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PaulSorensen
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PostPosted: Sun Mar 12, 2006 4:41 pm    Post subject: Upgrading to glibc requires nptlonly use flag Reply with quote

I was updating portage last night (I'm on ~x86) and noticed the the new glibc 2.4 ebuild requires that the "nptlonly" use flag is set. Has anyone had trouble with this lately? I'm using the testing keyword - but I don't want to screw up my system completely 8O
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PostPosted: Sun Mar 12, 2006 4:51 pm    Post subject: Reply with quote

You might like to take a look at this.. I am in the process of updating myself..
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PostPosted: Sun Mar 12, 2006 5:05 pm    Post subject: Reply with quote

Hi,

i updated yesterday and ran into a problem starting my X server. I got the following messages :

Code:
x relocation error: X symbol --guard, version GLIBC.2.3.2 not defined in file libc.so.6
with link time reference]


i searched the forum and found information in the following thread :
http://forums.gentoo.org/viewtopic-t-261679-highlight-prelink+afmr.html

I ran prelink -afmR which fixed it for me (my system was prelinked though)
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PaulSorensen
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PostPosted: Sun Mar 12, 2006 5:55 pm    Post subject: Reply with quote

Thanks - my system is also prelinked.

I think I'll take the "plunge" - it was nice knowing you all :)

Cybersorcerer wrote:
Hi,

i updated yesterday and ran into a problem starting my X server. I got the following messages :

Code:
x relocation error: X symbol --guard, version GLIBC.2.3.2 not defined in file libc.so.6
with link time reference]


i searched the forum and found information in the following thread :
http://forums.gentoo.org/viewtopic-t-261679-highlight-prelink+afmr.html

I ran prelink -afmR which fixed it for me (my system was prelinked though)
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TheRAt
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PostPosted: Sun Mar 12, 2006 5:59 pm    Post subject: Reply with quote

Post your experience / results..
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PostPosted: Sun Mar 12, 2006 6:43 pm    Post subject: Reply with quote

yep i am interested in your experiences as well !
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PostPosted: Sun Mar 12, 2006 10:00 pm    Post subject: Reply with quote

Cybersorcerer wrote:
Hi,

i updated yesterday and ran into a problem starting my X server. I got the following messages :

Code:
x relocation error: X symbol --guard, version GLIBC.2.3.2 not defined in file libc.so.6
with link time reference]


i searched the forum and found information in the following thread :
http://forums.gentoo.org/viewtopic-t-261679-highlight-prelink+afmr.html

I ran prelink -afmR which fixed it for me (my system was prelinked though)


I got the exact same problem, and the same fix did it for me...I did not initially have prelink installed, so I needed to do
Code:

emerge prelink
env-update

first (env-update creates /etc/prelink.conf for you). This seems to be a bit of a workaround though. Anybody know of a better solution?
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PaulSorensen
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PostPosted: Sun Mar 12, 2006 10:35 pm    Post subject: Everything is fine Reply with quote

It seems I must have been paranoid - everything seems to be fine. I haven't run into anything that doesn't execute yet, but I'll post here if I hit any problems.

I immediately ran:
- prelink -amfR
- revdep-rebuild

Thanks all
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russofris
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PostPosted: Mon Mar 13, 2006 12:17 am    Post subject: Reply with quote

Quote:
I got the exact same problem, and the same fix did it for me...I did not initially have prelink installed, so I needed to do
Code:

emerge prelink
env-update

first (env-update creates /etc/prelink.conf for you). This seems to be a bit of a workaround though. Anybody know of a better solution?


Same. Running without pre-link. I simply re-emerge xorg-x11 and all was well.

Frank
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hulmeman
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PostPosted: Mon Mar 13, 2006 8:11 pm    Post subject: Reply with quote

I've no problem with xorg-x11, but I'm running modular, xorg-server-1.0.1-r4 (xorg-7.0) but I'm getting the same error with other packages, for example:
Code:

/etc/init.d/sshd start
syslog-ng: relocation error: syslog-ng: symbol __guard, version
GLIBC_2.3.2 not defined in file libc.so.6 with link time reference
 * Configuration error. Please fix your configfile
(/etc/syslog-ng/syslog-ng.conf)              [ !! ]
Code:

 emerge --sync
>>> Starting rsync with rsync://137.226.34.228/gentoo-portage...
>>> Checking server timestamp ...
/usr/bin/rsync: relocation error: /usr/lib/libpopt.so.0: symbol __guard, version GLIBC_2.3.2
not defined in file libc.so.6 with link time reference
Code:

