Trouble with portage upgrade on amd64

[pkerwien]

When updating portage, emerge is first trying to install sandbox. Then the following error occurs:

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...
./configure --prefix=/usr --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --i                                       nfodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/v                                       ar/lib --libdir=/usr/lib32
configure: WARNING: If you wanted to set the --build type, don't use --host.
    If a cross compiler is detected then cross compile mode will be used.
checking for a BSD-compatible install... /bin/install -c
checking whether build environment is sane... yes
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for x86_64-pc-linux-gnu-strip... x86_64-pc-linux-gnu-strip
checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc
checking for C compiler default output file name... configure: error: C compiler                                        cannot create executables
See `config.log' for more details.

I then followed the tip printed out during installation:

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> FEATURES=-sandbox emerge sandbox
Calculating dependencies ...done!
>>> emerge (1 of 1) sys-apps/sandbox-1.2.9 to /
>>> md5 files   ;-) sandbox-1.2.9.ebuild
>>> md5 files   ;-) sandbox-1.2.10.ebuild
>>> md5 files   ;-) ChangeLog
>>> md5 files   ;-) metadata.xml
>>> md5 files   ;-) files/digest-sandbox-1.2.9
>>> md5 files   ;-) files/digest-sandbox-1.2.10
>>> md5 src_uri ;-) sandbox-1.2.9.tar.bz2
>>> Unpacking source...
>>> Unpacking sandbox-1.2.9.tar.bz2 to /var/tmp/portage/sandbox-1.2.9/work
 * Unpacking sandbox for ABI=x86...
>>> Unpacking sandbox-1.2.9.tar.bz2 to /var/tmp/portage/sandbox-1.2.9/work
 * Unpacking sandbox for ABI=amd64...
>>> Source unpacked.
 * If configure fails with a 'cannot run C compiled programs' error, try this:
 * FEATURES=-sandbox emerge sandbox
 * Configuring sandbox for ABI=x86...
 * econf: updating sandbox-1.2.9-amd64/config.guess with /usr/share/gnuconfig/config.guess
 * econf: updating sandbox-1.2.9-amd64/config.sub with /usr/share/gnuconfig/config.sub
 * econf: updating sandbox-1.2.9-x86/config.guess with /usr/share/gnuconfig/config.guess
 * econf: updating sandbox-1.2.9-x86/config.sub with /usr/share/gnuconfig/config.sub
./configure --prefix=/usr --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --libdir=/usr/lib32
configure: WARNING: If you wanted to set the --build type, don't use --host.
    If a cross compiler is detected then cross compile mode will be used.
checking for a BSD-compatible install... /bin/install -c
checking whether build environment is sane... yes
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for x86_64-pc-linux-gnu-strip... x86_64-pc-linux-gnu-strip
checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc
checking for C compiler default output file name... configure: error: C compiler cannot create executables
See `config.log' for more details.

!!! Please attach the config.log to your bug report:
!!! /var/tmp/portage/sandbox-1.2.9/work/sandbox-1.2.9-x86/config.log

!!! ERROR: sys-apps/sandbox-1.2.9 failed.
!!! Function econf, Line 485, Exitcode 0
!!! econf failed
!!! If you need support, post the topmost build error, NOT this status message.

I checked the config.log file and probably found the reason:

