[gentoo-user] Gentoo messed up after upgrade

[gentoo-user] Gentoo messed up after upgrade

[Miernik]

After running 'emerge -uD world' I have many things messed-up, besides
the unability of firefox to do DNS resolve for most (but not all) URLs.
ssh also can't DNS resolve some hosts (but ping can on the same hosts).

All my manpages look like this:

ESC[1mNAMEESC[0m
       ls - list directory contents

ESC[1mSYNOPSISESC[0m
       ESC[1mls ESC[22m[ESC[4mOPTIONESC[24m]... [ESC[4mFILEESC[24m]...

Many programs fail to start:

miernik@przehyba ~ $ gnumeric
gnumeric: symbol lookup error: /usr/lib/libspreadsheet-1.8.4.so: undefined symbol: g_dgettext

miernik@przehyba ~ $ oowriter
/usr/lib64/openoffice/program/soffice.bin: /usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/libstdc++.so.6: version LIBCXX_3.4.9' not found (required by /usr/lib64/openoffice/program/../basis-link/program/libbasegfxlx.so)

miernik@przehyba ~ $ eix glibc
eix: /usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/libstdc++.so.6: version LIBCXX_3.4.9' not found (required by eix)

Before I had ~amd64 in ACCEPT_KEYWORDS, but in the middle of this
upgrade I thought it was a bad idea, because many programs failed to
compile, so I removed that from make.conf, and did run
'emerge --empty-tree world'
which downgraded everything back to stable. But one thing I couldn't
downgrade was glibc which stayed at version
sys-libs/glibc-2.9_p20081201-r1

XTerm is not using my ~/.Xresources settings.

Is there any way I can possibly fix my system?

-- 
Miernik

Re: [gentoo-user] Gentoo messed up after upgrade

[Volker Armin Hemmann]

On Montag 02 Februar 2009, Miernik wrote:
> After running 'emerge -uD world' I have many things messed-up, besides
> the unability of firefox to do DNS resolve for most (but not all) URLs.
> ssh also can't DNS resolve some hosts (but ping can on the same hosts).
>
> All my manpages look like this:
>
> ESC[1mNAMEESC[0m
>        ls - list directory contents
>
> ESC[1mSYNOPSISESC[0m
>        ESC[1mls ESC[22m[ESC[4mOPTIONESC[24m]... [ESC[4mFILEESC[24m]...
>
> Many programs fail to start:
>
> miernik@przehyba ~ $ gnumeric
> gnumeric: symbol lookup error: /usr/lib/libspreadsheet-1.8.4.so: undefined
> symbol: g_dgettext
>
> miernik@przehyba ~ $ oowriter
> /usr/lib64/openoffice/program/soffice.bin:
> /usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/libstdc++.so.6: version
> LIBCXX_3.4.9' not found (required by
> /usr/lib64/openoffice/program/../basis-link/program/libbasegfxlx.so)
>
> miernik@przehyba ~ $ eix glibc
> eix: /usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/libstdc++.so.6: version
> LIBCXX_3.4.9' not found (required by eix)
>
> Before I had ~amd64 in ACCEPT_KEYWORDS, but in the middle of this
> upgrade I thought it was a bad idea, because many programs failed to
> compile, so I removed that from make.conf, and did run
> 'emerge --empty-tree world'
> which downgraded everything back to stable. But one thing I couldn't
> downgrade was glibc which stayed at version
> sys-libs/glibc-2.9_p20081201-r1
>
> XTerm is not using my ~/.Xresources settings.
>
> Is there any way I can possibly fix my system?

yes, revdep-rebuilt.

