614370 – sci-biology/tophat-2.1.1-r3 : file collision with dev-python/sortedcontainers-1.5.7

Bug 614370 - sci-biology/tophat-2.1.1-r3 : file collision with dev-python/sortedcontainers-1.5.7

Summary: sci-biology/tophat-2.1.1-r3 : file collision with dev-python/sortedcontainers...

Status:	RESOLVED FIXED

Alias:	None

Product:	Gentoo Linux
Classification:	Unclassified
Component:	Current packages (show other bugs)
Hardware:	All Linux

Importance:	Normal normal (vote)
Assignee:	Gentoo Science Biology related packages

URL:
Whiteboard:
Keywords:

Depends on:
Blocks:

Reported:	2017-03-31 17:58 UTC by Toralf Förster
Modified:	2017-04-01 12:10 UTC (History)
CC List:	1 user (show)

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

Attachments
emerge-info.txt (emerge-info.txt,6.13 KB, text/plain) 2017-03-31 17:58 UTC, Toralf Förster	Details
config.log.tbz2 (config.log.tbz2,7.20 KB, application/x-bzip) 2017-03-31 17:58 UTC, Toralf Förster	Details
emerge-history.txt (emerge-history.txt,317.90 KB, text/plain) 2017-03-31 17:58 UTC, Toralf Förster	Details
etc.portage.tbz2 (etc.portage.tbz2,28.96 KB, application/x-bzip) 2017-03-31 17:58 UTC, Toralf Förster	Details
sci-biology:tophat-2.1.1-r3:20170331-093123.log (sci-biology:tophat-2.1.1-r3:20170331-093123.log,27.06 KB, text/plain) 2017-03-31 17:58 UTC, Toralf Förster	Details
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Description Toralf Förster gentoo-dev

2017-03-31 17:58:10 UTC

 * 	/usr/lib64/python2.7/site-packages/sortedcontainers/__init__.py
 * 	/usr/lib64/python2.7/site-packages/sortedcontainers/sorteddict.py
 * 	/usr/lib64/python2.7/site-packages/sortedcontainers/sortedlist.py
 * 	/usr/lib64/python2.7/site-packages/sortedcontainers/sortedset.py
 * 
 * Searching all installed packages for file collisions...
 * 
 * Press Ctrl-C to Stop
 * 
 * dev-python/sortedcontainers-1.5.7:0::gentoo
 * 	/usr/lib64/python2.7/site-packages/sortedcontainers/__init__.py
 * 	/usr/lib64/python2.7/site-packages/sortedcontainers/sorteddict.py
 * 	/usr/lib64/python2.7/site-packages/sortedcontainers/sortedlist.py
 * 	/usr/lib64/python2.7/site-packages/sortedcontainers/sortedset.py
 * 
 * Package 'sci-biology/tophat-2.1.1-r3' NOT merged due to file

  -----------------------------------------------------------------

  This is an unstable amd64 chroot image (named gnome-libressl_20170325-144337) at a hardened host acting as a tinderbox.

  -----------------------------------------------------------------

gcc-config -l:
 [1] x86_64-pc-linux-gnu-5.4.0 *

Available Python interpreters, in order of preference:
  [1]   python3.4
  [2]   python3.6 (fallback)
  [3]   python2.7 (fallback)
  [4]   jython2.7 (fallback)

java-config:
The following VMs are available for generation-2:
*)	IcedTea JDK 3.3.0 [icedtea-bin-8]
Available Java Virtual Machines:
  [1]   icedtea-bin-8  system-vm

Comment 1 Toralf Förster gentoo-dev

2017-03-31 17:58:13 UTC

Created attachment 468802 [details]
emerge-info.txt

Comment 2 Toralf Förster gentoo-dev

2017-03-31 17:58:17 UTC

Created attachment 468804 [details]
config.log.tbz2

Comment 3 Toralf Förster gentoo-dev

2017-03-31 17:58:20 UTC

Created attachment 468806 [details]
emerge-history.txt

Comment 4 Toralf Förster gentoo-dev

2017-03-31 17:58:24 UTC

Created attachment 468808 [details]
etc.portage.tbz2

Comment 5 Toralf Förster gentoo-dev

2017-03-31 17:58:27 UTC

Created attachment 468810 [details]
sci-biology:tophat-2.1.1-r3:20170331-093123.log

Comment 6 David Seifert gentoo-dev

2017-04-01 12:10:47 UTC

commit d16351c8ea24af193b4fa3f7cd9321924ceffc40
Author: David Seifert <soap@gentoo.org>
Date:   Sat Apr 1 14:09:16 2017 +0200

    sci-biology/tophat: Unbundle python modules
    
    Bug: https://bugs.gentoo.org/show_bug.cgi?id=614370
    Package-Manager: Portage-2.3.5, Repoman-2.3.2