Bug#633406: dpkg-shlibdeps: error: couldn't find library libc.so.6
Jameson Graef Rollins
Version: 1.16.0.3
Severity: normal
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
For some reason I have recently been unable to build packages linked
against libc.so.6 or libpthread.so.0 because dpkg-shlibdeps keeps
failing with the following errors:
...
dh_shlibdeps
dpkg-shlibdeps: error: couldn't find library libpthread.so.0 needed by debian/notmuch/usr/bin/notmuch (ELF format: 'elf64-x86-64'; RPATH: '').
dpkg-shlibdeps: error: couldn't find library libc.so.6 needed by debian/notmuch/usr/bin/notmuch (ELF format: 'elf64-x86-64'; RPATH: '').
dpkg-shlibdeps: error: Cannot continue due to the errors listed above.
Note: libraries are not searched in other binary packages that do not have any shlibs or symbols file.
To help dpkg-shlibdeps find private libraries, you might need to set LD_LIBRARY_PATH.
dh_shlibdeps: dpkg-shlibdeps -Tdebian/notmuch.substvars debian/notmuch/usr/bin/notmuch returned exit code 2
make: *** [binary] Error 2
dpkg-buildpackage: error: fakeroot debian/rules binary gave error exit status 2
debuild: fatal error at line 1340:
dpkg-buildpackage -rfakeroot -D -us -uc -i -I failed
gbp:error: debuild -i -I returned 29
gbp:error: Couldn't run 'debuild -i -I -us -uc'
This is just one example, but I have other packages that are failing
to build with the same error. This has been going on for about a
month now, after just starting at some point, presumably due to some
upgrade that I didn't pay attention too.
This may very well be a bug in libc6 or libc6-i386 (both of which are
installed on my system) since both libpthread.so.0 and libc.so.6 are
provided by those packages (although in different paths).
I really don't know what's going on here, and nor does anyone else
I've ask. Please advise. Any debugging help would be much
appreciated.
Thanks so much for the help.
jamie.
- -- System Information:
Debian Release: wheezy/sid
APT prefers testing
APT policy: (600, 'testing'), (500, 'unstable'), (101, 'experimental')
Architecture: amd64 (x86_64)
Kernel: Linux 2.6.38-2-amd64 (SMP w/4 CPU cores)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Versions of packages dpkg-dev depends on:
ii base-files 6.3 Debian base system miscellaneous f
ii binutils 2.21.52.20110606-2 The GNU assembler, linker and bina
ii bzip2 1.0.5-6 high-quality block-sorting file co
ii libdpkg-perl 1.16.0.3 Dpkg perl modules
ii make 3.81-8.1 An utility for Directing compilati
ii patch 2.6.1-2 Apply a diff file to an original
ii xz-utils 5.0.0-2 XZ-format compression utilities
Versions of packages dpkg-dev recommends:
ii build-essential 11.5 Informational list of build-essent
ii fakeroot 1.16-1 tool for simulating superuser priv
ii gcc [c-compiler] 4:4.6.0-6 GNU C compiler
ii gcc-4.4 [c-compiler] 4.4.6-6 GNU C compiler
ii gcc-4.5 [c-compiler] 4.5.3-3 The GNU C compiler
ii gcc-4.6 [c-compiler] 4.6.1-1 GNU C compiler
ii gnupg 1.4.11-3 GNU privacy guard - a free PGP rep
ii gpgv 1.4.11-3 GNU privacy guard - signature veri
ii libalgorithm-merge-perl 0.08-2 Perl module for three-way merge of
Versions of packages dpkg-dev suggests:
ii debian-keyring 2011.03.03 GnuPG keys of Debian Developers
- -- no debconf information
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Jonathan Nieder
Jameson Graef Rollins wrote:
> dpkg-shlibdeps: error: couldn't find library libpthread.so.0 needed by debian/notmuch/usr/bin/notmuch (ELF format: 'elf64-x86-64'; RPATH: '').
What does
ldd debian/notmuch/usr/bin/notmuch
say?
Thanks for reporting,
Jonathan
Jameson Graef Rollins
> What does
>
> ldd debian/notmuch/usr/bin/notmuch
>
> say?
