Error(s) in re-building vignettes:
--- re-building ‘calcPhenotype.Rmd’ using rmarkdown
Warning in in_dir(input_dir(), expr) :
  You changed the working directory to /tmp/Rtmp5ZKysC/working_dir/RtmpYMEaF9 (probably via setwd()). It will be restored to /data/gannet/ripley/R/packages/tests-clang/oncoPredict.Rcheck/vign_test/oncoPredict/vignettes. See the Note section in ?knitr::knit
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘calcPhenotype.Rmd’

--- re-building ‘cnv.Rmd’ using rmarkdown

Quitting from cnv.Rmd:17-84 [setup]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `idwas()`:
! 
ERROR: A gene was not mutated in at least 10 patients. Recommend decreasing the n parameter.
---
Backtrace:
    ▆
 1. └─oncoPredict::idwas(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'cnv.Rmd' failed with diagnostics:

ERROR: A gene was not mutated in at least 10 patients. Recommend decreasing the n parameter.
--- failed re-building ‘cnv.Rmd’

--- re-building ‘glds.Rmd’ using rmarkdown
Warning in in_dir(input_dir(), expr) :
  You changed the working directory to /tmp/Rtmp5ZKysC/working_dir/RtmpqOYPLd (probably via setwd()). It will be restored to /data/gannet/ripley/R/packages/tests-clang/oncoPredict.Rcheck/vign_test/oncoPredict/vignettes. See the Note section in ?knitr::knit
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘glds.Rmd’

--- re-building ‘mut.Rmd’ using rmarkdown
Warning in in_dir(input_dir(), expr) :
  You changed the working directory to /tmp/Rtmp5ZKysC/working_dir/RtmpI5um1G (probably via setwd()). It will be restored to /data/gannet/ripley/R/packages/tests-clang/oncoPredict.Rcheck/vign_test/oncoPredict/vignettes. See the Note section in ?knitr::knit
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘mut.Rmd’

SUMMARY: processing the following file failed:
  ‘cnv.Rmd’

Error: Vignette re-building failed.
Execution halted