From tony.travis at abdn.ac.uk Fri Jun 6 04:54:31 2014 From: tony.travis at abdn.ac.uk (Tony Travis) Date: Fri, 6 Jun 2014 09:54:31 +0100 Subject: [Bio-linux-dev] x2go server Message-ID: <539181C7.5070106@abdn.ac.uk> Hi, Tim. I've been experimenting with the x2go server under a Bio-Linux 7 system that I've upgraded to Ubuntu 14.04 LTS. As I mentioned before, the Gnome fallback/flashback session does not work. The "x2go" client connects successfully, but all you get in the client window is a black screen instead of the remote fallback/flashback Gnome2-like desktop. I now realise that this is because Unity-2d does not work at all without hardware acceleration. Same for Gnome3-based sessions. However, KDE, XFCE, LXDE and other desktop sessions do work. At the moment, I'm trying out the MATE desktop that is soon going to be included in the official Ubuntu repositories. This may be important for CBL and other deployments of Bio-Linux using either OpenNX or x2go. My own preference is for a Gnome2-like desktop, which is why I'm looking at MATE. What remote desktop sessions will you include in Bio-Linux 8? Bye, Tony. -- 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 cl?raichte ann an Alba, ?ir. SC013683. From tbooth at ceh.ac.uk Fri Jun 6 05:51:20 2014 From: tbooth at ceh.ac.uk (Tim Booth) Date: Fri, 6 Jun 2014 10:51:20 +0100 Subject: [Bio-linux-dev] x2go server In-Reply-To: <539181C7.5070106@abdn.ac.uk> References: <539181C7.5070106@abdn.ac.uk> Message-ID: <1402048280.6733.138.camel@balisaur> Hi Tony, Good question. I'm only just at the point of properly experimenting with x2go on 14.04 myself. I agree that a gnome-type desktop is best so MATE might well be the way to go. Please let me know what you think of it. I've had at least two people say "use Cinnamon" but it seems to be totally enmeshed into Mint and porting it properly to Bio-Linux would probably take a sizeable chunk of my development time. I'm personally quite a fan of Xfce but it is quite dissimilar to Gnome/Unity. Cheers, TIM On Fri, 2014-06-06 at 09:54 +0100, Tony Travis wrote: > Hi, Tim. > > I've been experimenting with the x2go server under a Bio-Linux 7 system > that I've upgraded to Ubuntu 14.04 LTS. As I mentioned before, the Gnome > fallback/flashback session does not work. > > The "x2go" client connects successfully, but all you get in the client > window is a black screen instead of the remote fallback/flashback > Gnome2-like desktop. I now realise that this is because Unity-2d does > not work at all without hardware acceleration. Same for Gnome3-based > sessions. However, KDE, XFCE, LXDE and other desktop sessions do work. > > At the moment, I'm trying out the MATE desktop that is soon going to be > included in the official Ubuntu repositories. This may be important for > CBL and other deployments of Bio-Linux using either OpenNX or x2go. My > own preference is for a Gnome2-like desktop, which is why I'm looking at > MATE. What remote desktop sessions will you include in Bio-Linux 8? > > Bye, > > Tony. > > -- > 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 cl?raichte ann an Alba, ?ir. 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 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 From tbooth at ceh.ac.uk Fri Jun 27 07:49:18 2014 From: tbooth at ceh.ac.uk (Tim Booth) Date: Fri, 27 Jun 2014 12:49:18 +0100 Subject: [Bio-linux-dev] Bio-Linux 8 ready for Beta-testing Message-ID: <1403869758.6513.73.camel@balisaur> Dear Bio-Linux-Dev subscribers, It took longer than I planned, but I'm pleased to announce that the Bio-Linux 8 upgrade script (aka update to Ubuntu Trusty 14.04) is now available for testing. I have tried the script out on several machines here including my own, and nothing has blown up (much). However, as with any major upgrade you should be sure you have a reliable backup before proceeding. And as with any beta test you should be prepared for glitches, so don't run the upgrade 2 hours before you need your machine for some critical analysis! Please discuss any problems on this list and I will endeavour to respond helpfully as quickly as I can. Notes: * There is no ISO or OVA download