[gentoo-user] emerge error

[gentoo-user] emerge error

[James]

Hello,

I did a routine 'emerge sync' with no problems.
Then I did an ' emerge -uDNvp world' and it gives this
message:

Calculating system dependencies /Traceback (most recent call last):
  File "/usr/bin/emerge", line 6518, in ?
    retval = emerge_main()
  File "/usr/bin/emerge", line 6512, in emerge_main
    myopts, myaction, myfiles, spinner)
  File "/usr/bin/emerge", line 5813, in action_build
    mydepgraph = depgraph(settings, trees, myopts, myparams, spinner)
  File "/usr/bin/emerge", line 1174, in __init__
    vardb.aux_get(pkg, self._mydbapi_keys))))
  File "/usr/bin/emerge", line 948, in _aux_get_wrapper
    self._portdb.aux_get(pkg, self._portdb_keys)))
  File "/usr/lib/portage/pym/portage.py", line 6552, in aux_get
    try:                                del self.auxdb[mylocation][mycpv]
  File "/usr/lib/portage/pym/cache/template.py", line 82, in __delitem__
    self._delitem(cpv)
  File "/usr/lib/portage/pym/cache/flat_hash.py", line 98, in _delitem
    raise cache_errors.CacheCorruption(cpv, e)
cache.cache_errors.CacheCorruption: sys-apps/baselayout-1.12.10-r5 is corrupt:
[Errno 13] Permission denied:
'/var/cache/edb/dep/usr/portage/sys-apps/baselayout-1.12.10-r5'


revdep-rebuild is clean......

I cannot emerge (rebuild) anything. Never seen this problem before

Ideas on fixing this?


James

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Re: [gentoo-user] emerge error

[James Ausmus]

On Jan 22, 2008 7:08 PM, James <wireless@tampabay.rr.com> wrote:
> Hello,
>
> I did a routine 'emerge sync' with no problems.
> Then I did an ' emerge -uDNvp world' and it gives this
> message:

<snip>

> cache.cache_errors.CacheCorruption: sys-apps/baselayout-1.12.10-r5 is corrupt:
> [Errno 13] Permission denied:
> '/var/cache/edb/dep/usr/portage/sys-apps/baselayout-1.12.10-r5'
>
>
> revdep-rebuild is clean......
>
> I cannot emerge (rebuild) anything. Never seen this problem before
>
> Ideas on fixing this?

Hmm - not sure exactly, but two thoughts come to mind off the bat:

1. Check your disk space, make sure it's not full
2. As root, do a chown -R portage:portage /var/cache/edb

and see what happens.

-James


>
>
> James
>
> --
> gentoo-user@lists.gentoo.org mailing list
>
>
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Re: [gentoo-user] emerge error

[KH]

James Ausmus wrote:
> On Jan 22, 2008 7:08 PM, James <wireless@tampabay.rr.com> wrote:
>   
>> Hello,
>>
>> I did a routine 'emerge sync' with no problems.
>> Then I did an ' emerge -uDNvp world' and it gives this
>> message:
>>     
>
> <snip>
>
>   
>> cache.cache_errors.CacheCorruption: sys-apps/baselayout-1.12.10-r5 is corrupt:
>> [Errno 13] Permission denied:
>> '/var/cache/edb/dep/usr/portage/sys-apps/baselayout-1.12.10-r5'
>>
>>
>> revdep-rebuild is clean......
>>
>> I cannot emerge (rebuild) anything. Never seen this problem before
>>
>> Ideas on fixing this?
>>     
>
> Hmm - not sure exactly, but two thoughts come to mind off the bat:
>
> 1. Check your disk space, make sure it's not full
> 2. As root, do a chown -R portage:portage /var/cache/edb
>
> and see what happens.
>
> -James
>
>
>   
>> James
>>
>> --
>> gentoo-user@lists.gentoo.org mailing list
>>
>>
>>     
add the -c to chown
       -c, --changes
              like verbose but report only when a change is made

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[gentoo-user] Re: emerge error

[James]

KH <gentoo-user <at> konstantinhansen.de> writes:


> James Ausmus wrote:

> > 1. Check your disk space, make sure it's not full

Not a problem...

