From tony.travis at minke-informatics.co.uk Sat Mar 7 17:23:48 2015 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Sat, 7 Mar 2015 22:23:48 +0000 Subject: [Bio-linux-dev] USB-stick checksum failures Message-ID: <54FB7A74.5070508@minke-informatics.co.uk> Hi, Tim. We had some problems with the USB-sticks I supplied for the workshop at AAU in Jorhat recently and I replaced any USB-sticks that failed their 'self-test' (i.e. "Check stick for defects" on the boot menu). I noticed that they all seemed to fail on the same file, so I investigated using bio-linux-usb-checker and "md5sum". I tested the failed' sticks exhaustively using "badblocks" destructive write/read without any errors and remade them using "bio-linux-usb-maker". This stick passed its 'self-test' on first boot, but after using it a few times, it now fails its 'self-test', so I checked it 'live': > root at biolinux:~# cd /cdrom > root at biolinux:/cdrom# md5sum --quiet -c md5sum.txt > ./casper/initrd.lz: FAILED > md5sum: WARNING: 1 computed checksum did NOT match > root at biolinux:/cdrom# ls -rtl casper > total 3455124 > -rwxr-xr-x 1 root root 10 Mar 5 11:30 filesystem.size > -rwxr-xr-x 1 root root 1063 Mar 5 11:30 filesystem.manifest-remove > -rwxr-xr-x 1 root root 94031 Mar 5 11:30 filesystem.manifest > -rwxr-xr-x 1 root root 5815992 Mar 5 12:09 vmlinuz.efi > -rwxr-xr-x 1 root root 3511578624 Mar 5 12:09 filesystem.squashfs > -rwxr-xr-x 1 root root 20545577 Mar 7 2015 initrd.lz It's clear that "initrd.lz" is being written to and it's md5sum will change. Therefore, the 'self-test' using the original md5sum will always fail even though there is nothing wrong with the USB-stick. Some of the USB-sticks were physically bent and not working(!), but I don't think we had as many USB-stick failures as it seemed because of my over-zealous rejection of sticks that failed their 'self-test'. Any idea why "initrd.lz" is being written to? Bye, Tony. -- Minke Informatics Limited, Registered in Scotland - Company No. SC419028 Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK) tel. +44(0)19755 63548 http://minke-informatics.co.uk mob. +44(0)7985 078324 mailto:tony.travis at minke-informatics.co.uk From tony.travis at abdn.ac.uk Sat Mar 7 18:52:47 2015 From: tony.travis at abdn.ac.uk (Tony Travis) Date: Sat, 7 Mar 2015 23:52:47 +0000 Subject: [Bio-linux-dev] USB-stick checksum failures In-Reply-To: <54FB7A74.5070508@minke-informatics.co.uk> References: <54FB7A74.5070508@minke-informatics.co.uk> Message-ID: <54FB8F4F.6050700@abdn.ac.uk> On 07/03/15 22:23, Tony Travis wrote: > [...] > Any idea why "initrd.lz" is being written to? Hi, Tim. I've compared the original and updated initrd.lz's: > # extract original initrd.lz from original USB-stick > root at beluga:/media/ajt/bl-live-iso/casper# > cp -ai initrd.lz /var/tmp/original-initrd.lz > cd /var/tmp > mkdir original- > initrd > cd original-initrd > lzma -dc -S .lz ../original-initrd.lz | cpio -id > > # extract updated initrd.lz from updated USB-stick > root at beluga:/media/ajt/bl-live-iso/casper# > cp -ai initrd.lz /var/tmp > cd /var/tmp > mkdir updatedupdated-initrd > lzma -dc -S .lz ../updated-initrd.lz | cpio -id > > # compare contents of initrd's > root at beluga:/var/tmp# diff -r original-initrd updated-initrd > Binary files original-initrd/etc/console-setup/cached.kmap.gz and updated-initrd/etc/console-setup/cached.kmap.gz differ > diff -r original-initrd/etc/default/keyboard updated-initrd/etc/default/keyboard > 9c9 > < XKBLAYOUT="gb" > --- > > XKBLAYOUT="us" > Only in original-initrd/etc/ld.so.conf.d: zz_i386-biarch-compat.conf > Only in original-initrd/etc/modprobe.d: dkms.conf > Binary files original-initrd/usr/lib/x86_64-linux-gnu/libdrm.so.2 and updated-initrd/usr/lib/x86_64-linux-gnu/libdrm.so.2 differ The file is NOT being corrupted, but it is being updated by changes to the keyboard and kernel 'drm' (i.e. display) modules. This all seems quite normal, according to diferent hardware, and explains why the 'self-test' fails. On read-only media (e.g. DVD) these files would not be changed and the 'self-test' would not fail... 