[SOLVED] pacman, tar, startx, and others not running after sys update

Maosn · 2014-11-26 23:41:49

I have Arch Linux installed on a USB drive, and have been having some problems with it for a couple of weeks. Currently, after a system update, pacman fails with no error messages or output of any kind, as does vim. Startx fails with the following error:

 /usr/bin/Xorg.bin: error while loading shared libraries: /usr/lib/libpng16.so.16: file too short

I'm not sure if this could be causing the problem, but I did not see the announcement about the Intel microcode updates before updating (https://www.archlinux.org/news/changes- … deupdates/) and did not follow the instructions in the wiki. If that is the problem, I would appreciate instructions on how to fix it without pacman (which I would normally use to install the intel-ucode package).

this the log file for pacman (/var/log/pacman.log), starting at the system update:

[2014-11-24 11:35] [PACMAN] Running 'pacman -Syu'
[2014-11-24 11:35] [PACMAN] synchronizing package lists
[2014-11-24 11:35] [PACMAN] starting full system upgrade
[2014-11-24 11:54] [PACMAN] upgraded adwaita-icon-theme (3.14.0-1 -> 3.14.1-1)
[2014-11-24 11:54] [PACMAN] upgraded tzdata (2014h-1 -> 2014j-1)
[2014-11-24 11:54] [PACMAN] upgraded filesystem (2014.07-1 -> 2014.10-3)
[2014-11-24 11:55] [PACMAN] upgraded glibc (2.20-2 -> 2.20-3)
[2014-11-24 11:55] [PACMAN] upgraded libdbus (1.8.8-1 -> 1.8.10-1)
[2014-11-24 11:55] [PACMAN] upgraded dbus (1.8.8-1 -> 1.8.10-1)
[2014-11-24 11:55] [PACMAN] upgraded libffi (3.1-2 -> 3.1-3)
[2014-11-24 11:55] [PACMAN] upgraded glib2 (2.42.0-1 -> 2.42.1-1)
[2014-11-24 11:55] [PACMAN] upgraded at-spi2-core (2.14.0-1 -> 2.14.1-1)
[2014-11-24 11:55] [PACMAN] upgraded avahi (0.6.31-13 -> 0.6.31-14)
[2014-11-24 11:55] [PACMAN] upgraded binutils (2.24-7 -> 2.24-8)
[2014-11-24 11:55] [PACMAN] upgraded boost-libs (1.56.0-3 -> 1.57.0-2)
[2014-11-24 11:56] [PACMAN] upgraded boost (1.56.0-3 -> 1.57.0-2)
[2014-11-24 11:56] [PACMAN] upgraded ca-certificates-mozilla (3.17.1-1 -> 3.17.2-1)
[2014-11-24 11:56] [PACMAN] upgraded libpng (1.6.13-1 -> 1.6.14-1)
[2014-11-24 11:56] [PACMAN] upgraded kmod (18-1 -> 19-1)
[2014-11-24 11:56] [PACMAN] upgraded hwids (20140602-1 -> 20141030-1)
[2014-11-24 11:56] [PACMAN] upgraded libsystemd (216-3 -> 217-7)
[2014-11-24 11:56] [PACMAN] installed lz4 (123-1)
[2014-11-24 11:56] [PACMAN] upgraded libutil-linux (2.25.1-1 -> 2.25.2-1)
[2014-11-24 11:56] [PACMAN] upgraded util-linux (2.25.1-1 -> 2.25.2-1)
[2014-11-24 11:57] [PACMAN] upgraded systemd (216-3 -> 217-7)
[2014-11-24 11:57] [PACMAN] upgraded gcc-libs (4.9.1-2 -> 4.9.2-1)
[2014-11-24 11:57] [PACMAN] upgraded elfutils (0.159-1 -> 0.160-1)
[2014-11-24 11:57] [PACMAN] upgraded mesa-dri (10.3.1-1 -> 10.3.4-1)
[2014-11-24 11:58] [PACMAN] upgraded mesa (10.3.1-1 -> 10.3.4-1)
[2014-11-24 11:58] [PACMAN] upgraded mesa-libgl (10.3.1-1 -> 10.3.4-1)
[2014-11-24 11:58] [PACMAN] upgraded cairo (1.14.0-1 -> 1.14.0-2)
[2014-11-24 11:58] [PACMAN] upgraded sqlite (3.8.7-1 -> 3.8.7.2-1)
