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

[Bernd Klaus]

Hi Brian,

thanks a lot for your prompt response!

The select warning is fine, I have probe IDs and want to
get gene symbols and then some probes map to multiple genes.

However, I am actually chasing a very strange bug that only 
appears on the build system and not on my own computer.

It essentially seems that an object is set to NULL somehow during
the execution. This seems to be related to the downloaded data 
in some way, but I will write a separate and more extensive email to
the devel mailing list about this shortly.

Thanks again and best wishes,

Bernd

On Mi, 2015-12-02 at 21:08 +0000, Brian Long wrote:
> 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
>  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-MTA
> B-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-MTA
> B-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-MTA
> B-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-MTA
> B-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
> > > 
> >