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Bug 455010 - app-text/tree-1.6.0-r1, sci-biology/readseq-20080420 and sci-biology/meme-4.8.1 - file collisions in /usr/bin/tree /usr/bin/readseq
Summary: app-text/tree-1.6.0-r1, sci-biology/readseq-20080420 and sci-biology/meme-4.8...
Status: RESOLVED FIXED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: AMD64 Linux
: Normal normal (vote)
Assignee: Andrey Kislyuk (RETIRED)
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2013-02-01 12:17 UTC by Linlin Yan
Modified: 2013-02-01 14:55 UTC (History)
2 users (show)

See Also:
Package list:
Runtime testing required: ---

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Description Linlin Yan 2013-02-01 12:17:15 UTC 
When emerge(upgrade) sci-biology/meme (from 4.3.0 to 4.8.1) on amd64, it reports file collision:

 * app-text/tree-1.6.0-r1:0::gentoo
 *      /usr/bin/tree
 * 
 * sci-biology/readseq-20080420:0::gentoo
 *      /usr/bin/readseq

Within old version of sci-biology/meme, those files are in /opt/meme/bin/:

# equery f sci-biology/meme | grep readseq
/opt/meme/bin/readseq
/opt/meme/doc/readseq.html

# equery f sci-biology/meme | grep tree
/opt/meme/bin/reconcile-tree-alignment
/opt/meme/bin/tree
/opt/meme/doc/reconcile-tree-alignment.html
Comment 1 Justin Lecher (RETIRED) gentoo-dev 2013-02-01 14:51:29 UTC 
+*meme-4.8.1-r1 (01 Feb 2013)
+
+  01 Feb 2013; Justin Lecher <jlec@gentoo.org> meme-4.8.1.ebuild,
+  +meme-4.8.1-r1.ebuild:
+  Resolve file collision with app-text and sci-biology/readseq, #455010
+
Comment 2 Justin Lecher (RETIRED) gentoo-dev 2013-02-01 14:54:54 UTC 
+  01 Feb 2013; Justin Lecher <jlec@gentoo.org> tree-1.6.0-r1.ebuild,
+  metadata.xml:
+  Resolve file collision sci-biology/meme, #455010
+
Comment 3 Justin Lecher (RETIRED) gentoo-dev 2013-02-01 14:55:25 UTC 
+  01 Feb 2013; Justin Lecher <jlec@gentoo.org> -readseq-19930201.ebuild,
+  -readseq-19930201-r1.ebuild, readseq-20080420.ebuild, metadata.xml:
+  Drop old; Resolve file collision sci-biology/meme, #455010
+
Comment 4 Justin Lecher (RETIRED) gentoo-dev 2013-02-01 14:55:44 UTC 
Moved tree and readseq to meme-tree and meme-readseq.