Ubuntu – Segmentation fault dpkg: error processing package libc-bin (–configure)

aptdpkg

Similar/maybe the same error at dpkg: error processing package libc-bin (–configure).

Although my example below is for sudo apt-get install, note that it also happens for the commands

  • sudo apt-get -f install
  • sudo apt-get upgrade
  • sudo apt-get autoremove
  • sudo dpkg --configure -a
  • and maybe a few other more

I am working with the Ubuntu 16.04 with ARM 64-bit architecture (on Jetson TX2 board). Help on resolving the segmentation fault would be very much appreciated. Since I cannot even install new software (due to this issue), help on ignoring the upgrades would also be appreciated. I am quite unfamiliar with linux, so please do try to answer accordingly. Thanks.

sudo apt-get install
Reading package lists... Done
Building dependency tree
Reading state information... Done
0 upgraded, 0 newly installed, 0 to remove and 12 not upgraded.
1 not fully installed or removed.
After this operation, 0 B of additional disk space will be used.
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
        LANGUAGE = (unset),
        LC_ALL = (unset),
        LANG = "en_US.UTF-8"
    are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
locale: Cannot set LC_CTYPE to default locale: No such file or directory
locale: Cannot set LC_MESSAGES to default locale: No such file or directory
locale: Cannot set LC_ALL to default locale: No such file or directory
Setting up libc-bin (2.23-0ubuntu7) ...
Segmentation fault (core dumped)
/sbin/ldconfig.real: Path `/usr/lib/aarch64-linux-gnu/tegra' given more than once
/sbin/ldconfig.real: Path `/lib/aarch64-linux-gnu' given more than once
/sbin/ldconfig.real: Path `/usr/lib/aarch64-linux-gnu' given more than once
/lib/aarch64-linux-gnu:
        libssl.so.1.0.0 -> libssl.so.1.0.0
        libapparmor.so.1 -> libapparmor.so.1.4.0
        libiw.so.30 -> libiw.so.30
        liblvm2app.so.2.2 -> liblvm2app.so.2.2
        libcryptsetup.so.4 -> libcryptsetup.so.4.6.0
        libnss_mdns4.so.2 -> libnss_mdns4.so.2
        libusb-1.0.so.0 -> libusb-1.0.so.0.1.0
        libnss_files.so.2 -> libnss_files-2.23.so
        libhistory.so.6 -> libhistory.so.6.3
        libbrlapi.so.0.6 -> libbrlapi.so.0.6.4
        libatasmart.so.4 -> libatasmart.so.4.0.5
        libBrokenLocale.so.1 -> libBrokenLocale-2.23.so
        libdevmapper.so.1.02.1 -> libdevmapper.so.1.02.1
        libsystemd.so.0 -> libsystemd.so.0.14.0
        libcrypto.so.1.0.0 -> libcrypto.so.1.0.0
        libxtables.so.11 -> libxtables.so.11.0.0
        libwrap.so.0 -> libwrap.so.0.7.6
        libnih.so.1 -> libnih.so.1.0.0
        libnss_mdns6_minimal.so.2 -> libnss_mdns6_minimal.so.2
        libiptc.so.0 -> libiptc.so.0.0.0
        libisc-export.so.160 -> libisc-export.so.160.0.0
        libprocps.so.4 -> libprocps.so.4.0.0
        libaudit.so.1 -> libaudit.so.1.0.0
        libpam_misc.so.0 -> libpam_misc.so.0.82.0
        libnss_mdns.so.2 -> libnss_mdns.so.2
        libpci.so.3 -> libpci.so.3.3.1
        libgcc_s.so.1 -> libgcc_s.so.1
        libgcrypt.so.20 -> libgcrypt.so.20.0.5
        libpcsclite.so.1 -> libpcsclite.so.1.0.0
        liblzo2.so.2 -> liblzo2.so.2.0.0
        libnss_hesiod.so.2 -> libnss_hesiod-2.23.so
        libusb-0.1.so.4 -> libusb-0.1.so.4.4.4
        libseccomp.so.2 -> libseccomp.so.2.2.3
        libreadline.so.6 -> libreadline.so.6.3
        liblzma.so.5 -> liblzma.so.5.0.0
        libnewt.so.0.52 -> libnewt.so.0.52.18
        libacl.so.1 -> libacl.so.1.1.0
        libss.so.2 -> libss.so.2.0
        libpopt.so.0 -> libpopt.so.0.0.0
        libudev.so.1 -> libudev.so.1.6.4
        libdns-export.so.162 -> libdns-export.so.162.1.3
        libmemusage.so -> libmemusage.so
        libpcprofile.so -> libpcprofile.so
        libthread_db.so.1 -> libthread_db-1.0.so
        librt.so.1 -> librt-2.23.so
        libpthread.so.0 -> libpthread-2.23.so
        libreadline.so.5 -> libreadline.so.5.2
        libcrypt.so.1 -> libcrypt-2.23.so
        libncurses.so.5 -> libncurses.so.5.9
        libkeyutils.so.1 -> libkeyutils.so.1.5
        libz.so.1 -> libz.so.1.2.8
        libexpat.so.1 -> libexpat.so.1.6.0
        libply-splash-graphics.so.4 -> libply-splash-graphics.so.4.0.0
        libnss_nis.so.2 -> libnss_nis-2.23.so
        libparted.so.2 -> libparted.so.2.0.1
        libnss_nisplus.so.2 -> libnss_nisplus-2.23.so
        libnih-dbus.so.1 -> libnih-dbus.so.1.0.0
        libcidn.so.1 -> libcidn-2.23.so
        libnss_mdns4_minimal.so.2 -> libnss_mdns4_minimal.so.2
        libply-splash-core.so.4 -> libply-splash-core.so.4.0.0
        libjson-c.so.2 -> libjson-c.so.2.0.0
        libsepol.so.1 -> libsepol.so.1
/sbin/ldconfig.real: /lib/aarch64-linux-gnu/ld-2.23.so is the dynamic linker, ignoring