[2014-11-24 11:58] [PACMAN] upgraded nss (3.17.1-1 -> 3.17.2-1)
[2014-11-24 11:58] [PACMAN] upgraded harfbuzz (0.9.35-2 -> 0.9.36-1)
[2014-11-24 11:59] [PACMAN] upgraded chromium (38.0.2125.104-2 -> 39.0.2171.65-1)
[2014-11-24 11:59] [PACMAN] upgraded colord (1.2.3-1 -> 1.2.5-1)
[2014-11-24 11:59] [PACMAN] upgraded ctags (5.8-4 -> 5.8-5)
[2014-11-24 11:59] [PACMAN] upgraded gnutls (3.3.9-1 -> 3.3.10-1)
[2014-11-24 11:59] [PACMAN] upgraded krb5 (1.12.2-1 -> 1.13-1)
[2014-11-24 11:59] [ALPM] warning: /etc/cups/client.conf installed as /etc/cups/client.conf.pacnew
[2014-11-24 11:59] [PACMAN] upgraded libcups (1.7.5-1 -> 2.0.1-1)
[2014-11-24 11:59] [PACMAN] upgraded libjpeg-turbo (1.3.1-1 -> 1.3.1-2)
[2014-11-24 11:59] [PACMAN] upgraded poppler (0.26.5-1 -> 0.28.1-1)
[2014-11-24 11:59] [PACMAN] upgraded cups-filters (1.0.61-1 -> 1.0.61-3)
[2014-11-24 11:59] [ALPM] warning: directory permissions differ on /var/cache/cups/
filesystem: 775  package: 770
[2014-11-24 11:59] [ALPM-SCRIPTLET] > systemd unit names have been renamed
[2014-11-24 11:59] [ALPM-SCRIPTLET] > you should systemctl stop and disable cups.service and
[2014-11-24 11:59] [ALPM-SCRIPTLET] > systemctl daemon-reload, start and enable org.cups.cupsd.service
[2014-11-24 11:59] [PACMAN] upgraded cups (1.7.5-1 -> 2.0.1-1)
[2014-11-24 11:59] [PACMAN] upgraded curl (7.38.0-2 -> 7.39.0-1)
[2014-11-24 11:59] [PACMAN] upgraded device-mapper (2.02.111-1 -> 2.02.112-1)
[2014-11-24 11:59] [PACMAN] upgraded dhcpcd (6.5.1-1 -> 6.6.2-1)
[2014-11-24 11:59] [PACMAN] upgraded fakeroot (1.20.1-1 -> 1.20.2-1)
[2014-11-24 11:59] [PACMAN] upgraded file (5.20-1 -> 5.20-2)
[2014-11-24 12:00] [PACMAN] upgraded firefox (33.0-2 -> 33.1.1-1)
[2014-11-24 12:01] [PACMAN] upgraded gcc (4.9.1-2 -> 4.9.2-1)
[2014-11-24 12:01] [PACMAN] upgraded gettext (0.19.2-2 -> 0.19.3-1)
[2014-11-24 12:01] [PACMAN] upgraded git (2.1.2-1 -> 2.1.3-1)
[2014-11-24 12:01] [PACMAN] upgraded libxml2 (2.9.1-5 -> 2.9.2-2)
[2014-11-24 12:02] [PACMAN] upgraded gstreamer (1.4.3-1 -> 1.4.4-1)
[2014-11-24 12:02] [PACMAN] upgraded gst-plugins-base-libs (1.4.3-1 -> 1.4.4-1)
[2014-11-24 12:02] [PACMAN] upgraded libxkbcommon (0.4.3-1 -> 0.5.0-1)
[2014-11-24 12:02] [PACMAN] installed json-glib (1.0.2-1)
[2014-11-24 12:02] [PACMAN] installed libproxy (0.4.11-4)
[2014-11-24 12:02] [PACMAN] installed glib-networking (2.42.0-1)
[2014-11-24 12:02] [PACMAN] installed libsoup (2.48.0-1)
[2014-11-24 12:02] [PACMAN] installed rest (0.7.92-1)
[2014-11-24 12:04] [PACMAN] upgraded gtk3 (3.14.3-2 -> 3.14.5-1)
[2014-11-24 12:04] [PACMAN] upgraded harfbuzz-icu (0.9.35-2 -> 0.9.36-1)
[2014-11-24 12:04] [PACMAN] upgraded libltdl (2.4.2-14 -> 2.4.2-15)
[2014-11-24 12:04] [PACMAN] upgraded imagemagick (6.8.9.8-1 -> 6.9.0.0-1)
[2014-11-24 12:04] [PACMAN] upgraded java-environment-common (2-1 -> 2-2)
[2014-11-24 12:04] [PACMAN] upgraded java-runtime-common (2-1 -> 2-2)
[2014-11-24 12:04] [PACMAN] upgraded libaio (0.3.109-7 -> 0.3.110-1)
