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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/libbiod">Debian Med / libbiod</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/libbiod/commit/2cf5a6534a0f72640ae8d0d68a91865e0ecde1c4">2cf5a653</a></strong>
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<span>by Michael R. Crusoe</span>
<i>at 2019-01-18T19:29:50Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">apply "size_t is uint on 32-bits platform" patch
</pre>
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#7d4d2668a0f75bc51a2e4224b1e49c2da01ae4ce">
debian/patches/003_modernize_meson.patch
</a>
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<li class="file-stats">
<a href="#2fb822ef93ac5ebbd7bbda17cbcb1b4401d2d9b9">
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+
debian/patches/25068c1c439515a48f392bd85754a3465597c419.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/libbiod/commit/2cf5a6534a0f72640ae8d0d68a91865e0ecde1c4#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">libbiod (0.2.1-2) UNRELEASED; 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"> [ Andreas Tille ]</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * debhelper 12</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> * Standards-Version: 4.3.0</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"> [ Michael R. Crusoe ]</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * Apply patch from upstream: "size_t is uint on 32-bits platform"</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> Closes: #912077</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"> -- Andreas Tille <tille@debian.org> Fri, 18 Jan 2019 09:31:55 +0100</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">libbiod (0.2.1-1) unstable; urgency=medium</span>
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<li id="7d4d2668a0f75bc51a2e4224b1e49c2da01ae4ce">
<a href="https://salsa.debian.org/med-team/libbiod/commit/2cf5a6534a0f72640ae8d0d68a91865e0ecde1c4#7d4d2668a0f75bc51a2e4224b1e49c2da01ae4ce"><strong>debian/patches/003_modernize_meson.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">@@ -8,10 +8,8 @@ Origin: https://github.com/biod/BioD/pull/38/commits/c059165f359327c5a67aadabe18</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"> meson.build | 131 +++++++++++++++++++++++++++-------------------------</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> 1 file changed, 67 insertions(+), 64 deletions(-)</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/meson.build b/meson.build</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"><span class="gh" style="color: #999;">index 88f3bcc7..9d308efd 100644</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/meson.build</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/meson.build</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- libbiod.orig/meson.build</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ libbiod/meson.build</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,6 +1,9 @@</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-project('BioD', 'd')</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+project('BioD', 'd',</span></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">@@ -24,7 +22,7 @@ index 88f3bcc7..9d308efd 100644</td>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="diff"> project_soversion = '0'</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="diff"> src_dir = include_directories('.')</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -16,79 +19,83 @@<span class="idiff left right"> zlib_dep = dependency('zlib')</span></span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -16,79 +19,83 @@</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="diff"> # Sources</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="diff"> #</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="diff"> biod_src = [</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">@@ -163,7 +161,7 @@ index 88f3bcc7..9d308efd 100644</td>
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="diff"> bio2_src = [</span>
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="diff"> 'bio2/bam/header.d',</span>
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -114,18 +121,16 @@<span class="idiff left right"> install_subdir('bio2/', install_dir: 'include/d/bio/')</span></span></span>
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -114,18 +121,16 @@</span></span>
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="diff"> # Library and pkg-config</span>
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="diff"> #</span>
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="diff"> biod_lib = library('biod',</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">@@ -184,7 +182,7 @@ index 88f3bcc7..9d308efd 100644</td>
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="diff"> description: 'Bioinformatics library in D (utils for working with SAM, BAM, SFF formats).'</span>
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="diff"> )</span>
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -134,11 +139,9 @@<span class="idiff left right"> pkgc.generate(name: 'biod',</span></span></span>
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -134,11 +139,9 @@</span></span>
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="diff"> #</span>
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="diff"> biod_test_exe = executable('biod_test',</span>
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="diff"> ['test/unittests.d',</span>
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<li id="2fb822ef93ac5ebbd7bbda17cbcb1b4401d2d9b9">
<a href="https://salsa.debian.org/med-team/libbiod/commit/2cf5a6534a0f72640ae8d0d68a91865e0ecde1c4#2fb822ef93ac5ebbd7bbda17cbcb1b4401d2d9b9"><strong>debian/patches/25068c1c439515a48f392bd85754a3465597c419.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">From 25068c1c439515a48f392bd85754a3465597c419 Mon Sep 17 00:00:00 2001</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">From: Pjotr Prins <pjotr.guix@thebird.nl></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Date: Mon, 29 Oct 2018 11:23:07 -0500</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff">Subject: [PATCH] size_t is uint on 32-bits platform. Fixes #43. Thanks</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"> @tillea.</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">---</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> bio2/bgzf.d | 2 +-</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> 1 file changed, 1 insertion(+), 1 deletion(-)</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- libbiod.orig/bio2/bgzf.d</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ libbiod/bio2/bgzf.d</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -211,7 +211,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> f.rawRead(buf);</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> f.seek(lastpos);</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> if (buf == BGZF_EOF)</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return tuple(FilePos(),compressed_buf,cast(ulong)0,crc32); // sets fpos to null</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return tuple(FilePos(),compressed_buf,cast(size_t)0,crc32); // sets fpos to null</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> return tuple(FilePos(f.tell()),compressed_buf,cast(size_t)uncompressed_size,crc32);</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> } catch (Exception e) { throwBgzfException(e.msg,e.file,e.line); }</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- libbiod.orig/bio2/pileup.d</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ libbiod/bio2/pileup.d</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -89,7 +89,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> T[] _items;</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> RingBufferIndex _head;</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> RingBufferIndex _tail;</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- size_t max_size = 0;</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ulong max_size = 0;</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> /** initializes round buffer of size $(D n) */</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> this(size_t n) {</span></pre>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">001_fix_unit_tests.patch</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">002_include_bio2.patch</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">003_modernize_meson.patch</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">25068c1c439515a48f392bd85754a3465597c419.patch</span></pre>
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