[Bioc-devel] winbuilder1 in the workflow CI system offline ...

Brian Long brian at bioconductor.org
Wed Dec 2 22:08:40 CET 2015

Hi Bernd,

I've restarted winbuilder1.bioconductor.org .  Jenkins seemed to reconnect
to it as soon as it was back online, and your job started running
It's completed now.  Sad to say it seems to have failed (unrelated to the
Windows node) .  I remember some discussion about changes in `select()`,
but am not very familiar with those changes :

+ C:/Progra~1/R/R-3.2.2patched/bin/R CMD build c:/DOCBUILDER_TEMP/maEndToEnd

* checking for file 'c:/DOCBUILDER_TEMP/maEndToEnd/DESCRIPTION' ... OK
* preparing 'maEndToEnd':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ...Warning: running command
'"C:/Progra~1/R/R-3.2.2patched/bin/x64/Rscript" --vanilla
--default-packages= -e "tools::buildVignettes(dir = '.', tangle =
TRUE)"' had status 1
trying URL 'http://www.ebi.ac.uk/arrayexpress/files/A-AFFY-141/A-AFFY-141.adf.txt'
Content type 'text/plain' length 94175098 bytes (89.8 MB)
downloaded 89.8 MB

trying URL 'http://www.ebi.ac.uk/arrayexpress/files/E-MTAB-2967/E-MTAB-2967.sdrf.txt'
Content type 'text/plain' length 22516 bytes (21 KB)
downloaded 21 KB

trying URL 'http://www.ebi.ac.uk/arrayexpress/files/E-MTAB-2967/E-MTAB-2967.idf.txt'
Content type 'text/plain' length 3407 bytes
downloaded 3407 bytes

trying URL 'http://www.ebi.ac.uk/arrayexpress/files/E-MTAB-2967/E-MTAB-2967.raw.1.zip'
Content type 'application/zip' length 186452879 bytes (177.8 MB)
downloaded 177.8 MB

trying URL 'http://www.ebi.ac.uk/arrayexpress/files/E-MTAB-2967/E-MTAB-2967.raw.2.zip'
Content type 'application/zip' length 38447870 bytes (36.7 MB)
downloaded 36.7 MB

'select()' returned 1:many mapping between keys and columns
Quitting from lines 229-264 (dummy-Workflow.Rmd)
Error: processing vignette 'dummy-Workflow.Rmd' failed with diagnostics:
invalid genes selected
Execution halted
Build step 'Execute shell' marked build as failure

Hope this helps,

On Wed, Dec 2, 2015 at 3:54 PM, Brian Long <brian at bioconductor.org> wrote:

> Hi Bernd,
> We're working to resolve this issue.  We'll let you know once it's fixed
> and thank you for bringing it to our attention.
> Thanks,
> Brian
> On Wed, Dec 2, 2015 at 3:36 PM, Bernd Klaus <bernd.klaus at embl.de> wrote:
>> Dear all,
>> unfortunately, winbuilder1 is offline since a day or so,
>> so that new submissions to the svn are cannot be build in
>> the Jenkins system for the workflows.
>> Does anyone know when he will (most likely) be back up?
>> Thanks and best wishes,
>> Bernd
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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