        ld-linux-aarch64.so.1 -> ld-2.23.so
        libslang.so.2 -> libslang.so.2.3.0
        libkmod.so.2 -> libkmod.so.2.3.0
        libhistory.so.5 -> libhistory.so.5.2
        libfdisk.so.1 -> libfdisk.so.1.1.0
        libply-boot-client.so.4 -> libply-boot-client.so.4.0.0
        libm.so.6 -> libm-2.23.so
        libselinux.so.1 -> libselinux.so.1
        libpamc.so.0 -> libpamc.so.0.82.1
        libglib-2.0.so.0 -> libglib-2.0.so.0.4800.2
        libatm.so.1 -> libatm.so.1.0.0
        libnl-3.so.200 -> libnl-3.so.200.22.0
        libparted-fs-resize.so.0 -> libparted-fs-resize.so.0.0.1
        libsmartcols.so.1 -> libsmartcols.so.1.1.0
        libip4tc.so.0 -> libip4tc.so.0.1.0
        libmount.so.1 -> libmount.so.1.1.0
        libntfs-3g.so.861 -> libntfs-3g.so.861.0.0
        libcgmanager.so.0 -> libcgmanager.so.0.0.0
        libtinfo.so.5 -> libtinfo.so.5.9
        libmnl.so.0 -> libmnl.so.0.1.0
        liblvm2cmd.so.2.02 -> liblvm2cmd.so.2.02
        libresolv.so.2 -> libresolv-2.23.so
        libpng12.so.0 -> libpng12.so.0.54.0
        libdl.so.2 -> libdl-2.23.so
        libply.so.4 -> libply.so.4.0.0
        libgpg-error.so.0 -> libgpg-error.so.0.17.0
        libanl.so.1 -> libanl-2.23.so
        libcap.so.2 -> libcap.so.2.24
        libpcre.so.3 -> libpcre.so.3.13.2
        libnss_compat.so.2 -> libnss_compat-2.23.so
        libattr.so.1 -> libattr.so.1.1.0
        libnss_dns.so.2 -> libnss_dns-2.23.so
        libtirpc.so.1 -> libtirpc.so.1.0.10
        libdevmapper-event-lvm2.so.2.02 -> libdevmapper-event-lvm2.so.2.02
        libfuse.so.2 -> libfuse.so.2.9.4
        libncursesw.so.5 -> libncursesw.so.5.9
        libnss_mdns_minimal.so.2 -> libnss_mdns_minimal.so.2
        libdevmapper-event.so.1.02.1 -> libdevmapper-event.so.1.02.1
        libc.so.6 -> libc-2.23.so
        libdbus-1.so.3 -> libdbus-1.so.3.14.6
        libutil.so.1 -> libutil-2.23.so
        libnss_mdns6.so.2 -> libnss_mdns6.so.2
        libcom_err.so.2 -> libcom_err.so.2.1
        libuuid.so.1 -> libuuid.so.1.3.0
        libbz2.so.1.0 -> libbz2.so.1.0.4
        libulockmgr.so.1 -> libulockmgr.so.1.0.1
        libe2p.so.2 -> libe2p.so.2.3
        libnsl.so.1 -> libnsl-2.23.so
        libpam.so.0 -> libpam.so.0.83.1
        libip6tc.so.0 -> libip6tc.so.0.1.0
        libbsd.so.0 -> libbsd.so.0.8.2
        libnl-genl-3.so.200 -> libnl-genl-3.so.200.22.0
        libblkid.so.1 -> libblkid.so.1.1.0
        libSegFault.so -> libSegFault.so
        libext2fs.so.2 -> libext2fs.so.2.4
/usr/lib/aarch64-linux-gnu:
Segmentation fault (core dumped)
dpkg: error processing package libc-bin (--configure):
 subprocess installed post-installation script returned error exit status 139
Errors were encountered while processing:
 libc-bin
E: Sub-process /usr/bin/dpkg returned an error code (1)

Best Answer

I don't think it would have been easy for anyone to figure this one out.

I was trying to install cudnn onto the Jetson without JetPack flashing. I used the information found at How can I install CuDNN on Ubuntu 16.04?.

Unfortunately the symbolic links maintained must have caused some trouble (as we can probably tell from the ldconfig having problems). I have since removed those copied files as well as the original. This resolves the segmentation fault.

edit:

In response to the comment below, I'll provide example commands I made. Do keep in mind, though, that my problem is somewhat specific to me. I happened to copy over files to certain directories while maintaining the symbolic links (via cp -P). So it's unlikely those example commands will help you. Though regardless, I suspect it has to do with the symbolic links being messed up somewhere.

$ rm /usr/include/cudnn.h
$ rm /usr/lib/x86_64-linux-gnu/libcudnn*