[Bioc-devel] Workflow builder failing at postprocessing step

[Andrzej Oleś]

Dear Leo,

I'm happy to inform you that the issues with updating workflows have been
resolved. Apart from the problems with the postprocessing step which was
looking for the now disabled mac tar balls, there was also a similar issue
with the bioconductor website building script which prevented the build
artifacts from propagating and updating on the website. All this is
hopefully fixed now, and you should be able to see your recent changes at
https://master.bioconductor.org/help/workflows/recountWorkflow/

Cheers,
Andrzej

On Thu, Oct 12, 2017 at 4:42 PM, Leonardo Collado Torres <lcollado at jhu.edu>
wrote:

> 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
> >>
> >> _______________________________________________
> >> Bioc-devel at r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
> >
>

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