##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r piano -R && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data piano
###
##############################################################################
##############################################################################


* checking for file 'piano/DESCRIPTION' ... OK
* preparing 'piano':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'Running_gene-set_analysis_with_piano.Rmd' using rmarkdown
Running gene set analysis:
Final gene/gene-set association: 1136 genes and 50 gene sets
  Details:
  Calculating gene set statistics from 1136 out of 2000 gene-level statistics
  Using all 2000 gene-level statistics for significance estimation
  Removed 0 genes from GSC due to lack of matching gene statistics
  Removed 0 gene sets containing no genes after gene removal
  Removed additionally 0 gene sets not matching the size limits
  Loaded additional information for 0 gene sets
--- finished re-building 'Running_gene-set_analysis_with_piano.Rmd'

--- re-building 'piano-vignette.Rnw' using Sweave
Loading data in text file...
...done
Loading setup file...
...done
Text file data: No normalization performed.

Creating annotation...
...done
Removing unmapped probes...
..done
Warning in runQC(myArrayData) :
  can not run rnaDeg: argument arrayData does not contain dataRaw
Warning in runQC(myArrayData) :
  can not run nuseRle: argument arrayData does not contain dataRaw
Generating normalized data distribution plot...
...done
Generating normalized data boxplot...
dev.new(): using pdf(file="Rplots1.pdf")
...done
Generating PCA...
...done
dev.new(): using pdf(file="Rplots2.pdf")
dev.new(): using pdf(file="Rplots3.pdf")
dev.new(): using pdf(file="Rplots4.pdf")
dev.new(): using pdf(file="Rplots5.pdf")
Generating PCA...
...done
dev.new(): using pdf(file="Rplots6.pdf")
dev.new(): using pdf(file="Rplots7.pdf")
dev.new(): using pdf(file="Rplots8.pdf")
dev.new(): using pdf(file="Rplots9.pdf")
Generating PCA...
...done
dev.new(): using pdf(file="Rplots10.pdf")
dev.new(): using pdf(file="Rplots11.pdf")
dev.new(): using pdf(file="Rplots12.pdf")
dev.new(): using pdf(file="Rplots13.pdf")
Fitting linear models...
...done
Generating Venn diagrams...
dev.new(): using pdf(file="Rplots14.pdf")
dev.new(): using pdf(file="Rplots15.pdf")
...done
Calculating p-values for contrast aerobic_Clim - anaerobic_Clim...

Error: processing vignette 'piano-vignette.Rnw' failed with diagnostics:
 chunk 10 
Error in `[.data.frame`(topTab, , c("ID", "tmp", "logFC", "AveExpr", "t",  : 
  undefined columns selected

--- failed re-building 'piano-vignette.Rnw'

SUMMARY: processing the following file failed:
  'piano-vignette.Rnw'

Error: Vignette re-building failed.
Execution halted