full system upgrade destroys my system

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full system upgrade destroys my system

Postby phelbore » Fri Feb 24, 2012 9:59 pm

I'm having some issues after a full upgrade from a fresh install. No kernel modules load and my pcre library goes awol.

First, I get my system working, installing wireless-tools so that I can connect to the internet, no ethernet.
After that, I do pacman -Syyu and it wants to upgrade pacman, no issues there.
After that, I repeat the above command and get the following:

Code: Select all
:: Starting full system upgrade...
resolving dependencies...
looking for inter-conflicts...

Targets (40): coreutils-8.15-1  device-mapper-2.02.90-1  dhcpcd-5.5.4-1  e2fsprogs-1.42-1  filesystem-2012.2-2  gcc-libs-4.6.2-7  glib2-2.30.2-2  glibc-2.15-5  gmp-5.0.4-1  grep-2.10-3  inetutils-1.9.1-1  initscripts-2012.01.3-1  iproute2-3.2.0-2  kmod-5-4  less-444-3  libidn-1.24-1  libldap-2.4.28-2  libnl-3.2.7-1  libpcap-1.2.1-2  libsasl-2.1.23-9  linux-headers-omap-3.2.6-2  linux-omap-3.2.6-2  lvm2-2.02.90-1  man-db-2.6.1-1  mdadm-3.2.3-1  mkinitcpio-0.8.2-3  module-init-tools-3.16-3 [removal]  ncurses-5.9-3  openssl-1.0.0.g-1  pacman-mirrorlist-20120204-1  pciutils-3.1.9-1  pcre-8.30-1  perl-5.14.2-7  psmisc-22.15-1  run-parts-4.2.1-1  shadow-4.1.5-3  syslog-ng-3.3.4-2  udev-181-2  wpa_supplicant-0.7.3-5  zlib-1.2.6-1

Total Installed Size:   223.30 MiB
Net Upgrade Size:       2.51 MiB

checking package integrity...
loading package files...
checking for file conflicts...
checking available disk space...
removing module-init-tools...
upgrading glibc...
Generating locales...
  en_US.UTF-8... done
  en_US.ISO-8859-1... done
  de_DE.ISO-8859-1... done
  de_DE.ISO-8859-15@euro... done
  de_AT.ISO-8859-1... done
  de_AT.ISO-8859-15@euro... done
Generation complete.
upgrading shadow...
upgrading gcc-libs...
upgrading gmp...
upgrading coreutils...
upgrading pcre...
upgrading glib2...
upgrading zlib...
installing kmod...
upgrading pciutils...
upgrading udev...
ATTENTION UDEV:
----------
udev-compat has been removed, and should be uninstalled.
 --
Framebuffers are no longer blacklisted by default.
 --
binaries moved from /sbin to /usr/bin
---------------
upgrading device-mapper...
upgrading dhcpcd...
upgrading e2fsprogs...
upgrading filesystem...
grep: error while loading shared libraries: libpcre.so.0: cannot open shared object file: No such file or directory
groupadd: group 'optical' already exists
grep: error while loading shared libraries: libpcre.so.0: cannot open shared object file: No such file or directory
groupadd: group 'audio' already exists
grep: error while loading shared libraries: libpcre.so.0: cannot open shared object file: No such file or directory
groupadd: group 'video' already exists
grep: error while loading shared libraries: libpcre.so.0: cannot open shared object file: No such file or directory
groupadd: group 'floppy' already exists
grep: error while loading shared libraries: libpcre.so.0: cannot open shared object file: No such file or directory
groupadd: group 'storage' already exists
grep: error while loading shared libraries: libpcre.so.0: cannot open shared object file: No such file or directory
groupadd: group 'log' already exists
grep: error while loading shared libraries: libpcre.so.0: cannot open shared object file: No such file or directory
groupadd: group 'utmp' already exists
grep: error while loading shared libraries: libpcre.so.0: cannot open shared object file: No such file or directory
groupadd: group 'power' already exists
grep: error while loading shared libraries: libpcre.so.0: cannot open shared object file: No such file or directory
groupadd: group 'network' already exists
grep: error while loading shared libraries: libpcre.so.0: cannot open shared object file: No such file or directory
groupadd: group 'games' already exists
grep: error while loading shared libraries: libpcre.so.0: cannot open shared object file: No such file or directory
groupadd: group 'uucp' already exists
grep: error while loading shared libraries: libpcre.so.0: cannot open shared object file: No such file or directory
groupadd: group 'http' already exists
grep: error while loading shared libraries: libpcre.so.0: cannot open shared object file: No such file or directory
Usage: useradd [options] LOGIN
       useradd -D
       useradd -D [options]

