[Bioc-sig-seq] report error

[Wolfgang Huber]

Hi Joseph

have you checked that LaTeX is installed on your computer?

  Best wishes
	Wolfgang

> Hi
> 
> I need help with the error reported below; I got it when I
> tried to generate a report from the qaSummary in the vignette “An Introduction
> to ShortRead, 25 July, 2008”.
> Thanks
>  
>  
>> exptPath <- system.file("extdata", package
> = "ShortRead")
>> sp <- SolexaPath(exptPath)
>> aln <- readAligned(sp, "s_2_export.txt")
>> qaSummary <- qa(sp)
>> report(qaSummary, dest = "qa_report.pdf")
> Writing to file qa_solexa.tex
> Processing code chunks ...
>  1 : term verbatim
> (label=setup)
>  2 : term verbatim
> (label=utilities)
>  3 : term verbatim
> (label=qa-run)
>  4 : echo (label=code)
>  5 : echo term
> verbatim (label=read-counts)
>  6 : echo term
> verbatim (label=base-calls)
>  7 : echo term
> verbatim eps pdf (label=read-quality-raw)
>  8 : echo term
> verbatim eps pdf (label=read-distribution-occurrence)
>  9 : echo term
> verbatim (label=common-duplicate-reads)
> 10 : echo term verbatim
> (label=common-duplicate-mapped-reads)
> 11 : echo term verbatim eps pdf (label=per-cycle-base-call)
> 12 : echo term verbatim eps pdf (label=per-cycle-quality)
> 13 : echo term verbatim eps pdf (label=counts-histo)
> 14 : echo term verbatim eps pdf (label=read-counts-per-tile)
> 15 : echo term verbatim eps pdf (label=read-score-per-tile)
> 16 : echo term verbatim eps pdf
> (label=mapped-alignment-score)
> 17 : echo keep.source term verbatim (label=appendix)
>  
> You can now run LaTeX on 'qa_solexa.tex'
> Error in tools::texi2dvi(texFile, pdf = TRUE) : 
>   unable to run
> pdflatex on 'qa_solexa.tex'
> In addition: Warning message:
> In system(paste(shQuote(latex),
> "-interaction=nonstopmode", texfile)) :
>   "pdflatex"
> not found
>  
>  
>> sessionInfo()
> R version 2.8.1 Patched (2009-01-24 r47717) 
> i386-pc-mingw32 
> locale:
> LC_COLLATE=English_United
> States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
> attached base packages:
> [1] tools     stats     graphics  grDevices utils     datasets  methods   base     
> other attached packages:
> [1] ShortRead_1.0.6    lattice_0.17-20    Biobase_2.2.1      Biostrings_2.10.15
> [5] IRanges_1.0.9     
> loaded via a namespace (and not attached):
> [1] grid_2.8.1         Matrix_0.999375-18
> 
> 
>       
> 	[[alternative HTML version deleted]]
> 
> 
> 
> ------------------------------------------------------------------------
> 
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-- 
----------------------------------------------------
Wolfgang Huber  EMBL-EBI  http://www.ebi.ac.uk/huber