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Thread: apt-get -y upgrade fails apt-get -y dist-upgrade fails

  1. #1
    Join Date
    2016-Nov
    Location
    Dallas, TX USA
    Posts
    2

    apt-get -y upgrade fails apt-get -y dist-upgrade fails

    I have had this problem before, and the only solution was a new install. I'd like to find a better solution.

    I am running Kali in a virtual (VMware 12.5.1 build 4542065) environment on Windows 8.1.
    I last patched about 2 weeks ago.

    # cat /etc/*release*
    DISTRIB_ID=Kali
    DISTRIB_RELEASE=kali-rolling
    DISTRIB_CODENAME=kali-rolling
    DISTRIB_DESCRIPTION="Kali GNU/Linux Rolling"
    PRETTY_NAME="Kali GNU/Linux Rolling"
    NAME="Kali GNU/Linux"
    ID=kali
    VERSION="2016.2"
    VERSION_ID="2016.2"
    ID_LIKE=debian
    ANSI_COLOR="1;31"
    HOME_URL="http://www.kali.org/"
    SUPPORT_URL="http://forums.kali.org/"
    BUG_REPORT_URL="http://bugs.kali.org/"


    Took a snapshot, then booted

    I ran
    apt-get update
    apt-get -y upgrade -d
    (completes OK)
    apt-get -y upgrade