yet, so you can't test installing Bio-Linux 8 from scratch or running a "Live" boot. This is coming! * The bioinformatics menu in the Dash doesn't work, due to fundamental changes to the way this actually works under the hood. You can still search for tools but you can't just get a nice list of bioinf stuff - I'm working on this. Switch to MATE desktop to get a working bioinformatics menu (see below). * You should be able to run the script on a vanilla Ubuntu 14.04 box to Bio-Linux-ify it (minus a few things like default firewall settings and sudo/ssh/postgresql config) * All the bioinf packages have been updated for the new release, but testing is still ongoing so there may be issues * None of the docs and tutorials are updated yet, but things are broadly unchanged so experienced user shouldn't be baffled. * NX is nixed, and x2go is go for remote desktops! Please test this and let me know what you think. The lightweight MATE desktop is provided as it works well with x2go. * You should see one of a selection of lovely new desktop wallpapers. I will credit the submitters of those on the website when the other release material goes up. To actually do the upgrade: sudo runurl http://nebc.nerc.ac.uk/downloads/bl8_only/upgrade8.sh (or if the runurl command isn't found, just download the script and do "sudo sh upgrade8.sh" ). Enjoy, and let me know how you get on. TIM -- Tim Booth 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 From tony.travis at abdn.ac.uk Sat Jun 28 11:37:19 2014 From: tony.travis at abdn.ac.uk (Tony Travis) Date: Sat, 28 Jun 2014 16:37:19 +0100 Subject: [Bio-linux-dev] Bio-Linux 8 ready for Beta-testing In-Reply-To: <1403869758.6513.73.camel@balisaur> References: <1403869758.6513.73.camel@balisaur> Message-ID: <53AEE12F.9060006@abdn.ac.uk> On 27/06/14 12:49, Tim Booth wrote: > [...] > To actually do the upgrade: > > sudo runurl http://nebc.nerc.ac.uk/downloads/bl8_only/upgrade8.sh > > (or if the runurl command isn't found, just download the script and do > "sudo sh upgrade8.sh" ). > > Enjoy, and let me know how you get on. Hi, Tim. 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. I didn't get on so well with my workstation at home. However, I'd already upgraded it to Ubuntu 14.04 LTS and tried to manually update Bio-Linux before you posted your beta-test installation script. In particular, I had problems installing bio-linux-cruft-killer on my workstation and I had to remove it from the unpacked version of your installation script in /tmp. Fortunately, your script didn't remove the cached copy :-) I also had problems with bio-linux-emboss because the version of embassy-domsearch I already had installed was too new and needed to be downgraded. I also had to remove tigr-glimmer from my workstation before I could get bio-linux-glimmer3 to install. I realise that my workstation was in an unusual 'non-vanilla' state, but I only managed to get your upgrade script to work after fixing APT problems with: aptitude -f install I edited your script in /tmp to use "aptitude" except for the last one, which does the "autoremove", and it allowed me to complete the upgrade in a more complicated environment but one that people might encounter if running your script on a non-vanilla Ubuntu 14.04 LTS installation. I'll upgrade my Bio-Linux 7 workstation at work next week. This is just a standard Bio-Linux 7 installation like my laptop. I think your script worked very well for me and I'm looking forward to using Bio-Linux 8. BTW, I'm now using btrfs RAID10 on my workstation at home. I installed Bio-Linux 7 on it with boot and swap on btrfs RAID10 and upgraded it to Ubuntu 14.04 LTS. You have to mount a swap file on a loop device under btrfs (or use a separate swap partiton, but that is complicated with RAID10). GRUB2 can boot from btrfs RAID. Have you tried btrfs at all? Bye, Tony. -- 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 cl?raichte ann an Alba, ?ir. SC013683. From tony.travis at abdn.ac.uk Sat Jun 28 11:43:09 2014 From: tony.travis at abdn.ac.uk (Tony Travis) Date: Sat, 28 Jun 2014 16:43:09 +0100 Subject: [Bio-linux-dev] Bio-Linux 8 ready for Beta-testing In-Reply-To: <53AEE12F.9060006@abdn.ac.uk> References: <1403869758.6513.73.camel@balisaur> <53AEE12F.9060006@abdn.ac.uk> Message-ID: <53AEE28D.8020502@abdn.ac.uk> 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 cl?raichte ann an Alba, ?ir. SC013683. From tbooth at ceh.ac.uk Mon Jun 30 05:15:40 2014 From: tbooth at ceh.ac.uk (Tim Booth) Date: Mon, 30 Jun 2014 10:15:40 +0100 Subject: [Bio-linux-dev] Bio-Linux 8 ready for Beta-testing In-Reply-To: <53AEE28D.8020502@abdn.ac.uk> References: <1403869758.6513.73.camel@balisaur> <53AEE12F.9060006@abdn.ac.uk> <53AEE28D.8020502@abdn.ac.uk> Message-ID: <1404119740.4956.3.camel@balisaur> 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 cl?raichte ann an Alba, ?ir. 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 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 From tony.travis at abdn.ac.uk Mon Jun 30 05:53:15 2014 From: tony.travis at abdn.ac.uk (Tony Travis) Date: Mon, 30 Jun 2014 10:53:15 +0100 Subject: [Bio-linux-dev] Bio-Linux 8 ready for Beta-testing In-Reply-To: <1404119740.4956.3.camel@balisaur> References: <1403869758.6513.73.camel@balisaur> <53AEE12F.9060006@abdn.ac.uk> <53AEE28D.8020502@abdn.ac.uk> <1404119740.4956.3.camel@balisaur> Message-ID: <53B1338B.3090207@abdn.ac.uk> On 30/06/14 10:15, Tim Booth wrote: > 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. Hi, Tim. I already ran your script twice on my laptop "beluga" and it did not report any errors either time: That's why I was so impressed with it! > 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. I use "aptitude -f install" to check that the APT system is in a consistent state before doing any upgrades and again afterwards to check that the system is still in a stable state. The only time that aptitude removes stuff to satisfy dependencies is when it needs to in order to get the APT system back into a consistent state again. I don't think it's a 'magic' bullet, but it has saved me lots of time having to re-install systems that had become unmaintainable because of broken dependencies and partially installed packages after installing packages with "apt-get". I began to use "aptitude" instead when I read that "aptitude" is now the recommended package manager for Debian: https://www.debian.org/doc/manuals/debian-faq/ch-uptodate.en.html "aptitude is the recommended package manager for Debian GNU/Linux systems. It is a text-based interface to APT using the curses library, and can be used to perform management tasks in a fast and easy way" I've experienced severe problems from time to time when installing and upgrading Bio-Linux in what you might regard as 'unorthodox' ways. This is not unexpected in a complex distribution like Bio-Linux and I'm not criticising Bio-Linux because I've had problems. Instead, I advocate a 'defensive' strategy, using the best tools available for the task. I ran "aptitude -f install" before running your upgrade script, which I ran twice without any errors being reported. I subsequently checked for and fixed any inconsistencies in the APT system by running "aptitude -f install". My laptop then ran your upgrade script a third time without creating further inconsistencies detectable by "aptitude -f install". I'm upgrading my workstation today + I'll let you know how I get on. Bye, Tony. -- 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 cl?raichte ann an Alba, ?ir. SC013683. From tbooth at ceh.ac.uk Mon Jun 30 07:46:22 2014 From: tbooth at ceh.ac.uk (Tim Booth) Date: Mon, 30 Jun 2014 12:46:22 +0100 Subject: [Bio-linux-dev] Bio-Linux 8 ready for Beta-testing In-Reply-To: <53B1338B.3090207@abdn.ac.uk> References: <1403869758.6513.73.camel@balisaur> <53AEE12F.9060006@abdn.ac.uk> <53AEE28D.8020502@abdn.ac.uk> <1404119740.4956.3.camel@balisaur> <53B1338B.3090207@abdn.ac.uk> Message-ID: <1404128782.4956.49.camel@balisaur> Hi Tony, > I'm upgrading my workstation today + I'll let you know how I get on. OK, thanks, keep me posted. I've had another look at one of my test machines, and discovered that: apt-get -f install => reports no errors update-manager => reports no errors aptitude -f install => has a fit and wants to remove most of the