/dev/sd* missing after full system upgrade

[kldavis4]

I am running archlinux on a seagate dockstar. (I previously installed Plugbox-Linux-1.1.)

I decided to install a new package last night, and when I ran pacman -S <package> I got an error saying pluglinux.com was not found. So then I ran pacman -Su. There was a message about upgrading the pacman db, so I did pacman-db-upgrade. Then when I tried to install the package again, I got a message saying the pacman db could not be found. Then I ran pacman -Syyu. I ran into the issue with mtab needing to be replaced, so I copied mtab to a backup and then ran pacman -S --force filesystem and ran pacman -Syyu and got the first set of output below in pacman.log. During the rebuilding man pages step, I got kicked out of my ssh session. I attempted to reconnect and got an error saying something about a problem with 'ssh_exchange_identification'. Then I ran pacman -S openssh hoping that would fix the problem and it seemed to. I resumed the full system upgrade again (pacman -Syyu) and got the second set of output below.

At this point, everything seemed to be ok. I was able to install my package. Then I rebooted to make sure everything was ok. When I tried to ssh in again I got this error: PTY allocation request failed on channel 0. I googled and found this blog post: (http://fsk141.com/fix-pty-allocation-request-failed-on-channel-0) and followed the steps there. Once I did this I was able to ssh in again. Then I discovered that only my usb drive with the root filesystem was mounting. When I tried mounting my second usb hard drive, I got an error. I checked in /dev/ and found there were no longer any drives there, only the following: 'console initctl log null ptmx pts shm tty[0-9]* urandom zero'. I checked the dmesg and found the following:

$this->bbcode_second_pass_code('', '
[ 23.892573] Waiting 10sec before mounting root device...
[ 24.441017] scsi 0:0:0:0: Direct-Access TOSHIBA MK6026GAX PA20 PQ: 0 ANSI: 0
[ 24.450691] sd 0:0:0:0: Attached scsi generic sg0 type 0
[ 24.456582] sd 0:0:0:0: [sda] Adjusting the sector count from its reported value: 117210240
[ 24.465820] sd 0:0:0:0: [sda] 117210239 512-byte logical blocks: (60.0 GB/55.8 GiB)
[ 24.474441] sd 0:0:0:0: [sda] Write Protect is off
[ 24.479257] sd 0:0:0:0: [sda] Mode Sense: 03 00 00 00
[ 24.479267] sd 0:0:0:0: [sda] Assuming drive cache: write through
[ 24.486564] sd 0:0:0:0: [sda] Adjusting the sector count from its reported value: 117210240
[ 24.495812] sd 0:0:0:0: [sda] Assuming drive cache: write through
[ 24.502735] sda: sda1
[ 24.506817] sd 0:0:0:0: [sda] Adjusting the sector count from its reported value: 117210240
[ 24.516189] sd 0:0:0:0: [sda] Assuming drive cache: write through
[ 24.522351] sd 0:0:0:0: [sda] Attached SCSI disk
[ 24.650869] scsi 1:0:0:0: Direct-Access ST325082 3A PQ: 0 ANSI: 0
[ 24.660361] sd 1:0:0:0: Attached scsi generic sg1 type 0
[ 24.665969] sd 1:0:0:0: [sdb] 488397168 512-byte logical blocks: (250 GB/232 GiB)
[ 24.675189] sd 1:0:0:0: [sdb] Write Protect is off
[ 24.680040] sd 1:0:0:0: [sdb] Mode Sense: 33 00 00 00
[ 24.680052] sd 1:0:0:0: [sdb] Assuming drive cache: write through
[ 24.687936] sd 1:0:0:0: [sdb] Assuming drive cache: write through
[ 24.734699] sdb: sdb1 sdb2
[ 24.740195] sd 1:0:0:0: [sdb] Assuming drive cache: write through
[ 24.746342] sd 1:0:0:0: [sdb] Attached SCSI disk
[ 33.905206] EXT2-fs (sda1): warning: mounting unchecked fs, running e2fsck is recommended
[ 33.914229] VFS: Mounted root (ext2 filesystem) on device 8:1.
')

It looks it is seeing the second drive, but nothing shows up in /dev. I tried installing udev-automount as mentioned here: (http://archlinuxarm.org/article/20110807/re-enabling-automount-usb-drives) but that didn't have any effect.


pacman -Syyu output (first attempt):

