Re: [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

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--
----------------------------------------------------
Wolfgang Huber  EMBL-EBI  http://www.ebi.ac.uk/huber


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