emerging xorg borked my system [SOLVED toolchain problems]

[dakster]

I'm in the middle of a once in a blue moon emerge -e system && emerge -e system && emerge -e world && emerge -e world. I generally only apply security patches, and once every year or so I'll recompile everything with the line above (I know, it's overkill). I've gone through the two system rebuilds just fine. I'm on my first world rebuild which was going along ok until I hit xorg. The xorg that is maked stable (x11-base/xorg-x11-6.8.2-r7) is, it would seem, not so friendly to the lib symlinks in /usr. How this got marked stable is beyond me since there's a number of posts about it, but I digress...

So using the posts I "fixed" my symlinks and skipped the xorg build with emerge --resume --skipfirst so that I can come back to it later. However, just a few packages later my emerge -e world dies with some bizarre statements. It's on glut, and has died like so:

config.status: executing default-1 commands
/bin/sh ../libtool --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../include -DNDEBUG -march=k8 -O2 -pipe -frename-registers -Wall -fomit-frame-pointer -ffast-math -fexpensive-optimizations -fstrict-aliasing -D_REENTRANT -DPTHREADS -c glut_8x13.c
/bin/sh ../libtool --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../include -DNDEBUG -march=k8 -O2 -pipe -frename-registers -Wall -fomit-frame-pointer -ffast-math -fexpensive-optimizations -fstrict-aliasing -D_REENTRANT -DPTHREADS -c glut_9x15.c
/bin/sh ../libtool --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../include -DNDEBUG -march=k8 -O2 -pipe -frename-registers -Wall -fomit-frame-pointer -ffast-math -fexpensive-optimizations -fstrict-aliasing -D_REENTRANT -DPTHREADS -c glut_bitmap.c
../libtool: line 320: s,^.*/,,g: No such file or directory
../libtool: line 320: s,^.*/,,g: No such file or directory
../libtool: line 320: s,^.*/,,g: No such file or directory
../libtool: line 698: -e: command not found
*** Warning: inferring the mode of operation is deprecated.
*** Future versions of Libtool will require --mode=MODE be specified.
../libtool: line 992: -e: command not found
../libtool: line 992: -e: command not found
../libtool: line 992: -e: command not found
../libtool: line 992: -e: command not found
../libtool: line 992: -e: command not found
../libtool: line 992: -e: command not found
../libtool: line 992: -e: command not found
../libtool: line 992: -e: command not found
../libtool: line 992: -e: command not found
../libtool: line 698: -e: command not found
../libtool: line 992: -e: command not found
../libtool: line 992: -e: command not found
../libtool: line 992: -e: command not found
../libtool: line 992: -e: command not found
../libtool: line 992: -e: command not found
../libtool: line 992: -e: command not found
../libtool: line 992: -e: command not found
../libtool: line 992: -e: command not found
*** Warning: inferring the mode of operation is deprecated.
*** Future versions of Libtool will require --mode=MODE be specified.
../libtool: line 992: -e: command not found
../libtool: line 992: -e: command not found
../libtool: line 992: -e: command not found
../libtool: line 992: -e: command not found
../libtool: line 1020: -e: command not found
../libtool: line 992: -e: command not found
../libtool: line 1043: -e: command not found
../libtool: line 992: -e: command not found
: compile: cannot determine name of library object from `'
make: *** [glut_bitmap.lo] Error 1
make: *** Waiting for unfinished jobs....
../libtool: line 992: -e: command not found
../libtool: line 992: -e: command not found
../libtool: line 992: -e: command not found
../libtool: line 992: -e: command not found
../libtool: line 992: -e: command not found
../libtool: line 992: -e: command not found
../libtool: line 992: -e: command not found
../libtool: line 992: -e: command not found
../libtool: line 992: -e: command not found
../libtool: line 992: -e: command not found
../libtool: line 992: -e: command not found
../libtool: line 992: -e: command not found
../libtool: line 992: -e: command not found
../libtool: line 992: -e: command not found
../libtool: line 992: -e: command not found
../libtool: line 1020: -e: command not found
../libtool: line 1043: -e: command not found
: compile: cannot determine name of library object from `'
make: *** [glut_8x13.lo] Error 1
../libtool: line 698: -e: command not found
*** Warning: inferring the mode of operation is deprecated.
*** Future versions of Libtool will require --mode=MODE be specified.
../libtool: line 992: -e: command not found
../libtool: line 992: -e: command not found
../libtool: line 992: -e: command not found
../libtool: line 992: -e: command not found
../libtool: line 992: -e: command not found
../libtool: line 992: -e: command not found
../libtool: line 992: -e: command not found
../libtool: line 992: -e: command not found
../libtool: line 992: -e: command not found
../libtool: line 992: -e: command not found
../libtool: line 992: -e: command not found
../libtool: line 992: -e: command not found
../libtool: line 992: -e: command not found
../libtool: line 992: -e: command not found
../libtool: line 992: -e: command not found
../libtool: line 992: -e: command not found
../libtool: line 992: -e: command not found
../libtool: line 992: -e: command not found
../libtool: line 992: -e: command not found
../libtool: line 1020: -e: command not found
../libtool: line 1043: -e: command not found
: compile: cannot determine name of library object from `'
make: *** [glut_9x15.lo] Error 1

!!! ERROR: media-libs/glut-3.7.1 failed.
Call stack:
ebuild.sh, line 1539: Called dyn_compile
ebuild.sh, line 939: Called src_compile
glut-3.7.1.ebuild, line 35: Called die

!!! emake failed
!!! If you need support, post the topmost build error, and the call stack if relevant.



