[solved] Update Watch Out!

[doctordruidphd]

Did a sudo apt-get update and sudo apt-get -d dist-upgrade this morning; good thing I used the -d option. It is threatening to remove about 1/4 of my system, including most xorg packages (this IS maverick, not natty).

Tried blocking the backport, beta, experimental, xswat and xorg-edgers ppas, did not help.

Looks like a couple of mesa package updates might be responsible, though placing holds on them didn't help. Also noticed upstart is on the "not upgraded" list, that could also be a problem.

Wondering if anyone else has noticed this?

[thelonegunmen]

Re: Update Watch Out!

Do you think maybe you have a virus? I just checked and the only updats I have are for a program called subversion (non official). When's the last time you updated?

[doctordruidphd]

Re: Update Watch Out!

I would doubt there is a virus; rkhunter finds nothing.
Did an update/dist-upgrade yesterday, no problems.

I did notice one strange thing:
When I first ran the update/d-u this morning, I got an error message I haven't seen before.
It said it couldn't calculate the upgrade because of a problem with php5, and some unsatisfied dependencies that couldn't be resolved. I did a manual reinstall on one of them (php5-fpm), and the u/d-u again. This time it complained about ia32-libs, which I also reinstalled.
In both cases, it said the problem might be packages on hold. The only package on hold is mono-runtime, to keep it off the system. I did try removing the hold on it, but that didn't fix it.

After reinstalling ia32-libs, it's making this noise about removing most of the xorg packages, and everything that depends on them (which is a big part of the system). I can't figure out which package might be causing that.

[doctordruidphd]

Re: Update Watch Out!

Some additional info:

I tried an apt-get install --reinstall upstart, since it is apparently being held back for some reason.
This is the error message I got:

greenman@Wolfenstein:~$ sudo apt-get install --reinstall upstart
Reading package lists... Done
Building dependency tree    
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:

The following packages have unmet dependencies:
 debconf : Depends: debconf-i18n but it is not going to be installed or
          debconf-english but it is not going to be installed
      PreDepends: perl-base (>= 5.6.1-4) but it is not going to be installed
      Recommends: apt-utils (>= 0.5.1) but it is not going to be installed
 ghostscript : Depends: libgs8 (= 8.71.dfsg.2-0ubuntu7) but it is not going to be installed
        Depends: debianutils (>= 1.6) but it is not going to be installed
 ghostscript-x : Depends: libice6 (>= 1:1.0.0) but it is not going to be installed
         Depends: libpaper1 but it is not going to be installed
         Depends: libsm6 but it is not going to be installed
         Depends: libxext6 but it is not going to be installed
         Depends: libxt6 but it is not going to be installed
 libschroedinger-1.0-0 : Depends: liborc-0.4-0 (>= 0.4.6) but it is not going to be installed
 libsdl1.2debian : Depends: libsdl1.2debian-alsa (= 1.2.14-6ubuntu3) but it is not going to be installed or
              libsdl1.2debian-all (= 1.2.14-6ubuntu3) but it is not going to be installed or
              libsdl1.2debian-esd (= 1.2.14-6ubuntu3) but it is not going to be installed or
              libsdl1.2debian-oss (= 1.2.14-6ubuntu3) but it is not going to be installed or
              libsdl1.2debian-nas (= 1.2.14-6ubuntu3) but it is not going to be installed or
              libsdl1.2debian-pulseaudio (= 1.2.14-6ubuntu3) but it is not going to be installed
 libtheora0 : Depends: libogg0 (>= 1.1.0) but it is not going to be installed
 libvorbis0a : Depends: libogg0 (>= 1.1.0) but it is not going to be installed
 libvorbisenc2 : Depends: libogg0 (>= 1.0rc3) but it is not going to be installed
 libx11-6 : Depends: libxcb1 (>= 1.2) but it is not going to be installed
 sun-java6-bin : Depends: sun-java6-jre (>= 6.21dlj-0ubuntu1~maverick1~ppa1) but it is not going to be installed
         Depends: unixodbc but it is not going to be installed
         Recommends: libasound2
         Recommends: libxext6 but it is not going to be installed
         Recommends: libxi6 but it is not going to be installed
         Recommends: libxt6 but it is not going to be installed
         Recommends: libxtst6 but it is not going to be installed
         Recommends: libnss-mdns but it is not going to be installed
 upstart : Depends: libdbus-1-3 (>= 1.2.16) but it is not going to be installed
      Depends: libnih-dbus1 (>= 1.0.0) but it is not going to be installed
      Depends: libnih1 (>= 1.0.0) but it is not going to be installed
      Depends: libudev0 (>= 151) but it is not going to be installed
      Depends: sysvinit-utils but it is not going to be installed
      Depends: sysv-rc but it is not going to be installed
      Depends: initscripts but it is not going to be installed
      Depends: mountall but it is not going to be installed
      Depends: ifupdown (>= 0.6.8ubuntu29)
      Breaks: libc6 (< 2.12.1-0ubuntu10.2) but 2.12.1-0ubuntu10.1 is to be installed
E: Broken packages

