Segfault installing AUR Packages

Watnuss · 2014-01-17 15:15:04

Hi,

I am running arch on my vserver and installed yaourt for AUR Package installation. Running a system update using # yaourt -Syua got me a segfault on an AUR package update. I wanted to reinstall the yaourt and package-query packages by hand and even get segfaults trying that. Normal pacman -Syu updates work just fine.

The error I get building the package using makepkg is:

/usr/bin/fakeroot: line 181: 18123 Segmentation fault      (core dumped) FAKEROOTKEY=$FAKEROOTKEY LD_LIBRARY_PATH="$PATHS" LD_PRELOAD="$LIB" "$@"
$ echo $?
139

A try without the usage of fakeroot (# makepkg --asroot):

Segmentation fault (core dumped)
# echo $?
139

Do you have any ideas what might causes this issue or what I can try to fix it? Where can I get the core dump to investigate the issue further?

Best regards and thanks for your help,

Watnuss

Spider.007 · 2014-01-17 17:39:50

makepkg is just a bash script (which I wouldn't expect to segfault); try running it with `bash -vv /usr/bin/makepkg` to see what binary is segfaulting.

WorMzy · 2014-01-17 18:02:10

Check the health of your disk and filesystem, then reinstall fakeroot (assuming they're healthy).

As a sidenote: you don't need yaourt to install packages from the AUR, 'pacman -U' will install packages whether they're official or 'homemade'.

Spider.007 · 2014-01-17 18:04:40

WorMzy wrote:

Check the health of your disk and filesystem, then reinstall fakeroot (assuming they're healthy).

The op states it fails without fakeroot too; and the reason fakeroot is in that message is probably because of what fakeroot actually executes otoh; it won't make things worse

Last edited by Spider.007 (2014-01-17 18:04:58)

jasonwryan · 2014-01-17 19:18:20

Not a Sysadmin issue, moving to AUR Issues...

Watnuss · 2014-01-18 08:50:53

Hi,

I know, that I don't need to use yaourt but nevertheless I cannot install packages manually as 'makepkg' fails by itself. That was the reason why yaourt installations didn't work in the first place.

I tried to get any information by calling makepkg with bash -vv but the logfiles don't include any further information. (http://pastebin.com/3qe9ejwB if you wanna check by yourself. I called it with '$ bash -vv /usr/bin/makepkg >& logfile)
(see http://pastebin.com/s49YxRDx for calling with '# bash -vv /usr/bin/makepkg --asroot >& logfile'. The segfault message wasn't included to the log but given to the command line even though I used >& for redirection.)

Do you have any further ideas?

Best regards and thanks so far.

Watnuss

Last edited by Watnuss (2014-01-18 08:55:28)

Spider.007 · 2014-01-18 15:40:49

From the log it seems du is responsible for the segfault; could you try `pacman -S coreutils` to make sure it's not corrupted? Also; by default the segfault should also end up in the systemd-journal; have a look at systemd-coredumpctl (as root) and let us know if any segfaults are logged there

Watnuss · 2014-01-19 09:07:10

Hi,

reinstalling coreutils didn't solve the issue. Makepkg still fails with the same error.
You can find the output of coredumpctl below (calls with uid 0 are makepkg --asroot and calls with uid 1000 are normal makepkg calls. Output with the parameter dump results in a blob. How can I get further information out of coredumpctl (didn't got the information from the manpages)

