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

[Peter Cock]

On Sun, Aug 3, 2014 at 5:21 PM, Eric Talevich <eric.talevich at gmail.com> wrote:
> 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

Thanks Evan,

Maybe we should try getting TravisCI failure emails onto the mailing list...
although in this case we've not update the Biopython master branch in
this time period, so still would not have seen this problem yet.

> 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
> 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"

Good question Eric - let's find out (testing on a personal branch):

https://github.com/peterjc/biopython/commit/f4d510be1651ce8ba99906ba71e85841df0b4e07
https://travis-ci.org/peterjc/biopython/builds/31598172

That seems to work, so I applied it to the master branch with a
slightly more explicit commit comment:

https://travis-ci.org/biopython/biopython/builds/31598949
https://github.com/biopython/biopython/commit/091f4f8e9ec1808265c52c9de68090a9ef531684

Chris - since we're not using any of these optional bits of T-COFFEE
in our test suite, we don't need to try installing them via cpanm - but
that trick may be needed on another dependency one day.

Thanks all,

Peter