I'm really perplexed about what is going on here. If this is just a stuff-isn't-in-the-repository-yet problem, then others should be getting it, too. But no one else seems to be reporting the problem here, or on the ubuntu forums.

[dibl]

Re: Update Watch Out!

I'm only running 11.04 now, but it sounds as if you might have a "non-standard" repo, maybe, which is pulling in packages that are either earlier or later versions that 10.10. You might try commenting out all the repos that are not canonical's repos for 10.10, and update and then see what you get.

[doctordruidphd]

Re: Update Watch Out!

That's possible - I have a lot of non-standard ppas, but I think only xswat and edgers install x packages. Nonetheless, that's a good place to start, and I will try that.

Be forewarned, though -- I just did a u/d-u on natty, and it's threatening the same problem. I was expecting that, given the transition to xorg-1.10. But now is not the time to update there, either.

[doctordruidphd]

Re: Update Watch Out!

Oh well --

I tried removing ALL of the ppas, everything in sources.list.d, along with commenting out maverick-proposed and maverick-backports in sources.list. All that's there is the basic stuff. Doing an update, and then a -d dist-upgrade, still wants to remove just about all of xorg, and nearly 2000 other packages (most of the system).

Now I'm really stumped. I wonder if apt itself is corrupted, and if so, how and what to do about it.

[doctordruidphd]

Re: Update Watch Out!

OK further info:

Removing this line from sources.list solves the problem of removing the entire system:

deb http://us.archive.ubuntu.com/ubuntu/ maverick-updates main restricted

but that's a standard canonical repository!! Well maybe wait a few days. But why is no one else seeing this?

[claydoh]

Re: Update Watch Out!

nope, I just updated 2 Maverick boxes today and got just a few things as far as I remember - no problems at all.

[doctordruidphd]

Re: Update Watch Out!

Then something here is seriously messed up. Here is what I get:
-------------------------------------

