[gentoo-user] emerging gentoo-sources failing due to file collisions

[gentoo-user] emerging gentoo-sources failing due to file collisions

[Walt Rarus]

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I've never experienced this phenomenon prior to gentoo-sources-2.6.31.-r6.
I've always emerged gentoo-sources and they peacefully sat there and waited
until I built the corresponding kernel later when I felt like it - if ever.
With 2.6.31-r6, however, the emerge fails and consequently screws up 'emerge
world' attempts. PITA.

Any recommended workarounds or fixes?

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
I've pieced the following together from the console and elogv:

ERROR: preinst
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 http://bugs.gentoo.org unless you report exactly which
two packages install the same file(s). Once again, please do NOT file
a bug report unless you have completely understood the above message.

package sys-kernel/gentoo-sources-2.6.31-r6 NOT merged

Detected file collision(s):

*       /usr/src/linux-2.6.31-gentoo-r6/Makefile
*       /usr/src/linux-2.6.31-gentoo-r6/Kbuild
.... gazillion similar ellided
*      /usr/src/linux-2.6.31-gentoo-r6/include/asm-generic/bitops/lock.h
*      /usr/src/linux-2.6.31-gentoo-r6/include/asm-generic/bitops/hweight.h
*
/usr/src/linux-2.6.31-gentoo-r6/include/asm-generic/bitops/non-atomic.h
*
* Searching all installed packages for file collisions...
*
* Press Ctrl-C to Stop
*
* None of the installed packages claim the file(s).
*
* Package 'sys-kernel/gentoo-sources-2.6.31-r6' NOT merged due to file
* collisions. If necessary, refer to your elog messages for the whole
* content of the above message.

>>> Failed to install sys-kernel/gentoo-sources-2.6.31-r6, Log file:
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

WALRUS ~ # emerge
--info
Portage 2.1.6.13 (default/linux/amd64/10.0/desktop, gcc-4.3.4,
glibc-2.9_p20081201-r2, 2.6.30-gentoo-r4 x86_64)
=================================================================

System uname:
Linux-2.6.30-gentoo-r4-x86_64-AMD_Athlon-tm-_64_X2_Dual_Core_Processor_4200+-with-gentoo-1.12.13

Timestamp of tree: Wed, 06 Jan 2010 07:45:02
+0000
app-shells/bash:     4.0_p35
dev-java/java-config: 1.3.7-r1, 2.1.9-r2
dev-lang/python:     2.4.6, 2.5.4-r3, 2.6.4
dev-python/pycrypto: 2.0.1-r8
dev-util/cmake:      2.6.4-r3
sys-apps/baselayout: 1.12.13
sys-apps/sandbox:    1.6-r2
sys-devel/autoconf:  2.13, 2.63-r1
sys-devel/automake:  1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2,
1.10.2
sys-devel/binutils:  2.18-r3
sys-devel/gcc-config: 1.4.1
sys-devel/libtool:   2.2.6b
virtual/os-headers:  2.6.27-r2
ACCEPT_KEYWORDS="amd64"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=athlon64 -O2 -pipe -msse3"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/X11/xkb /usr/share/config"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/
/etc/fonts/fonts.conf /etc/gconf /etc/revdep-rebuild /etc/sandbox.d
/etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d
/etc/texmf/updmap.d /etc/texmf/web2c /etc/udev/rules.d"
CXXFLAGS="-march=athlon64 -O2 -pipe -msse3"
DISTDIR="/usr/portage/distfiles"
FEATURES="ccache collision-protect distlocks fixpackages parallel-fetch
protect-owned sandbox sfperms strict unmerge-orphans userfetch"
GENTOO_MIRRORS="http://gentoo.osuosl.org/
ftp://ftp.gtlib.gatech.edu/pub/gentoo http://mirrors.acm.cs.rpi.edu/gentoo/
http://open-systems.ufl.edu/mirrors/gentoo ftp://lug.mtu.edu/gentoo
ftp://gentoo.cites.uiuc.edu/pub/gentoo/
http://mirror.clarkson.edu/pub/distributions/gentoo/ "
LANG="en_US.utf8"
LDFLAGS="-Wl,-O1"
LINGUAS="en en_US"
MAKEOPTS="-j3"
PKGDIR="/usr/portage/packages"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times
--compress --force --whole-file --delete --stats --timeout=180
--exclude=/distfiles --exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/usr/local/portage/layman/java-binary
/usr/local/portage/layman/sunrise /usr/local/portage/layman/lisp"
SYNC="rsync://rsync.namerica.gentoo.org/gentoo-portage"
USE="X a52 aac acl acpi alsa amd64 apache2 berkdb blas bluetooth branding
bzip2 cairo cdr cjk cli consolekit cracklib crypt cups cxx dbus dri dts dvd
dvdr eds emacs emboss encode evo fam firefox flac fortran gdbm gif gpm
gstreamer gtk hal iconv ipv6 jpeg kde lapack ldap libnotify mad mikmod mmx
mng modules mp3 mp4 mpeg mudflap multilib ncurses nls nptl nptlonly nvidia
ogg opengl openmp oss pam pcre pdf perl png postgres ppds pppd python
qt3support qt4 quicktime readline reflection ruby sdl session spell spl
sqlite sse sse2 ssl startup-notification svg sysfs tcltk tcpd thunar tiff
truetype type1 unicode usb vorbis x264 xml xorg xulrunner xv xvid zlib"
ALSA_CARDS="intel8x0" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare
dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter
mmap_emul mulaw multi null plug rate route share shm softvol"
APACHE2_MODULES="actions alias auth_basic auth_digest authn_anon authn_dbd
authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile
authz_host authz_owner authz_user autoindex cache dav dav_fs dav_lock dbd
deflate dir disk_cache env expires ext_filter file_cache filter headers
ident imagemap include info log_config logio mem_cache mime mime_magic
negotiation proxy proxy_ajp proxy_balancer proxy_connect proxy_http rewrite
setenvif so speling status unique_id userdir usertrack vhost_alias"
ELIBC="glibc" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux"
LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb
ncurses text" LINGUAS="en en_US" RUBY_TARGETS="ruby18" USERLAND="GNU"
VIDEO_CARDS="nvidia vesa"
Unset:  CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK,
LC_ALL, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS