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...
configure:2254: $? = 0
configure:2256: x86_64-pc-linux-gnu-gcc -v </dev/null >&5
Reading specs from /usr/lib/gcc/x86_64-pc-linux-gnu/3.4.3/specs
Configured with: /var/tmp/portage/gcc-3.4.3-r1/work/gcc-3.4.3/configure --enable-version-specific-runtime-libs --prefix
=/usr --bindir=/usr/x86_64-pc-linux-gnu/gcc-bin/3.4.3 --includedir=/usr/lib/gcc/x86_64-pc-linux-gnu/3.4.3/include --dat
adir=/usr/share/gcc-data/x86_64-pc-linux-gnu/3.4.3 --mandir=/usr/share/gcc-data/x86_64-pc-linux-gnu/3.4.3/man --infodir
=/usr/share/gcc-data/x86_64-pc-linux-gnu/3.4.3/info --with-gxx-include-dir=/usr/lib/gcc/x86_64-pc-linux-gnu/3.4.3/inclu
de/g++-v3 --host=x86_64-pc-linux-gnu --disable-altivec --enable-nls --without-included-gettext --with-system-zlib --dis
able-checking --disable-werror --disable-libunwind-exceptions --enable-multilib --disable-libgcj --enable-languages=c,c
++,f77 --enable-shared --enable-threads=posix --enable-__cxa_atexit --enable-clocale=gnu
Thread model: posix
gcc version 3.4.3 20041125 (Gentoo 3.4.3-r1, ssp-3.4.3-0, pie-8.7.7)
configure:2259: $? = 0
configure:2261: x86_64-pc-linux-gnu-gcc -V </dev/null >&5
x86_64-pc-linux-gnu-gcc: `-V' must come at the start of the command line
configure:2264: $? = 1
configure:2287: checking for C compiler default output file name
configure:2290: x86_64-pc-linux-gnu-gcc -march=athlon64 -O2 -pipe -fomit-frame-pointer -DSB_HAVE_64BIT_ARCH   conftest.
c  >&5
/usr/lib/gcc/x86_64-pc-linux-gnu/3.4.3/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find /emul/linux/x86/lib/libc.so.
6
collect2: ld returned 1 exit status
configure:2293: $? = 1
configure: failed program was:
| /* confdefs.h.
...

If the missing file (/emul/linux/x86/lib/libc.so) is the reason, how do I restore it?

[OldTango]

I get the exact same error during a emerge -vuD system while compiling sandbox. My config.log shows the same missing libc.so file. I checked the path and it isn't there. I also got a message during the compile that said

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* If configure fails with a 'cannot run C compiled programs' error, try this:
 * FEATURES=-sandbox emerge sandbox

which I tried and the compile still failed with the same error.

Does anyone have a soultion to this problem, or know what the cause is???????????????

TIA

[OldTango]

pkerwien

I don't know if you have solved this problem yet. I filed a bug report on it and haven't found a fix or a way around it yet. You might try to

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emerge emul-linux-x86-glibc

which might help you. It didn't do a thing to fix my problem.

I will post back if I find a soultion.

BUG #98232

[pkerwien]

No, I haven't solved it.

Yes, I already have emul-linux-x86-glibc-1000 installed (which is empty). Yesterday I tried to upgrade glibc to 2.3.5, then I got the following error:

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...
checking for local label subtraction... yes
checking for __thread... yes
checking for tls_model attribute... yes
checking for libgd... no
checking for is_selinux_enabled in -lselinux... no
checking for egrep... grep -E
checking for ANSI C header files... no
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for long double... yes
checking size of long double... configure: error: cannot compute sizeof (long double), 77
See `config.log' for more details.

!!! ERROR: sys-libs/glibc-2.3.5 failed.
!!! Function glibc_do_configure, Line 928, Exitcode 1
!!! failed to configure glibc
!!! If you need support, post the topmost build error, NOT this status message.

[/quote]

[Maedhros]

This might help you with that: http://forums.gentoo.org/viewtopic-t-293507.html

[OldTango]

It apppears that when I upgraded to the 2005.0 profile back in April all did not go well. I followed the upgrade how-to exactly, but it gave you 2 options. The easy way and the long way. Being stupid I dececided to take the easy way. It failed to upgrade my system properly and left me scratching my head. Searching the forums I found the thread that Maedhros pointed to.

Maedhros

This might help you with that: http://forums.gentoo.org/viewtopic-t-293507.html

Using the info in that thread I reverted back to the 2004.3 profile and tried again. This time all seemed to go well, no errors and everything seemed to be ok, untill the recent changes in portage.

