[Bio-linux-dev] Bio-Linux 8 ready for Beta-testing

[Tony Travis]

On 28/06/14 16:37, Tony Travis wrote:
> [...]
> I've upgraded my Bio-Linux 7 laptop without any problems. One minor
> issue is that the boot splash screen still says Bio-Linux 7.

Hi, Tim.

Sorry, I spoke too soon: Your script didn't produce any errors on my
laptop during its execution, but I've just found this when I checked the
APT consistency using "aptitude -f install". I'll let you know how I get
on fixing the problems, but some of this could be pre-empted by using
"aptitude" in your script instead of "apt-get". These are similar to the
problems I had upgrading my workstation:

Bye,

  Tony.

> root at beluga:~# aptitude -f install
> The following NEW packages will be installed:
>   apache2.2-bin{b} apport-gtk{b} apport-symptoms bio-linux-estscan bio-linux-themes-v7{b} bluez-alsa:i386
>   compiz-plugins-main-default compizconfig-backend-gconf espeak foomatic-db-engine gcc-4.6-base:i386 gir1.2-dbusmenu-gtk-0.4
>   gir1.2-gst-plugins-base-0.10 gir1.2-gstreamer-0.10 gir1.2-gtk-2.0 gir1.2-indicate-0.7{b} glib-networking:i386{b}
>   gstreamer0.10-x:i386 gwibber-service hal-info html2text icedtea-6-jre-cacao icedtea-6-jre-jamvm icedtea-6-plugin
>   intel-gpu-tools libanydata-perl libbackport-util-concurrent-java libcommons-el-java libegl1-mesa-drivers-lts-saucy
>   libegl1-mesa-lts-saucy libfftw3-3{b} libfile-find-rule-perl libgbm1-lts-saucy libgcj-bc{b} libgl1-mesa-glx-lts-saucy
>   libgl1-mesa-glx-lts-saucy:i386 libglamor-ltss0 libglapi-mesa-lts-saucy libglapi-mesa-lts-saucy:i386 libgnujaf-java
>   libgphoto2-2-dev libjetty-java libkadm5srv-mit8 libmono-corlib4.0-cil libmotif4 libnumber-compare-perl
>   libopenvg1-mesa-lts-saucy libpam-ck-connector libperl-dev libquvi-scripts libservlet2.4-java libslf4j-java libsnmp-perl
>   libswitch-perl libtag1c2a:i386{b} libtasn1-3-dev libtext-glob-perl libtiff4-dev libtomcat6-java libusb-dev
>   libxatracker1-lts-saucy mothur-mpi openjdk-6-jdk openjdk-6-jre openjdk-6-jre-headless openjdk-6-jre-lib python-appindicator
>   python-brlapi python-gnupginterface python-gst0.10 python-keyring python-launchpadlib python-lazr.restfulclient
>   python-lazr.uri python-libproxy python-louis python-mako python-markupsafe python-oauth python-pexpect python-pyatspi2{b}
>   python-virtkey python-wadllib python-xkit sdparm slib ttf-dejavu-core ttf-dejavu-extra ttf-freefont unity-lens-video
>   unity-scope-video-remote x11-xserver-utils-lts-saucy x11vnc x11vnc-data xserver-common-lts-saucy xserver-xorg-core-lts-saucy
>   xserver-xorg-glamoregl-lts-saucy xserver-xorg-input-all-lts-saucy xserver-xorg-input-evdev-lts-saucy
>   xserver-xorg-input-mouse-lts-saucy xserver-xorg-input-synaptics-lts-saucy xserver-xorg-input-vmmouse-lts-saucy
>   xserver-xorg-input-wacom-lts-saucy xserver-xorg-video-all-lts-saucy xserver-xorg-video-ati-lts-saucy
>   xserver-xorg-video-cirrus-lts-saucy xserver-xorg-video-fbdev-lts-saucy xserver-xorg-video-intel-lts-saucy
>   xserver-xorg-video-mach64-lts-saucy xserver-xorg-video-mga-lts-saucy xserver-xorg-video-modesetting-lts-saucy
>   xserver-xorg-video-neomagic-lts-saucy xserver-xorg-video-nouveau-lts-saucy xserver-xorg-video-openchrome-lts-saucy
>   xserver-xorg-video-r128-lts-saucy xserver-xorg-video-radeon-lts-saucy xserver-xorg-video-s3-lts-saucy
