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Bug 70425 - dev-python/python-fchksum, sys-devel/flex, sys-apps/diffutils cannot be emerged during emerge system - Collision with stage1 files?
Summary: dev-python/python-fchksum, sys-devel/flex, sys-apps/diffutils cannot be emerg...
Status: RESOLVED FIXED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: High blocker
Assignee: SpanKY
URL:
Whiteboard:
Keywords: InVCS
: 75870 80868 81676 (view as bug list)
Depends on:
Blocks: 78241
  Show dependency tree
 
Reported: 2004-11-07 23:44 UTC by Alexander Skwar
Modified: 2005-04-14 19:03 UTC (History)
5 users (show)

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


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Description Alexander Skwar 2004-11-07 23:44:01 UTC
I'm currently setting up a new system and followed the instructions at http://forums.gentoo.org/viewtopic.php?t=169054. I added "FEATURES=collision-protect" to make.conf.


Reproducible: Always
Steps to Reproduce:
1. Follow instructions at http://forums.gentoo.org/viewtopic.php?t=169054
2. Do "emerge system"

Actual Results:  
copying build/lib.linux-i686-2.3/fchksum.so ->
/var/tmp/portage/python-fchksum-1.7.1/image/usr/lib/python2.3/site-packages
man:
prepallstrip:
strip:
strip:
   usr/lib/python2.3/site-packages/fchksum.so
>>> Completed installing into /var/tmp/portage/python-fchksum-1.7.1/image/

* checking 1 files for package collisions
existing file /usr/lib/python2.3/site-packages/fchksum.so is not owned by this
package
* spend 0.000676155090332 seconds checking for file collisions
* This package is blocked because it wants to overwrite
* files belonging to other packages (see messages above).
* If you have no clue what this is all about report it
* as a bug for this package on http://bugs.gentoo.org

package dev-python/python-fchksum-1.7.1 NOT merged

HOWEVER:
rescue build_system # epm -qf /usr/lib/python2.3/site-packages/fchksum.so
file /usr/lib/python2.3/site-packages/fchksum.so is not owned by any package





rescue build_system # emerge info
Portage 2.0.51-r3 (default-x86-2004.2, gcc-3.4.2, glibc-2.3.4.20041102-r0,
2.4.27-040930 i686)
=================================================================
System uname: 2.4.27-040930 i686 Intel(R) Celeron(R) CPU 2.00GHz
Gentoo Base System version 1.6.5
Autoconf: sys-devel/autoconf-2.59-r5
Automake: sys-devel/automake-1.8.5-r1
Binutils: sys-devel/binutils-2.15.92.0.2-r1
Headers:  sys-kernel/linux26-headers-2.6.8.1-r1
Libtools: sys-devel/libtool-1.5.2-r6
ACCEPT_KEYWORDS="x86 ~x86"
AUTOCLEAN="yes"
CFLAGS="-march=pentium4 -O3 -pipe -fomit-frame-pointer"
CHOST="i686-pc-linux-gnu"
COMPILER=""
CONFIG_PROTECT="/etc /usr/kde/2/share/config /usr/kde/3/share/config
/usr/share/config /var/qmail/control"
CONFIG_PROTECT_MASK="/etc/gconf /etc/terminfo /etc/env.d"
CXXFLAGS="-march=pentium4 -O3 -pipe -fomit-frame-pointer"
DISTDIR="/usr/portage/distfiles"
FEATURES="autoaddcvs ccache collision-protect distlocks sandbox"
GENTOO_MIRRORS="http://ftp-stud.fht-esslingen.de/pub/Mirrors/gentoo/
ftp://mirrors.sec.informatik.tu-darmstadt.de/gentoo/
ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gentoo
ftp://ftp.wh2.tu-dresden.de/pub/mirrors/gentoo http://194.117.158.29/"
MAKEOPTS="-j2"
PKGDIR="/usr/portage/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY=""
SYNC="rsync://rsync.europe.gentoo.org/gentoo-portage"
USE="X acl apache2 apm arts async avi bzlib crypt cscope cups curl curlwrappers
diet djbfft encode exif fam flash foomaticdb ftp fwdzone gd gdbm gif gnome gpm
gtk gtk2 hal iconv imagemagick imap imlib immqt-bc javascript jpeg kde libedit
libg++ libwww lzo lzw lzw-tiff mad maildir mailwrapper mbox mmap mmx mng mpeg
ncurses nls no-old-linux noantlr nobcel nobeanutils nobsh nocommonslogging
nocommonsnet nojdepend nojsch nojython nolog4j nooro noregexp norhino noxalan
noxerces offensive oggvorbis opengl oss pam parse-clocks pcntl pcre pdflib perl
pic pie png posix python qt quicktime readline recode sasl sdl shared slang
sockets spell sse ssl sysvipc tcpd tiff truetype unicode vim-with-x x86 xfs xml2
xmms xv zlib linguas_de"
Comment 1 Alexander Skwar 2004-11-07 23:49:14 UTC
Next package:

>>> emerge (2 of 55) sys-devel/flex-2.5.4a-r5 to /
>>> md5 src_uri ;-) flex-2.5.4a.tar.gz
* checking 6 files for package collisions
existing file /usr/bin/flex is not owned by this package

rescue build_system # epm -qf /usr/bin/flex
file /usr/bin/flex is not owned by any package

Hm. Are those the files, that were in the stage1 tar?
Comment 2 Alexander Skwar 2004-11-07 23:53:25 UTC
>>> emerge (3 of 54) sys-apps/diffutils-2.8.7 to /
>>> md5 src_uri ;-) diffutils-2.8.7.tar.gz
* checking 12 files for package collisions
existing file /usr/bin/cmp is not owned by this package
existing file /usr/bin/diff is not owned by this package
existing file /usr/bin/diff3 is not owned by this package
existing file /usr/bin/sdiff is not owned by this package


rescue build_system # epm -qf /usr/bin/cmp /usr/bin/diff /usr/bin/diff3 /usr/bin/sdiff
file /usr/bin/cmp is not owned by any package
file /usr/bin/diff is not owned by any package
file /usr/bin/diff3 is not owned by any package
file /usr/bin/sdiff is not owned by any package
Comment 3 SpanKY gentoo-dev 2005-01-04 00:44:38 UTC
why do we clean out /var/db/pkg in our stage1/stage2 ?

cant a better solution be found ?
Comment 4 Chris Gianelloni (RETIRED) gentoo-dev 2005-01-04 05:30:32 UTC
Since catalyst is the one doing the cleaning, I'm reassigning.

Personally, I think we should stop cleaning out /var/db/pkg in stage1 and stage2.  This will probably mean a change to the bootstrap.sh script to have it run a "emerge -e $list_of_packages" rather than just emerge, so that all of the packages get rebuilt with the user's USE/CFLAGS.
Comment 5 Chris Gianelloni (RETIRED) gentoo-dev 2005-01-11 05:52:05 UTC
As far as catalyst is concerned, this has been modified in CVS now.

What we need from here is a modified bootstap.sh script that works with the new stage files, as both stage1 and stage2 now have much more in their /var/db/pkg directory.
Comment 6 Chris Gianelloni (RETIRED) gentoo-dev 2005-01-14 11:50:59 UTC
Catalyst 1.1.2 is now out!
Comment 7 Chris Gianelloni (RETIRED) gentoo-dev 2005-01-14 11:54:48 UTC
Sorry... forgot that the bootstrap.sh script needs updating...

Reassigning to vapier...

I have been getting this to work myself, by adding a -e onto the baselayout/glibc emerge in bootstrap.sh, but I'm sure you can come up with a more elegant solution.  We will also have to figure out something for "emerge system", as catalyst uses "emerge -e system" now to ensure all packages get updated.
Comment 8 Chris Gianelloni (RETIRED) gentoo-dev 2005-01-27 09:57:45 UTC
This is resolved in newer stages created by catalyst and will be resolved when 2005.0 is released.

vapier: can you test the bootstrap-new.sh script in cvs and make sure it looks good (or fix it)... my tests have shown it to work as expected, so everything seems to be resolved.  If the bootstrap-new.sh script works, we will be replacing the old bootstrap.sh script with this new one.
Comment 9 SpanKY gentoo-dev 2005-02-11 16:41:42 UTC
*** Bug 81676 has been marked as a duplicate of this bug. ***
Comment 10 SpanKY gentoo-dev 2005-02-11 16:41:45 UTC
*** Bug 75870 has been marked as a duplicate of this bug. ***
Comment 11 SpanKY gentoo-dev 2005-02-14 05:47:49 UTC
*** Bug 80868 has been marked as a duplicate of this bug. ***
Comment 12 Chris Gianelloni (RETIRED) gentoo-dev 2005-04-13 08:43:19 UTC
You can RESOLVE this one now that 2005.0 is released.
Comment 13 Chris Gianelloni (RETIRED) gentoo-dev 2005-04-14 19:03:14 UTC
Fixed with the 2005.0 stages and new bootstrap.sh script.