[Bioc-devel] Workflow builder failing at postprocessing step

[Leonardo Collado Torres]

Thanks for looking into this Andrzej!

On Wed, Oct 11, 2017 at 6:02 PM, Andrzej Oleś <andrzej.oles at gmail.com> wrote:
> Thanks Leo for drawing our attention to this issue. It will probably require
> some additional modifications to the postprocessing scripts in order to
> account for the now missing Mac tar balls. I will look into this.
>
> Cheers,
> Andrzej
>
> On Wed, Oct 11, 2017 at 8:09 PM, Leonardo Collado Torres <lcollado at jhu.edu>
> wrote:
>>
>> Hi,
>>
>> I recently pushed some changes to recountWorkflow** that triggered new
>> "postprocessing" jobs by the workflow builder. The last few (#412 up
>> to 415) failed and I can see at
>>
>> http://docbuilder.bioconductor.org:8080/job/postprocessing/label=master/415/console
>> that the error is related to the retirement of the Mac workflow build
>> machine:
>>
>> + true
>> + MACREPO=/var/lib/jenkins/repository/CRANrepo/3.6/bin/macosx/contrib/3.4
>> + mkdir -p /var/lib/jenkins/repository/CRANrepo/3.6/bin/macosx/contrib/3.4
>> + rm -f
>> /var/lib/jenkins/repository/CRANrepo/3.6/bin/macosx/contrib/3.4/recountWorkflow_*.tgz
>> + cp /var/lib/jenkins/repository/recountWorkflow/*.tgz
>> /var/lib/jenkins/repository/CRANrepo/3.6/bin/macosx/contrib/3.4
>> cp: cannot stat '/var/lib/jenkins/repository/recountWorkflow/*.tgz':
>> No such file or directory
>> Build step 'Execute shell' marked build as failure
>>
>> Hopefully the Mac tar ball part can be ignored for now. I just wanted
>> to check if the recount workflow looked ok after I made some changes
>> suggested by Andrzej in another thread
>> https://stat.ethz.ch/pipermail/bioc-devel/2017-August/011444.html.
>>
>>
>> Thanks,
>> Leo
>>
>> ** Changes I made are from versions 0.99.32 to 0.99.37
>> https://github.com/LieberInstitute/recountWorkflow/commits/master
>>
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>
>