    it says:
    apt-get -y upgrade
    Reading package lists... Done
    Building dependency tree
    Reading state information... Done
    Calculating upgrade... Done
    The following packages were automatically installed and are no longer required:
    iceweasel libradcli4 python-pyregfi reglookup-doc
    Use 'apt autoremove' to remove them.
    The following packages have been kept back:
    gir1.2-mutter-3.0 gnome-shell gnome-shell-common gnome-software
    gnome-software-common imagemagick-common libdbd-mysql-perl libfbclient2
    libmagickcore-6.q16-2 libmagickcore-6.q16-2-extra libmagickwand-6.q16-2
    libmutter0i libvlc5 libvlccore8 mitmproxy mutter mutter-common udisks2 vlc
    vlc-data vlc-nox
    The following packages will be upgraded:
    apktool binutils bluez bluez-hcidump bluez-obexd bsdmainutils commix
    console-setup console-setup-linux cpp-5 cpp-6 cryptsetup cryptsetup-bin
    distro-info-data dkms dos2unix dwarfdump erlang-asn1 erlang-base
    erlang-crypto erlang-eunit erlang-inets erlang-mnesia erlang-os-mon
    erlang-public-key erlang-runtime-tools erlang-snmp erlang-ssl
    erlang-syntax-tools erlang-tools erlang-xmerl ethtool evince evince-common
    exploitdb file flex g++-5 g++-6 gcc-5 gcc-5-base gcc-6 gcc-6-base gdm3
    geoip-database geoip-database-extra gir1.2-gdm-1.0 gir1.2-gtk-3.0
    gir1.2-ibus-1.0 gir1.2-networkmanager-1.0 gir1.2-notify-0.7
    gir1.2-polkit-1.0 gir1.2-wnck-3.0 git git-man
    gnome-shell-extension-dashtodock gnome-shell-extension-refreshwifi
    gnome-shell-extension-workspacestodock gnome-shell-extensions gnome-terminal
    gnome-terminal-data gnuplot gnuplot-data gnuplot-qt
    greenbone-security-assistant grub-common grub-pc grub-pc-bin grub2-common
    gtk-update-icon-cache gvfs gvfs-backends gvfs-bin gvfs-common gvfs-daemons
    gvfs-fuse gvfs-libs hashdeep imagemagick imagemagick-6.q16 iproute iproute2
    jarwrapper keyboard-configuration libapache2-mod-php7.0 libapparmor1
    libappstream-glib8 libarchive13 libasan2 libasan3 libatomic1 libavcodec57
    libavfilter6 libavformat57 libavresample3 libavutil55 libbabeltrace-ctf1
    libbabeltrace1 libbluetooth-dev libbluetooth3 libboost-atomic1.61.0
    libboost-chrono1.61.0 libboost-date-time1.61.0 libboost-filesystem1.61.0
    libboost-system1.61.0 libboost-thread1.61.0 libbrlapi0.6 libc-bin
    libc-dev-bin libc-l10n libc6 libc6-dbg libc6-dev libcc1-0 libcilkrts5
    libclang-common-3.8-dev libcommons-lang3-java libcrypto++6 libcryptsetup4
    libdatrie1 libdw1 libegl1-mesa libelf1 libevdocument3-4 libevview3-3
    libfcgi-perl libfl-dev libflite1 libgail-3-0 libgbm1 libgcc-5-dev
    libgcc-6-dev libgcc1 libgdm1 libgeoip1 libgfortran3 libgif7 libgl1-mesa-dri
    libgl1-mesa-glx libglapi-mesa libgles1-mesa libgles2-mesa
    libgnutls-openssl27 libgnutls30 libgom-1.0-0 libgom-1.0-common libgomp1
    libgssdp-1.0-3 libgtk-3-0 libgtk-3-bin libgtk-3-common libgtksourceview2.0-0
    libgtksourceview2.0-common libgupnp-1.0-4 libgupnp-av-1.0-2 libhyphen0
    libibus-1.0-5 libio-socket-socks-perl libiptcdata0 libitm1 libjack-jackd2-0
    libjpeg-turbo-progs libjpeg62-turbo libjs-jquery libjs-sphinxdoc
    libjs-uglify libjsr305-java libllvm3.8 liblsan0 libmagic-dev libmagic-mgc
    libmagic1 libmdb2 libmdbsql2 libmodplug1 libmotif-common libmpx0 libmpx2
    libnautilus-extension1a libnet-ssh2-perl libnewt0.52 libnghttp2-14
    libnm-glib4 libnm-util2 libnm0 libnotify4 libobjc-5-dev libobjc4 libopenvas8
    libopus0 liborc-0.4-0 libosmesa6 libpackagekit-glib2-18 libpolkit-agent-1-0
    libpolkit-backend-1-0 libpolkit-gobject-1-0 libpostproc54 libqtwebkit4
    libquadmath0 libregfi1 librygel-core-2.6-2 librygel-db-2.6-2
    librygel-renderer-2.6-2 librygel-server-2.6-2 libsasl2-2 libsasl2-modules
    libsasl2-modules-db libsepol1 libsqlite3-0 libstdc++-5-dev libstdc++-6-dev
    libstdc++6 libsub-exporter-progressive-perl libswresample2 libswscale4
    libtag1v5 libtag1v5-vanilla libtagc0 libterm-readkey-perl libthai-data
    libthai0 libtracker-control-1.0-0 libtracker-miner-1.0-0
    libtracker-sparql-1.0-0 libtsan0 libturbojpeg0 libubsan0 libudisks2-0
    libupnp6 libuv1 libwayland-egl1-mesa libwnck-3-0 libwnck-3-common
    libwww-mechanize-perl libxapian30 libxatracker2 libxklavier16 libxm4
    libxslt1.1 libyara3 linux-compiler-gcc-5-x86 linux-headers-4.7.0-kali1-amd64
    linux-headers-4.7.0-kali1-common linux-image-4.7.0-kali1-amd64
    linux-kbuild-4.7 linux-libc-dev locales locales-all lsb-base lsb-release mc
    mc-data mdbtools mercurial mercurial-common mesa-opencl-icd
    mesa-vdpau-drivers metasploit-framework mimikatz multiarch-support
    munin-common munin-node munin-plugins-core munin-plugins-extra nautilus
    nautilus-data ndiff network-manager nmap ntp openjdk-8-jdk
    openjdk-8-jdk-headless openjdk-8-jre openjdk-8-jre-headless openvas-manager
    openvas-scanner packagekit packagekit-tools php7.0 php7.0-cli php7.0-common
    php7.0-json php7.0-mysql php7.0-opcache php7.0-readline policykit-1
    policykit-1-gnome python-dnspython python-git python-gitdb python-hyperframe
    python-libxslt1 python-pefile python-pyparsing python-pyregfi python-scipy
    python-smmap python-zope.interface python3-brlapi python3-pyparsing
    python3-scipy recon-ng redis-server redis-tools reglookup reglookup-doc
    responder rsyslog rygel smali sqlite3 t50 tmux tracker tracker-extract
    tracker-gui tracker-miner-fs tzdata volatility volatility-tools w3af
    w3af-console whiptail x11proto-core-dev xbrlapi xsltproc zenmap zlib1g
    328 upgraded, 0 newly installed, 0 to remove and 21 not upgraded.
    Need to get 0 B/453 MB of archives.
    After this operation, 7,874 kB disk space will be freed.
    apt-listchanges: Reading changelogs...
    apt-listchanges: News
    ---------------------