/etc/init.d/nfs restart
 * WARNING:  nfs has not yet been started.
 * Starting portmap ...
/sbin/portmap: relocation error: /sbin/portmap: symbol __guard, version GLIBC_2.3.2 not
defined in file libc.so.6 with link time reference
[ !! ]
 * Starting idmapd ...
[ ok ]
 * Starting NFS statd ...
 * Error starting NFS statd

emerging the offending packages solves the problem, but how to discover which are affected? Baffling!!!
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opopanax
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PostPosted: Mon Mar 13, 2006 8:44 pm    Post subject: Reply with quote

I'm not prelinked, so all I should have to do is emerge --newuse world (with nptl and nptlonly USE flags), then do a revdep-rebuild?
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PostPosted: Mon Mar 13, 2006 8:55 pm    Post subject: Reply with quote

I was getting some strange compile errors, after putting the new glibc on... in the process of an emerge -e world at the moment.. and about 1/3 of the way through.. without any problems..
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PostPosted: Mon Mar 13, 2006 9:16 pm    Post subject: Reply with quote

sketelsen wrote:
I'm not prelinked, so all I should have to do is emerge --newuse world (with nptl and nptlonly USE flags), then do a revdep-rebuild?


First thing I tried, but it didn't work for me. '--newuse' didn't detect many of the broken packages, for example, nfs, ssh rsync and more. I have to re-emerge manually each broken package when I encounter the "symbol __guard" error.
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PostPosted: Tue Mar 14, 2006 1:20 am    Post subject: Reply with quote

so, revdep-rebuild didn't work for you, hulmeman?
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destr0yr
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PostPosted: Tue Mar 14, 2006 1:47 am    Post subject: Reply with quote

Maybe somebody could point me in the right direction here... After doing my typical sync && uDv world, I see:
Code:
grep: relocation error: grep: symbol __guard, version GLIBC_2.3.2 not defined in file libc.so.6 with link time reference

Any attempt to do anything returns similar errors:
Code:
~ # grep
grep: relocation error: grep: symbol __guard, version GLIBC_2.3.2 not defined in file libc.so.6 with link time reference
~ # sed
sed: relocation error: sed: symbol __guard, version GLIBC_2.3.2 not defined in file libc.so.6 with link time reference
~ # vi
vi: relocation error: /usr/lib/libperl.so.1: symbol __guard, version GLIBC_2.3.2 not defined in file libc.so.6 with link time reference


emerge glibc (2.4.0) returns an error that linux-headers needs to be >=2.6.9 (I have 2.6.11-r3), however, this fails anyways since grep shoots itself in the head.

8O :?:
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opopanax
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PostPosted: Tue Mar 14, 2006 3:09 am    Post subject: Reply with quote

how about re-merging portage, then re-merging grep and giving it another try? -uD world won't do it, I don't think, because too much stuff in the toolchain is whacked out by that nptlonly thing. I'm just doing
Code:

# emerge -e system
# emerge -e system
# emerge -e world
# emerge -e world

as described many places in these forums to get a good toolchain built on a good toolchain, and then everything else properly built on top of that. I'll check back in a week when it's done... :-/ I've got a monster world file.
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Last edited by opopanax on Tue Mar 14, 2006 3:12 am; edited 1 time in total
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Grooby
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PostPosted: Tue Mar 14, 2006 3:11 am    Post subject: Reply with quote

I emerge the new glibc
and my xorg craps out
recompile xorg but was locking up as soon as X starts.
rebooted the box and now everything *seems* ok.
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PostPosted: Tue Mar 14, 2006 3:41 am    Post subject: Reply with quote

I upgraded to glibc 2.4.0 over the weekend (and moved to gcc 4.1.0). So far everything is working.

gecko-sdk and seamonkey didn't compile but after patching them they're working.
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PostPosted: Tue Mar 14, 2006 3:45 am    Post subject: Reply with quote

sketelsen wrote:
how about re-merging portage, then re-merging grep and giving it another try? -uD world won't do it, I don't think, because too much stuff in the toolchain is whacked out by that ...

portage:
Code:
# emerge portage
 * Applying 1070_r2864_bug_125993_mergelist_keyerror.patch ...
 * Applying 1080_r2865_bug_125942_postinst_env.patch ...
 * Setting portage.VERSION to 2.1_pre6-r2 ...
sed: relocation error: sed: symbol __guard, version GLIBC_2.3.2 not defined in file libc.so.6 with link time reference

!!! ERROR: sys-apps/portage-2.1_pre6-r2 failed.
Call stack:
  ebuild.sh, line 1557:   Called dyn_unpack

grep:
Code:
* Applying grep-2.5.1-fix-devices-skip.patch ...                                                                                                                                            [ ok ]
sed: relocation error: sed: symbol __guard, version GLIBC_2.3.2 not defined in file libc.so.6 with link time reference

-e system:
Code:
usr/bin/confcache --confcache-ignore /var/tmp/ccache:/var/tmp/.distcc --confcache-dir /var/tmp/confcache ./configure --prefix=/usr --host=i686-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --build=i686-pc-linux-gnu
no cache
sed: relocation error: sed: symbol __guard, version GLIBC_2.3.2 not defined in file libc.so.6 with link time reference
sed: relocation error: sed: symbol __guard, version GLIBC_2.3.2 not defined in file libc.so.6 with link time reference
sed: relocation error: sed: symbol __guard, version GLIBC_2.3.2 not defined in file libc.so.6 with link time reference
...

