Bug 602508

Summary:	sci-biology/seqan - fix file collision between multiple SLOTed versions
Product:	Gentoo Linux	Reporter:	Martin Mokrejš <mmokrejs>
Component:	Current packages	Assignee:	Gentoo Science Biology related packages <sci-biology>
Status:	RESOLVED FIXED
Severity:	normal
Priority:	Normal
Version:	unspecified
Hardware:	All
OS:	Linux
Whiteboard:
Package list:		Runtime testing required:	---

Description Martin Mokrejš 2016-12-13 07:23:42 UTC

* Messages for package sci-biology/seqan-2.2.0:

 * This package will overwrite one or more files that may belong to other
 * packages (see list below). You can use a command such as `portageq
 * owners / <filename>` to identify the installed package that owns a
 * file. If portageq reports that only one package owns a file then do
 * NOT file a bug report. A bug report is only useful if it identifies at
 * least two or more packages that are known to install the same file(s).
 * If a collision occurs and you can not explain where the file came from
 * then you should simply ignore the collision since there is not enough
 * information to determine if a real problem exists. Please do NOT file
 * a bug report at https://bugs.gentoo.org/ unless you report exactly
 * which two packages install the same file(s). See
 * https://wiki.gentoo.org/wiki/Knowledge_Base:Blockers for tips on how
 * to solve the problem. And once again, please do NOT file a bug report
 * unless you have completely understood the above message.
 * 
 * Detected file collision(s):
 * 
 *      /usr/share/cmake/Modules/FindSeqAn.cmake
 *      /usr/share/pkgconfig/seqan-2.pc
 * 
 * Searching all installed packages for file collisions...
 * 
 * Press Ctrl-C to Stop
 * 
 * sci-biology/seqan-2.1.1:2.1::gentoo
 *      /usr/share/cmake/Modules/FindSeqAn.cmake
 *      /usr/share/pkgconfig/seqan-2.pc

Comment 1 David Seifert gentoo-dev

2016-12-14 20:34:47 UTC

Should be fixed now.

commit da90f594219f91865c4310e86f154dbc7dd8d3cd
Author: David Seifert <soap@gentoo.org>
Date:   Wed Dec 14 21:28:14 2016 +0100

    sci-biology/seqan: Add blocker for older SLOTs
    
    Gentoo-bug: 602508

Comment 2 Martin Mokrejš 2016-12-15 23:43:53 UTC

Is the below the expected behaviour? Seems I am pushed to unmerge first existing 2.2.0 to upgrade to -r1?:

# emerge -uN seqan

 * IMPORTANT: 20 news items need reading for repository 'gentoo'.
 * Use eselect news read to view new items.

Calculating dependencies... done!
[ebuild  NS    ] sci-biology/seqan-2.2.0-r1 [2.2.0] USE="-doc {-test}" CPU_FLAGS_X86="sse4_1" PYTHON_TARGETS="python2_7" 
[blocks B      ] sci-biology/seqan:2.2 ("sci-biology/seqan:2.2" is hard blocking sci-biology/seqan-2.2.0-r1)

 * Error: The above package list contains packages which cannot be
 * installed at the same time on the same system.

  (sci-biology/seqan-2.2.0-r1:0/0::gentoo, ebuild scheduled for merge) pulled in by
    seqan
    sci-biology/seqan required by @selected