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 Mar 9 08:07:30 2015 From: tbooth at ceh.ac.uk (Tim Booth) Date: Mon, 9 Mar 2015 12:07:30 +0000 Subject: [Bio-linux-dev] USB-stick checksum failures In-Reply-To: <54FB8F4F.6050700@abdn.ac.uk> References: <54FB7A74.5070508@minke-informatics.co.uk> <54FB8F4F.6050700@abdn.ac.uk> Message-ID: <1425902850.4114.11.camel@wllt1771.nerc-wallingford.ac.uk> Hi Tony, As you say, that's pretty clear cut, and it came as a big surprise to me. Like you, I assumed that all the files in the casper/ directory were untouched and all writes went to casper-rw/ via the union FS. But then looking at the Deb changelog for the Casper package it talks about the casper-update-initramfs hook which does exactly this - supports updated kernels and initramfs on USB media - and apparently it's been in there since Jaunty which is forever! So if your users ran any kind of update on the USB stick the behaviour you saw is exactly as expected. So I guess the bug here is that the md5sums file isn't being updated. I could probably submit this as a simple bug report/patch to Ubuntu. On the other hand, I might well look into disabling this feature on the Bio-Linux sticks, because it seems to me that even if the md5sums file is fixed it's liable to cause more problems than it fixes modifying these files. What do you think? Cheers, TIM On Sat, 2015-03-07 at 23:52 +0000, Tony Travis wrote: > On 07/03/15 22:23, Tony Travis wrote: > > [...] > > Any idea why "initrd.lz" is being written to? > > Hi, Tim. > > I've compared the original and updated initrd.lz's: > > > # extract original initrd.lz from original USB-stick > > root at beluga:/media/ajt/bl-live-iso/casper# > > cp -ai initrd.lz /var/tmp/original-initrd.lz > > cd /var/tmp > > mkdir original- > > initrd > > cd original-initrd > > lzma -dc -S .lz ../original-initrd.lz | cpio -id > > > > # extract updated initrd.lz from updated USB-stick > > root at beluga:/media/ajt/bl-live-iso/casper# > > cp -ai initrd.lz /var/tmp > > cd /var/tmp > > mkdir updatedupdated-initrd > > lzma -dc -S .lz ../updated-initrd.lz | cpio -id > > > > # compare contents of initrd's > > root at beluga:/var/tmp# diff -r original-initrd updated-initrd > > Binary files original-initrd/etc/console-setup/cached.kmap.gz and updated-initrd/etc/console-setup/cached.kmap.gz differ > > diff -r original-initrd/etc/default/keyboard updated-initrd/etc/default/keyboard > > 9c9 > > < XKBLAYOUT="gb" > > --- > > > XKBLAYOUT="us" > > Only in original-initrd/etc/ld.so.conf.d: zz_i386-biarch-compat.conf > > Only in original-initrd/etc/modprobe.d: dkms.conf > > Binary files original-initrd/usr/lib/x86_64-linux-gnu/libdrm.so.2 and updated-initrd/usr/lib/x86_64-linux-gnu/libdrm.so.2 differ > > The file is NOT being corrupted, but it is being updated by changes to > the keyboard and kernel 'drm' (i.e. display) modules. This all seems > quite normal, according to diferent hardware, and explains why the > 'self-test' fails. On read-only media (e.g. DVD) these files would not > be changed and the 'self-test' would not fail... > > 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://environmentalomics.org/bio-linux +44 1491 69 2297 From tony.travis at minke-informatics.co.uk Mon Mar 9 09:09:35 2015 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Mon, 9 