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?
