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Plotting queue job report fails. Rscript can't find function 'arrow'.

CarlosBorrotoCarlosBorroto Member Posts: 46
edited February 2014 in Ask the GATK team

Hi,

I found if I add library(grid) to gatk-protected / public / R / scripts / org / broadinstitute / sting / queue / util / queueJobReport.R the error goes away.

INFO  15:49:53,263 QCommandLine - Writing final jobs report...
INFO  15:49:53,263 QJobsReporter - Writing JobLogging GATKReport to file /Users/cborroto/workspace/sciencemodule/data_processing/GenePeeksPipeline.jobreport.txt
INFO  15:49:53,270 QJobsReporter - Plotting JobLogging GATKReport to file /Users/cborroto/workspace/sciencemodule/data_processing/GenePeeksPipeline.jobreport.pdf
DEBUG 15:49:53,278 RScriptExecutor - Executing:
DEBUG 15:49:53,278 RScriptExecutor -   Rscript
DEBUG 15:49:53,278 RScriptExecutor -   -e
DEBUG 15:49:53,278 RScriptExecutor -   tempLibDir = '/Users/cborroto/workspace/sciencemodule/data_processing/tmp/Rlib.5689446532231761075';install.packages(pkgs=c('/Users/cborroto/workspace/sciencemodule/data_processing/tmp/RlibSources.4324191911112824298/gsalib'), lib=tempLibDir, repos=NULL, type='source', INSTALL_opts=c('--no-libs', '--no-data', '--no-help', '--no-demo', '--no-exec'));library('gsalib', lib.loc=tempLibDir);source('/Users/cborroto/workspace/sciencemodule/data_processing/tmp/queueJobReport.6856864909021911181.R');
DEBUG 15:49:53,278 RScriptExecutor -   /Users/cborroto/workspace/sciencemodule/data_processing/GenePeeksPipeline.jobreport.txt
DEBUG 15:49:53,278 RScriptExecutor -   /Users/cborroto/workspace/sciencemodule/data_processing/GenePeeksPipeline.jobreport.pdf
* installing *source* package ‘gsalib’ ...
** R
** preparing package for lazy loading
** building package indices
** testing if installed package can be loaded
* DONE (gsalib)
Loading required package: methods
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
Attaching package: ‘gplots’
The following object is masked from ‘package:stats’:
    lowess
Loading required package: plyr
Attaching package: ‘reshape’
The following objects are masked from ‘package:plyr’:
    rename, round_any
[1] "Report"
[1] "Project          : /Users/cborroto/workspace/sciencemodule/data_processing/GenePeeksPipeline.jobreport.txt"
Error in do.call("layer", list(mapping = mapping, data = data, stat = stat,  :
  could not find function "arrow"
Calls: source ... geom_segment -> <Anonymous> -> <Anonymous> -> do.call
Execution halted
DEBUG 15:49:55,207 RScriptExecutor - Result: 1
WARN  15:49:55,207 RScriptExecutor - RScript exited with 1

Thanks,
Carlos

Tagged:

Answers

  • byb121byb121 UKMember Posts: 24
    edited March 2014

    Hi,

    I have bumped into the same problem, exactly the same error. It seems the R script is not available on the GATK github anymore. Another workaround is to add 'grid' to default library list so it can be preloaded into R.

    I hope the requirements of running the Rscript (the one that produces Qscript job report, if there are other R scripts) can be described somewhere on this forum/website, although I understand this is not really a major concern.

    Thanks,

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,633 admin

    Hi there,

    I will put this on the documentation to-do list. To be honest this is not a priority, so it may be a while, but we will get it done eventually.

    Geraldine Van der Auwera, PhD

  • holgerbrandlholgerbrandl DresdenMember Posts: 2

    Hi,

    I've just started to work with QUeue and I've also stumbled over the problem, and indeed adding library(grid) is solving the problem. Do you accept pull requests on github to fix this and similar problems? The development there seems to be halted at he moment since there was no commit in the last six months.

    Thanks

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,633 admin

    @holgerbrandl yes we do take pull requests, thank you. Queue is pretty stable so there's not much development happening there, but improvements are always welcome.

    Geraldine Van der Auwera, PhD

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