CRAN Package Check Results for Package oncoPredict

Last updated on 2025-10-09 20:04:14 CEST.

Flavor	Version	Tinstall	Tcheck	Ttotal	Status	Flags
r-devel-linux-x86_64-debian-clang	1.2	58.20	590.76	648.96	OK
r-devel-linux-x86_64-debian-gcc	1.2	39.88	425.51	465.39	ERROR
r-devel-linux-x86_64-fedora-clang	1.2			1057.65	ERROR
r-devel-linux-x86_64-fedora-gcc	1.2			1052.92	ERROR
r-devel-windows-x86_64	1.2	59.00	474.00	533.00	OK
r-patched-linux-x86_64	1.2	51.69	562.87	614.56	OK
r-release-linux-x86_64	1.2	54.61	562.07	616.68	OK
r-release-macos-arm64	1.2			5.00	ERROR
r-release-macos-x86_64	1.2			14.00	ERROR
r-release-windows-x86_64	1.2	59.00	471.00	530.00	OK
r-oldrel-macos-arm64	1.2			9.00	ERROR
r-oldrel-macos-x86_64	1.2			12.00	ERROR
r-oldrel-windows-x86_64	1.2	78.00	638.00	716.00	OK

Check Details

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/Rtmp85QAaP/working_dir/RtmpkavpCQ (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/Rtmp85QAaP/working_dir/Rtmp3DLl7g (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/Rtmp85QAaP/working_dir/RtmpTaJ0sc (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/RtmpYcZiCT/working_dir/RtmpI1EtdV (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/RtmpYcZiCT/working_dir/RtmphY7Jc1 (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/RtmpYcZiCT/working_dir/RtmpcXJiIv (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