# systemd-coredumpctl
TIME                                         PID   UID   GID SIG EXE
              Tue 2014-01-07 19:52:57 CET  13537     0     0   7 /usr/bin/postconf
              Tue 2014-01-07 19:53:13 CET  13714     0     0  11 /usr/bin/bash
              Tue 2014-01-07 19:53:30 CET  14134     0     0  11 /usr/bin/bash
              Tue 2014-01-07 19:56:37 CET  14856     0     0  11 /usr/bin/bash
              Wed 2014-01-08 11:05:59 CET    551     0     0  11 /usr/bin/bash
              Thu 2014-01-09 17:59:42 CET  17576     0     0  11 /usr/bin/bash
              Thu 2014-01-09 18:00:14 CET  18052     0     0  11 /usr/bin/bash
              Sat 2014-01-11 17:17:13 CET   5473     0     0  11 /usr/bin/bash
              Fri 2014-01-17 15:50:15 CET  15003  1000  1000  11 /usr/bin/bash
              Fri 2014-01-17 15:54:21 CET  24771  1000  1000  11 /usr/bin/bash
              Fri 2014-01-17 15:59:18 CET   1238     0     0  11 /usr/bin/bash
              Fri 2014-01-17 15:59:38 CET   4158     0     0  11 /usr/bin/bash
              Fri 2014-01-17 16:03:37 CET   7847  1000  1000  11 /usr/bin/bash
              Fri 2014-01-17 16:05:56 CET  11969     0     0  11 /usr/bin/bash
              Fri 2014-01-17 16:06:41 CET  18123  1000  1000  11 /usr/bin/bash
              Sat 2014-01-18 09:31:56 CET  32561  1000  1000  11 /usr/bin/bash
              Sat 2014-01-18 09:32:21 CET   3217  1000  1000  11 /usr/bin/bash
              Sat 2014-01-18 09:32:45 CET   6339  1000  1000  11 /usr/bin/bash
              Sat 2014-01-18 09:33:54 CET  10745  1000  1000  11 /usr/bin/bash
              Sat 2014-01-18 09:34:11 CET  13603  1000  1000  11 /usr/bin/bash
              Sat 2014-01-18 09:35:22 CET  18052  1000  1000  11 /usr/bin/bash
              Sat 2014-01-18 09:35:30 CET   3625  1000  1000  11 /usr/bin/bash
              Sat 2014-01-18 09:36:38 CET  22721  1000  1000  11 /usr/bin/bash
              Sat 2014-01-18 09:36:52 CET  25511  1000  1000  11 /usr/bin/bash
              Sat 2014-01-18 09:38:48 CET  28919     0     0  11 /usr/bin/bash
              Sat 2014-01-18 09:39:03 CET  31675     0     0  11 /usr/bin/bash
              Sat 2014-01-18 09:39:58 CET   3213     0     0  11 /usr/bin/bash
              Sat 2014-01-18 09:41:49 CET  11315  1000  1000  11 /usr/bin/bash
              Sat 2014-01-18 09:43:45 CET  14733     0     0  11 /usr/bin/bash
              Sun 2014-01-19 09:21:27 CET  18613  1000  1000  11 /usr/bin/bash
              Sun 2014-01-19 09:22:23 CET  20312     0     0  11 /usr/bin/bash

Thanks for your help spider.

Watnuss

Spider.007 · 2014-01-19 10:20:17

This is very interesting; it seems bash is the one segfaulting. You can try `systemd-coredumpctl gdb 13714`; or use `systemd-coredumpctl dump 13714` to dump the coredump to disk; then upload it somewhere for someone else to look at (maybe I can tell what is happening from the output)

Watnuss · 2014-01-19 17:33:08

Calling 'systemd-coredumpctl gdb 13714' gives me an error:

# systemd-coredumpctl gdb 13714
TIME                                         PID   UID   GID SIG EXE
              Tue 2014-01-07 19:53:13 CET  13714     0     0  11 /usr/bin/bash
Failed to invoke gdb: No such file or directory
# echo $?
1

Writing the dump out to disk (using the -o parameter) gives the following file: http://watnuss.de/public/bash_segfault.dump

Watnuss · 2014-01-24 15:00:19

If noone has any further ideas I would appreciate any hints on what I could do and where I could ask else to resolve this issue. I don't really feel like reinstalling the system from scratch.

WorMzy · 2014-01-24 15:23:48

To be honest, I don't know what to do with dump files, and Spider seemed to have a better grasp of the situation than me, but I loaded it up with gdb and it gave the following output:

Core was generated by `/usr/bin/bash /usr/bin/makepkg --asroot -s -f -p ./PKGBUILD'.
Program terminated with signal 11, Segmentation fault.
#0  0x00007fadf95a72c8 in __collidx_table_lookup () from /usr/lib/libc.so.6

So I'd try reinstalling glibc.

Watnuss · 2014-01-24 15:28:31

Thanks for your answer WorMzy. Sadly reinstalling glibc didn't change anything.

Spider.007 · 2014-01-26 11:54:58

Well I found the same thing as WorMzy noted, glibc throwing strange errors. (it seems the collidx function does nothing special) Have you ever tried memtest86 on your machine? You could also have a look at mcelog to see if your processor has anything useful to tell.

Watnuss · 2014-01-27 14:27:16

Hi,

I was running memtest without any errors on a whole run using all test.
I installed and enabled the mcelog daemon. I checked outputs with 'mcelog --client' which didn't gave me any outputs. I hope that was the correct way to check MCEs.

Maybe it's time to forget about finding that rare error and reinstall the system. What do you think? (Don't want to waste your time any further.)

Best regards and thanks for your help.

Last edited by Watnuss (2014-01-27 14:27:47)

Spider.007 · 2014-01-28 17:28:25

Well; you're not wasting any time, it is an intriguing problem; but it's hard to debug.