Re: [gentoo-user] Gentoo messed up after upgrade

[Dale]

Volker Armin Hemmann wrote:
> On Montag 02 Februar 2009, Miernik wrote:
>   
>> After running 'emerge -uD world' I have many things messed-up, besides
>> the unability of firefox to do DNS resolve for most (but not all) URLs.
>> ssh also can't DNS resolve some hosts (but ping can on the same hosts).
>>
>> All my manpages look like this:
>>
>> ESC[1mNAMEESC[0m
>>        ls - list directory contents
>>
>> ESC[1mSYNOPSISESC[0m
>>        ESC[1mls ESC[22m[ESC[4mOPTIONESC[24m]... [ESC[4mFILEESC[24m]...
>>
>> Many programs fail to start:
>>
>> miernik@przehyba ~ $ gnumeric
>> gnumeric: symbol lookup error: /usr/lib/libspreadsheet-1.8.4.so: undefined
>> symbol: g_dgettext
>>
>> miernik@przehyba ~ $ oowriter
>> /usr/lib64/openoffice/program/soffice.bin:
>> /usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/libstdc++.so.6: version
>> LIBCXX_3.4.9' not found (required by
>> /usr/lib64/openoffice/program/../basis-link/program/libbasegfxlx.so)
>>
>> miernik@przehyba ~ $ eix glibc
>> eix: /usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/libstdc++.so.6: version
>> LIBCXX_3.4.9' not found (required by eix)
>>
>> Before I had ~amd64 in ACCEPT_KEYWORDS, but in the middle of this
>> upgrade I thought it was a bad idea, because many programs failed to
>> compile, so I removed that from make.conf, and did run
>> 'emerge --empty-tree world'
>> which downgraded everything back to stable. But one thing I couldn't
>> downgrade was glibc which stayed at version
>> sys-libs/glibc-2.9_p20081201-r1
>>
>> XTerm is not using my ~/.Xresources settings.
>>
>> Is there any way I can possibly fix my system?
>>     
>
> yes, revdep-rebuilt.
>
>
>   

Typo there I think.  Try revdep-rebuild -i and see if that helps.

Dale

:-)  :-)

[gentoo-user] Re: Gentoo messed up after upgrade

[Miernik]

Dale <rdalek1967@gmail.com> wrote:
> Typo there I think.  Try revdep-rebuild -i and see if that helps.

Unfortunately it didn't help:


przehyba ~ # revdep-rebuild -i
 * Configuring search environment for revdep-rebuild

 * Checking reverse dependencies
 * Packages containing binaries and libraries broken by a package update
 * will be emerged.

 * Collecting system binaries and libraries
 * Generated new 1_files.rr
 * Collecting complete LD_LIBRARY_PATH
 * Generated new 2_ldpath.rr
 * Checking dynamic linking consistency
[ 29% ]  *   broken /usr/kde/3.5/lib32/libqtmcop.so.1.0.0 (requires libqt-mt.so.3)
[ 100% ]
 * Generated new 3_broken.rr
 * Assigning files to packages
 *   /usr/kde/3.5/lib32/libqtmcop.so.1.0.0 -> app-emulation/emul-linux-x86-soundlibs
 * Generated new 4_raw.rr and 4_owners.rr
 * Cleaning list of packages to rebuild
 * Generated new 4_pkgs.rr
 * Assigning packages to ebuilds
 * Generated new 4_ebuilds.rr
 * Evaluating package order
!!! Invalid PORTDIR_OVERLAY (not a dir): '/usr/portage/local/layman/java-overlay'
 *
 * Portage could not find any version of the following packages it could build:
 *  app-emulation/emul-linux-x86-soundlibs:0
 *
 * (Perhaps they are masked, blocked, or removed from portage.)
 * Try to emerge them manually.
 *
 * Warning: Portage cannot rebuild any of the necessary packages.
przehyba ~ # 

Even if it could rebuild app-emulation/emul-linux-x86-soundlibs I doubt
that one package would fix it all, it is something for sound, and my
problems are not related to sound.

Any other ideas?

Re: [gentoo-user] Re: Gentoo messed up after upgrade

[Stroller]

On 2 Feb 2009, at 22:52, Miernik wrote:

> !!! Invalid PORTDIR_OVERLAY (not a dir): '/usr/portage/local/layman/ 
> java-overlay'

Have you tried removing that from your make.conf?

Stroller.

[gentoo-user] Re: Gentoo messed up after upgrade

[Miernik]

Stroller <stroller@stellar.eclipse.co.uk> wrote:
> 
> On 2 Feb 2009, at 22:52, Miernik wrote:
> 
>> !!! Invalid PORTDIR_OVERLAY (not a dir): '/usr/portage/local/layman/ 
>> java-overlay'
> 
> Have you tried removing that from your make.conf?

