Plotting queue job report fails. Rscript can't find function 'arrow'.
Posted in Ask the GATK team | Last updated on 2014-02-24 22:45:40


Comments (2)

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


Return to top Comment on this article in the forum