As you know I filed a bug report #98232 which has now been marked as a dupicate od bug #90846.

Right now I am in the process of attempting to repair my system and bring it up to date properly. If I can some how manage this I will post back with the info on how I managed to do it.

[OldTango]

Over the last 2 days I have tried repeatedly to repair the botched amd64-2005.0 profile upgrade. Going back and forth between 2004.3 and 2005.0 many times. I have been able to compile both gcc and glibc scussfully under the 2004.3 profile. Following the instructions located here. After multiple attempts I am left with this error

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/var/tmp/portage/glibc-2.3.5/work/build-x86-x86_64-pc-linux-gnu-linuxthreads/linuxthreads/libpthread.so: undefined reference to `errno@GLIBC_PRIVATE'
/var/tmp/portage/glibc-2.3.5/work/build-x86-x86_64-pc-linux-gnu-linuxthreads/linuxthreads/libpthread.so: undefined reference to `__libc_dl_error_tsd@GLIBC_PRIVATE'
/var/tmp/portage/glibc-2.3.5/work/build-x86-x86_64-pc-linux-gnu-linuxthreads/linuxthreads/libpthread.so: undefined reference to `__resp@GLIBC_PRIVATE'
/var/tmp/portage/glibc-2.3.5/work/build-x86-x86_64-pc-linux-gnu-linuxthreads/linuxthreads/libpthread.so: undefined reference to `h_errno@GLIBC_PRIVATE'
collect2: ld returned 1 exit status
make[2]: *** [/var/tmp/portage/glibc-2.3.5/work/build-x86-x86_64-pc-linux-gnu-linuxthreads/nscd/nscd] Error 1
make[2]: Leaving directory `/var/tmp/portage/glibc-2.3.5/work/glibc-2.3.5/nscd'
make[1]: *** [nscd/others] Error 2
make[1]: Leaving directory `/var/tmp/portage/glibc-2.3.5/work/glibc-2.3.5'
make: *** [all] Error 2

!!! ERROR: sys-libs/glibc-2.3.5 failed.
!!! Function toolchain-glibc_src_compile, Line 237, Exitcode 2
!!! (no error message)
!!! If you need support, post the topmost build error, NOT this status message.

after the switch to the 2005.0 profile. I can't get around this botched upgrade for some stupid reason that eludes me at this time.

Can anybody offer me some advice or soultion I haven't yet tried.

TIA

NOTE TO SELF: Never choose the easy method!!!!!!!!!!!!!!!!!!!!!!

[brainwash]

Hello.

I have just encountered this same bug, and after checking bug report #90846
(which was mentioned by OldTango), I found out that it's a make.defaults problem.

The CFLAGS_x86 and LDFLAGS_x86 in /etc/make.profile/make.defaults only point
to /emul/linux/x86/lib and /emul/linux/x86/usr/lib, while libc6.so gets installed in /lib32.

The correct settings are:

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CFLAGS_x86="-m32 -L/lib32 -L/usr/lib32 -L/emul/linux/x86/lib -L/emul/linux/x86/usr/lib"
LDFLAGS_x86="-L/lib32 -L/usr/lib32 -m elf_i386 -L/emul/linux/x86/lib -L/emul/linux/x86/usr/lib"

After doing this, emerging sandbox and upgrading portage worked for me.

[OldTango]

brainwash

Hey I would like you to post the first half of your

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emerge info

Also did you upgrade from 2004.3 to 2005.0 profile or was it a fresh install. If you upgraded using the Gentoo How-to did glibc compile cleanly after the profile switch. I am trying to track down some nasty problems I am having.