Mar 2015 13:09:35 +0000 Subject: [Bio-linux-dev] USB-stick checksum failures In-Reply-To: <1425902850.4114.11.camel@wllt1771.nerc-wallingford.ac.uk> References: <54FB7A74.5070508@minke-informatics.co.uk> <54FB8F4F.6050700@abdn.ac.uk> <1425902850.4114.11.camel@wllt1771.nerc-wallingford.ac.uk> Message-ID: <54FD9B8F.9000500@minke-informatics.co.uk> On 09/03/15 12:07, Tim Booth wrote: > [...] > So I guess the bug here is that the md5sums file isn't being updated. I > could probably submit this as a simple bug report/patch to Ubuntu. On > the other hand, I might well look into disabling this feature on the > Bio-Linux sticks, because it seems to me that even if the md5sums file > is fixed it's liable to cause more problems than it fixes modifying > these files. What do you think? Hi, Tim. I agree about disabling this feature, because I think the /cdrom filesystem on the 'live' USB-stick should be read-only. I think you might be right that some of the problems we had at the workshop in Jorhat were because of changes to the initramfs. At the time, some people thought it might be dodgy Minke Informatics USB-sticks :-) In fact, I bought the sticks from a reputable supplier: http://www.bespokeusb.com/ However, the sticks were physically vulnerable in a crowded classroom and some got bent or were simply knocked out by people walking by. We didn't have desks, we just had 'tablet-arm' chairs instead - not good! I did ask the participants to install "gdebi" and use it to install RStudio, but I expected all the changes to occur in /casper-rw. We were giving them experience of downloading and installing the software, then using it to learn about programming in R... Got good feedback from the AAU B4GD workshop despite these problems! Bye, Tony. -- Minke Informatics Limited, Registered in Scotland - Company No. SC419028 Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK) tel. +44(0)19755 63548 http://minke-informatics.co.uk mob. +44(0)7985 078324 mailto:tony.travis at minke-informatics.co.uk From tbooth at ceh.ac.uk Mon Mar 9 09:42:13 2015 From: tbooth at ceh.ac.uk (Tim Booth) Date: Mon, 9 Mar 2015 13:42:13 +0000 Subject: [Bio-linux-dev] USB-stick checksum failures In-Reply-To: <54FD9B8F.9000500@minke-informatics.co.uk> References: <54FB7A74.5070508@minke-informatics.co.uk> <54FB8F4F.6050700@abdn.ac.uk> <1425902850.4114.11.camel@wllt1771.nerc-wallingford.ac.uk> <54FD9B8F.9000500@minke-informatics.co.uk> Message-ID: <1425908533.4114.23.camel@wllt1771.nerc-wallingford.ac.uk> In fact, I bought the sticks from a reputable supplier: > > http://www.bespokeusb.com/ > I've started using Flashbay, and have had zero failures with their sticks. And they assure me they use a single supplier so the quality shouldn't fluctuate from batch to batch. Based on experience so far I'd definitely recommend them. Anyway, I'll look into disabling kernel updates for the next ISO release. TIM On Mon, 2015-03-09 at 13:09 +0000, Tony Travis wrote: > On 09/03/15 12:07, Tim Booth wrote: > > [...] > > So I guess the bug here is that the md5sums file isn't being updated. I > > could probably submit this as a simple bug report/patch to Ubuntu. On > > the other hand, I might well look into disabling this feature on the > > Bio-Linux sticks, because it seems to me that even if the md5sums file > > is fixed it's liable to cause more problems than it fixes modifying > > these files. What do you think? > > Hi, Tim. > > I agree about disabling this feature, because I think the /cdrom > filesystem on the 'live' USB-stick should be read-only. I think you > might be right that some of the problems we had at the workshop in > Jorhat were because of changes to the initramfs. At the time, some > people thought