greenman@Wolfenstein:~$ sudo apt-get -d dist-upgrade
Reading package lists... Done
Building dependency tree
Reading state information... Done
Calculating upgrade... Done
The following packages will be REMOVED:
a2ps abakus abiword abiword-plugin-grammar abiword-plugin-mathview abiword-plugins acetoneiso acidrip
aconnectgui acpi-support add-apt-key afterstep aisleriot akonadiconsole akregator alacarte alien
alsa-tools-gui alsamixergui alsaplayer-common alsaplayer-esd amarok anacron anjuta apache2
apache2-mpm-prefork apache2-suexec apache2-utils apache2.2-bin apache2.2-common apcalc apparmor-utils
appmenu-gtk apport-gtk apport-kde apport-qt apt-file apt-rdepends apt-show-versions apt-transport-https
apt-xapian-index aptdaemon aptitude aptoncd aptsh apturl-kde aqbanking-tools aqsis arista ark audacious
audacious-plugins audacity audex automoc autopsy avahi-daemon avahi-utils avidemux-plugins-common
avidemux-plugins-gtk avidemux-plugins-qt awesome axe barcode basket bb bc bind9-host biniax2 black-box
bleachbit blender blt bluedevil bluefish bluetooth bluez bluez-alsa bluez-cups bluez-gstreamer bluez-utils
bookwrite brasero brasero-cdrkit bubblemon bubbros build-essential byobu bzip2 caca-utils calibre
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checkbox-gtk cheese chkrootkit cifer cinelerra cinelerrasv-smp clamav-base clamav-daemon clamav-freshclam
clamav-getfiles clamfs clamtk clementine clicompanion cm-super-minimal cm-super-x11 cmake cmake-curses-gui
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openmovieeditor openshot openshot-doc opensonic openssh-client openssh-server openssl-blacklist opera oxine
packagekit packagekit-backend-apt packagekit-backend-aptcc packagekit-backend-smart packagesearch
padevchooser page-crunch pandora paprefs parted partimage partitionmanager patch patchage patchutils pciutils
pdf2djvu pdf2svg pdfcube pdfjam perlmagick pessulus pgadmin3 pgagent pgdesigner pgf pgsnap phatch phatch-cli
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php5-suhosin php5-sybase php5-tidy php5-xsl phpmyadmin phppgadmin phpreports phpsysinfo phpunit phpwebcounter
phpwebcounter-extra phpwiki pia pidgin pidgin-bot-sentry pidgin-encryption pidgin-extprefs
pidgin-guifications pidgin-libnotify pidgin-musictracker pidgin-openpgp pidgin-otr pidgin-plugin-pack
pidgin-privacy-please pidgin-skype pidgin-skype-dbg pidgin-themes pingus pitivi pixbros
plasma-dataengines-workspace plasma-desktop plasma-netbook plasma-runners-addons plasma-scriptengine-python
plasma-scriptengine-qedje plasma-scriptengine-ruby plasma-scriptengine-superkaramba plasma-scriptengines
plasma-wallpapers-addons plasma-widget-adjustableclock plasma-widget-drive-io-monitor plasma-widget-facebook
plasma-widget-folderview plasma-widget-googlecalendar plasma-widget-kepas plasma-widget-lancelot
plasma-widget-message-indicator plasma-widget-pgame plasma-widget-quickaccess plasma-widget-runcommand
plasma-widget-smooth-tasks plasma-widget-toggle-compositing plasma-widgets-addons plasma-widgets-workspace
plasmoid-toggle-compositing plymouth-label plymouth-theme-fade-in plymouth-theme-glow
plymouth-theme-kubuntu-logo plymouth-theme-kubuntu-text plymouth-theme-script plymouth-theme-solar
plymouth-theme-spinfinity plymouth-theme-text plymouth-theme-ubuntu-logo plymouth-theme-ubuntu-text
plymouth-x11 pm-utils po-debconf polkit-kde-1 poppler-utils pornview portaudio19-dev postgresql
postgresql-8.4 postgresql-client postgresql-client-8.4 postgresql-contrib postgresql-contrib-8.4
postgresql-plperl-8.4 postgresql-plpython-8.4 ppa-purge ppp pppconfig pppoeconf pptp-linux printer-applet
pskmail psutils ptop puddletag pulseaudio pulseaudio-dbg pulseaudio-equalizer pulseaudio-esound-compat
pulseaudio-esound-compat-dbg pulseaudio-module-bluetooth pulseaudio-module-gconf pulseaudio-module-gconf-dbg
pulseaudio-module-hal pulseaudio-module-hal-dbg pulseaudio-module-lirc pulseaudio-module-lirc-dbg
pulseaudio-module-x11 pulseaudio-module-x11-dbg pulseaudio-module-zeroconf pulseaudio-module-zeroconf-dbg
puredata pxlib1 pxljr pyqt4-dev-tools pysdm python-appindicator python-aptdaemon python-aptdaemon-gtk
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python-farsight python-foolscap python-gconf python-gksu2 python-glade2 python-gmenu python-gnome2
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ruby1.8 rubygems rubygems1.8 sabayon sane sane-utils satanic-kde-themes sbackup sbackup-gtk screen-profiles
screen-resolution-extra screenruler scribes scribus scrot seahorse seahorse-plugins secpanel seed
sessioninstaller sfftw2 shermans-aquarium shotwell showfoto shutter skanlite skype smart-notifier smc
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snowballz software-center software-properties-gtk software-properties-kde sooperlooper soundconvert
soundconverter soundkonverter sox speech-dispatcher speex splix squeeze sreadahead ssh ssh-askpass-gnome
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stardict-plugin-festival stardict-plugin-spell startupmanager stopmotion streamripper strigi-client
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telepathy-haze telepathy-idle telepathy-logger telepathy-mission-control-5 telepathy-salut tellico tetex-bin
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winff winff-doc wireshark wireshark-common wordgrinder wsjt wv x11-apps x11-xkb-utils xawtv xawtv-plugin-qt
xawtv-tools xbase-clients xdg-user-dirs xdg-user-dirs-gtk xdiskusage xfburn xfce4 xfce4-appfinder
xfce4-goodies xfce4-places-plugin xfce4-power-manager xfce4-session xfce4-settings xfce4-terminal
xfce4-xfapplet-plugin xfce4-xkb-plugin xfdesktop4 xfmedia xine-console xine-plugin xine-ui xjadeo xmms2
xmms2-plugin-mad xoo xorg xpdf xpdf-reader xpp xprint xprint-common xprint-utils xsane xscorch
xscreensaver-data-extra xserver-common xserver-xephyr xserver-xorg xserver-xorg-core xserver-xorg-dev
xserver-xorg-input-all xserver-xorg-input-evdev xserver-xorg-input-mouse xserver-xorg-input-synaptics
xserver-xorg-input-vmmouse xserver-xorg-input-wacom xserver-xorg-video-apm xserver-xorg-video-ark
xserver-xorg-video-ati xserver-xorg-video-chips xserver-xorg-video-cirrus xserver-xorg-video-fbdev
xserver-xorg-video-i128 xserver-xorg-video-intel xserver-xorg-video-mach64 xserver-xorg-video-mga
xserver-xorg-video-neomagic xserver-xorg-video-nv xserver-xorg-video-openchrome xserver-xorg-video-r128
xserver-xorg-video-radeon xserver-xorg-video-rendition xserver-xorg-video-s3 xserver-xorg-video-s3virge
xserver-xorg-video-savage xserver-xorg-video-siliconmotion xserver-xorg-video-sis xserver-xorg-video-sisusb
xserver-xorg-video-tdfx xserver-xorg-video-trident xserver-xorg-video-tseng xserver-xorg-video-v4l
xserver-xorg-video-vesa xserver-xorg-video-vmware xserver-xorg-video-voodoo xtartan xterm xulrunner-1.9.2 xye
yarssr yelp yofrankie zeitgeist zeitgeist-datahub zeitgeist-fts-extension zssh
The following NEW packages will be installed:
cdebootstrap-static celestia-glut clamav-data console-tools erlang-base-hipe gs libavdevice-extra-52
libavfilter-extra-1 libclutter-eglx-es20-1.0-0 libconsole libegl1-mesa libegl1-mesa-drivers
libgd-gd2-noxpm-perl libgd2-noxpm libgles2-mesa libgpod4-nogtk librcc0 librcd0 libxcb-xfixes0
The following packages have been kept back:
upstart
The following packages will be upgraded:
computer-janitor empathy-common nautilus-data portmap
4 upgraded, 19 newly installed, 2004 to remove and 1 not upgraded.
Need to get 36.3MB of archives.
After this operation, 5,622MB disk space will be freed.
Do you want to continue [Y/n]? n
Abort.

