Namespaces in Imports field not imported from:
  ‘TCGAbiolinks’ ‘gdata’ ‘genefilter’ ‘maftools’ ‘readxl’
  All declared Imports should be used.
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
Namespaces in Imports field not imported from:
  ‘TCGAbiolinks’ ‘gdata’ ‘genefilter’ ‘maftools’ ‘readxl’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'TCGAbiolinks' 'gdata' 'genefilter' 'maftools' 'readxl'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘TCGAbiolinks’ ‘gdata’ ‘genefilter’ ‘maftools’ ‘readxl’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘TCGAbiolinks’ ‘gdata’ ‘genefilter’ ‘maftools’ ‘readxl’
  All declared Imports should be used.
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.
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