.java</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"><span class="p">@@ -43,23 +43,6 @@</span></span>
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<li id="9126f334daf6ad90527cca2c80f2dc88b472204a">
<a href="https://salsa.debian.org/med-team/picard-tools/-/compare/5e179c294f3840f5f9c2edc282332af3f4aecfbe...d03515e4af88a91efb4c911bc65cef479b3d3814#9126f334daf6ad90527cca2c80f2dc88b472204a"><strong>debian/patches/fix_javadoc_ascii.patch</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff"><span class="p">Author: Olivier Sallou</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Last-Update: 2018-04-23 14:51:06 +0000</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Description: Fix some issues with JavaDoc</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"></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="gd" style="color: #000; background-color: #fdd;">--- a/src/main/java/picard/illumina/IlluminaBasecallsToFastq.java</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/main/java/picard/illumina/IlluminaBasecallsToFastq.java</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="p">@@ -23,7 +23,6 @@</span></span>
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<li id="2338e60d4382624824f4ac493301417b621e0a9d">
<a href="https://salsa.debian.org/med-team/picard-tools/-/compare/5e179c294f3840f5f9c2edc282332af3f4aecfbe...d03515e4af88a91efb4c911bc65cef479b3d3814#2338e60d4382624824f4ac493301417b621e0a9d"><strong>debian/patches/fix_unreadabletests.patch</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">@@ -4,7 +4,7 @@ Description: some tests try to check that a non readable file or directory</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"> and unreadable is not effective. This patch removes related tests</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="p">Last-Updated: 2019-01-18</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="p">Author: Olivier Sallou <osallou@debian.org></span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="p">Forwarded: no</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">Forwarded: no<span class="idiff left right">t-needed</span></span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/test/java/picard/illumina/ExtractIlluminaBarcodesTest.java</span></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/src/test/java/picard/illumina/ExtractIlluminaBarcodesTest.java</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"><span class="p">@@ -159,33 +159,6 @@</span></span>
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<a href="https://salsa.debian.org/med-team/picard-tools/-/compare/5e179c294f3840f5f9c2edc282332af3f4aecfbe...d03515e4af88a91efb4c911bc65cef479b3d3814#a19ab181f42f2952911fb425a841f9a77adf945f"><strong>debian/patches/remove_google_nio.patch</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff"><span class="p">Author: Olivier Sallou</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Last-Update: 2018-04-23 14:51:06</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Description: Remove Google cloud storage</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"></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="gd" style="color: #000; background-color: #fdd;">--- picard-tools.orig/src/main/java/picard/nio/GoogleStorageUtils.java</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ picard-tools/src/main/java/picard/nio/GoogleStorageUtils.java</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="p">@@ -25,14 +25,6 @@</span></span>
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<a href="https://salsa.debian.org/med-team/picard-tools/-/compare/5e179c294f3840f5f9c2edc282332af3f4aecfbe...d03515e4af88a91efb4c911bc65cef479b3d3814#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</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">@@ -6,3 +6,4 @@</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">remove_google_nio.patch</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">fix_unreadabletests.patch</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">60-tests-exclude-network.patch</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">#fix_javadoc_ascii.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/picard-tools/-/compare/5e179c294f3840f5f9c2edc282332af3f4aecfbe...d03515e4af88a91efb4c911bc65cef479b3d3814#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Tests: run-unit-test</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">Depends: <span class="idiff left right">@</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Restrictions: allow-stderr</span></pre>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Depends: <span class="idiff left right">picard-tools</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Restrictions: allow-stderr<span class="idiff left right">, skip-not-installable</span></span></pre>
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