##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/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
--- re-building ‘Running_gene-set_analysis_with_piano.Rmd’ using rmarkdown
--- 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...
...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
Running gene set analysis:
Final gene/gene-set association: 643 genes and 163 gene sets
  Details:
  Calculating gene set statistics from 643 out of 5705 gene-level statistics
  Removed 0 genes from GSC due to lack of matching gene statistics
  Removed 0 gene sets containing no genes after gene removal
  Removed additionally 656 gene sets not matching the size limits
  Loaded additional information for 0 gene sets
-------------------------------------------------------------------------------

  A newer function 'networkPlot2()' with the same purpose is now available!

-------------------------------------------------------------------------------


Error: processing vignette 'piano-vignette.Rnw' failed with diagnostics:
unable to run pdflatex on 'piano-vignette.tex'
LaTeX errors:
! Package babel Error: Unknown option `swedish'. Either you misspelled it
(babel)                or the language definition file swedish.ldf was not foun
d.

See the babel package documentation for explanation.
! LaTeX Error: File `tocloft.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.18 \usepackage
                {hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘piano-vignette.Rnw’

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

Error: Vignette re-building failed.
Execution halted