Last updated on 2025-10-11 12:49:37 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.2 | 58.77 | 598.01 | 656.78 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.2 | 43.40 | 420.25 | 463.65 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.2 | 954.85 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.2 | 1032.74 | ERROR | |||
| r-devel-windows-x86_64 | 1.2 | 57.00 | 470.00 | 527.00 | 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 | 7.00 | ERROR | |||
| r-release-windows-x86_64 | 1.2 | 59.00 | 471.00 | 530.00 | OK | |
| r-oldrel-macos-arm64 | 1.2 | 10.00 | 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 |
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/Rtmp9bdAB9 (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/RtmpNsgAnL (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/RtmpHEXXiT (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/RtmptForQ1/working_dir/Rtmpo4nLVc (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/RtmptForQ1/working_dir/RtmpFSdDK3 (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/RtmptForQ1/working_dir/RtmpipCey0 (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/Rtmpi7VMx3/working_dir/Rtmpgz3u91 (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/Rtmpi7VMx3/working_dir/RtmpoMYlg1 (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/Rtmpi7VMx3/working_dir/RtmpobDYoP (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