> > 2. As root, do a chown -R portage:portage /var/cache/edb

> add the -c to chown
>        -c, --changes
>               like verbose but report only when a change is made


Many of the files were owned by root:portage

Now they are owned by portage:portage, but that did not 
fix the error:



calculating world dependencies \Traceback (most recent call last)
  File "/usr/bin/emerge", line 6518, in ?
    retval = emerge_main()
  File "/usr/bin/emerge", line 6512, in emerge_main
    myopts, myaction, myfiles, spinner)
  File "/usr/bin/emerge", line 5813, in action_build
    mydepgraph = depgraph(settings, trees, myopts, myparams, spinner)
  File "/usr/bin/emerge", line 1174, in __init__
    vardb.aux_get(pkg, self._mydbapi_keys))))
  File "/usr/bin/emerge", line 948, in _aux_get_wrapper
    self._portdb.aux_get(pkg, self._portdb_keys)))
  File "/usr/lib/portage/pym/portage.py", line 6552, in aux_get
    try:                                
del self.auxdb[mylocation][mycpv]
  File "/usr/lib/portage/pym/cache/template.py", 
line 82, in __delitem__
    self._delitem(cpv)
  File "/usr/lib/portage/pym/cache/flat_hash.py", 
line 98, in _delitem
    raise cache_errors.CacheCorruption(cpv, e)
cache.cache_errors.CacheCorruption: 
sys-apps/baselayout-1.12.10-r5 is
 corrupt:[Errno 13] Permission denied:
var/cache/edb/dep/usr/portage/sys-apps/baselayout-1.12.10-r5'



The files that had their permissions changed were:

changed ownership of var/cache/edb/dep/usr/
portage/sec-policy/selinux-lpd-20070329' to portage:portage
changed ownership of var/cache/edb/dep/usr/
portage/sec-policy/selinux-lpd-20070928' to portage:portage
changed ownership of var/cache/edb/dep/usr/
portage/sec-policy/selinux-cups-20070329' to portage:portage
changed ownership of var/cache/edb/dep/usr/
portage/sec-policy/selinux-cups-20070928' to portage:portage

snip>
changed ownership of var/cache/edb/dep/usr/
portage/sec-policy/selinux-screen-20070329' to
portage:portage
changed ownership of var/cache/edb/dep/usr/
portage/sec-policy/selinux-screen-20070928' to
portage:portage
chown: cannot access var/cache/edb/dep/usr/
portage/sec-policy/selinux-bind-20050408': 
Permission denied
changed ownership of var/cache/edb/dep/usr/
portage/sec-policy/selinux-bind-20050626' to portage:portage
chown: cannot access var/cache/edb/dep/usr/
portage/sec-policy/selinux-bind-20061114': 
Permission denied
changed ownership of var/cache/edb/dep/usr/
portage/sec-policy/selinux-bind-20070329' to portage:portage



Maybe the '/usr/bin/emerge' executable is corrupted. Can I 
just scp over a copy from another similar arch machine?


Any other ideas?

James


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Re: [gentoo-user] Re: emerge error

[James Ausmus]

On Jan 23, 2008 8:03 AM, James <wireless@tampabay.rr.com> wrote:
> KH <gentoo-user <at> konstantinhansen.de> writes:
>
>
> > James Ausmus wrote:
>
> > > 1. Check your disk space, make sure it's not full
>
> Not a problem...
>
> > > 2. As root, do a chown -R portage:portage /var/cache/edb
>
> > add the -c to chown
> >        -c, --changes
> >               like verbose but report only when a change is made
>
>
> Many of the files were owned by root:portage
>
> Now they are owned by portage:portage, but that did not
> fix the error:

<snip>

OK, try doing:

emerge --metadata

Also, have you done a emerge --sync since this started?

Sounds like it might just be a cache corruption - if the cache was
corrupted during the rsync process in an emerge--sync, then just doing
a emerge --metadata won't help, but if was just corrupted on disk (in
the /var/cache/edb dir), then a emerge --metadata might do it.

HTH-

James
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[gentoo-user] Re: emerge error

[James]

James Ausmus <james.ausmus <at> gmail.com> writes:


> OK, try doing:

> emerge --metadata

> Also, have you done a emerge --sync since this started?