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Re: [gentoo-user] emerging gentoo-sources failing due to file collisions

[Helmut Jarausch]

On  6 Jan, Walt Rarus wrote:
> I've never experienced this phenomenon prior to gentoo-sources-2.6.31.-r6.
> I've always emerged gentoo-sources and they peacefully sat there and waited
> until I built the corresponding kernel later when I felt like it - if ever.
> With 2.6.31-r6, however, the emerge fails and consequently screws up 'emerge
> world' attempts. PITA.
> 
> Any recommended workarounds or fixes?
> 
> ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
> I've pieced the following together from the console and elogv:
> 
> ERROR: preinst
> 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 http://bugs.gentoo.org unless you report exactly which
> two packages install the same file(s). Once again, please do NOT file
> a bug report unless you have completely understood the above message.
> 
> package sys-kernel/gentoo-sources-2.6.31-r6 NOT merged
> 
> Detected file collision(s):
> 
> *       /usr/src/linux-2.6.31-gentoo-r6/Makefile
> *       /usr/src/linux-2.6.31-gentoo-r6/Kbuild
> .... gazillion similar ellided
*** SNIP ***

So, please check where these files came from by

qfile /usr/src/linux-2.6.31-gentoo-r6/Makefile

Have you installed this kernel 'by hand' i.e. outside of portage?

Check by uname -a   if you are not currently running linux-2.6.31-r6

If not, it's safe to rm -rf /usr/src/linux-2.6.31-gentoo-r6
and emerge it again.

Helmut.

-- 
Helmut Jarausch

Lehrstuhl fuer Numerische Mathematik
RWTH - Aachen University
D 52056 Aachen, Germany

Re: [gentoo-user] emerging gentoo-sources failing due to file collisions

[Walt Rarus]

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> So, please check where these files came from by
>
> qfile /usr/src/linux-2.6.31-gentoo-r6/Makefile
>
> WALRUS ~ # qfile /usr/src/linux-2.6.31-gentoo-r6/Makefile
sys-kernel/-MERGING-gentoo-sources
(/usr/src/linux-2.6.31-gentoo-r6/Makefile)

Whatever that means.

Have you installed this kernel 'by hand' i.e. outside of portage?
>
> No. I've not built nor installed *any* 2.6.31 kernel. I've never succeeded
in emerging the sources.

Helmut, thanks for your rapid attention!

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Re: [gentoo-user] [SOLVED] emerging gentoo-sources failing due to file collisions

[Walt Rarus]

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per Helmut Jarausch:
rm -rf /usr/src/linux-2.6.31-gentoo-r6
followed by re-emerge of gentoo-sources-2.6.31-r6
worked!
Thanks, Helmut
P.S. The mystery remains how those conflicting files got there in the first
place. Certainly not by any conscious act on my part.
But, at this point I don't really care because things are back in balance
again.

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Re: [gentoo-user] emerging gentoo-sources failing due to file collisions

[Alan McKinnon]

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An earlier attempt to merge those sources failed and the install is left
incomplete. Do a --depclean to be safe, delete the source tree, merge it
again

On 06 Jan 2010 9:33 PM, "Walt Rarus" <geeked.up@gmail.com> wrote:


> So, please check where these files came from by > > qfile
/usr/src/linux-2.6.31-gentoo-r6/Makefile...
WALRUS ~ # qfile /usr/src/linux-2.6.31-gentoo-r6/Makefile
sys-kernel/-MERGING-gentoo-sources
(/usr/src/linux-2.6.31-gentoo-r6/Makefile)

Whatever that means.

> Have you installed this kernel 'by hand' i.e. outside of portage? >
No. I've not built nor installed *any* 2.6.31 kernel. I've never succeeded
in emerging the sources.

Helmut, thanks for your rapid attention!

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