Last updated on 2025-10-23 07:49:54 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.2 | 57.20 | 584.16 | 641.36 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.2 | 41.35 | 422.62 | 463.97 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.2 | 367.00 | 736.60 | 1103.60 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 1.2 | 253.00 | 802.92 | 1055.92 | ERROR | |
| r-devel-windows-x86_64 | 1.2 | 58.00 | 475.00 | 533.00 | OK | |
| r-patched-linux-x86_64 | 1.2 | 57.36 | 562.54 | 619.90 | OK | |
| r-release-linux-x86_64 | 1.2 | 53.54 | 562.15 | 615.69 | OK | |
| r-release-macos-arm64 | 1.2 | 5.00 | ERROR | |||
| r-release-macos-x86_64 | 1.2 | 8.00 | 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 | 13.00 | ERROR | |||
| r-oldrel-windows-x86_64 | 1.2 | 81.00 | 633.00 | 714.00 | 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/RtmpgpTNbG (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/Rtmpgo4ZnT (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/RtmprpnfWu (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: HTML version of manual
Result: NOTE
Found the following HTML validation problems:
glds.html:81:1 (glds.Rd:33): Warning: missing </ul> before </div>
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/RtmpTZRqda (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/RtmpSUPiRo (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/RtmpSJtAdv (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/RtmpTiN7yF/working_dir/Rtmp8LMRdH (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/RtmpTiN7yF/working_dir/Rtmp04nTyN (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/RtmpTiN7yF/working_dir/RtmpiFmhYO (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/RtmpbCNcM1/working_dir/Rtmp4tVzsP (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/RtmpbCNcM1/working_dir/Rtmp1s2n88 (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/RtmpbCNcM1/working_dir/Rtmp6GGQ96 (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