Last updated on 2025-10-13 01:49:18 CEST.
| Package | ERROR | OK |
|---|---|---|
| oncoPredict | 8 | 5 |
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/RtmpX5f8O4 (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/Rtmpdh4OTf (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/RtmpwWiHSI (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/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
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/RtmpvODzgN/working_dir/RtmpUgyN6g (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/RtmpvODzgN/working_dir/RtmpHvfmKv (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/RtmpvODzgN/working_dir/Rtmpbjdzk7 (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