Hey, Jonathan. I think this is what you're looking for (gbp specifies
./debian-build as the export-dir):
servo:~/src/notmuch/git [personal] 0$ ldd debian-build/notmuch-0.6/debian/notmuch/usr/bin/notmuch
linux-vdso.so.1 => (0x00007fff41f5d000)
libnotmuch.so.1 => /usr/lib/libnotmuch.so.1 (0x00007f7fa1f7b000)
libgmime-2.4.so.2 => /usr/lib/libgmime-2.4.so.2 (0x00007f7fa1d15000)
libgobject-2.0.so.0 => /usr/lib/libgobject-2.0.so.0 (0x00007f7fa1ac2000)
libglib-2.0.so.0 => /lib/libglib-2.0.so.0 (0x00007f7fa17d1000)
libtalloc.so.2 => /usr/lib/libtalloc.so.2 (0x00007f7fa15c7000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f7fa13aa000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f7fa1027000)
libxapian.so.22 => /usr/lib/libxapian.so.22 (0x00007f7fa0c09000)
libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007f7fa08fe000)
libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f7fa06e8000)
libgmodule-2.0.so.0 => /usr/lib/libgmodule-2.0.so.0 (0x00007f7fa04e5000)
libgthread-2.0.so.0 => /usr/lib/libgthread-2.0.so.0 (0x00007f7fa02e0000)
librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f7fa00d8000)
libz.so.1 => /usr/lib/libz.so.1 (0x00007f7f9fec1000)
libnsl.so.1 => /lib/x86_64-linux-gnu/libnsl.so.1 (0x00007f7f9fca8000)
libpcre.so.3 => /lib/libpcre.so.3 (0x00007f7f9fa6d000)
/lib64/ld-linux-x86-64.so.2 (0x00007f7fa21b5000)
libuuid.so.1 => /lib/libuuid.so.1 (0x00007f7f9f868000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f7f9f5e6000)
libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f7f9f3e2000)
servo:~/src/notmuch/git [personal] 0$
Both the libc.so.0 and libpthread.so.0 libraries exist on my system:
servo:~ 0$ ls -al /lib/x86_64-linux-gnu/libc.so.6 /lib/x86_64-linux-gnu/libpthread.so.0
lrwxrwxrwx 1 root root 12 Jun 12 12:38 /lib/x86_64-linux-gnu/libc.so.6 -> libc-2.13.so
lrwxrwxrwx 1 root root 18 Jun 12 12:38 /lib/x86_64-linux-gnu/libpthread.so.0 -> libpthread-2.13.so
servo:~ 0$
Please let me know what other info I can provide.
jamie.
Raphael Hertzog
> Package: dpkg-dev
> Version: 1.16.0.3
> Severity: normal
>
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA256
>
> For some reason I have recently been unable to build packages linked
> against libc.so.6 or libpthread.so.0 because dpkg-shlibdeps keeps
> failing with the following errors:
>
> ...
> dh_shlibdeps
> dpkg-shlibdeps: error: couldn't find library libpthread.so.0 needed by debian/notmuch/usr/bin/notmuch (ELF format: 'elf64-x86-64'; RPATH: '').
> dpkg-shlibdeps: error: couldn't find library libc.so.6 needed by debian/notmuch/usr/bin/notmuch (ELF format: 'elf64-x86-64'; RPATH: '').
If that error was more than a local problem, we would have noticed it by
now. :-)
Please paste the output of the failing dpkg-shlibdeps run with "-v -v".
And also paste the output of this:
$ ls -al /etc/ld.so.conf*
$ cat /etc/ld.so.conf
$ cat /etc/ld.so.conf.d/x86_64-linux-gnu.conf
> This is just one example, but I have other packages that are failing
> to build with the same error. This has been going on for about a
> month now, after just starting at some point, presumably due to some
> upgrade that I didn't pay attention too.
How are you building your packages ? Are they built in the same environment
that you used to report your bug ?
Cheers,
--
Raphaël Hertzog ◈ Debian Developer
Follow my Debian News ▶ http://RaphaelHertzog.com (English)
▶ http://RaphaelHertzog.fr (Français)
Jameson Graef Rollins
> If that error was more than a local problem, we would have noticed it by
> now. :-)
Maybe, or I'm just the first person to report it.
> Please paste the output of the failing dpkg-shlibdeps run with "-v -v".