Yes, no effect:

przehyba ~ # revdep-rebuild -i
 * Configuring search environment for revdep-rebuild

 * Checking reverse dependencies
 * Packages containing binaries and libraries broken by a package update
 * will be emerged.

 * Collecting system binaries and libraries
 * Generated new 1_files.rr
 * Collecting complete LD_LIBRARY_PATH
 * Generated new 2_ldpath.rr
 * Checking dynamic linking consistency
[ 29% ]  *   broken /usr/kde/3.5/lib32/libqtmcop.so.1.0.0 (requires libqt-mt.so.3)
[ 100% ]
 * Generated new 3_broken.rr
 * Assigning files to packages
 *   /usr/kde/3.5/lib32/libqtmcop.so.1.0.0 -> app-emulation/emul-linux-x86-soundlibs
 * Generated new 4_raw.rr and 4_owners.rr
 * Cleaning list of packages to rebuild
 * Generated new 4_pkgs.rr
 * Assigning packages to ebuilds
 * Generated new 4_ebuilds.rr
 * Evaluating package order

 *
 * Portage could not find any version of the following packages it could build:
 *  app-emulation/emul-linux-x86-soundlibs:0
 *
 * (Perhaps they are masked, blocked, or removed from portage.)
 * Try to emerge them manually.
 *
 * Warning: Portage cannot rebuild any of the necessary packages.
przehyba ~ # 

[gentoo-user] Re: Gentoo messed up after upgrade

[Miernik]

Stroller <stroller@stellar.eclipse.co.uk> wrote:
> 
> On 2 Feb 2009, at 22:52, Miernik wrote:
> 
>> !!! Invalid PORTDIR_OVERLAY (not a dir): '/usr/portage/local/layman/ 
>> java-overlay'
> 
> Have you tried removing that from your make.conf?

And after restarting squash_portage (no idea why it didn't start before)
it even built that sound thing:

 * Configuring search environment for revdep-rebuild

 * Checking reverse dependencies
 * Packages containing binaries and libraries broken by a package update
 * will be emerged.

 * Collecting system binaries and libraries
 * Generated new 1_files.rr
 * Collecting complete LD_LIBRARY_PATH
 * Generated new 2_ldpath.rr
 * Checking dynamic linking consistency
[ 29% ]  *   broken /usr/kde/3.5/lib32/libqtmcop.so.1.0.0 (requires libqt-mt.so.3)
[ 100% ]
 * Generated new 3_broken.rr
 * Assigning files to packages
 *   /usr/kde/3.5/lib32/libqtmcop.so.1.0.0 -> app-emulation/emul-linux-x86-soundlibs
 * Generated new 4_raw.rr and 4_owners.rr
 * Cleaning list of packages to rebuild
 * Generated new 4_pkgs.rr
 * Assigning packages to ebuilds
 * Generated new 4_ebuilds.rr
 * Evaluating package order
 * Generated new 5_order.rr
 * All prepared. Starting rebuild
emerge --oneshot  app-emulation/emul-linux-x86-soundlibs:0
..........
Calculating dependencies... done!

>>> Verifying ebuild manifests

>>> Emerging (1 of 1) app-emulation/emul-linux-x86-soundlibs-20080418
 * emul-linux-x86-soundlibs-20080418.tar.bz2 RMD160 SHA1 SHA256 size ;-) ...                                                                                                            [ ok ]
 * checking ebuild checksums ;-) ...                                                                                                                                                    [ ok ]
 * checking auxfile checksums ;-) ...                                                                                                                                                   [ ok ]
 * checking miscfile checksums ;-) ...                                                                                                                                                  [ ok ]
>>> Unpacking source...
>>> Unpacking emul-linux-x86-soundlibs-20080418.tar.bz2 to /var/tmp/portage/app-emulation/emul-linux-x86-soundlibs-20080418/work
mv: cannot stat var/tmp/portage/app-emulation/emul-linux-x86-soundlibs-20080418/work/usr/bin/esddsp': No such file or directory
>>> Source unpacked.
>>> Compiling source in /var/tmp/portage/app-emulation/emul-linux-x86-soundlibs-20080418/work ...
>>> Source compiled.
>>> Test phase [not enabled]: app-emulation/emul-linux-x86-soundlibs-20080418

