Package: cytofWorkflow

Version: 1.7.1

Command: chmod a+r cytofWorkflow -R && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data cytofWorkflow

StartedAt: 2019-01-30 09:40:24 -0500 (Wed, 30 Jan 2019)

EndedAt: 2019-01-30 09:42:33 -0500 (Wed, 30 Jan 2019)

EllapsedTime: 128.6 seconds

RetCode: 1

Status:  ERROR

PackageFile: None

PackageFileSize: NA

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### Running command:
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###   chmod a+r cytofWorkflow -R && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data cytofWorkflow
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* checking for file 'cytofWorkflow/DESCRIPTION' ... OK
* preparing 'cytofWorkflow':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'cytofWorkflow.Rmd' using rmarkdown
Warning: replacing previous import 'ggplot2::scale_discrete_manual' by 'ggridges::scale_discrete_manual' when loading 'cytofWorkflow'
trying URL 'http://imlspenticton.uzh.ch/robinson_lab/cytofWorkflow/PBMC8_metadata.xlsx'
Content type 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet' length 56676 bytes (55 KB)
==================================================
downloaded 55 KB

trying URL 'http://imlspenticton.uzh.ch/robinson_lab/cytofWorkflow/PBMC8_fcs_files.zip'
Content type 'application/zip' length 21513634 bytes (20.5 MB)
==================================================
downloaded 20.5 MB

trying URL 'http://imlspenticton.uzh.ch/robinson_lab/cytofWorkflow/PBMC8_panel.xlsx'
Content type 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet' length 44134 bytes (43 KB)
==================================================
downloaded 43 KB

Invalid Parameter - /plot-merker-expression-distribution-1.png"
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "figure/plot-merker-expression-distribution-1.png" -trim "figure/plot-merker-expression-distribution-1.png"' execution failed with error code 4
Invalid Parameter - /plot-number-of-cells-1.png"
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "figure/plot-number-of-cells-1.png" -trim "figure/plot-number-of-cells-1.png"' execution failed with error code 4
Invalid Parameter - /plot-mds-1.png"
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "figure/plot-mds-1.png" -trim "figure/plot-mds-1.png"' execution failed with error code 4
Invalid Parameter - /plot-dendogram-1.png"
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "figure/plot-dendogram-1.png" -trim "figure/plot-dendogram-1.png"' execution failed with error code 4
Invalid Parameter - /nrs-1.png"
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "figure/nrs-1.png" -trim "figure/nrs-1.png"' execution failed with error code 4
Building SOM

Mapping data to SOM

end fraction
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Invalid Parameter - /plot-clustering-heatmap1-1.png"
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "figure/plot-clustering-heatmap1-1.png" -trim "figure/plot-clustering-heatmap1-1.png"' execution failed with error code 4
Picking joint bandwidth of 0.127
Picking joint bandwidth of 0.128
Picking joint bandwidth of 0.164
Picking joint bandwidth of 0.142
Picking joint bandwidth of 0.113
Picking joint bandwidth of 0.0553
Picking joint bandwidth of 0.092
Picking joint bandwidth of 0.107
Picking joint bandwidth of 0.111
Picking joint bandwidth of 0.136
Invalid Parameter - /plot-clustering-distribution1-1.png"
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "figure/plot-clustering-distribution1-1.png" -trim "figure/plot-clustering-distribution1-1.png"' execution failed with error code 4
Warning: The input is a data frame, convert it to the matrix.
Quitting from lines 644-762 (cytofWorkflow.Rmd) 
Error: processing vignette 'cytofWorkflow.Rmd' failed with diagnostics:
`axis_gp` is removed from the arguments. Use `axis_param = list(gp =
...)` instead.
--- failed re-building 'cytofWorkflow.Rmd'

SUMMARY: processing the following file failed:
  'cytofWorkflow.Rmd'

Error: Vignette re-building failed.
Execution halted