-------------------------------------------------

This is not good.

[claydoh]

Re: Update Watch Out!

did you add back the standard repo you removed?

[doctordruidphd]

Re: Update Watch Out!

Yes, I did. Without it in there, there is none of this mess.

I am wondering if this is somehow connected with aptitude. I NEVER use it, because it always threatens to remove my entire system, and I have no idea why. Apt-get has always worked properly. Yesterday, I ran aptitude to check a feature I read about somewhere, and yep, it wanted to flush the entire system, upgrade OOo (which has been removed), and a bunch of other really stupid things that say to me aptitude is broken somewhere. I am wondering if somehow the problems with aptitude got written to apt-get's configuration somewhere, and now apt-get is broken.

I think I am looking at a restore from backup here, unless there is some way to flush out whatever aptitude's problem is.

[Snowhog]

Re: Update Watch Out!

I'd say, show us your sources.list as well as any other non-standard lists you have. We might be able to see something you are missing.

[doctordruidphd]

Re: Update Watch Out!

Here is sources.list:

-----------------------
greenman@Wolfenstein:/etc/apt$ cat sources.list
# deb cdrom:[Kubuntu 8.10 _Intrepid Ibex_ - Release i386 (20081029.1)]/ intrepid main restricted
# See http://help.ubuntu.com/community/UpgradeNotes for how to upgrade to
# newer versions of the distribution.

deb http://us.archive.ubuntu.com/ubuntu/ maverick main restricted
# deb-src http://us.archive.ubuntu.com/ubuntu/ maverick main restricted

## Major bug fix updates produced after the final release of the
## distribution.
deb http://us.archive.ubuntu.com/ubuntu/ maverick-updates main restricted
# deb-src http://us.archive.ubuntu.com/ubuntu/ maverick-updates main restricted