Output of the following attached below:
servo:~/src/notmuch/git [personal] 0$ dpkg-shlibdeps -v -v debian-build/notmuch-0.6/debian/notmuch/usr/bin/notmuch &> dpkgs-shlibdeps.output
servo:~/src/notmuch/git [personal] 2$
>
> And also paste the output of this:
> $ ls -al /etc/ld.so.conf*
> $ cat /etc/ld.so.conf
> $ cat /etc/ld.so.conf.d/x86_64-linux-gnu.conf
servo:~ 0$ ls -al /etc/ld.so.conf*
-rw-r--r-- 1 root root 34 Apr 14 13:15 /etc/ld.so.conf
/etc/ld.so.conf.d:
total 28
drwxr-xr-x 2 root root 4096 Jul 6 08:21 .
drwxr-xr-x 159 root root 12288 Jul 10 02:13 ..
-rw-r--r-- 1 root root 64 Jan 31 17:01 i486-linux-gnu.conf
-rw-r--r-- 1 root root 44 Jan 31 14:27 libc.conf
-rw-r--r-- 1 root root 56 Jun 12 12:38 zz_i386-biarch-compat.conf
servo:~ 0$ cat /etc/ld.so.conf
include /etc/ld.so.conf.d/*.conf
servo:~ 0$ cat /etc/ld.so.conf.d/x86_64-linux-gnu.conf
cat: /etc/ld.so.conf.d/x86_64-linux-gnu.conf: No such file or directory
servo:~ 1$ cat /etc/ld.so.conf.d/i486-linux-gnu.conf
# Multiarch support
/lib/i486-linux-gnu
/usr/lib/i486-linux-gnu
servo:~ 0$
So that last bit looks very suspicious to me. Should I not have the
x86_64-linux-gnu.conf file? dpkg also doesn't seem to know where
/etc/ld.so.conf.d/i486-linux-gnu.conf came from.
I unfortunately don't understand what's going on with all of this
multiarch stuff, which I assume is at the root of the issues here.
> How are you building your packages ? Are they built in the same environment
> that you used to report your bug ?
It depends on the package, but git-buildpackage was what was used in the
reported example. And yes, they are built in the same environment that
the bug was reported from. I am not currently using any sort of special
build environment.
jamie.
Jonathan Nieder
reassign 633406 libc6
tags 633406 + moreinfo
quit
Raphaël Hertzog wrote:
> On Sun, 10 Jul 2011, Jameson Graef Rollins wrote:
>> Maybe, or I'm just the first person to report it.
>
> If all builds were failing since a month, we would have noticed it. :-)
That's true. But an upgrade path somewhere or some documentation
could be broken. Since it is not clear to me that this bug has been
fixed in Debian, I'm reopening it (after all, "it's definitely not a
bug in dpkg" is not a reason to close a bug against the Debian OS).
Jamie, I'm tagging the bug moreinfo because I'm having trouble
imagining how this system came to be the way it is and that would be
important information for solving it. Do you know when this started
happening? Was there an upgrade or something soon before? Are there
other libc-related symptoms showing up? What are the versions of all
installed 'libc*' packages, and have you ever installed a version of
libc from another architecture or outside the packaging system?
Please feel free to send relevant logs to help with investigating.
Thanks and regards,
Jonathan
Jameson Graef Rollins
> What version of libc6 do you have? Please show me the output of "dpkg
> -s libc6".
I've got 2.13-7 installed.
> $ dpkg -S /etc/ld.so.conf.d/x86_64-linux-gnu.conf
> libc6: /etc/ld.so.conf.d/x86_64-linux-gnu.conf
>
> $ sudo dpkg -Gi --force-confmiss /var/cache/apt/archives/libc6_*.deb
Ah! dpkg noticed the x86_64-linux-gnu.conf was missing and reinstalled
it, which seems to have fixed the problem. Thanks so much, Raphael.
> Something removed that file and created all your problems. It might be
> libc6-i386 that did something wrong at some point. Not sure. Anyway
> reinstalling that file will fix your problem, it's definitely not a bug in
> dpkg.
Very strange. I wonder if it was something in the multiarch
transition. In any event, it seems to be fixed for me now. Thank you
very much for the help.
jamie.
Jonathan Nieder
> And even if there's something, it's not going to show up in a
> squeeeze->wheezy upgrade, it would be more likely a problem with an
> upgrade to a broken version that did not exist for very long.
Which would be, well, a bug, right?
I'm sorry, this kind of attitude seems really demotivating to me. I
don't understand what you think being dismissive and antagonistic to
people before a bug has been well understood nor much time passed
accomplishes.