[2014-11-24 12:04] [PACMAN] upgraded libevdev (1.3-1 -> 1.3.1-1)
[2014-11-24 12:04] [PACMAN] upgraded libgpg-error (1.16-1 -> 1.17-1)
[2014-11-24 12:04] [PACMAN] upgraded libpipeline (1.3.1-1 -> 1.4.0-1)
[2014-11-24 12:04] [PACMAN] upgraded neon (0.30.0-1 -> 0.30.1-1)
[2014-11-24 12:07] [PACMAN] upgraded libreoffice-fresh (4.3.2-3 -> 4.3.4-1)
[2014-11-24 12:07] [PACMAN] upgraded libtool (2.4.2-14 -> 2.4.2-15)
[2014-11-24 12:07] [PACMAN] upgraded libxdg-basedir (1.2.0-2 -> 1.2.0-3)
[2014-11-24 12:07] [PACMAN] upgraded libxkbcommon-x11 (0.4.3-1 -> 0.5.0-1)
[2014-11-24 12:07] [ALPM-SCRIPTLET] >>> Updating module dependencies. Please wait ...
[2014-11-24 12:07] [ALPM-SCRIPTLET] >>> Generating initial ramdisk, using mkinitcpio.  Please wait...
[2014-11-24 12:07] [ALPM-SCRIPTLET] ==> Building image from preset: /etc/mkinitcpio.d/linux.preset: 'default'
[2014-11-24 12:07] [ALPM-SCRIPTLET]   -> -k /boot/vmlinuz-linux -c /etc/mkinitcpio.conf -g /boot/initramfs-linux.img
[2014-11-24 12:07] [ALPM-SCRIPTLET] ==> Starting build: 3.17.3-1-ARCH
[2014-11-24 12:07] [ALPM-SCRIPTLET]   -> Running build hook: [base]
[2014-11-24 12:07] [ALPM-SCRIPTLET]   -> Running build hook: [udev]
[2014-11-24 12:07] [ALPM-SCRIPTLET]   -> Running build hook: [block]
[2014-11-24 12:07] [ALPM-SCRIPTLET] ==> WARNING: Possibly missing firmware for module: aic94xx
[2014-11-24 12:07] [ALPM-SCRIPTLET] ==> WARNING: Possibly missing firmware for module: smsmdtv
[2014-11-24 12:07] [ALPM-SCRIPTLET] ==> WARNING: Hook 'usb' is deprecated. Replace it with 'block' in your config
[2014-11-24 12:07] [ALPM-SCRIPTLET]   -> Running build hook: [block]
[2014-11-24 12:07] [ALPM-SCRIPTLET]   -> Running build hook: [autodetect]
[2014-11-24 12:07] [ALPM-SCRIPTLET]   -> Running build hook: [modconf]
[2014-11-24 12:07] [ALPM-SCRIPTLET]   -> Running build hook: [filesystems]
[2014-11-24 12:07] [ALPM-SCRIPTLET]   -> Running build hook: [keyboard]
[2014-11-24 12:07] [ALPM-SCRIPTLET]   -> Running build hook: [fsck]
[2014-11-24 12:07] [ALPM-SCRIPTLET] ==> Generating module dependencies
[2014-11-24 12:07] [ALPM-SCRIPTLET] ==> Creating gzip-compressed initcpio image: /boot/initramfs-linux.img
[2014-11-24 12:07] [ALPM-SCRIPTLET] ==> Image generation successful
[2014-11-24 12:07] [ALPM-SCRIPTLET] ==> Building image from preset: /etc/mkinitcpio.d/linux.preset: 'fallback'
[2014-11-24 12:07] [ALPM-SCRIPTLET]   -> -k /boot/vmlinuz-linux -c /etc/mkinitcpio.conf -g /boot/initramfs-linux-fallback.img -S autodetect
[2014-11-24 12:07] [ALPM-SCRIPTLET] ==> Starting build: 3.17.3-1-ARCH
[2014-11-24 12:07] [ALPM-SCRIPTLET]   -> Running build hook: [base]
[2014-11-24 12:07] [ALPM-SCRIPTLET]   -> Running build hook: [udev]
[2014-11-24 12:07] [ALPM-SCRIPTLET]   -> Running build hook: [block]
[2014-11-24 12:07] [ALPM-SCRIPTLET] ==> WARNING: Possibly missing firmware for module: aic94xx
[2014-11-24 12:07] [ALPM-SCRIPTLET] ==> WARNING: Possibly missing firmware for module: smsmdtv
[2014-11-24 12:07] [ALPM-SCRIPTLET] ==> WARNING: Hook 'usb' is deprecated. Replace it with 'block' in your config