Thanks

[brainwash]

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iguana jannik # emerge info
Portage 2.0.51.22-r1 (default-linux/amd64/2005.0, gcc-3.4.3, glibc-2.3.4.20041102-r1, 2.6.11-gentoo-r7 x86_64)
=================================================================
System uname: 2.6.11-gentoo-r7 x86_64 AMD Athlon(tm) 64 Processor 3200+
Gentoo Base System version 1.6.12
distcc 2.18.3 x86_64-pc-linux-gnu (protocols 1 and 2) (default port 3632) [disabled]
ccache version 2.3 [enabled]
dev-lang/python:     2.3.5
sys-apps/sandbox:    1.2.9
sys-devel/autoconf:  2.13, 2.59-r6
sys-devel/automake:  1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.5
sys-devel/binutils:  2.15.92.0.2-r10
sys-devel/libtool:   1.5.18-r1
virtual/os-headers:  2.6.11-r2
ACCEPT_KEYWORDS="amd64"
AUTOCLEAN="yes"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=k8 -O2 -fomit-frame-pointer -frename-registers -fPIC -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/kde/2/share/config /usr/kde/3.4/env /usr/kde/3.4/share/config /usr/kde/3.4/shutdown /usr/kde/3/share/config /usr/lib/X11/xkb /usr/lib/mozilla/defaults/pref /usr/share/config /usr/share/texmf/dvipdfm/config/ /usr/share/texmf/dvips/config/ /usr/share/texmf/tex/generic/config/ /usr/share/texmf/tex/platex/config/ /usr/share/texmf/xdvi/ /var/qmail/control"
CONFIG_PROTECT_MASK="/etc/gconf /etc/terminfo /etc/env.d"
CXXFLAGS="-march=k8 -O2 -fomit-frame-pointer -frename-registers -fPIC -pipe"
DISTDIR="/usr/portage/distfiles"
FEATURES="autoconfig ccache distlocks sandbox sfperms strict userpriv"
GENTOO_MIRRORS="http://iguana/ ftp://ftp.tu-clausthal.de/pub/linux/gentoo http://gentoo.oregonstate.edu http://www.ibiblio.org/pub/Linux/distributions/gentoo"
MAKEOPTS="-j2"
PKGDIR="/usr/portage/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="amd64 X aalib acpi aim alsa arts audiofile avi berkdb bitmap-fonts cdparanoia cdr crypt cups curl doc dvd dvdr encode esd fam fbcon fftw flac font-server foomaticdb fortran gd gdbm gif gpm gstreamer gtk gtk2 gtkhtml guile hal icq imagemagick imlib ipv6 jack java jp2 jpeg junit kde lcms lesstif libwww lzw lzw-tiff mad maildir mikmod motif mozilla mp3 mpeg ncurses nls offensive ogg oggvorbis opengl oscar oss pam pdflib perl png python qt quicktime readline samba sdl slang spell ssl svg tcltk tcpd tetex theora tidy tiff truetype truetype-fonts type1-fonts unicode usb userlocales vorbis xine xinerama xml xml2 xmms xpm xprint xrandr xscreensaver xv zeroconf zlib userland_GNU kernel_linux elibc_glibc"
Unset:  ASFLAGS, CTARGET, LANG, LC_ALL, LDFLAGS, LINGUAS, PORTDIR_OVERLAY

There you go.

Yes, I did an upgrade from 2004.3 to 2005.0 - multiple times actually

I'm not really sure what was the problem, but upgrading was a mess. Even with PORTAGE_FEATURES="-sandbox", I had some problems with the conventional upgrade procedure which broke multilib and then proceeded to break my entire toolchain.

I'm sorry I can't recall what solved the problem for me, but maybe one of the threads about 2005.0 can help you.

But I think it was something about emerging glibc by hand, then gcc, then glibc again, maybe even involving gcc-config...

Profile upgrading seems to me like some kind of voodoo black magic or maybe lsd shamanism

[brainwash]

Ahh, now that I'm reading your log I remember something.

If you have nptl in your USE setting when building glibc on AMD64, glibc is built 4 times,
64 bit without nptl, with nptl, the same for 32 bit. At least one of those builds usually
fails for some obscure reason...

