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] Workflow builder failing at postprocessing step
4 messages · Leonardo Collado Torres, Andrzej Oleś
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
Thanks for looking into this Andrzej!
On Wed, Oct 11, 2017 at 6:02 PM, Andrzej Ole? <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
1 day later
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 Ole? <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