update conflicts: system broken [Solved]

Kern · 2006-05-02 12:46:14

ok ive been off-scene a few months. system worked - no probs with anything.
trying to install a simple package f-spot, i get so many updates flagged i do a pacman -Syu.

first update pacman = Y : then restart

i get the old [
:: Replace mawk with gawk from "current"? [Y/n] n
:: Replace kernel26-scsi with kernel26 from "current"? [Y/n] n
:: Replace openoffice-en with openoffice-base from "extra"? [Y/n] n
] i got this ages ago anyways, and always declined.

but then :
:: libgl-dri conflicts with nvidia. Remove nvidia? [Y/n]
if n then exits with "error: package conflicts detected"
if Y then next error is
:: ttf-bitstream-vera conflicts with xorg. Remove xorg? [Y/n] n

"error: package conflicts detected"

for nvidia upgrade:

pacman -S nvidia

Targets: nvidia-1.0.8178-16

Total Package Size: 5.9 MB

Proceed with upgrade? [Y/n] y

checking package integrity... done.
loading package data... done.
checking for file conflicts...
error: the following file conflicts were found:
nvidia: /usr/lib/libGL.so: exists in filesystem
nvidia: /usr/lib/libGL.so.1: exists in filesystem
nvidia: /usr/lib/libGLcore.so.1: exists in filesystem
nvidia: /usr/lib/libnvidia-tls.so.1: exists in filesystem

errors occurred, no packages were upgraded.

i think i stopped upgrades just before this initscripts thing came along.
how far up sh*creek am i if ive fallen behind a few months.
dare i answer Y to all these and find i cant use the system.
i dont have the luxury of being "Down" and "experimenting" as i used to.

tia

kern

Cerebral · 2006-05-02 12:52:47

The problem you're seeing is the upgrade to Xorg 7.

Usually this can be best fixed by:

1) force your nvidia upgrade with pacman -Sf nvidia
2) remove xorg forcibly: pacman -Rd xorg
3) update your system with pacman -Syu
4) ensure xorg is uptodate with pacman -S xorg-server

By the way, if you're doing a full system update, then you really should read about initrd and answer "y" to:

:: Replace mawk with gawk from "current"? [Y/n]
:: Replace kernel26-scsi with kernel26 from "current"? [Y/n]
:: Replace openoffice-en with openoffice-base from "extra"? [Y/n]

The scsi kernel is no more; it's all handled by initrd and kernel26 now - everything in one package. Openoffice updated and afaik the english package is included in the base now. Gawk is now the 'standard' awk interpreter for arch, as certain packages won't compile without it.

Moo-Crumpus · 2006-05-02 13:39:58

Kern wrote:

ok ive been off-scene a few months.

I allways considered running bleeding edge linux and be off-scene as a trap...

Kern · 2006-05-02 14:37:07

Cerebral: many thanks for quick reply - will implement asap.

Pink/Moo : re trap, lol yes very much so. as you probably saw, i was quite active, but unforseen events conspired to upset hobbies and interests.

Nice to know ppl are around to help one out of said traps, and so quickly.
thanks folks.

8)

edit:

eeeek !
Total Package Size: 707.3 MB

Proceed with upgrade? [Y/n]

here we go!

Kern · 2006-05-02 17:04:31

ok - shit and fan have met:

the entire process rolled along and ended with similar "exists in filesytem" error messages.

no programs would then run from my own login terminal.
managed to copy the tail of the report to a text file using vim inside root terminal.
rebooted: dumps me.

Booting 'Arch linux [/boot/vmlinuz26]'

root (hda0,2)
filesystem is reiserfs, partiton type 0x83
kernel /boot/vmlinuz26
root= /dev/hda3 ro

Error 15: file not found

press any key to continue ...

(repeats loop if pressed)

gonna try and dig out live cd and check files / forum etc but any help or pointers meantime would be appreciated.

thanks
Kern

sputnik · 2006-05-02 17:37:02

I think you have to setup initrd in grub/lilo. check the wiki.

Kern · 2006-05-02 18:04:11

thanks for the pointer sputnik, but im after a little more detail. wiki is already printed out and on the desk.

....

from LiveCD

should we have a vmlinuz file in here and or a initrd26.img ? long time since i did boot thingies.

