Package: ggcyto

Version: 1.15.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ggcyto

StartedAt: 2020-01-15 22:25:45 -0500 (Wed, 15 Jan 2020)

EndedAt: 2020-01-15 22:28:27 -0500 (Wed, 15 Jan 2020)

EllapsedTime: 162.4 seconds

RetCode: 1

Status:  ERROR

PackageFile: None

PackageFileSize: NA

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ggcyto
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* checking for file ‘ggcyto/DESCRIPTION’ ... OK
* preparing ‘ggcyto’:
* checking DESCRIPTION meta-information ... OK
* installing the package to process help pages
* saving partial Rd database
* creating vignettes ... ERROR
--- re-building ‘Top_features_of_ggcyto.Rmd’ using rmarkdown
Loading required package: ggplot2
Loading required package: flowCore
Loading required package: ncdfFlow
Loading required package: RcppArmadillo
Loading required package: BH
Loading required package: flowWorkspace
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")
Quitting from lines 50-52 (Top_features_of_ggcyto.Rmd) 
Error: processing vignette 'Top_features_of_ggcyto.Rmd' failed with diagnostics:
Unknown colour name: transparent
--- failed re-building ‘Top_features_of_ggcyto.Rmd’

--- re-building ‘autoplot.Rmd’ using rmarkdown
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.
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.
--- finished re-building ‘autoplot.Rmd’

--- re-building ‘ggcyto.GatingSet.Rmd’ using rmarkdown
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.
--- finished re-building ‘ggcyto.GatingSet.Rmd’

--- re-building ‘ggcyto.flowSet.Rmd’ using rmarkdown
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Loading required package: ggridges
Picking joint bandwidth of 16.4
Picking joint bandwidth of 29.2
Picking joint bandwidth of 12.1
Picking joint bandwidth of 7.74
Warning: Removed 865 rows containing non-finite values (stat_binhex).
Warning: Removed 34 rows containing missing values (geom_hex).
Scale for 'fill' is already present. Adding another scale for 'fill', which
will replace the existing scale.
Warning: Removed 865 rows containing non-finite values (stat_binhex).
Warning: Removed 34 rows containing missing values (geom_hex).
Scale for 'fill' is already present. Adding another scale for 'fill', which
will replace the existing scale.
Warning: Removed 865 rows containing non-finite values (stat_binhex).
Warning: Removed 34 rows containing missing values (geom_hex).
Warning: Removed 865 rows containing non-finite values (stat_binhex).
Warning: Removed 34 rows containing missing values (geom_hex).
Warning: Removed 865 rows containing non-finite values (stat_binhex).
Warning: Removed 34 rows containing missing values (geom_hex).
Warning: Removed 865 rows containing non-finite values (stat_binhex).
Warning: Removed 34 rows containing missing values (geom_hex).
Warning: Removed 865 rows containing non-finite values (stat_binhex).
Warning: Removed 34 rows containing missing values (geom_hex).
Warning: Removed 865 rows containing non-finite values (stat_binhex).
Warning: Removed 34 rows containing missing values (geom_hex).
Warning: Removed 865 rows containing non-finite values (stat_binhex).
Warning: Removed 34 rows containing missing values (geom_hex).
Warning: Removed 865 rows containing non-finite values (stat_binhex).
Warning: Removed 34 rows containing missing values (geom_hex).
--- finished re-building ‘ggcyto.flowSet.Rmd’

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

Error: Vignette re-building failed.
Execution halted