[2014-11-24 12:07] [ALPM-SCRIPTLET]   -> Running build hook: [block]
[2014-11-24 12:07] [ALPM-SCRIPTLET]   -> Running build hook: [modconf]
[2014-11-24 12:07] [ALPM-SCRIPTLET]   -> Running build hook: [filesystems]
[2014-11-24 12:07] [ALPM-SCRIPTLET]   -> Running build hook: [keyboard]
[2014-11-24 12:07] [ALPM-SCRIPTLET]   -> Running build hook: [fsck]
[2014-11-24 12:08] [ALPM-SCRIPTLET] ==> Generating module dependencies
[2014-11-24 12:08] [ALPM-SCRIPTLET] ==> Creating gzip-compressed initcpio image: /boot/initramfs-linux-fallback.img
[2014-11-24 12:08] [ALPM-SCRIPTLET] ==> Image generation successful
[2014-11-24 12:08] [PACMAN] upgraded linux (3.17.1-1 -> 3.17.3-1)
[2014-11-24 12:08] [PACMAN] upgraded logrotate (3.8.7-3 -> 3.8.8-2)
[2014-11-24 12:08] [PACMAN] upgraded lvm2 (2.02.111-1 -> 2.02.112-1)
[2014-11-24 12:08] [PACMAN] upgraded make (4.0-2 -> 4.1-1)
[2014-11-24 12:08] [PACMAN] upgraded man-db (2.7.0.2-2 -> 2.7.1-1)
[2014-11-24 12:08] [ALPM] warning: /etc/pacman.d/mirrorlist installed as /etc/pacman.d/mirrorlist.pacnew
[2014-11-24 12:08] [PACMAN] upgraded pacman-mirrorlist (20140901-1 -> 20141116-1)
[2014-11-24 12:08] [PACMAN] upgraded pinentry (0.8.3-1 -> 0.8.4-1)
[2014-11-24 12:08] [PACMAN] upgraded procps-ng (3.3.9-3 -> 3.3.10-1)
[2014-11-24 12:08] [PACMAN] upgraded protobuf (2.6.0-2 -> 2.6.1-1)
[2014-11-24 12:08] [PACMAN] upgraded python2-lxml (3.4.0-1 -> 3.4.1-1)
[2014-11-24 12:08] [PACMAN] upgraded ruby (2.1.3-2 -> 2.1.5-1)
[2014-11-24 12:08] [PACMAN] upgraded sudo (1.8.11.p1-1 -> 1.8.11.p2-1)
[2014-11-24 12:08] [PACMAN] upgraded systemd-sysvcompat (216-3 -> 217-7)
[2014-11-24 12:08] [PACMAN] upgraded tdb (1.3.0-2 -> 1.3.1-1)
[2014-11-24 12:08] [PACMAN] upgraded usbutils (007-1 -> 008-1)
[2014-11-24 12:08] [PACMAN] upgraded wget (1.15-1 -> 1.16-2)
[2014-11-24 12:08] [PACMAN] upgraded xorg-xkbcomp (1.2.4-2 -> 1.3.0-1)
[2014-11-24 12:08] [PACMAN] upgraded xorg-server-common (1.16.1-1 -> 1.16.2-1)
[2014-11-24 12:08] [PACMAN] upgraded xorg-server (1.16.1-1 -> 1.16.2-1)
[2014-11-24 12:08] [PACMAN] upgraded xterm (312-1 -> 312-2)
[2014-11-24 12:08] [PACMAN] upgraded zathura (0.3.0-1 -> 0.3.2-1)
[2014-11-25 12:45] [PACMAN] Running 'pacman -Syu'
[2014-11-25 12:45] [PACMAN] synchronizing package lists
[2014-11-25 12:45] [PACMAN] starting full system upgrade
[2014-11-25 12:49] [PACMAN] removed dirmngr (1.1.1-3)
[2014-11-25 12:49] [PACMAN] installed npth (1.1-1)
[2014-11-25 12:49] [PACMAN] upgraded gnupg (2.0.26-1 -> 2.1.0-4)
[2014-11-25 12:49] [PACMAN] upgraded glibc (2.20-3 -> 2.20-4)
[2014-11-25 12:49] [PACMAN] upgraded groff (1.22.2-7 -> 1.22.3-2)
[2014-11-25 12:49] [PACMAN] upgraded vim-runtime (7.4.473-1 -> 7.4.525-1)
[2014-11-25 12:49] [PACMAN] upgraded gvim (7.4.473-1 -> 7.4.525-1)
[2014-11-25 12:49] [PACMAN] upgraded libcdr (0.1.0-2 -> 0.1.1-1)
[2014-11-25 12:49] [PACMAN] upgraded libodfgen (0.1.1-1 -> 0.1.2-1)
[2014-11-25 12:49] [PACMAN] upgraded libpng (1.6.14-1 -> 1.6.15-1)
[2014-11-25 12:49] [PACMAN] upgraded pacman (4.1.2-6 -> 4.1.2-7)