Jonathan Nieder
Jameson Graef Rollins wrote:
> On Sun, 10 Jul 2011 20:47:11 +0200, Raphael Hertzog <her...@debian.org> wrote:
>> $ sudo dpkg -Gi --force-confmiss /var/cache/apt/archives/libc6_*.deb
>
> Ah! dpkg noticed the x86_64-linux-gnu.conf was missing and reinstalled
> it, which seems to have fixed the problem. Thanks so much, Raphael.
Could you grep through /var/log/dpkg.log* for the upgrade history of
libc6? I would like to learn what caused this so we can prevent it
from happening again.
To others: sorry for the noise.
Jameson Graef Rollins
> Could you grep through /var/log/dpkg.log* for the upgrade history of
> libc6? I would like to learn what caused this so we can prevent it
> from happening again.
Hi, Jonathan. Thanks for trying to figure this out. I believe I
started noticing the problem around 06-24 [0]. My dpkg log [1] shows
that on the 24th I did an upgrade that appears to have sequentially
applied versions 2.13-4 and 2.13-7 of both libc6-dev and libc6-i386.
libc6 itself was updated to 2.13-7 the next day (06-25).
Please let me know if there's anything else I can do to help solve the
mystery.
jamie.
[0]
http://mid.gmane.org/87y60qb...@servo.factory.finestructure.net
[1]
servo:~ 0$ grep libc6 /var/log/dpkg.log* | sort -u
/var/log/dpkg.log.1:2011-06-24 15:45:35 status half-configured libc6-dev 2.13-4
/var/log/dpkg.log.1:2011-06-24 15:45:35 status half-configured libc6-i386 2.13-4
/var/log/dpkg.log.1:2011-06-24 15:45:35 status half-installed libc6-dev 2.13-4
/var/log/dpkg.log.1:2011-06-24 15:45:35 status half-installed libc6-i386 2.13-4
/var/log/dpkg.log.1:2011-06-24 15:45:35 status unpacked libc6-dev 2.13-4
/var/log/dpkg.log.1:2011-06-24 15:45:35 status unpacked libc6-i386 2.13-4
/var/log/dpkg.log.1:2011-06-24 15:45:35 status unpacked libc6-i386 2.13-7
/var/log/dpkg.log.1:2011-06-24 15:45:35 upgrade libc6-dev 2.13-4 2.13-7
/var/log/dpkg.log.1:2011-06-24 15:45:35 upgrade libc6-i386 2.13-4 2.13-7
/var/log/dpkg.log.1:2011-06-24 15:45:36 status half-installed libc6-dev 2.13-4
/var/log/dpkg.log.1:2011-06-24 15:45:36 status unpacked libc6-dev 2.13-7
/var/log/dpkg.log.1:2011-06-24 15:45:38 status half-configured libc6 2.13-4
/var/log/dpkg.log.1:2011-06-24 15:45:38 status half-installed libc6 2.13-4
/var/log/dpkg.log.1:2011-06-24 15:45:38 status unpacked libc6 2.13-4
/var/log/dpkg.log.1:2011-06-24 15:45:38 status unpacked libc6 2.13-7
/var/log/dpkg.log.1:2011-06-24 15:45:38 upgrade libc6 2.13-4 2.13-7
/var/log/dpkg.log.1:2011-06-24 15:45:39 configure libc6 2.13-7 <none>
/var/log/dpkg.log.1:2011-06-24 15:45:39 status half-configured libc6 2.13-7
/var/log/dpkg.log.1:2011-06-24 15:45:39 status unpacked libc6 2.13-7
/var/log/dpkg.log.1:2011-06-24 15:45:40 status installed libc6 2.13-7
/var/log/dpkg.log.1:2011-06-24 15:46:06 configure libc6-i386 2.13-7 <none>
/var/log/dpkg.log.1:2011-06-24 15:46:06 status half-configured libc6-i386 2.13-7
/var/log/dpkg.log.1:2011-06-24 15:46:06 status unpacked libc6-i386 2.13-7
/var/log/dpkg.log.1:2011-06-24 15:46:07 configure libc6-dev 2.13-7 <none>