    brltty (5.4-1~1) experimental; urgency=medium

    Authenticating BrlAPI clients now defaults to using policykit too.
    It means that logged-in users can now run orca and similar programs
    using brlapi without having to be able to read /etc/brlapi.key,
    which is thus not world-readable by default any more.

    ...


    during the unpack/install phase, I get:
    Preparing to unpack .../164-libgl1-mesa-dri_12.0.3-3_amd64.deb ...

    Unpacking libgl1-mesa-dri:amd64 (12.0.3-3) over (12.0.3-1) ...
    dpkg: error processing archive /tmp/apt-dpkg-install-pi5qlW/164-libgl1-mesa-dri_12.0.3-3_amd64.deb (--unpack):
    unable to stat './usr/share/bug/libgl1-mesa-dri/control' (which I was about to install): Structure needs cleaning
    E: Sub-process /usr/bin/dpkg received a segmentation fault.
    W: Problem unlinking the file /var/cache/apt/pkgcache.bin - pkgDPkgPM::Go (30: Read-only file system)

    I have disk space:
    # df -h
    Filesystem Size Used Avail Use% Mounted on
    udev 3.9G 0 3.9G 0% /dev
    tmpfs 798M 11M 788M 2% /run
    /dev/sda1 38G 18G 19G 49% /
    tmpfs 3.9G 300K 3.9G 1% /dev/shm
    tmpfs 5.0M 0 5.0M 0% /run/lock
    tmpfs 3.9G 0 3.9G 0% /sys/fs/cgroup
    tmpfs 798M 28K 798M 1% /run/user/133
    tmpfs 798M 20K 798M 1% /run/user/0

    I have 8GB RAM, 4 CPUs.
    There is nothing else running on the PC


    if I revert to the snapshot and try again, it fails in the same place.
    What is going on?

  2. #2
    Join Date
    2013-Apr
    Location
    Kali forums
    Posts
    805
    From the error, it appears dpkg is crashing. Anything in dmesg or /var/log?

    You might also try running apt-get autoclean, based on the "Structure needs cleaning". The read-only file system warning makes me wonder if you might have a hard drive issue.

  3. #3
    Join Date
    2016-Nov
    Location
    Dallas, TX USA
    Posts
    2
    the package causing problems is: libgl1-mesa-dri
    in a test, I did the following:
    apt-get update
    apt-get -y upgrade -d
    made a list of the packages to be upgraded
    applied each individually via
    apt-get -y install PKGNAME --only-upgrade
    upgraded each package but the one named above, then expecting it to crash, I did
    apt-get -y upgrade
    apt-get -y dist-upgrade
    No problems

    If instead, I applied any combination of other packages and then the above package, it went read-only

  4. #4
    Join Date
    2013-Mar
    Posts
    28
    do what it tells you then try

    Code:
    apt autoremove
    Reading package lists... Done
    Building dependency tree
    Reading state information... Done
    Calculating upgrade... Done
    The following packages were automatically installed and are no longer required:
    iceweasel libradcli4 python-pyregfi reglookup-doc
    Use 'apt autoremove' to remove them.
    Last edited by sml156; 2016-11-04 at 03:49.

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