Also some of my applications are acting strangely, so I think I still have some libs screwed up. Here's my symlinks:

shadowcat(root)> ls -l /usr/
total 284
lrwxrwxrwx 1 root root 6 Jun 29 2005 X11R6 -> ../usr/
drwxr-xr-x 2 root root 53248 Jun 20 10:51 bin/
drwxr-xr-x 3 root root 19 Nov 22 2004 com/
drwxr-xr-x 4 root root 32 Nov 2 2005 cs/
lrwxrwxrwx 1 root root 9 Jun 29 2005 doc -> share/doc/
drwxr-x--- 4 root games 26 Nov 12 2004 games/
drwxr-xr-x 229 root root 20480 Jun 20 10:50 include/
lrwxrwxrwx 1 root root 10 Jun 29 2005 info -> share/info/
drwxr-xr-x 5 root root 36 Sep 8 2005 kde/
drwxr-xr-x 6 root root 51 Sep 8 2005 kdevbdb/
drwxr-xr-x 117 root root 69632 Jun 20 10:51 lib/
lrwxrwxrwx 1 root root 25 Jun 20 10:35 lib32 -> ../emul/linux/x86/usr/lib/
drwxr-xr-x 11 root root 4096 Jun 20 09:52 lib32-old/
lrwxrwxrwx 1 root root 3 Jun 20 10:39 lib64 -> lib/
lrwxrwxrwx 1 root root 8 Jun 20 09:08 lib64.oldLink -> ../lib64/
drwxr-xr-x 8 root root 4096 Jun 19 13:00 libexec/
drwxrwxrwx 24 pat dev 4096 Jan 24 10:56 local/
lrwxrwxrwx 1 root root 9 Jun 29 2005 man -> share/man/
drwxr-xr-x 155 root root 4096 Jun 18 21:57 portage/
drwxr-xr-x 3 root root 14 Jul 26 2004 qt/
drwxr-xr-x 2 root root 8192 Jun 20 10:41 sbin/
drwxr-xr-x 193 root root 8192 Jun 19 17:32 share/
drwxr-xr-x 7 root root 4096 Jun 15 08:31 src/
lrwxrwxrwx 1 root root 10 Jun 29 2005 tmp -> ../var/tmp/
drwxr-xr-x 6 root root 59 Sep 29 2005 x86_64-pc-linux-gnu/


According to the postings this looks like the way it should be after "Fixing" what xorg does to the symlinks. I did grab a backup before I started this process, but I'd hate to go back. Stable portage shouldn't be giving me such fits I wouldn't think. Here's my emerge info:


shadowcat(root)> emerge --info
Portage 2.1 (default-linux/amd64/2006.0, gcc-3.4.5, glibc-2.3.6-r3, 2.6.16-gentoo-r9 x86_64)
=================================================================
System uname: 2.6.16-gentoo-r9 x86_64 AMD Athlon(tm) 64 X2 Dual Core Processor 4400+
Gentoo Base System version 1.6.14
dev-lang/python: 2.3.5-r2, 2.4.2
dev-python/pycrypto: 2.0.1-r5
dev-util/ccache: [Not Present]
dev-util/confcache: [Not Present]
sys-apps/sandbox: 1.2.17
sys-devel/autoconf: 2.13, 2.59-r7
sys-devel/automake: 1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r1
sys-devel/binutils: 2.16.1-r2
sys-devel/gcc-config: 1.3.13-r2
sys-devel/libtool: 1.5.22
virtual/os-headers: 2.6.11-r2
ACCEPT_KEYWORDS="amd64"
AUTOCLEAN="yes"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=k8 -O2 -pipe -frename-registers"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/kde/3.2/share/config /usr/kde/3.3/env /usr/kde/3.3/share/config /usr/kde/3.3/shutdown /usr/kde/3.4/env /usr/kde/3.4/share/config /usr/kde/3.4/shutdown /usr/lib/X11/xkb /usr/share/config"
CONFIG_PROTECT_MASK="/etc/env.d /etc/gconf /etc/terminfo"
CXXFLAGS="-march=k8 -O2 -pipe -frename-registers"
DISTDIR="/usr/portage/distfiles"
FEATURES="autoconfig distlocks metadata-transfer sandbox sfperms strict"
GENTOO_MIRRORS="http://mirror.datapipe.net/gentoo http://gentoo.mirrors.pair.com/"
LANG="C"
MAKEOPTS="-j3"
PKGDIR="/usr/portage/packages"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --delete-after --stats --timeout=180 --exclude='/distfiles' --exclude='/local' --exclude='/packages'"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="X aalib alsa amd64 avi berkdb bitmap-fonts cdparanoia cdr cli crypt cups dga divx4linux dri dvd dvdr eds emboss encode firefox foomaticdb fortran gif gnome gpm gstreamer gtk gtk2 imlib ipv6 isdnlog jpeg jpg kde lzw lzw-tiff mad mp3 mpeg ncurses nls nptl nvidia oggvorbis opengl pam pcre pdflib perl png ppds pppd python qt quicktime readline reflection sdl session spell spl ssl tcpd theora threads tiff truetype truetype-fonts type1-fonts udev usb xinerama xorg xpm xv xvid xvmn zlib elibc_glibc kernel_linux userland_GNU"
Unset: CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, LDFLAGS, LINGUAS, PORTAGE_RSYNC_EXTRA_OPTS, PORTDIR_OVERLAY



