##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data openCyto
###
##############################################################################
##############################################################################


* checking for file ‘openCyto/DESCRIPTION’ ... OK
* preparing ‘openCyto’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘HowToAutoGating.Rmd’ using rmarkdown
As part of improvements to flowWorkspace, some behavior of
GatingSet objects has changed. For details, please read the section
titled "The cytoframe and cytoset classes" in the package vignette:

  vignette("flowWorkspace-Introduction", "flowWorkspace")
Warning: replacing previous import 'flowViz::contour' by 'graphics::contour' when loading 'flowStats'
Loading required package: ggplot2
Loading required package: ncdfFlow
Loading required package: RcppArmadillo
Loading required package: BH
Coordinate system already present. Adding new coordinate system, which will replace the existing one.
Coordinate system already present. Adding new coordinate system, which will replace the existing one.
Coordinate system already present. Adding new coordinate system, which will replace the existing one.
The prior specification has no effect when usePrior=no
Using the serial version of flowClust
Coordinate system already present. Adding new coordinate system, which will replace the existing one.
The prior specification has no effect when usePrior=no
Using the serial version of flowClust
Coordinate system already present. Adding new coordinate system, which will replace the existing one.
The prior specification has no effect when usePrior=no
Using the serial version of flowClust
--- finished re-building ‘HowToAutoGating.Rmd’

--- re-building ‘HowToWriteCSVTemplate.Rmd’ using rmarkdown
expanding pop: +/- to cd4+/cd4-

expanding pop: +/-+/-

splitting the row that has multiple parents: 'cd4,cd8'
--- finished re-building ‘HowToWriteCSVTemplate.Rmd’

--- re-building ‘openCytoVignette.Rmd’ using knitr
Coordinate system already present. Adding new coordinate system, which will replace the existing one.
Coordinate system already present. Adding new coordinate system, which will replace the existing one.
Coordinate system already present. Adding new coordinate system, which will replace the existing one.
Coordinate system already present. Adding new coordinate system, which will replace the existing one.
Coordinate system already present. Adding new coordinate system, which will replace the existing one.
Coordinate system already present. Adding new coordinate system, which will replace the existing one.
Coordinate system already present. Adding new coordinate system, which will replace the existing one.
Coordinate system already present. Adding new coordinate system, which will replace the existing one.
Quitting from lines 69-71 (openCytoVignette.Rmd) 
Error: processing vignette 'openCytoVignette.Rmd' failed with diagnostics:
Metric information not available for this family/device
--- failed re-building ‘openCytoVignette.Rmd’

SUMMARY: processing the following file failed:
  ‘openCytoVignette.Rmd’

Error: Vignette re-building failed.
Execution halted