/var/log/dpkg.log.1:2011-06-24 15:46:07 status half-configured libc6-dev 2.13-7
/var/log/dpkg.log.1:2011-06-24 15:46:07 status installed libc6-dev 2.13-7
/var/log/dpkg.log.1:2011-06-24 15:46:07 status installed libc6-i386 2.13-7
/var/log/dpkg.log.1:2011-06-24 15:46:07 status unpacked libc6-dev 2.13-7
/var/log/dpkg.log.1:2011-06-25 11:12:05 status half-configured libc6 2.13-7
/var/log/dpkg.log.1:2011-06-25 11:12:05 status half-installed libc6 2.13-7
/var/log/dpkg.log.1:2011-06-25 11:12:05 status unpacked libc6 2.13-7
/var/log/dpkg.log.1:2011-06-25 11:12:05 upgrade libc6 2.13-7 2.13-7
/var/log/dpkg.log.1:2011-06-25 11:12:06 configure libc6 2.13-7 <none>
/var/log/dpkg.log.1:2011-06-25 11:12:06 status half-configured libc6 2.13-7
/var/log/dpkg.log.1:2011-06-25 11:12:06 status unpacked libc6 2.13-7
/var/log/dpkg.log.1:2011-06-25 11:12:07 status installed libc6 2.13-7
/var/log/dpkg.log.1:2011-06-25 11:17:31 status installed libc6-i386 2.13-7
/var/log/dpkg.log.1:2011-06-25 11:17:32 purge libc6-i386 2.13-7 <none>
/var/log/dpkg.log.1:2011-06-25 11:17:32 remove libc6-i386 2.13-7 <none>
/var/log/dpkg.log.1:2011-06-25 11:17:32 status config-files libc6-i386 2.13-7
/var/log/dpkg.log.1:2011-06-25 11:17:32 status half-configured libc6-i386 2.13-7
/var/log/dpkg.log.1:2011-06-25 11:17:32 status half-installed libc6-i386 2.13-7
/var/log/dpkg.log.1:2011-06-25 11:17:32 status installed libc6-i386 2.13-7
/var/log/dpkg.log.1:2011-06-25 11:17:32 status not-installed libc6-i386 <none>
/var/log/dpkg.log:2011-07-06 08:21:33 install libc6-i386 <none> 2.13-7
/var/log/dpkg.log:2011-07-06 08:21:33 status half-installed libc6-i386 2.13-7
/var/log/dpkg.log:2011-07-06 08:21:33 status unpacked libc6-i386 2.13-7
/var/log/dpkg.log:2011-07-06 08:21:34 configure libc6-i386 2.13-7 <none>
/var/log/dpkg.log:2011-07-06 08:21:34 status half-configured libc6-i386 2.13-7
/var/log/dpkg.log:2011-07-06 08:21:34 status installed libc6-i386 2.13-7
/var/log/dpkg.log:2011-07-06 08:21:34 status unpacked libc6-i386 2.13-7
/var/log/dpkg.log:2011-07-10 11:54:13 status half-configured libc6 2.13-7
/var/log/dpkg.log:2011-07-10 11:54:13 status half-installed libc6 2.13-7
/var/log/dpkg.log:2011-07-10 11:54:13 status unpacked libc6 2.13-7
/var/log/dpkg.log:2011-07-10 11:54:13 upgrade libc6 2.13-7 2.13-7
/var/log/dpkg.log:2011-07-10 11:54:14 configure libc6 2.13-7 2.13-7
/var/log/dpkg.log:2011-07-10 11:54:14 status half-configured libc6 2.13-7
/var/log/dpkg.log:2011-07-10 11:54:14 status half-installed libc6 2.13-7
/var/log/dpkg.log:2011-07-10 11:54:14 status unpacked libc6 2.13-7
/var/log/dpkg.log:2011-07-10 11:54:15 status installed libc6 2.13-7
/var/log/dpkg.log:2011-07-10 11:58:07 configure libc6-i386 2.13-7 2.13-7
/var/log/dpkg.log:2011-07-10 11:58:07 status half-configured libc6-i386 2.13-7
/var/log/dpkg.log:2011-07-10 11:58:07 status half-installed libc6-i386 2.13-7
/var/log/dpkg.log:2011-07-10 11:58:07 status installed libc6-i386 2.13-7
/var/log/dpkg.log:2011-07-10 11:58:07 status unpacked libc6-i386 2.13-7
/var/log/dpkg.log:2011-07-10 11:58:07 upgrade libc6-i386 2.13-7 2.13-7
servo:~ 0$