Options:
  -b, --base-dir BASE_DIR       base directory for the home directory of the
                                new account
  -c, --comment COMMENT         GECOS field of the new account
  -d, --home-dir HOME_DIR       home directory of the new account
  -D, --defaults                print or change default useradd configuration
  -e, --expiredate EXPIRE_DATE  expiration date of the new account
  -f, --inactive INACTIVE       password inactivity period of the new account
  -g, --gid GROUP               name or ID of the primary group of the new
                                account
  -G, --groups GROUPS           list of supplementary groups of the new
                                account
  -h, --help                    display this help message and exit
  -k, --skel SKEL_DIR           use this alternative skeleton directory
  -K, --key KEY=VALUE           override /etc/login.defs defaults
  -l, --no-log-init             do not add the user to the lastlog and
                                faillog databases
  -m, --create-home             create the user's home directory
  -M, --no-create-home          do not create the user's home directory
  -N, --no-user-group           do not create a group with the same name as
                                the user
  -o, --non-unique              allow to create users with duplicate
                                (non-unique) UID
  -p, --password PASSWORD       encrypted password of the new account
  -r, --system                  create a system account
  -R, --root CHROOT_DIR         directory to chroot into
  -s, --shell SHELL             login shell of the new account
  -u, --uid UID                 user ID of the new account
  -U, --user-group              create a group with the same name as the user

grep: error while loading shared libraries: libpcre.so.0: cannot open shared object file: No such file or directory
groupadd: group 'scanner' already exists
grep: error while loading shared libraries: libpcre.so.0: cannot open shared object file: No such file or directory
groupadd: group 'rfkill' already exists
grep: error while loading shared libraries: libpcre.so.0: cannot open shared object file: No such file or directory
grep: error while loading shared libraries: libpcre.so.0: cannot open shared object file: No such file or directory
grep: error while loading shared libraries: libpcre.so.0: cannot open shared object file: No such file or directory
grep: error while loading shared libraries: libpcre.so.0: cannot open shared object file: No such file or directory
grep: error while loading shared libraries: libpcre.so.0: cannot open shared object file: No such file or directory
grep: error while loading shared libraries: libpcre.so.0: cannot open shared object file: No such file or directory
grep: error while loading shared libraries: libpcre.so.0: cannot open shared object file: No such file or directory
grep: error while loading shared libraries: libpcre.so.0: cannot open shared object file: No such file or directory
upgrading grep...
upgrading ncurses...
upgrading inetutils...
upgrading iproute2...
upgrading initscripts...
If using non-bash-compatible shell, please set LANG in /etc/locale.conf,
as LOCALE in /etc/rc.conf no longer works.
upgrading less...
upgrading libidn...
upgrading perl...
upgrading openssl...
upgrading libsasl...
upgrading libldap...
upgrading libnl...
upgrading libpcap...
upgrading linux-headers-omap...
upgrading mkinitcpio...
upgrading linux-omap...
>>> Updating module dependencies. Please wait ...
upgrading lvm2...
upgrading man-db...
upgrading mdadm...
upgrading pacman-mirrorlist...
upgrading psmisc...
upgrading run-parts...
upgrading syslog-ng...
upgrading wpa_supplicant...


Grep and man throw errors about being unable to find libpcre.so.0.
I reboot, and no kernel modules load, and it throws errors I'm unable to copy/paste at this time since I've just restored to the standard ArchLinuxArm download. Sorry about that, but it's looking for the kernel modules in the old modules directory.

Any ideas?

Oh, I've also tried upgrading pcre first, same results.
phelbore
 
Posts: 13
Joined: Thu Feb 23, 2012 3:33 pm

Re: full system upgrade destroys my system

Postby WarheadsSE » Fri Feb 24, 2012 10:02 pm

Psst. What device?

Also, I saw this myself the other day. The issue is with the order in which the packages get upgraded pissing it off. Filesystem is the only package actually complaining, so once that is done, just Sf filesystem to forcibly re-install filesystem.
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Re: full system upgrade destroys my system

Postby phelbore » Sat Feb 25, 2012 9:38 am

I had tried to reinstall filesystem before I posted :) no such luck. BTW, this is an Overo Firestorm. Awesome little device, I'm turning this into a toy to take to Defcon.

I finally got it to work by upgrading everything BUT linux-omap and linux-headers-omap, which isn't an ideal solution. Below is the log I got when I do a full upgrade, force reinstall filesystem and reboot. This is from minicom, so kinda messy.

From what I can tell, this is booting an old kernel with a new set of modules, which it can't find. Maybe?

Code: Select all
## Booting kernel from Legacy Image at 82000000 ...
   Image Name:   Linux-3.1.6-1-ARCH
   Image Type:   ARM Linux Kernel Image (uncompressed)
   Data Size:    4409180 Bytes = 4.2 MiB
   Load Address: 80008000
   Entry Point:  80008000
   Verifying Checksum ... OK
   Loading Kernel Image ... OK
OK

Starting kernel ...