>>> Install emul-linux-x86-soundlibs-20080418 into /var/tmp/portage/app-emulation/emul-linux-x86-soundlibs-20080418/image/ category app-emulation
>>> Completed installing emul-linux-x86-soundlibs-20080418 into /var/tmp/portage/app-emulation/emul-linux-x86-soundlibs-20080418/image/


>>> Installing app-emulation/emul-linux-x86-soundlibs-20080418
>>> Auto-cleaning packages...

>>> No outdated packages were found on your system.

 * GNU info directory index is up-to-date.

 * IMPORTANT: 3 config files in '/etc' need updating.
 * See the CONFIGURATION FILES section of the emerge
 * man page to learn how to update config files.
 * Build finished correctly. Removing temporary files...
 *
 * You can re-run revdep-rebuild to verify that all libraries and binaries
 * are fixed. If some inconsistency remains, it can be orphaned file, deep
 * dependency, binary package or specially evaluated library.
przehyba ~ # 


But it didn't fix anything:

miernik@przehyba ~ $ gnumeric
gnumeric: symbol lookup error: /usr/lib/libspreadsheet-1.8.4.so:
undefined symbol: g_dgettext
miernik@przehyba ~ $ ssh miernik@ogai.org
ssh: Could not resolve hostname ogai.org: Name or service not known
miernik@przehyba ~ $ ping ogai.org
PING ogai.org (85.25.152.157) 56(84) bytes of data.
64 bytes from india854 (85.25.152.157): icmp_seq=1 ttl=55 time=1165 ms
64 bytes from india854 (85.25.152.157): icmp_seq=2 ttl=55 time=391 ms
^C
--- ogai.org ping statistics ---
2 packets transmitted, 2 received, 0% packet loss, time 1013ms
rtt min/avg/max/mdev = 391.952/778.779/1165.606/386.827 ms, pipe 2
miernik@przehyba ~ $ 

How can ping resolve a host, and ssh not?

[gentoo-user] Re: Gentoo messed up after upgrade

[Nikos Chantziaras]

Miernik wrote:
> 
> Before I had ~amd64 in ACCEPT_KEYWORDS, but in the middle of this
> upgrade I thought it was a bad idea, because many programs failed to
> compile, so I removed that from make.conf, and did run
> 'emerge --empty-tree world'
> which downgraded everything back to stable. But one thing I couldn't
> downgrade was glibc which stayed at version
> sys-libs/glibc-2.9_p20081201-r1
> 
> XTerm is not using my ~/.Xresources settings.
> 
> Is there any way I can possibly fix my system?

The only thing I can recommend is rebuilding system, and then rebuilding 
world to make sure everything is rebuilt using the same toolchain, 
including the toolchain itself.  Pretty much the same as installing from 
scratch though, but at least you won't have to configure everything again.

I suspect changing ACCEPT_KEYWORDS in the middle was not a good idea.

[gentoo-user] Re: Gentoo messed up after upgrade

[Nikos Chantziaras]

Nikos Chantziaras wrote:
> [...]
> The only thing I can recommend is rebuilding system, and then rebuilding 
> world to make sure everything is rebuilt using the same toolchain, 
> including the toolchain itself.  Pretty much the same as installing from 
> scratch though, but at least you won't have to configure everything again.
> 
> I suspect changing ACCEPT_KEYWORDS in the middle was not a good idea.

Another thing.  Since you're now on glibc-2.9_p20081201-r1, before you 
rebuild system and world, make sure to upgrade your kernel to 2.6.28-r1 
and also upgrade to linux-headers-2.6.28-r1.  Rebuild 
glibc-2.9_p20081201-r1 after that and reboot.  If that won't help, 
continue with the plan of rebuilding system and world :P

I've had mysterious issues when running newest glibc with older kernels 
and linux-headers that were similar to yours.