> Sounds like it might just be a cache corruption - if the cache was
> corrupted during the rsync process in an emerge--sync, then just doing
> a emerge --metadata won't help, but if was just corrupted on disk (in
> the /var/cache/edb dir), then a emerge --metadata might do it.


'emerge' sync almost ran to completion:



Number of files: 131430
Number of files transferred: 270
Total file size: 175763417 bytes
Total transferred file size: 1202283 bytes
Literal data: 1202283 bytes
Matched data: 0 bytes
File list size: 3192393
File list generation time: 4.092 seconds
File list transfer time: 0.000 seconds
Total bytes sent: 8817
Total bytes received: 4410697

sent 8817 bytes  received 4410697 bytes  34393.11 bytes/sec
total size is 175763417  speedup is 39.77

>>> Updating Portage cache:      Traceback (most recent call last):
  File "/usr/bin/emerge", line 6518, in ?
    retval = emerge_main()
  File "/usr/bin/emerge", line 6473, in emerge_main
    action_sync(settings, trees, mtimedb, myopts, myaction)
  File "/usr/bin/emerge", line 5010, in action_sync
    action_metadata(settings, portdb, myopts)
  File "/usr/bin/emerge", line 5104, in action_metadata
    eclass_cache=ec, verbose_instance=noise_maker)
  File "/usr/lib/portage/pym/cache/util.py", line 21, in mirror_cache
    dead_nodes = set(trg_cache)
  File "/usr/lib/python2.4/sets.py", line 429, in __init__
    self._update(iterable)
  File "/usr/lib/python2.4/sets.py", line 383, in _update
    for element in iterable:
  File "/usr/lib/portage/pym/cache/flat_hash.py", line 122, in __iter__
    st = os.lstat(p)
OSError: [Errno 13] Permission denied: 
'/var/cache/edb/dep/usr/portage/net-zope'

ideas?

James


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[gentoo-user] Re: emerge error

[James]

James <wireless <at> tampabay.rr.com> writes:


> James Ausmus <james.ausmus <at> gmail.com> writes:

>   File "/usr/lib/portage/pym/cache/flat_hash.py", line 122, in __iter__
>     st = os.lstat(p)
> OSError: [Errno 13] Permission denied: 
> '/var/cache/edb/dep/usr/portage/net-zope'


Well here is the problem:
in '/var/cache/edb/dep/usr/portage'

drwxrwsr-x 2 root portage  1480 Jan 10 13:41 net-www
?????????? ? ?    ?           ?            ? net-zope
drwxrwsr-x 2 root portage  3024 Jan 22 22:29 perl-core


But I cannot remove it?

rm -rf ./net-zope
rm: cannot remove `./net-zope': Permission denied

cp /dev/null net-zope
cp: accessing `net-zope': Permission denied

rmdir net-zope
rmdir: net-zope: Permission denied

chown root:portage net-zope
chown: cannot access `net-zope': Permission denied


ideas?

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Re: [gentoo-user] Re: emerge error

[Neil Bothwick]

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On Wed, 23 Jan 2008 16:39:51 +0000 (UTC), James wrote:

> ideas?

fsck. If that fails, copy off the data you can and reformat, the
filesystem is screwed.


-- 
Neil Bothwick

You shall know the truth, and you shall freak.

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[gentoo-user] Re: emerge error

[James]

Neil Bothwick <neil <at> digimed.co.uk> writes:


> > ideas?

> fsck. If that fails, copy off the data you can and reformat, the
> filesystem is screwed.

Roger that. 

Here's an idea, since it's a minimal firewall, that I'm currently using,
and scp works.

dd  over ssh everything onto a 8G Compact Flash card  that is plugged
into another system and then install the CF card into an ide-to-cf socket
reboot and then emerge-sync? think this will work?


The partions are simple on the existing firewall:
/dev/hda3              18G  2.1G   16G  12% /
udev                  125M  2.6M  123M   3% /dev
shm                   125M     0  125M   0% /dev/shm
/dev/hda1             393M   46M  347M  12% /boot

Next format the CF card similar to the above scheme.

<not sure exactly how to run dd over ssh any (syntax) ideas? >


Then install CF disk into similar arch machine (amd k6)and boot it
up.

Since I have quite a few of these machine and several friends
running on similar firewalls, it's time I start using CF drvies
and develop a procedure to replicate the firewalls, without
3 days of install, configuring and compiling.

