[Biopython-dev] Travis-CI failing due to t-coffee dependency

[Eric Talevich]

On Sat, Aug 2, 2014 at 9:56 PM, Evan Parker <eparker05 at gmail.com> wrote:

> Hey Biopython-Dev,
>
> I was pushing some commits today and I noticed failures on Travis-CI due
> to dependency failures. Travis was giving me the following error:
> * > The command "sudo apt-get install t-coffee
> *  muscle mafft probcons wise emboss" failed
> *  and exited with 100 during .
> I have a link to the error below. I broke apart the dependencies and tried
> again and I identified t-coffee as the issue. I'm not exactly sure of how
> to proceed from this point or if others have experienced this or are
> currently experiencing this.
>
> A Travis-CI job that failed due to this error:
> https://travis-ci.org/eparker05/biopython/jobs/31520799
>
> My latest feature-branch commit that identified the specific Travis-CI
> dependency failure
>
> https://github.com/eparker05/biopython/commit/2149fa15e89bb6833097b8db74e3a77badac2ccd
>
> -Evan Parker
>
>
It looks like this affected all 5 builds on the two commits before your fix
(beginning within the last day), so I suppose it's not just a transient
network error on Travis's side?

The apt-get failure is for only one package in the main Ubuntu US
repository, libxml-sax-perl, which is a dependency of libxml-simple-perl
<http://packages.ubuntu.com/precise/libxml-simple-perl> which t-coffee
"recommends":
http://packages.ubuntu.com/precise/t-coffee

What if we tried adding the "--no-install-recommends" flag to the Travis
configuration?
"sudo apt-get install --no-install-recommends t-coffee"
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