$this->bbcode_second_pass_code('', '
[2012-02-09 21:13] starting full system upgrade
[2012-02-09 21:14] removed util-linux-ng (2.18-2)
[2012-02-09 21:14] removed module-init-tools (3.11.1-2)
[2012-02-09 21:14] removed heimdal (1.3.3-1)
[2012-02-09 21:14] removed mailx (8.1.1-7)
[2012-02-09 21:14] removed fam (2.7.0-14)
[2012-02-09 21:14] upgraded attr (2.4.44-1 -> 2.4.46-1)
[2012-02-09 21:14] upgraded acl (2.2.49-1 -> 2.2.51-1)
[2012-02-09 21:14] upgraded expat (2.0.1-5 -> 2.0.1-7)
[2012-02-09 21:14] upgraded libdaemon (0.14-1 -> 0.14-2)
[2012-02-09 21:14] upgraded gcc-libs (4.4.3-5 -> 4.6.2-7)
[2012-02-09 21:14] upgraded pcre (8.10-1 -> 8.21-1)
[2012-02-09 21:14] installed libffi (3.0.10-1)
[2012-02-09 21:14] upgraded glib2 (2.26.0-2 -> 2.30.2-1)
[2012-02-09 21:14] upgraded libcap (2.19-1 -> 2.22-2)
[2012-02-09 21:14] upgraded ncurses (5.7-3 -> 5.9-2)
[2012-02-09 21:14] upgraded readline (6.1.002-1 -> 6.2.002-1)
[2012-02-09 21:14] warning: /etc/bash.bashrc installed as /etc/bash.bashrc.pacnew
[2012-02-09 21:14] upgraded bash (4.1.007-1 -> 4.2.020-1)
[2012-02-09 21:14] >> Major version update. Consider running db_upgrade on Berkeley DB databases.
[2012-02-09 21:14] upgraded db (4.8.26-2 -> 5.3.15-1)
[2012-02-09 21:14] upgraded zlib (1.2.5-2 -> 1.2.6-1)
[2012-02-09 21:14] upgraded cracklib (2.8.16-1 -> 2.8.18-2)
[2012-02-09 21:14] upgraded libgssglue (0.1-2 -> 0.3-1)
[2012-02-09 21:14] upgraded libtirpc (0.2.1-1 -> 0.2.2-2)
[2012-02-09 21:14] upgraded pam (1.1.1-1 -> 1.1.5-2)
[2012-02-09 21:14] upgraded shadow (4.1.4.2-3 -> 4.1.4.3-5)
[2012-02-09 21:14] upgraded gmp (5.0.1-1 -> 5.0.3-1)
[2012-02-09 21:14] upgraded coreutils (8.5-2 -> 8.15-1)
[2012-02-09 21:14] upgraded dbus-core (1.2.24-1 -> 1.4.16-1)
[2012-02-09 21:14] upgraded xproto (7.0.18-1 -> 7.0.22-1)
[2012-02-09 21:14] upgraded libxdmcp (1.0.3-1 -> 1.1.0-1)
[2012-02-09 21:14] upgraded libxau (1.0.5-1 -> 1.0.6-1)
[2012-02-09 21:14] upgraded libxcb (1.7-1 -> 1.7-2)
[2012-02-09 21:15] upgraded libx11 (1.3.5-1 -> 1.4.4-1)
[2012-02-09 21:15] upgraded dbus (1.2.24-1 -> 1.4.16-1)
[2012-02-09 21:15] upgraded gdbm (1.8.3-7 -> 1.10-1)
[2012-02-09 21:15] upgraded avahi (0.6.25-3 -> 0.6.30-7)
[2012-02-09 21:15] upgraded binutils (2.20.1-1 -> 2.22-4)
[2012-02-09 21:15] upgraded bzip2 (1.0.6-1 -> 1.0.6-3)
[2012-02-09 21:15] upgraded run-parts (3.2.2-1 -> 4.2.1-1)

[2012-02-09 21:15] upgraded perl (5.10.1-5 -> 5.14.2-7)
[2012-02-09 21:15] upgraded openssl (1.0.0.a-2 -> 1.0.0.g-1)
[2012-02-09 21:15] upgraded findutils (4.4.2-2 -> 4.4.2-4)
[2012-02-09 21:15] upgraded sed (4.2.1-2 -> 4.2.1-4)
[2012-02-09 21:15] Updating certificates. This might take a while...
[2012-02-09 21:15] upgraded ca-certificates (20090814-3 -> 20111211-1)
[2012-02-09 21:15] installed util-linux (2.20.1-2)
[2012-02-09 21:15] installed kmod (4-2.1)
[2012-02-09 21:15] upgraded pciutils (3.1.7-1 -> 3.1.8-1)
[2012-02-09 21:15] upgraded libusb (0.1.12-4 -> 1.0.8-2)
[2012-02-09 21:15] upgraded usbutils (0.87-1 -> 004-1)
[2012-02-09 21:15] ATTENTION UDEV:
[2012-02-09 21:15] ----------
[2012-02-09 21:15] Kernel 2.6.32 or newer is now required.
[2012-02-09 21:15] --
[2012-02-09 21:15] OSS emulation modules are not loaded by default, add to rc.conf if needed.
[2012-02-09 21:15] --
[2012-02-09 21:15] Arch specific cd symlinks are now no longer created.
[2012-02-09 21:15] --
[2012-02-09 21:15] cd and net persistent rules will no longer be autogenerated,
[2012-02-09 21:15] see <[url]https://wiki.archlinux.org/index.php/Udev[/url]> for details.
[2012-02-09 21:15] --