For future reference; here is the backtrace from gdb:

#0  0x00007fadf95a72c8 in __collidx_table_lookup () from /usr/lib/libc.so.6
#1  0x00007fadf961d245 in get_next_seq () from /usr/lib/libc.so.6
#2  0x00007fadf961def7 in wcscoll_l () from /usr/lib/libc.so.6
#3  0x000000000047aa38 in ?? ()
#4  0x000000000043e77d in ?? ()
#5  0x00000000004486a4 in ?? ()
#6  0x00000000004496ef in ?? ()
#7  0x000000000044ac9c in ?? ()
#8  0x000000000044b1fe in ?? ()
#9  0x0000000000446035 in expand_string ()
#10 0x0000000000444f7e in ?? ()
#11 0x0000000000447c4b in ?? ()
#12 0x00000000004496ef in ?? ()
#13 0x000000000044a3c2 in ?? ()
#14 0x000000000044ac9c in ?? ()
#15 0x000000000044b0fa in expand_string_assignment ()
#16 0x0000000000444f7e in ?? ()
#17 0x000000000044536f in ?? ()
#18 0x000000000044bd26 in ?? ()
#19 0x000000000042b0c0 in ?? ()
#20 0x000000000042cbaa in execute_command_internal ()
#21 0x000000000042c9e9 in execute_command_internal ()
#22 0x000000000042e12e in execute_command ()
.....
#138 0x000000000042e12e in execute_command ()
#139 0x00000000004192b3 in reader_loop ()
#140 0x000000000041793e in main ()

Miha · 2014-02-05 13:54:45

My machine (VM) also segfaults on bash. I couldnt even login. I had to change default shell to zsh.

tobias_ · 2014-02-08 13:33:58

It also happens for me, I'm not sure why, but it seems to be connected to the locale. My default locale is de_DE.utf8, when I switch to en_US.utf8 or C, i.e. "LANG=C makepkg", it works.1

Watnuss · 2014-02-08 13:59:07

Thanks tobias_,

[edit: double thanks actually as I was just making a backup to reinstall the server. This won't be necessary now I guess. So really HUGE thanks as you save me a lot of time.]

I was able to build the packages setting the LANG variable to 'C'. Setting it to 'en_US.UTF-8', which I originally had, still results in the segfault above.

Can anyone explain this behaviour?

Last edited by Watnuss (2014-02-08 14:00:40)

x33a · 2014-02-08 14:05:55

This is probably a bug. You should report this on the Arch bugtracker.

tobias_ · 2014-02-08 23:55:02

I found the source of the issue: I did not generate locales with locale-gen for de-DE.UTF-8
I'm not sure if segfaulting applications is a wanted or buggy behaviour then…

WorMzy · 2014-02-08 23:57:28

Someone did find a similar locale bug with pacman/makepkg a while back. I'll see if I can find the related topic.

I'll also say the archivist's name three times into a mirror in three minutes time (midnight here) and see if he appears with the link.

EDIT: Er, I think it worked.. https://bbs.archlinux.org/viewtopic.php?id=173500

Last edited by WorMzy (2014-02-09 00:01:08)

Arch Linux

#1 2014-01-17 15:15:04

Segfault installing AUR Packages

#2 2014-01-17 17:39:50

Re: Segfault installing AUR Packages

#3 2014-01-17 18:02:10

Re: Segfault installing AUR Packages

#4 2014-01-17 18:04:40

Re: Segfault installing AUR Packages

#5 2014-01-17 19:18:20

Re: Segfault installing AUR Packages

#6 2014-01-18 08:50:53

Re: Segfault installing AUR Packages

#7 2014-01-18 15:40:49

Re: Segfault installing AUR Packages

#8 2014-01-19 09:07:10

Re: Segfault installing AUR Packages

#9 2014-01-19 10:20:17

Re: Segfault installing AUR Packages

#10 2014-01-19 17:33:08

Re: Segfault installing AUR Packages

#11 2014-01-24 15:00:19

Re: Segfault installing AUR Packages

#12 2014-01-24 15:23:48

Re: Segfault installing AUR Packages

#13 2014-01-24 15:28:31

Re: Segfault installing AUR Packages

#14 2014-01-26 11:54:58

Re: Segfault installing AUR Packages

#15 2014-01-27 14:27:16

Re: Segfault installing AUR Packages

#16 2014-01-28 17:28:25

Re: Segfault installing AUR Packages

#17 2014-02-05 13:54:45

Re: Segfault installing AUR Packages

#18 2014-02-08 13:33:58

Re: Segfault installing AUR Packages

#19 2014-02-08 13:59:07

Re: Segfault installing AUR Packages

#20 2014-02-08 14:05:55

Re: Segfault installing AUR Packages

#21 2014-02-08 23:55:02

Re: Segfault installing AUR Packages

#22 2014-02-08 23:57:28

Re: Segfault installing AUR Packages

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