CRAN Package Check Results for Package oncoPredict

Last updated on 2021-09-18 10:52:48 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.1 50.55 544.77 595.32 OK
r-devel-linux-x86_64-debian-gcc 0.1 44.11 406.83 450.94 OK
r-devel-linux-x86_64-fedora-clang 0.1 719.69 WARN
r-devel-linux-x86_64-fedora-gcc 0.1 716.95 NOTE
r-devel-windows-x86_64 0.1 64.00 608.00 672.00 OK
r-devel-windows-x86_64-gcc10-UCRT 0.1 NOTE
r-patched-linux-x86_64 0.1 52.80 572.87 625.67 OK
r-patched-solaris-x86 0.1 704.90 NOTE
r-release-linux-x86_64 0.1 48.21 570.51 618.72 OK
r-release-macos-arm64 0.1 NOTE
r-release-macos-x86_64 0.1 ERROR
r-release-windows-ix86+x86_64 0.1 121.00 482.00 603.00 WARN

Check Details

Version: 0.1
Check: dependencies in R code
Result: NOTE
    Namespaces in Imports field not imported from:
     ‘TCGAbiolinks’ ‘gdata’ ‘genefilter’ ‘maftools’ ‘readxl’
     All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64-gcc10-UCRT, r-patched-solaris-x86, r-release-macos-arm64

Version: 0.1
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘calcPhenotype.Rmd’ using rmarkdown
    Warning in in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE, :
     You changed the working directory to /tmp/RtmpYv6J9y/working_dir/RtmpCKntJc (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
    --- finished re-building ‘calcPhenotype.Rmd’
    
    --- re-building ‘cnv.Rmd’ using rmarkdown
    Warning in in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE, :
     You changed the working directory to /tmp/RtmpYv6J9y/working_dir/RtmpCKntJc (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
    --- finished re-building ‘cnv.Rmd’
    
    --- re-building ‘glds.Rmd’ using rmarkdown
    Warning in in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE, :
     You changed the working directory to /tmp/RtmpYv6J9y/working_dir/RtmpCKntJc (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
    --- finished re-building ‘glds.Rmd’
    
    --- re-building ‘mut.Rmd’ using rmarkdown
    Quitting from lines 18-58 (mut.Rmd)
    Error: processing vignette 'mut.Rmd' failed with diagnostics:
    GDC server down, try to use this package later
    --- failed re-building ‘mut.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘mut.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 0.1
Check: package dependencies
Result: ERROR
    Packages required but not available:
     'org.Hs.eg.db', 'TxDb.Hsapiens.UCSC.hg19.knownGene', 'maftools',
     'TCGAbiolinks'
    
    See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
    manual.
Flavor: r-release-macos-x86_64

Version: 0.1
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building 'calcPhenotype.Rmd' using rmarkdown
    Warning in in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE, :
     You changed the working directory to D:/temp/Rtmpq0tgQ1 (probably via setwd()). It will be restored to d:/RCompile/CRANpkg/local/4.1/oncoPredict.Rcheck/vign_test/oncoPredict/vignettes. See the Note section in ?knitr::knit
    --- finished re-building 'calcPhenotype.Rmd'
    
    --- re-building 'cnv.Rmd' using rmarkdown
    Warning in in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE, :
     You changed the working directory to D:/temp/RtmpQVJw1p (probably via setwd()). It will be restored to d:/RCompile/CRANpkg/local/4.1/oncoPredict.Rcheck/vign_test/oncoPredict/vignettes. See the Note section in ?knitr::knit
    --- finished re-building 'cnv.Rmd'
    
    --- re-building 'glds.Rmd' using rmarkdown
    Warning in in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE, :
     You changed the working directory to D:/temp/Rtmp8GFvH9 (probably via setwd()). It will be restored to d:/RCompile/CRANpkg/local/4.1/oncoPredict.Rcheck/vign_test/oncoPredict/vignettes. See the Note section in ?knitr::knit
    --- finished re-building 'glds.Rmd'
    
    --- re-building 'mut.Rmd' using rmarkdown
    Quitting from lines 18-58 (mut.Rmd)
    Error: processing vignette 'mut.Rmd' failed with diagnostics:
    GDC server down, try to use this package later
    --- failed re-building 'mut.Rmd'
    
    SUMMARY: processing the following file failed:
     'mut.Rmd'
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-release-windows-ix86+x86_64