[2012-02-09 21:15] Errors are now logged (possibly to the console) by default.
[2012-02-09 21:15] --
[2012-02-09 21:15] Arch's custom blacklisting logic has been removed. MOD_AUTOLOAD and
[2012-02-09 21:15] blacklisting in MODULES no longer works.
[2012-02-09 21:15] See 'man modprobe.conf' for a replacement to blacklisting.
[2012-02-09 21:15] To disable a module mod1 on the kernel command line, use
[2012-02-09 21:15] mod1.disable=1
[2012-02-09 21:15] or
[2012-02-09 21:15] modprobe.blacklist=mod1
[2012-02-09 21:15] --
[2012-02-09 21:15] The following modules are no longer unconditionally loaded:
[2012-02-09 21:15] pcspkr irtty-sir analog lp ppdev ide-generic
[2012-02-09 21:15] Add them to MODULES in rc.conf if you need them.
[2012-02-09 21:15] --
[2012-02-09 21:15] Blacklisting of framebuffer devices has moved from /etc/modprobe.d to
[2012-02-09 21:15] /lib/modprobe.d. Any customizations shoud be done to the file in /etc, as it
[2012-02-09 21:15] takes precedence.
[2012-02-09 21:15] --
[2012-02-09 21:15] kbd and rtc devices are no longer world readable.
[2012-02-09 21:15] --
[2012-02-09 21:15] rtc is no longer in the audio group and fb devices are no longer in
[2012-02-09 21:15] the video group, as permissions and ownership of fb devices are controlled

[2012-02-09 21:15] by X.
[2012-02-09 21:15] --
[2012-02-09 21:15] We now use upstream rules for assigning devices to the 'disk', 'optical',
[2012-02-09 21:15] 'scanner' and 'video' groups. Beware of any changes.
[2012-02-09 21:15] --
[2012-02-09 21:15] We no longer create symlinks from /dev/<dev> to /dev/<dev>0.
[2012-02-09 21:15] --
[2012-02-09 21:15] For security reasons, we no longer add devices to the 'storage' group. Use
[2012-02-09 21:15] udisks and friends, or add custom rules to /etc/udev.d/rules/, if you want
[2012-02-09 21:15] this functionality back.
[2012-02-09 21:15] --
[2012-02-09 21:15] We no longer create the static nodes on install needed for an initrd-less boot
[2012-02-09 21:15] where devtmpfs is not mounted by the kernel, this only affects fresh installs.
[2012-02-09 21:15] --
[2012-02-09 21:15] devtmpfs support is now a hard requirement. Users of the official Arch kernels
[2012-02-09 21:15] have this enabled.
[2012-02-09 21:15] ---------------
[2012-02-09 21:15] upgraded udev (157-2 -> 180-1)
[2012-02-09 21:15] upgraded device-mapper (2.02.70-1 -> 2.02.88-1)
[2012-02-09 21:15] upgraded libgpg-error (1.7-3 -> 1.10-1)
[2012-02-09 21:15] upgraded libgcrypt (1.4.6-1 -> 1.5.0-1)
[2012-02-09 21:15] upgraded popt (1.16-2 -> 1.16-4)

