CRAN Package Check Results for Maintainer ‘Robert Gruener <rgruener at umn.edu>’

Last updated on 2025-10-10 15:50:25 CEST.

Package	ERROR	OK
oncoPredict	8	5

Package oncoPredict

Current CRAN status: ERROR: 8, OK: 5

Version: 1.2
Check: re-building of vignette outputs
Result: 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 /home/hornik/tmp/scratch/RtmpLsLOjT (probably via setwd()). It will be restored to /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/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 /home/hornik/tmp/scratch/Rtmpxq6Awi (probably via setwd()). It will be restored to /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/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 /home/hornik/tmp/scratch/Rtmp92QZ4k (probably via setwd()). It will be restored to /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/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 Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.2
Check: re-building of vignette outputs
Result: 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/RtmpRjmNST (probably via setwd()). It will be restored to /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/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/Rtmpm5J3ip (probably via setwd()). It will be restored to /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/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/RtmpsgD5pa (probably via setwd()). It will be restored to /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/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 Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.2
Check: re-building of vignette outputs
Result: 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/RtmpyJM7ei/working_dir/RtmpcJpPR0 (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/RtmpyJM7ei/working_dir/RtmpDnDwEa (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/RtmpyJM7ei/working_dir/RtmpLQl0RC (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 Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.2
Check: re-building of vignette outputs
Result: 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/RtmpKmQRtX/working_dir/Rtmp9TkZhB (probably via setwd()). It will be restored to /data/gannet/ripley/R/packages/tests-devel/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/RtmpKmQRtX/working_dir/Rtmp1Jp2Os (probably via setwd()). It will be restored to /data/gannet/ripley/R/packages/tests-devel/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/RtmpKmQRtX/working_dir/RtmprLpkBz (probably via setwd()). It will be restored to /data/gannet/ripley/R/packages/tests-devel/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 Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 1.2
Check: package dependencies
Result: ERROR Packages required but not available: 'org.Hs.eg.db', 'TxDb.Hsapiens.UCSC.hg19.knownGene', 'TCGAbiolinks' See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. Flavor: r-release-macos-arm64

Version: 1.2
Check: package dependencies
Result: ERROR Packages required but not available: 'TxDb.Hsapiens.UCSC.hg19.knownGene', 'TCGAbiolinks' See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. Flavors: r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64