crashed on upgrade - unresolvable dependencies

[cement_head]

The script crashed on me, but asked me to reboot and run again, which I did and it seemed to pick up where I left off.

I do get one error message that I can't solve:

Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:

The following packages have unmet dependencies:
 galaxy-server-all : Depends: python-rpy but it is not going to be installed
                     Recommends: ucsc-tools-non-free but it is not installable
                     Recommends: laj but it is not installable
E: Unable to correct problems, you have held broken packages.
Not all packages installed properly - exiting.

Attempting to install python-rpy fails as it claims that it will break r-base.

Any Ideas?

Thanks,
CH

[Tony Travis (ajtravis)]

On 02/10/12 18:51, cement_head wrote:
> Public bug reported:
>
> The script crashed on me, but asked me to reboot and run again, which I
> did and it seemed to pick up where I left off.
>
> I do get one error message that I can't solve:
>
> Some packages could not be installed. This may mean that you have
> requested an impossible situation or if you are using the unstable
> distribution that some required packages have not yet been created
> or been moved out of Incoming.
> The following information may help to resolve the situation:
>
> The following packages have unmet dependencies:
> galaxy-server-all : Depends: python-rpy but it is not going to be installed
> Recommends: ucsc-tools-non-free but it is not installable
> Recommends: laj but it is not installable
> E: Unable to correct problems, you have held broken packages.
> Not all packages installed properly - exiting.
>
> Attempting to install python-rpy fails as it claims that it will break
> r-base.
>
> Any Ideas?

Hi,

Try forcing a check of APT consistency using:

   aptitude update
   aptitude -f install

The "-f" option means makes "aptitude" try hard to fix the dependencies
of broken packages. In this respect, "aptitude" is more robust than
"apt-get". Indeed, aptitude is the recommended package manager for
Debian GNU/Linux systems:

   http://www.debian.org/doc/manuals/debian-faq/ch-uptodate.en.html

Unfortunately, "aptitude" is not installed by default in Ubuntu 12.04
LTS Desktop.

HTH,

   Tony.

[Tim Booth (tbooth)]

Hi,

I recognise this problem. It's one I thought I'd resolved and it won't be fixed by using aptitude instead of apt-get.

You can diagnose it using:

  apt-cache policy r-base

And you should, all being well, see this:

tbooth@balisaur[gwt]apt-cache policy r-base
r-base:
  Installed: 2.15.1-1precise2
  Candidate: 2.15.1-1precise2
  Version table:
 *** 2.15.1-1precise2 0
        500 http://www.stats.bris.ac.uk/R/bin/linux/ubuntu/ precise/ Packages
        100 /var/lib/dpkg/status
     2.15.0-1precise0 0
        500 http://www.stats.bris.ac.uk/R/bin/linux/ubuntu/ precise/ Packages
     2.14.1-1 0
        500 http://gb.archive.ubuntu.com/ubuntu/ precise/universe amd64 Packages

So on my test machine, the CRAN package repository is set up and providing R version 2.15.1. You, unless I'm much mistaken, won't see any of the stats.bris.ac.uk lines and furthermore you'll see that the "Installed" version doesn't match the version from gb.archive.ubuntu.com. This is the problem, and you have two options to fix it:

1 - apt-get remove r-base and r-base core, then install python-rpy using apt-get (or aptitude). This should install the default, older Ubuntu-supported version of R and everything will then be fine.

or

2 - add the CRAN repository lines to /etc/apt/sources.list.d/bio-linux.list - we use the UK mirror by default but you can use whatever you like:

#UK mirror for R-cran packages
deb http://www.stats.bris.ac.uk/R/bin/linux/ubuntu precise/
deb-src http://www.stats.bris.ac.uk/R/bin/linux/ubuntu precise/

This gives you the default Bio-Linux setup.

Now the upgrade script is supposed to detect if you are using CRAN or not and stick with that set-up, so I'm not sure what went wrong here. I could have it remove R before the update and then put it back but this seems like a kludge. I'll wait for you to confirm if my diagnosis is right and then try and have another look and see if I can spot the problem.

Cheers,

TIM

[cement_head (andorjkiss)]

Hi,

Okay, so I re-enabled the CRAN repositories (disabled on upgrade) and changed the version to precise:

#UK mirror for R-cran packages
deb http://www.stats.bris.ac.uk/R/bin/linux/ubuntu precise/
deb-src http://www.stats.bris.ac.uk/R/bin/linux/ubuntu precise/

The I did:

$ sudo apt-get update
$ sudo apt-get upgrade

Once that completed and upgraded all the R packages, I re-ran the bio-linux 7 upgrade script.

This completed and I am now on bio-linux 7 from bio-linux 6. And I did have quite a few thrid-party PPAs (compiz, X-SWAT, to name a few).

Looking forward to using the new bio-linux 7!

Also, will try upgrading / converting a 12.04 machine to bio-linux 7 soon.

Regards,
CH

[cement_head (andorjkiss)]

Please mark as solved for me.

[Tim Booth (tbooth)]

Marked as solved. Thanks for reporting this issue.

TIM

[Tony Travis (ajtravis)]

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
> 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-seavie...

[Tim Booth (tbooth)]

Created a new bug report for Ton's comment as this is not an R/CRAN issue. Leaving this bug closed.