Error(s) in re-building vignettes:
  ...
--- re-building ‘basis_comparison.Rmd’ using rmarkdown
data(canprot): attached environment "canprot"
human_base: 21006 proteins
human_additional: 71173 proteins
human_extra: 337 proteins
Quitting from lines 50-53 (basis_comparison.Rmd) 
Error: processing vignette 'basis_comparison.Rmd' failed with diagnostics:
object of type ‘closure’ is not subsettable
--- failed re-building ‘basis_comparison.Rmd’

--- re-building ‘colorectal.Rmd’ using rmarkdown
data(canprot): attached environment "canprot"
human_base: 21006 proteins
human_additional: 71173 proteins
human_extra: 337 proteins
lapply_canprot: loading CHNOSZ
lapply_canprot: loading canprot and setting up canprot environment
lapply_canprot: running 36 calculations on 2 cores
Quitting from lines 137-146 (colorectal.Rmd) 
Error: processing vignette 'colorectal.Rmd' failed with diagnostics:
object of type ‘closure’ is not subsettable
--- failed re-building ‘colorectal.Rmd’

--- re-building ‘hyperosmotic.Rmd’ using rmarkdown
data(canprot): attached environment "canprot"
human_base: 21006 proteins
human_additional: 71173 proteins
human_extra: 337 proteins
lapply_canprot: loading CHNOSZ
lapply_canprot: loading canprot and setting up canprot environment
lapply_canprot: running 26 calculations on 2 cores
--- finished re-building ‘hyperosmotic.Rmd’

--- re-building ‘hypoxia.Rmd’ using rmarkdown
data(canprot): attached environment "canprot"
human_base: 21006 proteins
human_additional: 71173 proteins
human_extra: 337 proteins
lapply_canprot: loading CHNOSZ
lapply_canprot: loading canprot and setting up canprot environment
lapply_canprot: running 31 calculations on 2 cores
--- finished re-building ‘hypoxia.Rmd’

--- re-building ‘pancreatic.Rmd’ using rmarkdown
data(canprot): attached environment "canprot"
human_base: 21006 proteins
human_additional: 71173 proteins
human_extra: 337 proteins
lapply_canprot: loading CHNOSZ
lapply_canprot: loading canprot and setting up canprot environment
lapply_canprot: running 23 calculations on 2 cores
--- finished re-building ‘pancreatic.Rmd’

--- re-building ‘potential_diagrams.Rmd’ using rmarkdown
data(canprot): attached environment "canprot"
human_base: 21006 proteins
human_additional: 71173 proteins
human_extra: 337 proteins
lapply_canprot: loading CHNOSZ
lapply_canprot: loading canprot and setting up canprot environment
lapply_canprot: running 8 calculations on 2 cores
lapply_canprot: loading CHNOSZ
lapply_canprot: loading canprot and setting up canprot environment
lapply_canprot: running 8 calculations on 2 cores
--- finished re-building ‘potential_diagrams.Rmd’

SUMMARY: processing the following files failed:
  ‘basis_comparison.Rmd’ ‘colorectal.Rmd’

Error: Vignette re-building failed.
Execution halted