• 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