===================

[root (boot)]# ls -alR
.:
total 117
drwxr-xr-x 3 root root 184 May 2 09:41 .
drwxrwxrwx 25 root root 648 Apr 27 03:57 ..
-rw-r--r-- 1 root root 5032 Sep 21 2005 diag1.img
drwxr-xr-x 2 root root 512 Oct 16 2005 grub
-rw-r--r-- 1 root root 53952 Oct 16 2005 kconfig26-rlegate
-rw-r--r-- 1 root root 51107 Jun 14 2005 kconfig26.pacsave

./grub:
total 305
drwxr-xr-x 2 root root 512 Oct 16 2005 .
drwxr-xr-x 3 root root 184 May 2 09:41 ..
-rw-r--r-- 1 root root 8020 Feb 2 2005 e2fs_stage1_5
-rw-r--r-- 1 root root 7780 Feb 2 2005 fat_stage1_5
-rw-r--r-- 1 root root 7060 Feb 2 2005 ffs_stage1_5
-rw-r--r-- 1 root root 7092 Feb 2 2005 iso9660_stage1_5
-rw-r--r-- 1 root root 8544 Feb 2 2005 jfs_stage1_5
-rw-r--r-- 1 root root 1262 Oct 16 2005 menu.lst
-rw-r--r-- 1 root root 1408 May 10 2005 menu.lst.pacnew
-rw-r--r-- 1 root root 7252 Feb 2 2005 minix_stage1_5
-rw-r--r-- 1 root root 9524 Feb 2 2005 reiserfs_stage1_5
-rw-r--r-- 1 root root 512 Feb 2 2005 stage1
-rw-r--r-- 1 root root 101490 Feb 2 2005 stage2
-rw-r--r-- 1 root root 101490 Feb 2 2005 stage2_eltorito
-rw-r--r-- 1 root root 7336 Feb 2 2005 ufs2_stage1_5
-rw-r--r-- 1 root root 6676 Feb 2 2005 vstafs_stage1_5
-rw-r--r-- 1 root root 9372 Feb 2 2005 xfs_stage1_5

Kern · 2006-05-02 19:24:24

last pacman text output recovered :

:: Retrieving packages from current...
gawk-3.1.5-2 [################] 100% 539K 147.7K/s 00:00:03
mkinitrd-1.01-29 [################] 100% 368K 125.5K/s 00:00:02
kernel26-2.6.16.12-1 [################] 100% 17666K 224.7K/s 00:01:18
<snip>
xmms-1.2.10-7 [################] 100% 1886K 200.2K/s 00:00:09
zip-2.31-1 [################] 100% 69K 42.3K/s 00:00:01

:: Retrieving packages from extra...
openoffice-base-2.0.2-2 [################] 100% 120568K 230.3K/s 00:00:11
<snip>

checking package integrity... done.
removing mawk... done.
removing kernel26-scsi...
warning: /boot/kconfig26 saved as /boot/kconfig26.pacsave
done.
removing openoffice-en... done.

/sbin/ldconfig: File /usr/lib/libnvidia-cfg.so.1 is empty, not checked.
/sbin/ldconfig: File /usr/lib/libXvMCNVIDIA.so.1.0.8178 is empty, not checked.
/sbin/ldconfig: File /usr/lib/libnvidia-tls.so.1 is empty, not checked.
/sbin/ldconfig: File /usr/lib/libXvMCNVIDIA_dynamic.so.1 is empty, not checked.
/sbin/ldconfig: File /usr/lib/libnvidia-cfg.so is empty, not checked.
/sbin/ldconfig: File /usr/lib/libnvidia-tls.so.1.0.8178 is empty, not checked.
/sbin/ldconfig: File /usr/lib/libGL.so.1.0.8178 is empty, not checked.
/sbin/ldconfig: File /usr/lib/libnvidia-cfg.so.1.0.8178 is empty, not checked.
/sbin/ldconfig: File /usr/lib/libGLcore.so.1 is empty, not checked.
/sbin/ldconfig: File /usr/lib/libGLcore.so.1.0.8178 is empty, not checked.
/sbin/ldconfig: /usr/lib/libGLcore.so.1 is not a symbolic link

/sbin/ldconfig: /usr/lib/libnvidia-tls.so.1 is not a symbolic link

loading package data... done.
checking for file conflicts...
error: the following file conflicts were found:
ntp: /etc/ntp.conf: exists in filesystem
errors occurred, no packages were upgraded.