## N.B. software from this repository is ENTIRELY UNSUPPORTED by the Ubuntu
## team. Also, please note that software in universe WILL NOT receive any
## review or updates from the Ubuntu security team.
deb http://us.archive.ubuntu.com/ubuntu/ maverick universe
# deb-src http://us.archive.ubuntu.com/ubuntu/ maverick universe
deb http://us.archive.ubuntu.com/ubuntu/ maverick-updates universe
# deb-src http://us.archive.ubuntu.com/ubuntu/ maverick-updates universe

## N.B. software from this repository is ENTIRELY UNSUPPORTED by the Ubuntu
## team, and may not be under a free licence. Please satisfy yourself as to
## your rights to use the software. Also, please note that software in
## multiverse WILL NOT receive any review or updates from the Ubuntu
## security team.
deb http://us.archive.ubuntu.com/ubuntu/ maverick multiverse
# deb-src http://us.archive.ubuntu.com/ubuntu/ maverick multiverse
deb http://us.archive.ubuntu.com/ubuntu/ maverick-updates multiverse
# deb-src http://us.archive.ubuntu.com/ubuntu/ maverick-updates multiverse

## Uncomment the following two lines to add software from the 'backports'
## repository.
## N.B. software from this repository may not have been tested as
## extensively as that contained in the main release, although it includes
## newer versions of some applications which may provide useful features.
## Also, please note that software in backports WILL NOT receive any review
## or updates from the Ubuntu security team.
deb http://us.archive.ubuntu.com/ubuntu/ maverick-backports main restricted universe multiverse
# deb-src http://us.archive.ubuntu.com/ubuntu/ maverick-backports main restricted universe multiverse

## Uncomment the following two lines to add software from Canonical's
## 'partner' repository. This software is not part of Ubuntu, but is
## offered by Canonical and the respective vendors as a service to Ubuntu
## users.
# deb http://archive.canonical.com/ubuntu/ maverick partner
# deb-src http://archive.canonical.com/ubuntu/ intrepid partner

## Ubuntu extras repository
deb http://extras.ubuntu.com/ubuntu/ maverick main

## Update repositories
deb http://security.ubuntu.com/ubuntu/ maverick-security main restricted
# deb-src http://security.ubuntu.com/ubuntu/ maverick-security main restricted
deb http://security.ubuntu.com/ubuntu/ maverick-security universe
# deb-src http://security.ubuntu.com/ubuntu/ maverick-security universe
deb http://security.ubuntu.com/ubuntu/ maverick-security multiverse
# deb-src http://security.ubuntu.com/ubuntu/ maverick-security multiverse
deb http://us.archive.ubuntu.com/ubuntu/ maverick-proposed restricted main multiverse universe
# deb-src http://us.archive.ubuntu.com/ubuntu/ maverick-proposed restricted main multiverse universe

-----------------------

I moved everything out of sources.list.d, did the update and -d dist-upgrade, and here is the error message I got:

greenman@Wolfenstein:/etc/apt/sources.list.d$ sudo apt-get -d dist-upgrade
Reading package lists... Done
Building dependency tree    
Reading state information... Done
Calculating upgrade... Failed
The following packages have unmet dependencies:
 php5 : Depends: libapache2-mod-php5 (>= 5.3.3-1ubuntu9.3) but it is not going to be installed or
         libapache2-mod-php5filter (>= 5.3.3-1ubuntu9.3) but it is not going to be installed or
         php5-cgi (>= 5.3.3-1ubuntu9.3) but it is not going to be installed or
         php5-fpm (>= 5.3.3-1ubuntu9.3) but it is not going to be installed
 php5-mcrypt : Depends: phpapi-20090626
 php5-sqlite : Depends: phpapi-20090626
 php5-xsl : Depends: phpapi-20090626
N: Ignoring file 'noinstall' in directory '/etc/apt/sources.list.d/' as it has no filename extension
E: Error, pkgProblemResolver::Resolve generated breaks, this may be caused by held packages.

This is how it all started this morning. I reinstalled the php5 packages, then it complained about ia32-libs, which I reinstalled, then I got the mess.

There are a whole bunch of sources.list.d list files, too many to list all their contents. But as I said, I have moved all of them out for purposes of this test.

Edit: PS this is on the system I just restored from backup, so it isn't aptitude's fault. Or anything else that happened in the last 4 days.

[Snowhog]

Re: Update Watch Out!

Why do you have commented:

# deb http://archive.canonical.com/ubuntu/ maverick partner

in sources.list?