>   xserver-xorg-video-savage-lts-saucy xserver-xorg-video-siliconmotion-lts-saucy xserver-xorg-video-sis-lts-saucy
>   xserver-xorg-video-sisusb-lts-saucy xserver-xorg-video-tdfx-lts-saucy xserver-xorg-video-trident-lts-saucy
>   xserver-xorg-video-vesa-lts-saucy
> The following packages are RECOMMENDED but will NOT be installed:
>   apport python-secretstorage
> 0 packages upgraded, 124 newly installed, 0 to remove and 0 not upgraded.
> Need to get 6,350 kB/70.7 MB of archives. After unpacking 145 MB will be used.
> The following packages have unmet dependencies:
>  python-pyatspi2 : Depends: python-pyatspi (= 2.10.0+dfsg-1) but it is not going to be installed.
>  bio-linux-themes-v7 : Conflicts: bio-linux-themes which is a virtual package.
>  bio-linux-themes-v8 : Conflicts: bio-linux-themes which is a virtual package.
>                        Conflicts: bio-linux-themes-v7 but 7.0-12 is to be installed.
>  libtag1c2a:i386 : Depends: libtag1-vanilla:i386 (= 1.9.1-2) but it is not going to be installed.
>  apache2.2-bin : Breaks: gnome-user-share (< 3.8.0-2~) but 3.0.4-0ubuntu1 is installed.
>  bio-linux-cruft-killer : Conflicts: unity-lens-video but 0.3.15+13.10.20130920-0ubuntu1 is to be installed.
>                           Conflicts: unity-scope-video-remote but 0.3.15+13.10.20130920-0ubuntu1 is to be installed.
>                           Conflicts: apport-gtk but 2.14.1-0ubuntu3.2 is to be installed.
>  libtomcat7-java : Conflicts: libtomcat6-java but 6.0.39-1 is to be installed.
>  libfftw3-3 : Depends: libfftw3-long3 (= 3.3.3-7ubuntu3) but it is not going to be installed.
>  gir1.2-indicate-0.7 : Depends: libindicate5 (>= 12.10.1-0ubuntu3) but it is not going to be installed.
>  apport-gtk : Depends: python3-apport (>= 2.14.1-0ubuntu3.2) but it is not going to be installed.
>               Depends: apport (>= 0.41) but it is not going to be installed.
>  libgcj-bc : Depends: libgcj-common (>= 1:4.8.2-1ubuntu6) but it is not going to be installed.
>              Depends: libgcj14 (>= 4.8.2-5~) but it is not going to be installed.
>  glib-networking:i386 : Depends: libproxy1:i386 (>= 0.4.7) but it is not going to be installed.
> The following actions will resolve these dependencies:
>
>       Remove the following packages:
> 1)      eclipse
> 2)      eclipse-jdt
> 3)      eclipse-pde
> 4)      eclipse-platform
> 5)      eclipse-platform-data
> 6)      libtomcat7-java
>
>       Keep the following packages at their current version:
> 7)      apache2.2-bin [Not Installed]
> 8)      apport-gtk [Not Installed]
> 9)      bio-linux-themes-v7 [Not Installed]
> 10)     gir1.2-indicate-0.7 [Not Installed]
> 11)     glib-networking:i386 [Not Installed]
> 12)     libfftw3-3 [Not Installed]
> 13)     libgcj-bc [Not Installed]
> 14)     libtag1c2a:i386 [Not Installed]
> 15)     python-pyatspi2 [Not Installed]
> 16)     unity-lens-video [Not Installed]
> 17)     unity-scope-video-remote [Not Installed]
>
>
>
> Accept this solution? [Y/n/q/?]

--
Dr. A.J.Travis, University of Aberdeen, Institute of Biological and
Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen
AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396
http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis


The University of Aberdeen is a charity registered in Scotland, No SC013683.
Tha Oilthigh Obar Dheathain na charthannas clàraichte ann an Alba, Àir. SC013683.