BioC 3.2: BUILD report for piano on perceval

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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 piano
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* checking for file ‘piano/DESCRIPTION’ ... OK
* preparing ‘piano’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Warning: replacing previous import by ‘igraph::union’ when loading ‘piano’
Warning: replacing previous import by ‘igraph::normalize’ when loading ‘piano’
Loading data in text file...
...done
Loading setup file...
...done
Text file data: No normalization performed.
Loading required package: DBI

Creating annotation...
...done
Removing unmapped probes...
..done
Creating a generic function for ‘boxplot’ from package ‘graphics’ in package ‘affyPLM’
Creating a generic function for ‘hist’ from package ‘graphics’ in package ‘affyPLM’
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...
...done
Calculating p-values for contrast aerobic_Nlim - anaerobic_Nlim...
...done
Generating heatmap...
dev.new(): using pdf(file="Rplots16.pdf")
dev.new(): using pdf(file="Rplots17.pdf")
...done
Generating merged polar plot...
dev.new(): using pdf(file="Rplots18.pdf")
...done
Generating separate polar plots...
dev.new(): using pdf(file="Rplots19.pdf")
dev.new(): using pdf(file="Rplots20.pdf")
...done
Generating polar plot legend...
dev.new(): using pdf(file="Rplots21.pdf")
...done
Generating volcano plot...
dev.new(): using pdf(file="Rplots22.pdf")
dev.new(): using pdf(file="Rplots23.pdf")
...done
Running gene set analysis:
Final gene/gene-set association: 4 genes and 4 gene sets
  Details:
  Calculating gene set statistics from 4 out of 4 gene-level statistics
  Using all 4 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

Error: processing vignette 'piano-vignette.Rnw' failed with diagnostics:
 chunk 25 
Error : 1: Space required after the Public Identifier
2: SystemLiteral " or ' expected
3: SYSTEM or PUBLIC, the URI is missing
4: Opening and ending tag mismatch: hr line 7 and body
5: Opening and ending tag mismatch: body line 4 and html
6: Premature end of data in tag html line 2

Execution halted
BioC 3.2: BUILD report for piano on perceval

Summary

Command output