Let me know if there's any other info you need, and thanks in advance for any help.

Last edited by Maosn (2014-11-28 21:17:42)

jasonwryan · 2014-11-26 23:52:08

The error suggests that some/all of the files on the drive are corrupted: you could try rerunning the update, but I wouldn't trust that drive with any valuable data...

Maosn · 2014-11-27 00:01:34

I have practically all of the files on the drive backed up. I just need it as a portable Linux installation, which it has generally worked as until now. Do you know what would have caused it to become corrupted? And how I can fix it if that is the case? As to rerunning the update, I'm not entirely sure how to do that with pacman not working.

Scimmia · 2014-11-27 00:04:13

Simply reinstall the package.

As for why it happened, could be a number of things. From simply not syncing to disk to full blown filesystem corruption.

Maosn · 2014-11-27 00:25:41

Simply reinstall the package.

which package?

and for what its worth, fsck didn't find anything wrong with the filesystem.

ids1024 · 2014-11-27 00:31:42

Maosn wrote:

which package?

The error message is complaining about libpng, so it makes sense to reinstall that.

Allan · 2014-11-27 00:48:52

Use "pacman -Qkk" to find files with issues and reinstall their packages.

Maosn · 2014-11-27 00:51:34

Ok, since pacman doesn't work I tried reinstalling it manually, and using that to install libpng. The good news is pacman actually did something this time. The bad news is that something was printing out an error message:

pacman: error while loading shared libraries: libarchive.so.13: wrong ELF class: ELFCLASS64

Last edited by Maosn (2014-11-27 01:35:24)

Maosn · 2014-11-27 00:57:58

Should I just keep reinstalling the broken packages manually and hope things start working again at some point?