it might be dodgy Minke Informatics USB-sticks :-) > > In fact, I bought the sticks from a reputable supplier: > > http://www.bespokeusb.com/ > > However, the sticks were physically vulnerable in a crowded classroom > and some got bent or were simply knocked out by people walking by. We > didn't have desks, we just had 'tablet-arm' chairs instead - not good! > > I did ask the participants to install "gdebi" and use it to install > RStudio, but I expected all the changes to occur in /casper-rw. We were > giving them experience of downloading and installing the software, then > using it to learn about programming in R... > > Got good feedback from the AAU B4GD workshop despite these problems! > > Bye, > > Tony. > -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://environmentalomics.org/bio-linux +44 1491 69 2297 From tony.travis at abdn.ac.uk Mon Mar 16 06:42:48 2015 From: tony.travis at abdn.ac.uk (Tony Travis) Date: Mon, 16 Mar 2015 10:42:48 +0000 Subject: [Bio-linux-dev] "x2go-server" upgrade problems Message-ID: <5506B3A8.8060208@abdn.ac.uk> Hi, A recent upgrade has broken the "x2go-server" installation on three of our servers. Several 'mainstream' packages now conflict with those in the "x2go" PPA. You can force the new packages to be installed in order to resolve the conflicts: > root at wildcat:~# aptitude -f install > The following NEW packages will be installed: > king libbcmail-java libbcpkix-java libbcprov-java libcapture-tiny-perl libitext-java libjogl-java libjogl-jni libnx-x11{b} > libxcompext3{b} libxcompshad3{b} linux-headers-3.13.0-40 linux-headers-3.13.0-40-generic linux-headers-3.13.0-43 > linux-headers-3.13.0-43-generic linux-image-3.13.0-40-generic linux-image-3.13.0-43-generic > linux-image-extra-3.13.0-40-generic linux-image-extra-3.13.0-43-generic nxagent{b} pwgen x2goagent x2goserver > x2goserver-extensions x2goserver-xsession > The following packages will be REMOVED: > libxcb-xf86dri0{u} libxcb-xv0{u} > 0 packages upgraded, 25 newly installed, 2 to remove and 2 not upgraded. > Need to get 132 MB of archives. After unpacking 558 MB will be used. > The following packages have unmet dependencies: > libnx-x11 : Depends: libnx-x11-6 (>= 2:3.5.0.30-0~595~ubuntu14.04.1) but it is not going to be installed. > Depends: libnx-x11-6 (< 2:3.5.0.30-0~595~ubuntu14.04.1.1) but it is not going to be installed. > libxcompshad3 : Depends: libnx-x11-6 (>= 3.5.0.29) but it is not going to be installed. > Depends: libnx-xdamage1 (>= 3.5.0.29) but it is not going to be installed. > Depends: libnx-xrandr2 (>= 3.5.0.29) but it is not going to be installed. > Depends: libnx-xtst6 (>= 3.5.0.29) but it is not going to be installed. > libxcompext3 : Depends: libnx-x11-6 (>= 3.5.0.29) but it is not going to be installed. > nxagent : Depends: libnx-x11-6 (>= 3.5.0.29) but it is not going to be installed. > Depends: libnx-xcomposite1 (>= 3.5.0.29) but it is not going to be installed. > Depends: libnx-xdmcp6 (>= 3.5.0.29) but it is not going to be installed. > Depends: libnx-xext6 (>= 3.5.0.29) but it is not going to be installed. > Depends: libnx-xfixes3 (>= 3.5.0.29) but it is not going to be installed. > Depends: libnx-xpm4 (>= 3.5.0.29) but it is not going to be installed. > Depends: libnx-xrender1 (>= 3.5.0.29) but it is not going to be installed. > Internal error: found 2 (choice -> promotion) mappings for a single choice. > Internal error: found 2 (choice -> promotion) mappings for a single choice. > Internal error: found 2 (choice -> promotion) mappings for a single choice. > Internal error: found 2 (choice -> promotion) mappings for a single choice. > Internal error: found 2 (choice -> promotion) mappings for a single choice. > Internal error: found 2 (choice -> promotion) mappings for a single choice. > Internal error: found 2 (choice -> promotion) mappings for a single choice. > Internal error: found 2 (choice -> promotion) mappings for a single choice. > Internal error: found 2 (choice -> promotion) mappings for a single choice. > The following actions will resolve these dependencies: > > Keep the following packages at their current version: > 1) libnx-x11 [Not Installed] > 2) libxcompext3 [Not Installed] > 3) libxcompshad3 [Not Installed] > 4) nxagent [Not Installed] > 5) x2goagent [Not Installed] > 6) x2goserver [Not Installed] > 7) x2goserver-extensions [Not Installed] > 8) x2goserver-xsession [Not Installed] > > > > Accept this solution? [Y/n/q/?] n > The following actions will resolve these dependencies: > > Install the following packages: > 1) libnx-x11-6 [2:3.5.0.30-0~595~ubuntu14.04.1 (trusty)] > 2) libnx-xcomposite1 [2:3.5.0.30-0~595~ubuntu14.04.1 (trusty)] > 3) libnx-xdamage1 [2:3.5.0.30-0~595~ubuntu14.04.1 (trusty)] > 4) libnx-xdmcp6 [2:3.5.0.30-0~595~ubuntu14.04.1 (trusty)] > 5) libnx-xext6 [2:3.5.0.30-0~595~ubuntu14.04.1 (trusty)] > 6) libnx-xfixes3 [2:3.5.0.30-0~595~ubuntu14.04.1 (trusty)] > 7) libnx-xpm4 [2:3.5.0.30-0~595~ubuntu14.04.1 (trusty)] > 8) libnx-xrandr2 [2:3.5.0.30-0~595~ubuntu14.04.1 (trusty)] > 9) libnx-xrender1 [2:3.5.0.30-0~595~ubuntu14.04.1 (trusty)] > 10) libnx-xtst6 [2:3.5.0.30-0~595~ubuntu14.04.1 (trusty)] > 11) nx-x11-common [2:3.5.0.30-0~595~ubuntu14.04.1 (trusty)] > > > > Accept this solution? [Y/n/q/?] > The following NEW packages will be installed: > king libbcmail-java libbcpkix-java libbcprov-java libcapture-tiny-perl libitext-java libjogl-java libjogl-jni libnx-x11 > libnx-x11-6{a} libnx-xcomposite1{a} libnx-xdamage1{a} libnx-xdmcp6{a} libnx-xext6{a} libnx-xfixes3{a} libnx-xpm4{a} > libnx-xrandr2{a} libnx-xrender1{a} libnx-xtst6{a} libxcompext3 libxcompshad3 linux-headers-3.13.0-40 > linux-headers-3.13.0-40-generic linux-headers-3.13.0-43 linux-headers-3.13.0-43-generic linux-image-3.13.0-40-generic > linux-image-3.13.0-43-generic linux-image-extra-3.13.0-40-generic linux-image-extra-3.13.0-43-generic nx-x11-common{a} > nxagent pwgen x2goagent x2goserver x2goserver-extensions x2goserver-xsession > The following packages will be REMOVED: > libxcb-xf86dri0{u} libxcb-xv0{u} > 0 packages upgraded, 36 newly installed, 2 to remove and 2 not upgraded. > Need to get 133 MB of archives. After unpacking 560 MB will be used. > Do you want to continue? [Y/n/?] HTH, 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 Tue Mar 17 08:09:53 2015 From: tbooth at ceh.ac.uk (Booth, Timothy G.) Date: Tue, 17 Mar 2015 12:09:53 +0000 Subject: [Bio-linux-dev] "x2go-server" upgrade problems In-Reply-To: <5506B3A8.8060208@abdn.ac.uk> References: <5506B3A8.8060208@abdn.ac.uk> Message-ID: <8C33D34D431A974EAEA913101DDA194407E83C9E06@nerckwmbc.ad.nerc.ac.uk> Hi Tony, I had a look just now and I can install both the newest x2go and the libxcb-xf86dri0 and libxcb-xv0 packages (which are needed for vlc and a couple of other things) so I'm wondering if this is just a transient issue with the package indices getting out-of-sync? If anyone else on the list is still seeing upgrade problems please let me know. TIM ________________________________________ From: Tony Travis [tony.travis at abdn.ac.uk] Sent: 16 March 2015 10:42 To: Bio-Linux technical discussion Subject: [Bio-linux-dev] "x2go-server" upgrade problems Hi, A recent upgrade has broken the "x2go-server" installation on three of our servers. Several 'mainstream' packages now conflict with those in the "x2go" PPA. You can force the new packages to be installed in order to resolve the conflicts: > root at wildcat:~# aptitude -f install > The following NEW packages will be installed: > king libbcmail-java libbcpkix-java libbcprov-java libcapture-tiny-perl libitext-java libjogl-java libjogl-jni libnx-x11{b} > libxcompext3{b} libxcompshad3{b} linux-headers-3.13.0-40 linux-headers-3.13.0-40-generic linux-headers-3.13.0-43 > linux-headers-3.13.0-43-generic linux-image-3.13.0-40-generic linux-image-3.13.0-43-generic > linux-image-extra-3.13.0-40-generic linux-image-extra-3.13.0-43-generic nxagent{b} pwgen x2goagent x2goserver > x2goserver-extensions x2goserver-xsession > The following packages will be REMOVED: > libxcb-xf86dri0{u} libxcb-xv0{u} > 0 packages upgraded, 25 newly installed, 2 to remove and 2 not upgraded. > Need to get 132 MB of archives. After unpacking 558 MB will be used. > The following packages have unmet dependencies: > libnx-x11 : Depends: libnx-x11-6 (>= 2:3.5.0.30-0~595~ubuntu14.04.1) but it is not going to be installed. > Depends: libnx-x11-6 (< 2:3.5.0.30-0~595~ubuntu14.04.1.1) but it is not going to be installed. > libxcompshad3 : Depends: libnx-x11-6 (>= 3.5.0.29) but it is not going to be installed. > Depends: libnx-xdamage1 (>= 3.5.0.29) but it is not going to be installed. > Depends: libnx-xrandr2 (>= 3.5.0.29) but it is not going to be installed. > Depends: libnx-xtst6 (>= 3.5.0.29) but it is not going to be installed. > libxcompext3 : Depends: libnx-x11-6 (>= 3.5.0.29) but it is not going to be installed. > nxagent : Depends: libnx-x11-6 (>= 3.5.0.29) but it is not going to be installed. > Depends: libnx-xcomposite1 (>= 3.5.0.29) but it is not going to be installed. > Depends: libnx-xdmcp6 (>= 3.5.0.29) but it is not going to be installed. > Depends: libnx-xext6 (>= 3.5.0.29) but it is not going to be installed. > Depends: libnx-xfixes3 (>= 3.5.0.29) but it is not going to be installed. > Depends: libnx-xpm4 (>= 3.5.0.29) but it is not going to be installed. > Depends: libnx-xrender1 (>= 3.5.0.29) but it is not going to be installed. > Internal error: found 2 (choice -> promotion) mappings for a single choice. > Internal error: found 2 (choice -> promotion) mappings for a single choice. > Internal error: found 2 (choice -> promotion) mappings for a single choice. > Internal error: found 2 (choice -> promotion) mappings for a single choice. > Internal error: found 2 (choice -> promotion) mappings for a single choice. > Internal error: found 2 (choice -> promotion) mappings for a single choice. > Internal error: found 2 (choice -> promotion) mappings for a single choice. > Internal error: found 2 (choice -> promotion) mappings for a single choice. > Internal error: found 2 (choice -> promotion) mappings for a single choice. > The following actions will resolve these dependencies: > > Keep the following packages at their current version: > 1) libnx-x11 [Not Installed] > 2) libxcompext3 [Not Installed] > 3) libxcompshad3 [Not Installed] > 4) nxagent [Not Installed] > 5) x2goagent [Not Installed] > 6) x2goserver [Not Installed] > 7) x2goserver-extensions [Not Installed] > 8) x2goserver-xsession [Not Installed] > > > > Accept this solution? [Y/n/q/?] n > The following actions will resolve these dependencies: > > Install the following packages: > 1) libnx-x11-6 [2:3.5.0.30-0~595~ubuntu14.04.1 (trusty)] > 2) libnx-xcomposite1 [2:3.5.0.30-0~595~ubuntu14.04.1 (trusty)] > 3) libnx-xdamage1 [2:3.5.0.30-0~595~ubuntu14.04.1 (trusty)] > 4) libnx-xdmcp6 [2:3.5.0.30-0~595~ubuntu14.04.1 (trusty)] > 5) libnx-xext6 [2:3.5.0.30-0~595~ubuntu14.04.1 (trusty)] > 6) libnx-xfixes3 [2:3.5.0.30-0~595~ubuntu14.04.1 (trusty)] > 7) libnx-xpm4 [2:3.5.0.30-0~595~ubuntu14.04.1 (trusty)] > 8) libnx-xrandr2 [2:3.5.0.30-0~595~ubuntu14.04.1 (trusty)] > 9) libnx-xrender1 [2:3.5.0.30-0~595~ubuntu14.04.1 (trusty)] > 10) libnx-xtst6 [2:3.5.0.30-0~595~ubuntu14.04.1 (trusty)] > 11) nx-x11-common [2:3.5.0.30-0~595~ubuntu14.04.1 (trusty)] > > > > Accept this solution? [Y/n/q/?] > The following NEW packages will be installed: > king libbcmail-java libbcpkix-java libbcprov-java libcapture-tiny-perl libitext-java libjogl-java libjogl-jni libnx-x11 > libnx-x11-6{a} libnx-xcomposite1{a} libnx-xdamage1{a} libnx-xdmcp6{a} libnx-xext6{a} libnx-xfixes3{a} libnx-xpm4{a} > libnx-xrandr2{a} libnx-xrender1{a} libnx-xtst6{a} libxcompext3 libxcompshad3 linux-headers-3.13.0-40 > linux-headers-3.13.0-40-generic linux-headers-3.13.0-43 linux-headers-3.13.0-43-generic linux-image-3.13.0-40-generic > linux-image-3.13.0-43-generic linux-image-extra-3.13.0-40-generic linux-image-extra-3.13.0-43-generic nx-x11-common{a} > nxagent pwgen x2goagent x2goserver x2goserver-extensions x2goserver-xsession > The following packages will be REMOVED: > libxcb-xf86dri0{u} libxcb-xv0{u} > 0 packages upgraded, 36 newly installed, 2 to remove and 2 not upgraded. > Need to get 133 MB of archives. After unpacking 560 MB will be used. > Do you want to continue? [Y/n/?] HTH, 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 This message (and any attachments) is for the recipient only. NERC is subject to the Freedom of Information Act 2000 and the contents of this email and any reply you make may be disclosed by NERC unless it is exempt from release under the Act. Any material supplied to NERC may be stored in an electronic records management system. From tony.travis at abdn.ac.uk Wed Mar 18 07:03:22 2015 From: tony.travis at abdn.ac.uk (Tony Travis) Date: Wed, 18 Mar 2015 11:03:22 +0000 Subject: [Bio-linux-dev] "x2go-server" upgrade problems In-Reply-To: <8C33D34D431A974EAEA913101DDA194407E83C9E06@nerckwmbc.ad.nerc.ac.uk> References: <5506B3A8.8060208@abdn.ac.uk> <8C33D34D431A974EAEA913101DDA194407E83C9E06@nerckwmbc.ad.nerc.ac.uk> Message-ID: <55095B7A.6080702@abdn.ac.uk> On 17/03/15 12:09, Booth, Timothy G. wrote: > Hi Tony, > > I had a look just now and I can install both the newest x2go and the > libxcb-xf86dri0 and libxcb-xv0 packages (which are needed for vlc and > a couple of other things) so I'm wondering if this is just a > transient issue with the package indices getting out-of-sync? > > If anyone else on the list is still seeing upgrade problems please > let me know. Hi, Tim. We had the same problem upgrading "x2go" on Mahendra Modi's server "Aryabhatta" at AAU in Jorhat - Just fixed it the same way... 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 Wed Mar 18 08:25:26 2015 From: tony.travis at abdn.ac.uk (Tony Travis) Date: Wed, 18 Mar 2015 12:25:26 +0000 Subject: [Bio-linux-dev] "x2go-server" upgrade problems In-Reply-To: <55095B7A.6080702@abdn.ac.uk> References: <5506B3A8.8060208@abdn.ac.uk> <8C33D34D431A974EAEA913101DDA194407E83C9E06@nerckwmbc.ad.nerc.ac.uk> <55095B7A.6080702@abdn.ac.uk> Message-ID: <55096EB6.3050405@abdn.ac.uk> On 18/03/15 11:03, Tony Travis wrote: > On 17/03/15 12:09, Booth, Timothy G. wrote: >> Hi Tony, >> >> I had a look just now and I can install both the newest x2go and the >> libxcb-xf86dri0 and libxcb-xv0 packages (which are needed for vlc and >> a couple of other things) so I'm wondering if this is just a >> transient issue with the package indices getting out-of-sync? >> >> If anyone else on the list is still seeing upgrade problems please >> let me know. > > Hi, Tim. > > We had the same problem upgrading "x2go" on Mahendra Modi's server > "Aryabhatta" at AAU in Jorhat - Just fixed it the same way... Hi, Tim. Same problem on Mahendra's other server "khorana" - fixed it now. 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.