[2012-02-09 21:15] upgraded cryptsetup (1.1.3-1 -> 1.4.1-1)
[2012-02-09 21:15] installed libssh2 (1.4.0-1)
[2012-02-09 21:15] upgraded curl (7.21.1-1 -> 7.24.0-2)
[2012-02-09 21:15] upgraded dash (0.5.6.1-1 -> 0.5.7-2)
[2012-02-09 21:15] upgraded dcron (4.4-2 -> 4.5-2)
[2012-02-09 21:15] upgraded dhcpcd (5.2.5-1 -> 5.2.12-4)
[2012-02-09 21:15] upgraded libsigsegv (2.6-1 -> 2.6-2)
[2012-02-09 21:15] upgraded diffutils (3.0-3 -> 3.2-1)
[2012-02-09 21:15] upgraded e2fsprogs (1.41.12-2 -> 1.42-1)
[2012-02-09 21:15] upgraded eventlog (0.2.12-1 -> 0.2.12-3)
[2012-02-09 21:15] upgraded file (5.04-2 -> 5.10-1)
[2012-02-09 21:15] upgraded gawk (3.1.8-1 -> 4.0.0-2)
[2012-02-09 21:16] upgraded gettext (0.18.1.1-1 -> 0.18.1.1-4)
[2012-02-09 21:16] upgraded gzip (1.4-1 -> 1.4-4)
[2012-02-09 21:16] upgraded texinfo (4.13a-4 -> 4.13a-7)
[2012-02-09 21:16] upgraded libtasn1 (2.6-1 -> 2.9-1)
[2012-02-09 21:16] installed nettle (2.4-1)
[2012-02-09 21:16] installed p11-kit (0.9-1)
[2012-02-09 21:16] upgraded gnutls (2.8.6-1 -> 3.0.12-1)
[2012-02-09 21:16] upgraded grep (2.6.3-1 -> 2.10-1)
[2012-02-09 21:16] upgraded groff (1.20.1-4 -> 1.21-2)
[2012-02-09 21:16] upgraded hdparm (9.28-1 -> 9.38-1)

[2012-02-09 21:16] upgraded libsasl (2.1.23-4 -> 2.1.23-9)
[2012-02-09 21:16] upgraded libfetch (2.32-1 -> 2.33-1)
[2012-02-09 21:16] upgraded libldap (2.4.22-1 -> 2.4.28-2)
[2012-02-09 21:16] installed keyutils (1.5.5-1)
[2012-02-09 21:16] installed krb5 (1.9.2-2)
[2012-02-09 21:16] installed iproute2 (3.2.0-2)
[2012-02-09 21:16] upgraded kbd (1.15.2-1 -> 1.15.3-2)
[2012-02-09 21:16] upgraded sysvinit (2.86-5 -> 2.88-3)
[2012-02-09 21:16] warning: /etc/rc.conf installed as /etc/rc.conf.pacnew
[2012-02-09 21:16] Blacklisting of modules is no longer supported in rc.conf,
[2012-02-09 21:16] please add blacklist entries to /etc/modprobe.d/ instead.
[2012-02-09 21:16] VERBOSE= in rc.conf no longer has any effect.
[2012-02-09 21:16] Please append 'quiet' to your kernel command line.
[2012-02-09 21:16] If using non-bash-compatible shell, please set LANG in /etc/locale.conf,
[2012-02-09 21:16] as LOCALE in /etc/rc.conf no longer works.
[2012-02-09 21:16] upgraded initscripts (2010.11-1 -> 2012.01.3-1)
[2012-02-09 21:16] upgraded iputils (20100214-2 -> 20101006-2)
[2012-02-09 21:16] upgraded jfsutils (1.1.14-1 -> 1.1.15-3)
[2012-02-09 21:16] upgraded less (436-1 -> 444-2)
[2012-02-09 21:16] upgraded libjpeg (8.0.2-1 -> 8.3.0-1)
[2012-02-09 21:16] upgraded libtiff (3.9.4-1 -> 4.0.0-1)
[2012-02-09 21:16] upgraded libpng (1.4.4-1 -> 1.5.8-1)
[2012-02-09 21:16] upgraded libcups (1.4.3-2 -> 1.5.2-1)
[2012-02-09 21:16] upgraded libevent (1.4.14b-1 -> 2.0.16-1)
[2012-02-09 21:16] upgraded libidn (1.16-1 -> 1.24-1)
[2012-02-09 21:16] upgraded libpcap (1.1.1-2 -> 1.2.1-1)
[2012-02-09 21:16] upgraded licenses (2.6-1 -> 2.9-1)
[2012-02-09 21:16] upgraded logrotate (3.7.8-1 -> 3.8.1-1)
[2012-02-09 21:16] upgraded lvm2 (2.02.70-1 -> 2.02.88-1)
[2012-02-09 21:16] upgraded lzo2 (2.03-1 -> 2.06-1)
[2012-02-09 21:16] installed heirloom-mailx (12.5-3)
[2012-02-09 21:16] installed libpipeline (1.2.0-2)
[2012-02-09 21:16] (re)building database...
[2012-02-09 21:19] upgraded man-db (2.5.7-1 -> 2.6.0.2-3)
[2012-02-09 21:19] upgraded man-pages (3.25-1 -> 3.32-1)
')

pacman -Syyu output (second attempt):