==========================================
i think the relevant lines are

mkinitrd-1.01-29 [################] 100% 368K 125.5K/s 00:00:02
kernel26-2.6.16.12-1 [################] 100% 17666K 224.7K/s 00:01:18

removing kernel26-scsi...
warning: /boot/kconfig26 saved as /boot/kconfig26.pacsave
done.

errors occurred, no packages were upgraded.
==========================================

mpie · 2006-05-02 19:26:36

root (hda0,2)
filesystem is reiserfs, partiton type 0x83
kernel /boot/vmlinuz26 root= /dev/hda3 ro [/code]

add initrd6-full.img as an extra line
[code]root (hda0,2)
kernel /boot/vmlinuz26 root= /dev/hda3 ro
initrd /boot/initrd26-full.img[/code]

Kern · 2006-05-02 19:52:27

unless its me being dim, which has been known, grub points at the file to load.

from my last post ( ls -alR) there are no vmlinuz26, initrd26.img initrd26-full.img files.

hence error: file not found
(yes i added the initrd line to no avail)
looks like pacman removed stuff, then dumped out before replacing anything new.

am i looking at grabbing an Arch install CD again and running a kernel from that ?
is it just a simple matter (as if anythings ever simple) of then copying the vmlinuz and initrd files over?

thanks for the replies, keep em coming

cheers

kern

sputnik · 2006-05-02 20:31:46

First check to make sure mkinitrd & kernel26-2.6.16.12-1 are installed. Then edit /etc/mkinitrd.conf. then run "mkinitrd full". Then add mpie's initrd line in grub. And it should boot.

Kern · 2006-05-02 21:31:41

First check to make sure mkinitrd & kernel26-2.6.16.12-1 are installed. .....

yes .. indeed. i dont think they are, therein lies the problem

an interesting night lies ahead for sure

thanks for suggestions

K

Kern · 2006-05-03 01:20:15

downloaded an archlinux base image iso. (after finding, trying and failing with my original Arch.iso with the old system before udev)
ran it to repair mode. boot root=/dev/hda3
this then found the hard disk, filesystem .......

and then dumped me into a "fresh install" menu. tried again same thing. dmesg reveals no clues. is this normal repair mode? i thought it should have allowed me to run the old sys ?

different angle : install Arch base to a spare h/d.
fell into the same crap as i did when first installing Arch. (after setting up the network and getting the list of files from FTP, most of the tries to download files were abortive had to use CD install )

config scripts end up empty. god knows why. reinstalled from scratch and got it right.
mounted the old arch drive
checked newly created boot directory and sure enough it shows im missing a shedload of files from the old drive /boot.

with more hope than knowledge i copy the vmlinuz and initrd files from the new install into the old boot dir and guess what. boots, so far. then dumps me into a busybox ash shell.
its now 2:20 am and the initial worry i had re updating the system has been justified.
im out of ideas.

any system gurus out there point me in the right direction ?

off to bed. tomorrows got to be a better day.
thanks for the responses.
Kern

Cerebral · 2006-05-03 12:08:34

Allrighty, boot from your install CD normally, but instead of running arch/setup, just mount your regular root and chroot into it.

ie.

$ mount /dev/hda3 /mnt
$ chroot /mnt

Now you should have your regular arch filesystem. You'll need to run:

$ pacman -Sf ntp
$ pacman -Su

from in there to get your system updated.

If that doesn't work, you'll need to do something like:

$ cd /var/cache/pacman/pkg
$ pacman -U mkinitrd-1.01-29.pkg.tar.gz
$ pacman -U initscripts-0.7.1-24.pkg.tar.gz
$ pacman -U kernel26-2.6.16.13-1.pkg.tar.gz
$ pacman -U udev-091-2.pkg.tar.gz

Note, those might not be the versions you downloaded; I just used the latest version numbers from my system. If one of those packages doesn't exist, just find the latest version of the package in /var/cache/pacman/pkg and install that.

With those packages installed, ensure you have the proper initrd entry in your grub config, and try rebooting.

You were right in your suspicions, though - because of the file conflict in the ntp package, the update didn't happen; but since kernel26 replaced kernel26-scsi, it removed your old kernel before checking file conflicts. When the update died, you were left kernel-less.

Kern · 2006-05-03 15:58:44

thx cerebral. i got in similar to how u said. the main issue was getting to boot and run the vmlinuz so to use the CD kernel in my own sys.
the command arch root=/dev/hda3 dumped me into an install new arch menu.
however, i found that running vmlinuz root=/dev/hda3 got me in.

removed and replaced ntp. did a full pacman -Syu which seems to have updated stuff ok. seems that theres a lot of mirrors down.

every package install echoed that files in /usr/lib/lib*.so.1 were empty. these were mainl GL files or Nvidia . tried to remove them, no avail.

im at the stage now of i can login, boot the system but cant get a GUI as there are no screens available.

installing nvidia tells me it fails, re modules iirc, maybe i'll try a nvidia file directly not via pacman.

at least we have progress. will print your reply out, and check it over as i reboot into the blackscreen.

think i still have to boot via the CD, but at least theres progress.
thanks for taking the time to reply.

cheers
Kern

Cerebral · 2006-05-03 16:53:26

Kern: you boot directly into an X login manager? Ouch... that's gotta make things tough. Do you use the DAEMONS array in rc.conf or runlevel 5 in inittab? If you use runlevel 5, you can force a boot into runlevel 3 by appending a '3' at the end of your kernel line; ie:

kernel /boot/vmlinuz26 root=/dev/hda3 ro 3

The nvidia thing is a known problem that's happened before - you need to install the nvidia package when not running X, but even then sometimes it screws up for people. Try removing nvidia (pacman -Rd nvidia) and reinstalling it.

