[Bio-linux-dev] Bio-Linux 8 ready for Beta-testing
Tim Booth
tbooth at ceh.ac.uk
Mon Jun 30 05:15:40 EDT 2014
Hi Tony,
You have to run the script at least twice, until it says "Your system
has been fully upgraded". Could you please tell me what errors the
script produced? Seeing a report like this from Aptitude is not much
use to me.
And, no, I refuse to believe that s/apt-get/aptitude/g is a magic bullet
fix. Aptitude has a nasty habit of aggressively removing stuff in order
to satisfy dependencies.
TIM
On Sat, 2014-06-28 at 16:43 +0100, Tony Travis wrote:
> 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.
> _______________________________________________
> Bio-Linux-dev mailing list
> Bio-Linux-dev at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev
--
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre
Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB
http://nebc.nerc.ac.uk
+44 1491 69 2705
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