Problems running upgrade script

[Tim Booth]

Bug reported by TT:

Hi, Tim.

I've just done a Bio-Linux 7 upgrade on a clean install of 64-bit Ubuntu
12.04 LTS server, using your script and had some problems:

[...]
> dpkg: dependency problems prevent configuration of bio-linux-emboss:
> bio-linux-emboss depends on emboss (>= 6.5.0); however:
> Package emboss is not installed.
> bio-linux-emboss depends on emboss-doc (>= 6.5.0); however:
> Package emboss-doc is not installed.
> bio-linux-emboss depends on jemboss (>= 6.5.0); however:
> Package jemboss is not installed.
> bio-linux-emboss depends on embassy-domainatrix; however:
> Package embassy-domainatrix is not installed.
> bio-linux-emboss depends on embassy-domalign; however:
> Package embassy-domalign is not installed.
> bio-linux-emboss depends on embassy-domsearch; however:
> Package embassy-domsearch is not installed.
> bio-linux-emboss depends on embassy-phylip; however:
> Package embassy-phylip is not installed.
> bio-linux-emboss depends on clustalw; however:
> Package clustalw is not installed.
> dpkg: error processing bio-linux-emboss (--install):
> dependency problems - leaving unconfigured
> dpkg: dependency problems prevent configuration of bio-linux-estscan:
> bio-linux-estscan depends on estscan2; however:
> Package estscan2 is not installed.
> dpkg: error processing bio-linux-estscan (--install):
> dependency problems - leaving unconfigured
> Setting up bio-linux-keyring (5) ...
> gpg: key "EADA2460" not found: eof
> gpg: EADA2460: delete key failed: eof
> OK
> OK
> OK
> dpkg: dependency problems prevent configuration of bio-linux-mothur:
> bio-linux-mothur depends on mothur (>= 1.27.0); however:
> Package mothur is not installed.
> dpkg: error processing bio-linux-mothur (--install):
> dependency problems - leaving unconfigured
> dpkg: dependency problems prevent configuration of bio-linux-paml:
> bio-linux-paml depends on paml; however:
> Package paml is not installed.
> bio-linux-paml depends on paml-doc; however:
> Package paml-doc is not installed.
> bio-linux-paml depends on paml-data-extra; however:
> Package paml-data-extra is not installed.
> dpkg: error processing bio-linux-paml (--install):
> dependency problems - leaving unconfigured
> dpkg: dependency problems prevent configuration of bio-linux-prank:
> bio-linux-prank depends on prank (>= 0.0.120716); however:
> Package prank is not installed.
> dpkg: error processing bio-linux-prank (--install):
> dependency problems - leaving unconfigured
> dpkg: dependency problems prevent configuration of bio-linux-rdp-classifier:
> bio-linux-rdp-classifier depends on rdp-classifier; however:
> Package rdp-classifier is not installed.
> bio-linux-rdp-classifier depends on rdp-classifier-doc; however:
> Package rdp-classifier-doc is not installed.
> dpkg: error processing bio-linux-rdp-classifier (--install):
> dependency problems - leaving unconfigured
> dpkg: dependency problems prevent configuration of bio-linux-seaview:
> bio-linux-seaview depends on seaview; however:
> Package seaview is not installed.
> dpkg: error processing bio-linux-seaview (--install):
> dependency problems - leaving unconfigured
> dpkg: dependency problems prevent configuration of bio-linux-transterm-hp:
> bio-linux-transterm-hp depends on transtermhp; however:
> Package transtermhp is not installed.
> dpkg: error processing bio-linux-transterm-hp (--install):
> dependency problems - leaving unconfigured
> dpkg: dependency problems prevent configuration of bio-linux-trnascan:
> bio-linux-trnascan depends on trnascan-se; however:
> Package trnascan-se is not installed.
> dpkg: error processing bio-linux-trnascan (--install):
> dependency problems - leaving unconfigured
> dpkg: dependency problems prevent configuration of bio-linux-wise2:
> bio-linux-wise2 depends on wise; however:
> Package wise is not installed.
> bio-linux-wise2 depends on wise-doc; however:
> Package wise-doc is not installed.
> dpkg: error processing bio-linux-wise2 (--install):
> dependency problems - leaving unconfigured
> Errors were encountered while processing:
> bio-linux-emboss
> bio-linux-estscan
> bio-linux-mothur
> bio-linux-paml
> bio-linux-prank
> bio-linux-rdp-classifier
> bio-linux-seaview
> bio-linux-transterm-hp
> bio-linux-trnascan
> bio-linux-wise2
    [...]
> dpkg: libgd2-noxpm: dependency problems, but removing anyway as you requested:^M
> emboss-lib depends on libgd2-noxpm (>= 2.0.36~rc1~dfsg) | libgd2-xpm (>= 2.0.36~rc1~dfsg); however:^M
> Package libgd2-noxpm is to be removed.^M
> Package libgd2-xpm is not installed.^M

[Tim Booth (tbooth)]

Hi Tony,

This is not the same bug, as it's not reporting any problems with R/CRAN
packages. I've made a new bug report.