Search around the forum for nvidia troubles - they may have gotten this fixed and I didn't notice.

Kern · 2006-05-04 00:33:59

Kern: you boot directly into an X login manager? Ouch... that's gotta make things tough.

nope, ive always booted to a terminal. then login (ie blackscreen) then run xcfe4.

anywaaays !!!

solutions. (omitting the hairpulling and things that just wouldnt work)
from the bootup disk, i ran vmlinuz /dev/hda3
then setup network then re ran pacman - 700meg +

your pacman -U stuff got me a kernel running, and filled in the missing bits in /boot ie the .img files

next: rebooted ok without the CD but couldnt get any network connection tho, so after many other things attempted added hwd to the DAEMONS . no idea why it wasnt there or if it was the cause. worked ok so i could then update again, properly

nvidia always failed using pacman, so i d/l from nvidia direct and ran it. installed ok.

tried to start X but then couldnt find modules for keyboard mouse etc so checked the Xorg7 stuff pointed to earlier. Xorg -config

hey presto, im back up and running.
small glitch i cant run a vt from inside xfce4. ctrl-alt-F2 will get me one outside of X , so theres no real hardship. just a tweak.
running ps2 keyboard/mouse but will try the change back to USB asap.
was unsure if usb would run rightaway. lets get basics going first huh ?

a BIG thanks, Cerebral, for the intensive tutorial and to all who made the effort to reply.

cheers

Kern

Cerebral · 2006-05-04 01:01:46

to get your term back inside xfce4 you might need to reinstall xterm, which was split into a seperate package with xorg 7:

pacman -S xterm

Instead of hwd, try adding the line:

MOD_AUTOLOAD="yes"

to your rc.conf - this will allow udev to do module autoloading.

In any case, glad to hear you're back up and running!

Kern · 2006-05-04 01:33:56

xterm worked thanks. eeeh what a thing this Xorg is, being split. !

any pointers for getting the usb keyboard and mouse working ? im scouring the forums but wont last much longer - 2:30 am

scratch that last - added autoload, usb k/b and mouse now work.

Bedtime !

laters

elasticdog · 2006-05-04 02:16:53

Good work matey! I did an update on one of my machines after having it sitting for about 6 months and luckly didn't have nearly as much trouble as you...of course it was just being used as a test server and didn't have X on it, but that's beside the point

Arch Linux

#1 2006-05-02 12:46:14

update conflicts: system broken [Solved]

#2 2006-05-02 12:52:47

Re: update conflicts: system broken [Solved]

#3 2006-05-02 13:39:58

Re: update conflicts: system broken [Solved]

#4 2006-05-02 14:37:07

Re: update conflicts: system broken [Solved]

#5 2006-05-02 17:04:31

Re: update conflicts: system broken [Solved]

#6 2006-05-02 17:37:02

Re: update conflicts: system broken [Solved]

#7 2006-05-02 18:04:11

Re: update conflicts: system broken [Solved]

#8 2006-05-02 19:24:24

Re: update conflicts: system broken [Solved]

#9 2006-05-02 19:26:36

Re: update conflicts: system broken [Solved]

#10 2006-05-02 19:52:27

Re: update conflicts: system broken [Solved]

#11 2006-05-02 20:31:46

Re: update conflicts: system broken [Solved]

#12 2006-05-02 21:31:41

Re: update conflicts: system broken [Solved]

#13 2006-05-03 01:20:15

Re: update conflicts: system broken [Solved]

#14 2006-05-03 12:08:34

Re: update conflicts: system broken [Solved]

#15 2006-05-03 15:58:44

Re: update conflicts: system broken [Solved]

#16 2006-05-03 16:53:26

Re: update conflicts: system broken [Solved]

#17 2006-05-04 00:33:59

Re: update conflicts: system broken [Solved]

#18 2006-05-04 01:01:46

Re: update conflicts: system broken [Solved]

#19 2006-05-04 01:33:56

Re: update conflicts: system broken [Solved]

#20 2006-05-04 02:16:53

Re: update conflicts: system broken [Solved]

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