Uncompressing Linux... done, booting the kernel.
[    1.834869] twl4030_wdt twl4030_wdt: Failed to register misc device
[    2.199737] omap_hsmmc omap_hsmmc.1: could not set regulator OCR (-22)
INIT: version 2.88 booting
 
 > Arch Linux ARM
 
 > http://www.archlinuxarm.org

   ------------------------------
:: Mounting Root Read-Only    [BUSY]    [DONE]
:: Adjusting system time and setting kernel timezone    [BUSY] libkmod: index_mm_open: open(/lib/modules/3.1.6-1-ARCH/modules.dep.bin, O_RDONLY|O_CLOEXEC): No such file or directory
libkmod: kmod_search_moddep: could not open moddep file '/lib/modules/3.1.6-1-ARCH/modules.dep.bin'
libkmod: kmod_search_moddep: could not open moddep file '/lib/modules/3.1.6-1-ARCH/modules.dep.bin'
libkmod: kmod_search_moddep: could not open moddep file '/lib/modules/3.1.6-1-ARCH/modules.dep.bin'
   [DONE]
:: Starting UDev Daemon    [BUSY]    [DONE]
:: Triggering UDev uevents    [BUSY] udevd[85]: open(/lib/modules/3.1.6-1-ARCH/modules.dep.bin, O_RDONLY|O_CLOEXEC): No such file or directory

   [DONE]
:: Waiting for UDev uevents to be processed    [BUSY]    [DONE]
:: Bringing up loopback interface    [BUSY]    [DONE]
:: Checking Filesystems    [BUSY]    [DONE]
:: Remounting Root    [BUSY]    [DONE]
:: Mounting Local Filesystems    [BUSY]    [DONE]
:: Activating Swap    [BUSY]    [DONE]
:: Configuring Time Zone    [BUSY]    [DONE]
:: Initializing Random Seed    [BUSY]    [DONE]
:: Removing Leftover Files    [BUSY]    [DONE]
:: Setting Hostname: alarm    [BUSY]    [DONE]
:: Setting Consoles to UTF-8 mode    [BUSY] G   [DONE]
:: Loading Keyboard Map: us    [BUSY]    [DONE]
:: Saving dmesg Log    [BUSY]    [DONE]
INIT: Entering runlevel: 3
:: Starting Syslog-NG    [BUSY]    [DONE]
:: Starting Network    [BUSY]
Error: unknown interface in /etc/rc.conf: `eth0'
   [DONE]
:: Mounting Network Filesystems    [BUSY]    [DONE]
:: Starting crond daemon    [BUSY]    [DONE]
:: Starting Secure Shell Daemon    [BUSY]    [DONE]

Arch Linux 3.1.6-1-ARCH (ttyO2)

alarm login: root
Password:
Last login: Fri Dec 31 18:24:26 CST 1999 on ttyO2
[root@alarm ~]# lsmod
Module                  Size  Used by
[root@alarm ~]#
phelbore
 
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Re: full system upgrade destroys my system

Postby WarheadsSE » Sat Feb 25, 2012 8:19 pm

Right... did you make sure that the kernel was in the right place after updating? That would cause this de-sync.
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Re: full system upgrade destroys my system

Postby phelbore » Mon Feb 27, 2012 5:29 pm

I'm still here, I just can't test this for a couple more days. Working too much. I'll post more Wednesday or maybe Thursday.
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Re: full system upgrade destroys my system

Postby WarheadsSE » Mon Feb 27, 2012 6:21 pm

Know the feeling, we'll still be here :geek:
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Re: full system upgrade destroys my system

Postby phelbore » Fri Mar 02, 2012 12:42 pm

You are wise beyond my years. I boot from an SD card, and following the instructions, I have it set up with 2 partitions, only the second remains mounted after boot. Once I copied the kernel from /boot/uImage to the first partition's uImage, everything worked fine. I'd better add that to my notes to self folder.
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Re: full system upgrade destroys my system

Postby glenno » Wed Mar 07, 2012 7:16 am

Running on a Goflex Net I think I have a similar issue following an upgrade on Saturday. Its been about 4 weeks since I last did a full upgrade (old kernel was 3.1.10-2) and I was upgrading to 3.1.10-4).

Since running pacman -Syu my system boots up, watching UBIT and kernel boot debugs via nc. But I have no Ethernet.

Ive mounted the ROOTFS drive on my PC and copied over 3.1.10-3 and tried that, same problem.

So the question is, where to from here? Do I need to do a full rebuild, or is there some other way around it?

If I put in another drive in the goflex, boot up, then chroot my normal drive and re pacman it, is that the way to go?

thanks heaps.
Glenn.
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