So maybe try to remove the nptl USE flag from your make.conf and compile glibc again.

[brainwash]

Ok, now I'm seeing this bug too.

This seems to be related to a patch that was dropped between glibc-2.3.4-2004-11-01-r1 and glibc-2.3.5.

The relevant bug is http://bugs.gentoo.org/show_bug.cgi?id=90091.

Let me know if something works for you, I'm currently pondering a reinstall which is long
overdue for me anyway.

[OldTango]

Well the problem I am running into is this. Under the 2004.3 profile I can compile any program marked stable for my amd64 system and all my 32bit programs function normally. After I move to the 2005.0 profile using the the HOW-TO guide and carefully checking every setp. glibc bails with the above mentioned errors. Whats worse is my 32bit porgrams no longer function at all.

It was mentioned to me that it could be a versioning problem, so I went back to 2004.3 and made sure I rebuilt with glibc-2.3.4.20041102 matching the emul-linux-x86 version. Gcc and glibc built error free and my 32bit programs working great. An important NOTE to keep in mind is that I have benn able to build any version of gcc and glibc under the 2004.3 profile error free and my 32bit programs always function. I took this a step further just to test things out and discovered that if I try to re-build gcc under the 2005.0 profile it will also error out, with ignoring incompatible lib (something,something) while searching for -lm, can't find -lm

My problem, like many other users had, started back in April if I recall when the 2005.0 profile first arrived on the seen. The HOW-TO at that time offered 2 methods of updating, the scripted way and the long way. I first chose the scripted way and it broked. So like everyone else suffering form this problem I began searching the forums and bug reports. At that time I went back to the 2004.3 profile and used the hand method to upgrading. I recall that there were problems with gcc and glibc even then. Using the forums and ideas from other users it appeared that I had made the switch to the 2005.0 profile and everything was working ok. BUT WAS IT?????????? I suspect it wasn't.

About a week ago an update to portage came out and sandbox was marked stable for amd64. During a normal

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emerge -vuD system

sandbox bailed with pkerwien's above mentioned post in this forum. Following the same advise he was before I had even read this forum, I got the exact same errors he did. I had gotton this advise when searching bug-reports. I also filed a report #98232 which might be worth reading.

I suspect that users like me who had problems upgrading to the 2005.0 profile and need or want a mixed environment (32bit and 64 bit) will discover that if they attempt to re-build gcc (not that I reccomend doing this) its going to fail. This could be a result of too many other updates to important programs that have occured over time sinse I first upgraded, or just missing libs.

I have spent days trying to make the upgrade work without sucess. There are a couple more ideas I am going to try out and hope I don't hose my whole system in the process. But I am quickly running out of ideas. I could use some expert linux input right about now. This problem is beyond my linux background and knowlege.......

[brainwash]

Okay, as far as the GLIBC_PRIVATE problem goes, I just got that fixed.

Reading through some bug reports I found out that it's really an nptl thing.
According to those bug reports you have to add nptl and nptlonly to your USE setting,
but glibc w/ nptl would not build on my machine.

Now I've tried an emerge -ev glibc, and it did actually build. So maybe you can try
this approach too.

As to your gcc problem, I remember having a similiar problem too. If you've got the 2005.0
profile, you have gcc 2.4.x. Try fiddling around with gcc-config, switch back to the older gcc,
emerge gcc with this and then switch to the newer version, emerge glibc and then gcc again.

I think that was the solution for me back then.

If you could post the build error for gcc this would also be helpful...

[OldTango]

Another update on this problem

I saw the new script was out for upgrading to the 2005.0 profile. I opened it and took a look inside, (not that I have any real clue of what I was looking at) it appeared to address most if not all of the bug reports filed on this subject. Also additional error warnings for the various steps involed in the upgrade. So if nothing else I felt it could be a nice debugging tool. Well all went well untill the final glibc emerge and there I sat looking at this error that will not go away.