All these look like warnings to me - the dependency problems are
expected but should be mopped up later in the script. And the final
warning is about swapping libgd2-noxpm for libgd2-xpm which is expected
behaviour.

Where does the thing actually stick? Does it bomb out after the final
output you sent?

Cheers,

TIM

On Tue, 2012-10-09 at 18:35 +0100, Tony Travis wrote:
> On 09/10/12 12:28, Tim Booth wrote:
> > Marked as solved. Thanks for reporting this issue.
>
> Hi, Tim.
>
> I've just done a Bio-Linux 7 upgrade on a clean install of 64-bit Ubuntu
> 12.04 LTS server, using your script and had some problems:
>
> > dpkg: dependency problems prevent configuration of bio-linux-emboss:
> > bio-linux-emboss depends on emboss (>= 6.5.0); however:
> > Package emboss is not installed.
> > bio-linux-emboss depends on emboss-doc (>= 6.5.0); however:
> > Package emboss-doc is not installed.
> > bio-linux-emboss depends on jemboss (>= 6.5.0); however:
> > Package jemboss is not installed.
> > bio-linux-emboss depends on embassy-domainatrix; however:
> > Package embassy-domainatrix is not installed.
> > bio-linux-emboss depends on embassy-domalign; however:
> > Package embassy-domalign is not installed.
> > bio-linux-emboss depends on embassy-domsearch; however:
> > Package embassy-domsearch is not installed.
> > bio-linux-emboss depends on embassy-phylip; however:
> > Package embassy-phylip is not installed.
> > bio-linux-emboss depends on clustalw; however:
> > Package clustalw is not installed.
> > dpkg: error processing bio-linux-emboss (--install):
> > dependency problems - leaving unconfigured
> > dpkg: dependency problems prevent configuration of bio-linux-estscan:
> > bio-linux-estscan depends on estscan2; however:
> > Package estscan2 is not installed.
> > dpkg: error processing bio-linux-estscan (--install):
> > dependency problems - leaving unconfigured
> > Setting up bio-linux-keyring (5) ...
> > gpg: key "EADA2460" not found: eof
> > gpg: EADA2460: delete key failed: eof
> > OK
> > OK
> > OK
> > dpkg: dependency problems prevent configuration of bio-linux-mothur:
> > bio-linux-mothur depends on mothur (>= 1.27.0); however:
> > Package mothur is not installed.
> > dpkg: error processing bio-linux-mothur (--install):
> > dependency problems - leaving unconfigured
> > dpkg: dependency problems prevent configuration of bio-linux-paml:
> > bio-linux-paml depends on paml; however:
> > Package paml is not installed.
> > bio-linux-paml depends on paml-doc; however:
> > Package paml-doc is not installed.
> > bio-linux-paml depends on paml-data-extra; however:
> > Package paml-data-extra is not installed.
> > dpkg: error processing bio-linux-paml (--install):
> > dependency problems - leaving unconfigured
> > dpkg: dependency problems prevent configuration of bio-linux-prank:
> > bio-linux-prank depends on prank (>= 0.0.120716); however:
> > Package prank is not installed.
> > dpkg: error processing bio-linux-prank (--install):
> > dependency problems - leaving unconfigured
> >...

[Tony Travis (ajtravis)]

On 10/10/12 11:08, Tim Booth wrote:
> Hi Tony,
>
> This is not the same bug, as it's not reporting any problems with R/CRAN
> packages. I've made a new bug report.

Hi, Tim.

Sorry about that - Hope I'm replying about the new bug now...

> All these look like warnings to me - the dependency problems are
> expected but should be mopped up later in the script. And the final
> warning is about swapping libgd2-noxpm for libgd2-xpm which is expected
> behaviour.

I think this is an error, not a warning:

   "dependency problems - leaving unconfigured"

> Where does the thing actually stick? Does it bomb out after the final
> output you sent?