Do you think this will work?
Did I miss any steps?


I do not want to reboot until I get an second firewall working.....


James



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Re: [gentoo-user] Re: emerge error

[Neil Bothwick]

[-- Attachment #1: Type: text/plain, Size: 530 bytes --]

On Wed, 23 Jan 2008 18:33:19 +0000 (UTC), James wrote:

> dd  over ssh everything onto a 8G Compact Flash card  that is plugged
> into another system and then install the CF card into an ide-to-cf
> socket reboot and then emerge-sync? think this will work?

No, because it will copy the corruption too. You'll end up with a byte
for byte copy of your broken filesystem. If fsck won't fix it, backup,
reformat, restore is the only safe fix.


-- 
Neil Bothwick

To whom the gods destroy, they first teach Windows...

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[gentoo-user] Re: emerge error

[James]

Neil Bothwick <neil <at> digimed.co.uk> writes:


> > dd  over ssh everything onto a 8G Compact Flash card  that is plugged
> > into another system and then install the CF card into an ide-to-cf
> > socket reboot and then emerge-sync? think this will work?

> No, because it will copy the corruption too. You'll end up with a byte
> for byte copy of your broken filesystem. If fsck won't fix it, backup,
> reformat, restore is the only safe fix.


If I reboot, I *may* loose the firewall completely, depending on what the
drive does. The only safe thing is to build another firewall before
rebooting the current firewall (then see if fsck will fix it).......

Either way, once I build a new firewall, I'm going to copy it
to CF and be done with these old ide drives.........

thx


James







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Re: [gentoo-user] Re: emerge error

[Neil Bothwick]

[-- Attachment #1: Type: text/plain, Size: 1010 bytes --]

On Wed, 23 Jan 2008 20:08:00 +0000 (UTC), James wrote:

> > No, because it will copy the corruption too. You'll end up with a byte
> > for byte copy of your broken filesystem. If fsck won't fix it, backup,
> > reformat, restore is the only safe fix.  
 
> If I reboot, I *may* loose the firewall completely, depending on what
> the drive does. The only safe thing is to build another firewall before
> rebooting the current firewall (then see if fsck will fix it).......

Then don't reboot. Mount another drive somewhere temporary, copy the
contents of /var to it, then unmount /var and mount the new drive
on /var. Reformat the original filesystem and reverse the process.

> Either way, once I build a new firewall, I'm going to copy it
> to CF and be done with these old ide drives.........

Use a suitable filesystem, or the flash memory will die very quickly,
especially if you put /var on it.


-- 
Neil Bothwick

New Intel opcode #007 PUKE: Put unmeaningful keywords everywhere

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Re: [gentoo-user] Re: emerge error

[Hal Martin]

If you need another firewall in the interim, I would suggest giving
IPCop a try. I've been using it as a gateway OS for 5 years now and it's
been solid for the entire time.

Or, if you'd really rather stick with Gentoo, you could run IPCop on
another of your K6 machines until you rebuild the Gentoo one.

-Hal

Neil Bothwick wrote:
> On Wed, 23 Jan 2008 20:08:00 +0000 (UTC), James wrote:
>
>   
>>> No, because it will copy the corruption too. You'll end up with a byte
>>> for byte copy of your broken filesystem. If fsck won't fix it, backup,
>>> reformat, restore is the only safe fix.  
>>>       
>  
>   
>> If I reboot, I *may* loose the firewall completely, depending on what
>> the drive does. The only safe thing is to build another firewall before
>> rebooting the current firewall (then see if fsck will fix it).......
>>     
>
> Then don't reboot. Mount another drive somewhere temporary, copy the
> contents of /var to it, then unmount /var and mount the new drive
> on /var. Reformat the original filesystem and reverse the process.
>
>   
>> Either way, once I build a new firewall, I'm going to copy it
>> to CF and be done with these old ide drives.........
>>     
>
> Use a suitable filesystem, or the flash memory will die very quickly,
> especially if you put /var on it.
>
>
>   

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[gentoo-user] Re: emerge error

[James]

Neil Bothwick <neil <at> digimed.co.uk> writes:


> > If I reboot, I *may* loose the firewall completely, depending on what
> > the drive does. The only safe thing is to build another firewall before
> > rebooting the current firewall (then see if fsck will fix it).......

