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

CarlosBorrotoCarlosBorroto Posts: 33Member
edited February 24 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

Post edited by CarlosBorroto on
Tagged:

Answers

  • byb121byb121 UKPosts: 21Member
    edited March 10

    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,

    Post edited by byb121 on
  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,169Administrator, GATK Developer 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

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