Suggestions? I'm thinking boot to cd, update portage, emerge glibc, grep and others, then carry on with -e system, etc...
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PostPosted: Tue Mar 14, 2006 4:27 am    Post subject: Reply with quote

sketelsen wrote:
so, revdep-rebuild didn't work for you, hulmeman?


Nope, it found one or two, but it missed ~40. ssh, nfs, gnome-terminal amongst others. Happily I got a response on bugzilla, Bug #125909

Quote:
------- Comment #14 From ********** 2006-03-13 13:41 PST [reply] -------
(In reply to comment #13)
> Re-emerging the failing packages resolves the problem, but how to find
> which are affected, other than wait untill I try to execute something?

One liner.
qlist -o $(qlist -ICv) | scanelf -Bs__guard -qf - -F%F#s | xargs qfile

This found 28 packages, which Ive emerged, things seem OK now. I had to do a revdep-rebuild afterwards, cos 'glib' was broken.
emerge -e world'is a bit like overkill I think?
Wonder why its different packages for different folks? Maybe the borked packages were installed pre nptl?
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PostPosted: Tue Mar 14, 2006 11:54 pm    Post subject: Reply with quote

I don't know if it is overkill or not. I'm debating that myself--however, if revdep-rebuild is not working for this particular issue, i'm not sure what else I might do instead. I wonder how long it would take? emerge -e system took about 16 hours--and I have about 1500 packages in world...
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opopanax
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PostPosted: Tue Mar 14, 2006 11:59 pm    Post subject: Reply with quote

I had a similar problem, although probably was unrelated. Try re-merging sed, and then the rest.
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PostPosted: Wed Mar 15, 2006 1:27 am    Post subject: Reply with quote

sketelsen wrote:
I had a similar problem, although probably was unrelated. Try re-merging sed, and then the rest.

emerging sed uses sed during the emerge process and fails.

I downloaded the linux livecd, burned it, boot it, built a binary of glibc-2.3.5 (emerge -B sys-libs/glibc-2.3.5) within the environment, copied it to my packages dir, chrooted into the env, emerged the glibc binary and then i was able to start bringing things back to life. I've taken the opportunity to move from gcc 3.4.5 to 4.1 and am working on moving to glibc 2.4 again, although i'm preparing for the worst and building a new binary of glibc-2.3.6-r3 just incase the doggy doodoo hits the fan again.
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PostPosted: Wed Mar 15, 2006 7:52 pm    Post subject: Reply with quote

good call--I completely forgot to do that, mostly because I didn't realize it'd be an issue and impossible to revert back.

BTW, can anyone point out a good chroot howto? I'd like to run zsnes w/different libraries, since my g/f loves the old nintendo, and snes9x doesn't run well on my box.
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PostPosted: Fri Mar 17, 2006 11:36 am    Post subject: Solution found in bug 125988 Reply with quote

Several of my machines got bit by this bug to various degrees. The machine hit the worst would not run emerge, grep, wget, ... nada... and it is 2500 miles away from me so I really needed to find a solution that did not involve inserting a CD in it. Everything I tried gave the __guard error.

I followed the (modified) advice from SpanKY at the end of the chain for bug 125988:

Quote:

ok, glibc-2.4-r1 should resolve this

if you guys have a broken system and are unable to sync/re-emerge glibc, then
you can grab prebuilt lib's to work around this issue:
# bb
# wget http://dev.gentoo.org/~vapier/amd64_libssp_simple.so
# mv amd64_libssp_simple.so /lib/libssp_simple.so
# echo /lib/libssp_simple.so > /etc/ld.so.preload

for x86 users, just change the "amd64" to "x86"

once you've installed glibc-2.4-r1, then just delete /lib/libssp_simple.so and
/etc/ld.so.preload and you should be all set


...except I could not get "bb" to work on any of three machines I tried, so I tried "/bin/busybox wget..." and that finally worked. I was able to then "emerge --sync" and now the machine is compiling glibc-2.4-r1. :-)
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