From anton.gossner at roslin.ed.ac.uk Fri Nov 30 05:40:40 2012 From: anton.gossner at roslin.ed.ac.uk (GOSSNER Anton) Date: Fri, 30 Nov 2012 10:40:40 +0000 Subject: [Bio-Linux] Upgrading to Bio-Linux 7 from 6 Message-ID: <4B2DE8422AF25D40820C088EF2AE5D27216883C45A@EXSEEDMD.is.ed.ac.uk> Hi, Just wondered if anybody is having the same problem and has solved it or if need to do a full install. Following Tims instructions for upgrading, all gone well with initial upgrade of Ubuntu and start of Bio-Linux packages but always stops and exits with; Verifying that everything installed... python-biopython failed to install python-biopython-doc failed to install Not all packages installed properly - exiting. despite the fact python is installed; Reading package lists... Done Building dependency tree Reading state information... Done python-software-properties is already the newest version. Have removed and reinstalled via Synaptic Package Manager, restarted and rerun the script numerous times and various different combinations of installing and uninstalling python but to no avail also run "apt-get autoremove" No joy, any ideas?, also seems to uninstall Coffee and reinstall in every time I run the script. Anton -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From tbooth at ceh.ac.uk Fri Nov 30 12:13:01 2012 From: tbooth at ceh.ac.uk (Tim Booth) Date: Fri, 30 Nov 2012 17:13:01 +0000 Subject: [Bio-Linux] Upgrading to Bio-Linux 7 from 6 In-Reply-To: <4B2DE8422AF25D40820C088EF2AE5D27216883C45A@EXSEEDMD.is.ed.ac.uk> References: <4B2DE8422AF25D40820C088EF2AE5D27216883C45A@EXSEEDMD.is.ed.ac.uk> Message-ID: <1354295581.7749.45.camel@balisaur> Hi Anton, This is more likely a problem with my script than with your system, or rather there is some minor issue and my script is making a meal of it. What do you get when you ask dpkg specifically about biopython? - ie: dpkg -s python-biopython Also the thing with removing and reinstalling t-coffee is expected - it's a crude workaround to a problem someone spotted during beta testing. Cheers, TIM On Fri, 2012-11-30 at 10:40 +0000, GOSSNER Anton wrote: > Hi, > > Just wondered if anybody is having the same problem and has solved it or if need to do a full install. > > Following Tims instructions for upgrading, all gone well with initial upgrade of Ubuntu and start of Bio-Linux packages but always stops and exits with; > > Verifying that everything installed... > python-biopython failed to install > python-biopython-doc failed to install > Not all packages installed properly - exiting. > > despite the fact python is installed; > > Reading package lists... Done > Building dependency tree > Reading state information... Done > python-software-properties is already the newest version. > > > Have removed and reinstalled via Synaptic Package Manager, restarted and rerun the script numerous times and various different combinations of installing and uninstalling python but to no avail also run "apt-get autoremove" > > No joy, any ideas?, also seems to uninstall Coffee and reinstall in every time I run the script. > > Anton -- 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