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 âAn Introduction
to ShortRead, 25 July, 2008â.
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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