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

[Brian Long]

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
<http://docbuilder.bioconductor.org:8080/job/maEndToEnd/label=winbuilder1/55/console>.
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
 ERROR
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,
Brian

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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