It runs to completions, but I noticed the errors in the installation
log. Another issue is that although NX works, there is no logout button
on the NX Gnome. fall-back session. That means you have to terminate the
session to end it or disconnect leaving it running. I'll install Ubuntu
desktop to see if that fixes the problem and report back.

Bye,

   Tony

[Tim Booth (tbooth)]

Hi Tony,

> I think this is an error, not a warning:
>
> "dependency problems - leaving unconfigured"

This is actually a warning, in this context. Dpkg by itself doesn't know how to satisfy dependencies from APT repositories so it emits this message, then waits for apt-get to run later and clean up the mess. When apt-get runs it either decides that the dependency problems are unsolvable and removes the package or it fixes the dependencies, finishes the configuration, and everything is fine. The underlying problem is that these packages should be in the repository with all their friends, and I will do that, but this will also cause warnings to appear in the update manager for existing users of BL6. So I'm holding off until I have properly announced the update instructions and advised people of what is going on.

A sticking plaster fix would be to hide these messages when the script runs, but then I risk losing genuinely useful info.

Thanks for looking into NX. My priorities are the bootable ISO (I have a working version but it's not yet fit for release) and sorting the obvious problems with Galaxy server, but a properly working NX is important before I can call BL7 done.

Cheers,

TIM

[Tim Booth (tbooth)]

The log messages are misleading but I want them for debugging. Therefore I'll just document that users should ignore these.

Also once I tidy up the repo a lot of these warnings will go away.

[Tony Travis (ajtravis)]

On 30/10/12 15:49, Tim Booth wrote:
> The log messages are misleading but I want them for debugging.
> Therefore I'll just document that users should ignore these.
>
> Also once I tidy up the repo a lot of these warnings will go away.
>
> ** Changed in: bio-linux
> Status: New => Won't Fix
>

Hi, Tim.

We've got a problem that is not Bio-Linux related, but might have an
impact on people's perception of the stability of Bio-Linux under NX.

One computer-literate biologist here told me that he thought it was a
reason for him not to use Bio-Linux on our servers...

I pointed out that this is actually a bug in Ubuntu, not Bio-Linux:

Bye,

   Tony.

> Problems with Gnome-fallback Indicator-session crashing
> root@bifx-rta:~# tail -4 /var/log/kern.log
> Oct 30 08:19:38 bifx-rta kernel: [1712165.082612] indicator-sessi[46007] trap int3 ip:7f12e7a26fdb sp:7ffff3e609b0 error:0
> Oct 30 08:46:24 bifx-rta kernel: [1713771.117436] indicator-sessi[47528] trap int3 ip:7feb7a056fdb sp:7fff7dc33cc0 error:0
> Oct 30 09:29:33 bifx-rta kernel: [1716359.192861] indicator-sessi[51908] trap int3 ip:7fb85d93efdb sp:7fffb1ae14c0 error:0
> Oct 30 09:59:38 bifx-rta kernel: [1718164.194575] indicator-sessi[56721] trap int3 ip:7ff3478aefdb sp:7fff910ea690 error:0
>
>
> root@bifx-rta:~# dpkg -S indicator-session
> indicator-session: /usr/share/doc/indicator-session/copyright
> indicator-session: /usr/share/doc/indicator-session/AUTHORS
> indicator-session: /usr/share/doc/indicator-session
> indicator-session: /usr/lib/indicator-session
> indicator-session: /usr/share/doc/indicator-session/changelog.Debian.gz
> indicator-session: /usr/lib/indicator-session/indicator-session-service
> indicator-session: /usr/share/dbus-1/services/indicator-session.service
> indicator-session: /usr/share/GConf/gsettings/indicator-session.convert
> indicator-session: /usr/lib/indicator-session/gtk-logout-helper
>
> root@bifx-rta:~# apt-cache rdepends indicator-session
> indicator-session
> Reverse Depends:
> unity-2d-panel
> libdbusmenu-glib4:i386
> unity-greeter
> unity-2d-panel
> unity
> libdbusmenu-glib4
> indicator-session-gtk2:i386
> libdbusmenu-glib4:i386
> indicator-session:i386
> indicator-session-gtk2
> indicator-session-gtk2
> indicator-applet-session
> indicator-applet-complete
> unity-greeter
> unity-2d-panel
> unity
> libdbusmenu-glib4
>
> # Try re-installing indicator-applet
> aptitude purge indicator-applet
> aptitude install indicator-applet