Edit:
I guess my actual question here is does this look like a problem with a bunch of individual packages, or a single more centralized problem that is causing all of those packages to fail?

Last edited by Maosn (2014-11-27 02:25:11)

fsckd · 2014-11-27 03:57:25

If you still have the install image you can boot from, you can use it to reinstall packages.

As for your actual question, I don't know. I would start by checking the disk and/or filesystem for errors.

Maosn · 2014-11-27 23:17:05

Ok, Thanks for the help. It turns out I had a 64 bit version of libarchive installed, while the rest of the drive is a 32 bit system. I uninstalled libarchive, and am now trying to reinstall a 32 bit version of it (and the packages that depended on it). pacman is giving me the following error message:

$ sudo pacman -r /mnt --cachedir /mnt/var/cache/pacman/pkg --config /mnt/etc/pacman.conf -S libarchive
error: failed to prepare transaction (package architecture is not valid)
:: package libarchive-3.1.2-8-x86_64 does not have a valid architecture

the system that I'm trying to repair it from is 64 bit, which may have something to do with this... how do I get it to install 32 bit packages?

Last edited by Maosn (2014-11-27 23:24:19)

berbae · 2014-11-28 11:11:49

~~[hand holding]~~
man pacman:

--arch <arch>
Specify an alternate architecture.

~~[/hand holding]~~
~~Really do you ask that?~~
With the --arch=i686, pacman should download the right package directly from the repository.

Last edited by berbae (2014-11-28 15:17:26)

Lone_Wolf · 2014-11-28 14:14:59

berbae, using that won't help Maosn . his architectue is i686, he just doesn't have a i686 libarchive package in that cache folder.

Maosn, search for the i686 libarchive page using the packages tab.
At the right of that page, you'll see an option called "download from mirror" .

Maosn · 2014-11-28 21:14:20

berbae, the architecture is specified in that config file, and I have tried using the --arch flag on the command line. As far as I know you're right, and that should tell pacman to download the right package, but for whatever reason it isn't working.

Anyway, I was able to get pacman working again using packages downloaded from this website, and used that to reinstall a bunch of libraries that seemed to have problems (a situation very similar to this: https://bbs.archlinux.org/viewtopic.php?id=167926). Vim is still a mess (totally my fault; I may or may not have forced pacman to reinstall it even though it told me there were file conflicts), but otherwise things appear to be working again.

Thanks for all the help everyone

Arch Linux

#1 2014-11-26 23:41:49

[SOLVED] pacman, tar, startx, and others not running after sys update

#2 2014-11-26 23:52:08

Re: [SOLVED] pacman, tar, startx, and others not running after sys update

#3 2014-11-27 00:01:34

Re: [SOLVED] pacman, tar, startx, and others not running after sys update

#4 2014-11-27 00:04:13

Re: [SOLVED] pacman, tar, startx, and others not running after sys update

#5 2014-11-27 00:25:41

Re: [SOLVED] pacman, tar, startx, and others not running after sys update

#6 2014-11-27 00:31:42

Re: [SOLVED] pacman, tar, startx, and others not running after sys update

#7 2014-11-27 00:48:52

Re: [SOLVED] pacman, tar, startx, and others not running after sys update

#8 2014-11-27 00:51:34

Re: [SOLVED] pacman, tar, startx, and others not running after sys update

#9 2014-11-27 00:57:58

Re: [SOLVED] pacman, tar, startx, and others not running after sys update

#10 2014-11-27 03:57:25

Re: [SOLVED] pacman, tar, startx, and others not running after sys update

#11 2014-11-27 23:17:05

Re: [SOLVED] pacman, tar, startx, and others not running after sys update

#12 2014-11-28 11:11:49

Re: [SOLVED] pacman, tar, startx, and others not running after sys update

#13 2014-11-28 14:14:59

Re: [SOLVED] pacman, tar, startx, and others not running after sys update

#14 2014-11-28 21:14:20

Re: [SOLVED] pacman, tar, startx, and others not running after sys update

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