- using R Under development (unstable) (2025-10-21 r88957)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
clang version 21.1.2
flang version 21.1.2
- running under: Fedora Linux 42 (Workstation Edition)
- using session charset: UTF-8
- using option ‘--no-stop-on-test-error’
- checking for file ‘oncoPredict/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘oncoPredict’ version ‘1.2’
- package encoding: UTF-8
- checking package namespace information ... OK
- checking package dependencies ... OK
- checking if this is a source package ... OK
- checking if there is a namespace ... OK
- checking for executable files ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... OK
- checking whether package ‘oncoPredict’ can be installed ... [104s/280s] OK
See the install log for details.
- checking installed package size ... OK
- checking package directory ... OK
- checking ‘build’ directory ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking for left-over files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking code files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... [35s/96s] OK
- checking whether the package can be loaded with stated dependencies ... [33s/93s] OK
- checking whether the package can be unloaded cleanly ... [32s/74s] OK
- checking whether the namespace can be loaded with stated dependencies ... [33s/92s] OK
- checking whether the namespace can be unloaded cleanly ... [34s/82s] OK
- checking loading without being on the library search path ... [33s/100s] OK
- checking use of S3 registration ... OK
- checking dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... [141s/197s] OK
- checking Rd files ... OK
- checking Rd metadata ... OK
- checking Rd line widths ... OK
- checking Rd cross-references ... OK
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... OK
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- checking for unstated dependencies in examples ... OK
- checking installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... NONE
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [252s/261s] ERROR
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/RtmpVdwzhT/working_dir/RtmpCsh9jB (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/RtmpVdwzhT/working_dir/Rtmp7MeSKn (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/RtmpVdwzhT/working_dir/RtmpGz7wJY (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
- checking PDF version of manual ... OK
- checking HTML version of manual ... OK
- checking for non-standard things in the check directory ... OK
- checking for detritus in the temp directory ... OK
- DONE
Status: 1 ERROR