I'm at wits end with this thing, anyone have any tips on how to fix my system?

[spielc]

What do you mean with " I generally only apply security patches"? Does this mean that you sync regularly but you only do a update your world ONCE a year?!?

[dakster]

Exactly, I sync daily (during the week) and apply security patches. Been doing this for years, keeps a nice stable system, which is important at work.

[spielc]

Did you search bugzilla if this is a know problem of glut? Btw. you should definitely update more often once a year is DEFINITELY not enough... Over a year a TON of things can change

[dakster]

I don't see any bugs using the keywords glut and libtool, which is what's spitting out tons of errors.

I'm sure there are tons of changes in a year of world updates, which is precisely why I don't do it. I'm running a multi-terabyte fileserver for a number of users I tend to want to make the least number of changes possible, until I have some down time (like now) in which I can calmly do the updates when downtime won't hamper the users as much.

I generally only do the full world and system updates when I move profiles, or when something gets out of sorts. It's just a conservative means of manageing a gentoo box. I'm pretty sure I'm not the only one who manages a gentoo server this way, and it's worked well for me for years.

So I guess "enough" updates lies in the eye of the beholder eh?

[spielc]

[dakster]

I don't run X on that server, however it's in a locked down room by itself, so sometimes it's convenient to start X on it and fire off a firefox browser to check things in the forums. Anyways, things seems to have settled down on the box well enough that I'm going through the emerge -e world again, and skipping problematic ebuilds with emerge --resume --skipfirst. Hopefully these will "fix" themselves prior to my second emerge -e world passthrough. Those print statements from libtool are just bizarre. Maybe it wasn't the fault of Xorg screwing up the symlinks. I'll see what happens on that second pass through the emerge -e world...

[uxbod]

If passed the emerge -e system, how about revdep-rebuild first ?

[dakster]

Good idea, I'll try that first thing in the morning...

[dakster]

It's becoming clear to me that my main problem assides from Xorg messing up some symlinks is that my toolchain is screwed up. I did have a bunch of memory errors before which are fixed now, maybe having bad memory over time led to some corruptions. I'm going back to fixing my toolchain so I know I have a good compiler and libraries and then start over. Good thing the machine is still pluggin away happily with all this running in the background

[dakster]

Doh, looks like I can't even rebuild my toolchain. I'm looking to snag avenj's binary's to use to rebuild my toolchain, then when I get a good toolchain build redo the whole system to be safe. I'm still looking for some instructions on how to utilize the binary's, but I'm thinking along the lines of doing this:

BTW, my portage still seems to work, so that does help. Anyway, my plan with binary's from http://dev.gentoo.org/~avenj/bins/

# emerge glibc binutils gcc && emerge glibc binutils gcc

switch to my rebuilt compiler using gcc-config and:

# emerge glibc binutils gcc && emerge glibc binutils gcc

If this works out, I should have a good toolchain again. For kicks and giggles, I think I'm going to follow this up with:

# emerge libtool m4 && emerge libtool m4

A lot of the errors I've been seeing seem like they should revolve around these packages. Anyway, assuming everything is hunky dory up to this point, I'm
going full blown rebuild with the hopefully good toolchain:

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



If anyone knows how to use the avenj binary's I'm all ears, the README seems to have disappeared from his directories, and he's not answering on irc as of yet....
If anyone has any comments on this I'm all ears. I don't particularly care how long this takes, I've got a amd X2, so it should be too bad.

[dakster]

Now that I look at what I've actually downloaded from avenj's binary site, there is no gcc binary for amd64. I think tonight after work I'm going to boot into a livecd and use that CD's toolchain to rebuild my systems initial toolchain. I'll report back if it works....

[dakster]

Doh, no compiler on the livecd's. Ok, I have a spare partition, I'm untaring the stage3 there like a fresh install, then migrating my stuff over like in this thread:

http://forums.gentoo.org/viewtopic-p-3286323-highlight-.html#3286323

Should work out fine. When it's done re-compiling everything (I'll chroot into it just like doing an install) I'll simply fix up my grub and reboot. Problem solved, basically a new install except I keep my world file and /etc. I'll just run off my broken gentoo install which I can't upgrade or maintain anymore, but most software works, while I wait for the new one to finish compiling. Go-go gadget gentoo....