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/var/tmp/portage/glibc-2.3.5/work/build-x86-x86_64-pc-linux-gnu-linuxthreads/linuxthreads/libpthread.so: undefined reference to `errno@GLIBC_PRIVATE'
/var/tmp/portage/glibc-2.3.5/work/build-x86-x86_64-pc-linux-gnu-linuxthreads/linuxthreads/libpthread.so: undefined reference to `__libc_dl_error_tsd@GLIBC_PRIVATE'
/var/tmp/portage/glibc-2.3.5/work/build-x86-x86_64-pc-linux-gnu-linuxthreads/linuxthreads/libpthread.so: undefined reference to `__resp@GLIBC_PRIVATE'
/var/tmp/portage/glibc-2.3.5/work/build-x86-x86_64-pc-linux-gnu-linuxthreads/linuxthreads/libpthread.so: undefined reference to `h_errno@GLIBC_PRIVATE'
collect2: ld returned 1 exit status
make[2]: *** [/var/tmp/portage/glibc-2.3.5/work/build-x86-x86_64-pc-linux-gnu-linuxthreads/nscd/nscd] Error 1
make[2]: Leaving directory `/var/tmp/portage/glibc-2.3.5/work/glibc-2.3.5/nscd'
make[1]: *** [nscd/others] Error 2
make[1]: Leaving directory `/var/tmp/portage/glibc-2.3.5/work/glibc-2.3.5'
make: *** [all] Error 2

!!! ERROR: sys-libs/glibc-2.3.5 failed.
!!! Function toolchain-glibc_src_compile, Line 237, Exitcode 2
!!! (no error message)
!!! If you need support, post the topmost build error, NOT this status message. 

Now I have been able to find and fix all the other errors that have happened when performing this upgrade except this one. As it stands right now I can't get past this one.

brainwash
WROTE"

Okay, as far as the GLIBC_PRIVATE problem goes, I just got that fixed.

Reading through some bug reports I found out that it's really an nptl thing.
According to those bug reports you have to add nptl and nptlonly to your USE setting,
but glibc w/ nptl would not build on my machine.

which I had already tested my self yesterday. I noticed that it always broked here at this point. So while in the 2004.3 profile I converted to using ntplonly, so threads would'nt be built into glibc. Everything built fine in 2004.3. After again moving to the 2005.0 profile as per the upgrade guide, to my surprise I got the exact same error only this time it was ntpl complaining about undefined rreferences to these same files.

brainwash: This evening I will once again try the upgrade, and after the move to 2005.0 I will try using

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emerge -ev gilbc

and let you know what the results are.

The only other question I have, is do all your 32bit programs function correctly.

[OldTango]

I have fixed all my problems with the upgrade to 2005.0 profile. I am sure most of them were caused by the first upgrade I had made back in April, which didn't go well. While all appeared to be ok at that time it in fact wasn't.

I was also runnig a buggy gcc back then so I switched back to my old version of gcc and ran

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unset GCC_SPECS && emerge gcc

gcc emerged with almost no warnings and no errors. This may not have been necessary but I was grasping at any straw.

Also during the time I had done the first upgrade up to the point I started getting emerge errors I had already upgraded a lot of other important files. This I belive was stopping me from getting the upgrade to work properly. The correct versions and libs were just not where they needed to be. There has been an update to portage that has the correct packages to make the upgrade work. THANK YOU GENTOO DEVS!!!!!

If you have the problems I had follow this guide and pay particular attention to the common problems section. This guide has been updated as of 7/12/2005 and following it will insure you get upgraded properly.

After completing the upgrade and everything goes as planed you may notice your 32bit games ie.....quake3 or doom3 won't start up correctly. If this is the case simply re- emerge your nvidia-glx package.

Thanks to all for their help and thanks to the GENTOO DEVS as well.