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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data FlowSOM
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* checking for file ‘FlowSOM/DESCRIPTION’ ... OK
* preparing ‘FlowSOM’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘FlowSOM.Rnw’ using Sweave
Loading required package: igraph

Attaching package: ‘igraph’

The following objects are masked from ‘package:stats’:

    decompose, spectrum

The following object is masked from ‘package:base’:

    union

Thanks for using FlowSOM. From version 2.1.4 on, the scale 
parameter in the FlowSOM function defaults to FALSE
Plot FlowSOM trees
Calculate t-SNE
Plot cluster per metacluster distribution
Plot heatmap
Make tables
Printing

Attaching package: ‘flowCore’

The following object is masked from ‘package:igraph’:

    normalize

Reading file /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpilAfsq/Rinstcd18362e48e9/FlowSOM/extdata/68983.fcs

Scaling the data

Scaling the data

Building SOM

Mapping data to SOM

Building MST

The packages "CytoML" and "flowWorkspace" are necessary for the function GetFlowJoLabels, but are not available.

Error: processing vignette 'FlowSOM.Rnw' failed with diagnostics:
 chunk 17 
Error in PlotPies(fSOM, cellTypes = gatingResult$manual) : 
  There are 19225 cells, while you provided 0 labels. These numbers should match.

--- failed re-building ‘FlowSOM.Rnw’

SUMMARY: processing the following file failed:
  ‘FlowSOM.Rnw’

Error: Vignette re-building failed.
Execution halted