[Bioc-sig-seq] report error

[Martin Morgan]

Hi Joseph --

Wolfgang Huber <huber at ebi.ac.uk> writes:

> Hi Joseph
>
> have you checked that LaTeX is installed on your computer?

The MiKTEX installation is perhaps the easiest way to get latex on
Windows http://miktex.org.

Also, users of the development version of R and ShortRead can generate
HTML reports, and so do not need latex.

Martin

>   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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>> Bioc-sig-sequencing at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing

-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M2 B169
Phone: (206) 667-2793