system (including the aptitude package!) So either this system is in a mess that apt-get can't see or else aptitude is wrong. I accept that either case is possible but I would note that Aptitude has had some real issues relating to multi-arch dependency resolution in the past: https://bugs.launchpad.net/ubuntu/+source/aptitude/+bug/831768 On my other test systems, aptitude is happy. I need to do more digging on this. Apart from this, you say you are still seeing the BL7 boot splash. What I did was to put both versions into bio-linux-plymouth-theme and have them switch based on [ `lsb_release -cs` != "precise" ]. What does lsb_release say on your system? And does "dpkg-reconfigure"-ing this package help? If so, I'll do this at the end of the upgrade script. Cheers, TIM From tony.travis at abdn.ac.uk Mon Jun 30 08:20:35 2014 From: tony.travis at abdn.ac.uk (Tony Travis) Date: Mon, 30 Jun 2014 13:20:35 +0100 Subject: [Bio-linux-dev] Bio-Linux 8 ready for Beta-testing In-Reply-To: <1404128782.4956.49.camel@balisaur> References: <1403869758.6513.73.camel@balisaur> <53AEE12F.9060006@abdn.ac.uk> <53AEE28D.8020502@abdn.ac.uk> <1404119740.4956.3.camel@balisaur> <53B1338B.3090207@abdn.ac.uk> <1404128782.4956.49.camel@balisaur> Message-ID: <53B15613.4060300@abdn.ac.uk> On 30/06/14 12:46, Tim Booth wrote: > [...] > apt-get -f install => reports no errors > update-manager => reports no errors > aptitude -f install => has a fit and wants to remove most of the system > (including the aptitude package!) Hi, Tim. I've quite often been in that situation, but I've learnt to trust it :-) > So either this system is in a mess that apt-get can't see or else > aptitude is wrong. I accept that either case is possible but I would > note that Aptitude has had some real issues relating to multi-arch > dependency resolution in the past: > > https://bugs.launchpad.net/ubuntu/+source/aptitude/+bug/831768 OK, but that bug was fixed in 2012 soon after it was reported... > On my other test systems, aptitude is happy. I need to do more digging > on this. I'm still having problems installing "bio-linux-cruft-killer" on my workstation at home, but that system was the one that I upgraded BL7 to Ubuntu 14.04 LTS while you were still working on the Bio-Linux PPA. > Apart from this, you say you are still seeing the BL7 boot splash. What > I did was to put both versions into bio-linux-plymouth-theme and have > them switch based on [ `lsb_release -cs` != "precise" ]. > > What does lsb_release say on your system? ajt at beluga:~$ lsb_release -cs trusty > And does > "dpkg-reconfigure"-ing this package help? Looks promising: ajt at beluga:~$ sudo dpkg-reconfigure bio-linux-plymouth-theme [sudo] password for ajt: update-alternatives: using /lib/plymouth/themes/bl8-logo/ubuntu-logo.plymouth to provide /lib/plymouth/themes/default.plymouth (default.plymouth) in auto mode update-alternatives: using /lib/plymouth/themes/bl8-text/ubuntu-text.plymouth to provide /lib/plymouth/themes/text.plymouth (text.plymouth) in auto mode update-initramfs: deferring update (trigger activated) Processing triggers for initramfs-tools (0.103ubuntu4.2) ... update-initramfs: Generating /boot/initrd.img-3.13.0-30-generic > If so, I'll do this at the > end of the upgrade script. Have to re-boot to find out... I'll let you know if that fixes it. Bye, Tony. -- 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 cl?raichte ann an Alba, ?ir. SC013683. From tony.travis at abdn.ac.uk Mon Jun 30 08:36:58 2014 From: tony.travis at abdn.ac.uk (Tony Travis) Date: Mon, 30 Jun 2014 13:36:58 +0100 Subject: [Bio-linux-dev] Bio-Linux 8 ready for Beta-testing In-Reply-To: <53B15613.4060300@abdn.ac.uk> References: <1403869758.6513.73.camel@balisaur> <53AEE12F.9060006@abdn.ac.uk> <53AEE28D.8020502@abdn.ac.uk> <1404119740.4956.3.camel@balisaur> <53B1338B.3090207@abdn.ac.uk> <1404128782.4956.49.camel@balisaur> <53B15613.4060300@abdn.ac.uk> Message-ID: <53B159EA.6080404@abdn.ac.uk> On 30/06/14 13:20, Tony Travis wrote: > [...] > Have to re-boot to find out... > > I'll let you know if that fixes it. Hi, Tim. OK, that fixed it - The italic '8' looks a bit odd to my eyes: Was the '7' you used before the same font? I also noticed that on the 'greeter' screen the (dotted) version of the current desktop wallpaper is not stretched or zoomed to fill the screen as it was before on a 1600x900 external monitor connected to my laptop. Although this is a trivial in one sense, it's the first impression that new people get of Bio-Linux. First impressions can, and often do, make a difference so I think it's worth getting it right. I'm still upgrading my 'work' workstation "wildcat"... Bye, Tony. -- 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 cl?raichte ann an Alba, ?ir. SC013683. From tony.travis at abdn.ac.uk Mon Jun 30 09:40:35 2014 From: tony.travis at abdn.ac.uk (Tony Travis) Date: Mon, 30 Jun 2014 14:40:35 +0100 Subject: [Bio-linux-dev] Bio-Linux 8 ready for Beta-testing In-Reply-To: <53B159EA.6080404@abdn.ac.uk> References: <1403869758.6513.73.camel@balisaur> <53AEE12F.9060006@abdn.ac.uk> <53AEE28D.8020502@abdn.ac.uk> <1404119740.4956.3.camel@balisaur> <53B1338B.3090207@abdn.ac.uk> <1404128782.4956.49.camel@balisaur> <53B15613.4060300@abdn.ac.uk> <53B159EA.6080404@abdn.ac.uk> Message-ID: <53B168D3.3050101@abdn.ac.uk> Hi, Tim. There is a bug in Unity/iBus under Ubuntu 14.04 LTS. The GUI keyboard layout defaults to US, even if it is set to and displayed as e.g. "English UK": https://bugs.launchpad.net/ubuntu/+source/ibus/+bug/1284635 I followed the advice here and disabled keyboard input via iBus: Settings / Language Support / Keyboard input method system: none [The bug doesn't seem to affect the keyboard layout in Gnome Terminal] Still upgrading my workstation... Bye, Tony. -- 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 cl?raichte ann an Alba, ?ir. SC013683. From tbooth at ceh.ac.uk Mon Jun 30 10:17:50 2014 From: tbooth at ceh.ac.uk (Tim Booth) Date: Mon, 30 Jun 2014 15:17:50 +0100 Subject: [Bio-linux-dev] Bio-Linux 8 ready for Beta-testing In-Reply-To: <53B159EA.6080404@abdn.ac.uk> References: <1403869758.6513.73.camel@balisaur> <53AEE12F.9060006@abdn.ac.uk> <53AEE28D.8020502@abdn.ac.uk> <1404119740.4956.3.camel@balisaur> <53B1338B.3090207@abdn.ac.uk> <1404128782.4956.49.camel@balisaur> <53B15613.4060300@abdn.ac.uk> <53B159EA.6080404@abdn.ac.uk> Message-ID: <1404137870.24510.3.camel@balisaur> Hi Tony, > OK, that fixed it - The italic '8' looks a bit odd to my eyes: Was the > '7' you used before the same font? Not sure - I did it pretty quickly just to get it saying "8". Probably need to do a more careful job at some point. > I also noticed that on the 'greeter' screen the (dotted) version of the > current desktop wallpaper is not stretched or zoomed to fill the screen > as it was before on a 1600x900 external monitor connected to my laptop. No idea what I need to do to fix this. I'll see if I can reproduce the problem. Yes, I do want to make the system make a good impression if I can. Cheers, TIM From tony.travis at abdn.ac.uk Mon Jun 30 10:59:26 2014 From: tony.travis at abdn.ac.uk (Tony Travis) Date: Mon, 30 Jun 2014 15:59:26 +0100 Subject: [Bio-linux-dev] Bio-Linux 8 ready for Beta-testing In-Reply-To: <1404137870.24510.3.camel@balisaur> References: <1403869758.6513.73.camel@balisaur> <53AEE12F.9060006@abdn.ac.uk> <53AEE28D.8020502@abdn.ac.uk> <1404119740.4956.3.camel@balisaur> <53B1338B.3090207@abdn.ac.uk> <1404128782.4956.49.camel@balisaur> <53B15613.4060300@abdn.ac.uk> <53B159EA.6080404@abdn.ac.uk> <1404137870.24510.3.camel@balisaur> Message-ID: <53B17B4E.6040008@abdn.ac.uk> On 30/06/14 15:17, Tim Booth wrote: > [...] >> I also noticed that on the 'greeter' screen the (dotted) version of the >> current desktop wallpaper is not stretched or zoomed to fill the screen >> as it was before on a 1600x900 external monitor connected to my laptop. > > No idea what I need to do to fix this. I'll see if I can reproduce the > problem. Yes, I do want to make the system make a good impression if I > can. Hi, Tim. The problem only seems to happen when booting: If I just logout/in, the greeter doesn't have the BL desktop wallpaper - Just the default one... Bye, Tony. -- 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 cl?raichte ann an Alba, ?ir. SC013683.