> Then don't reboot. Mount another drive somewhere temporary, copy the
> contents of /var to it, then unmount /var and mount the new drive
> on /var. Reformat the original filesystem and reverse the process.

Earlier I posted the partitions:
/dev/hda3              18G  2.1G   16G  12% /
udev                  125M  2.6M  123M   3% /dev
shm                   125M     0  125M   0% /dev/shm
/dev/hda1             393M   46M  347M  12% /boot

since /var is part of / (on the same partition) will this still work?

> > Either way, once I build a new firewall, I'm going to copy it
> > to CF and be done with these old ide drives.........

> Use a suitable filesystem, or the flash memory will die very quickly,
> especially if you put /var on it.


What would be the best file system to use on said CF HD to extend the life?
I usually use the reiserfs on  boot and root (simple partioning scheme).
But, I'm open to suggestions here.


The other thing I'm going to do is keep a master (k6) system with
a good HD for compiling updates and start  distributing binaries
to all of the other k6 (586) firewalls.... That should greatly
help extend the life too..... (any ideas on the caveats of this
scheme are most welcome).....

James




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Re: [gentoo-user] Re: emerge error

[Neil Bothwick]

[-- Attachment #1: Type: text/plain, Size: 1170 bytes --]

On Thu, 24 Jan 2008 13:46:04 +0000 (UTC), James wrote:

> > Then don't reboot. Mount another drive somewhere temporary, copy the
> > contents of /var to it, then unmount /var and mount the new drive
> > on /var. Reformat the original filesystem and reverse the process.  
> 
> Earlier I posted the partitions:
> /dev/hda3              18G  2.1G   16G  12% /
> udev                  125M  2.6M  123M   3% /dev
> shm                   125M     0  125M   0% /dev/shm
> /dev/hda1             393M   46M  347M  12% /boot
> 
> since /var is part of / (on the same partition) will this still work?

No, another reason to keep /var, and as much else as possible, away
from /.

> > Use a suitable filesystem, or the flash memory will die very quickly,
> > especially if you put /var on it.  

> What would be the best file system to use on said CF HD to extend the
> life? I usually use the reiserfs on  boot and root (simple partioning
> scheme). But, I'm open to suggestions here.

JFFS2, or budget on replacing the cards every couple of months.


-- 
Neil Bothwick

First Law of Laboratory Work:
Hot glass looks exactly the same as cold glass.

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[gentoo-user] Re: emerge error

[James]

Neil Bothwick <neil <at> digimed.co.uk> writes:


> JFFS2, or budget on replacing the cards every couple of months.


Thanks to everyone that helps,

thx Neil,


James






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Re: [gentoo-user] Re: emerge error

[Joseph]

On 01/23/08 16:39, James wrote:
>> OSError: [Errno 13] Permission denied: 
>> '/var/cache/edb/dep/usr/portage/net-zope'
>
>
>Well here is the problem:
>in '/var/cache/edb/dep/usr/portage'
>
>drwxrwsr-x 2 root portage  1480 Jan 10 13:41 net-www
>?????????? ? ?    ?           ?            ? net-zope
>drwxrwsr-x 2 root portage  3024 Jan 22 22:29 perl-core
>
>
>But I cannot remove it?
>
>rm -rf ./net-zope
>rm: cannot remove `./net-zope': Permission denied
>
>cp /dev/null net-zope
>cp: accessing `net-zope': Permission denied
>
>rmdir net-zope
>rmdir: net-zope: Permission denied
>
>chown root:portage net-zope
>chown: cannot access `net-zope': Permission denied
>
>
>ideas?

Try booting from Live Gentoo CD (or Knopix) mount the partition and delete that file.

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GPG KeyID: ED0E1FB7
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Re: [gentoo-user] Re: emerge error

[Dale]

James wrote:
> <<  SNIP >>
>
> Maybe the '/usr/bin/emerge' executable is corrupted. Can I 
> just scp over a copy from another similar arch machine?
>
>
> Any other ideas?
>
> James
>
>
>   

http://www.gentoo.org/proj/en/portage/doc/manually-fixing-portage.xml

Dale

:-)  :-) 
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