$this->bbcode_second_pass_code('', '
[2012-02-09 21:34] synchronizing package lists
[2012-02-09 21:34] starting full system upgrade
[2012-02-09 21:34] grep: /etc/mkinitcpio.conf: No such file or directory
[2012-02-09 21:34] upgraded mdadm (3.1.2-2 -> 3.2.3-1)
[2012-02-09 21:34] upgraded nano (2.2.4-1 -> 2.2.6-2)
[2012-02-09 21:34] hostname and {,yp,nis}domainname has moved:
[2012-02-09 21:34] ----------
[2012-02-09 21:34] hostname is now in coreutils
[2012-02-09 21:34] domainname is now in yp-tools
[2012-02-09 21:34] their functionality might have changed slightly
[2012-02-09 21:34]
[2012-02-09 21:34] dnsdomainname remains in net-tools
[2012-02-09 21:34] ----------
[2012-02-09 21:34] upgraded net-tools (1.60-14 -> 1.60.20110819cvs-3)
[2012-02-09 21:34] adding new group: ntp
[2012-02-09 21:34] upgraded openntpd (3.9p1-12 -> 3.9p1-13)
[2012-02-09 21:34] warning: /etc/pacman.d/mirrorlist saved as /etc/pacman.d/mirrorlist.pacsave

[2012-02-09 21:34] upgraded pacman-mirrorlist (20100608-1 -> 20120204-1)
[2012-02-09 21:34] upgraded ppp (2.4.5-1 -> 2.4.5-3)
[2012-02-09 21:34] upgraded procps (3.2.8-1 -> 3.2.8-4)
[2012-02-09 21:34] upgraded psmisc (22.11-1 -> 22.15-1)
[2012-02-09 21:34] upgraded reiserfsprogs (3.6.21-2 -> 3.6.21-4)
[2012-02-09 21:34] >>> The kernel-mode plugin has a new place.
[2012-02-09 21:34] >>> It's now located under /usr/lib/rp-pppoe/rp-pppoe.so
[2012-02-09 21:34] >>> Change LINUX_PLUGIN to the new path in your /etc/ppp/pppoe.conf
[2012-02-09 21:34] upgraded rp-pppoe (3.10-5 -> 3.10-7)
[2012-02-09 21:34] upgraded rpcbind (0.2.0-1 -> 0.2.0-6)
[2012-02-09 21:34] upgraded tdb (1.2.1-1 -> 1.2.9-2)
[2012-02-09 21:34] upgraded talloc (2.0.1-1 -> 2.0.7-1)
[2012-02-09 21:34] installed libcap-ng (0.6.6-1)
[2012-02-09 21:34] installed cifs-utils (5.3-1)
[2012-02-09 21:34] upgraded smbclient (3.5.4-2 -> 3.6.3-1)
[2012-02-09 21:34] installed gamin (0.1.10-6)
[2012-02-09 21:34] upgraded samba (3.5.4-2 -> 3.6.3-1)
[2012-02-09 21:34] upgraded sqlite3 (3.6.23.1-1 -> 3.7.10-1)
[2012-02-09 21:34] upgraded syslog-ng (3.1.1-1 -> 3.3.4-1)
[2012-02-09 21:34] upgraded tar (1.23-3 -> 1.26-2)
[2012-02-09 21:34] warning: /etc/conf.d/transmissiond installed as /etc/conf.d/transmissiond.pacnew
[2012-02-09 21:34] upgraded transmission-cli (2.10-1 -> 2.42-2)
[2012-02-09 21:34] upgraded tzdata (2010j-1 -> 2011n-1)
[2012-02-09 21:34] upgraded vi (050325-3 -> 1:050325-2)
[2012-02-09 21:34] upgraded wget (1.12-3 -> 1.13.4-1)
[2012-02-09 21:34] upgraded which (2.20-3 -> 2.20-5)
[2012-02-09 21:34] upgraded wpa_supplicant (0.6.10-2 -> 0.7.3-4)
[2012-02-09 21:34] upgraded xfsprogs (3.1.1-1 -> 3.1.7-1)
')

[kldavis4]

The following resolved it for me:

$this->bbcode_second_pass_code('', '
pacman -S linux
')

[weisl]

I had the same problem with my custom kernel after "pacman -Syu". The solution for me was to enable "devtmpfs" in the kernel-config.

[wkatastrof]

I'm having the same issue after the full sys upgrade on the pogoplug.

I tried pacman -S linux unsuccessfully.

How do I edit the kernel-config to enable devtmpfs?

[gdkags]

did you copy the new linux image over to to your sd card or whatever you are booting from?