Thank you. That fixed the problem.
________________________________ From: Wolfgang Huber <[email protected]> Cc: [email protected] Sent: Sunday, March 8, 2009 12:38:14 PM Subject: Re: [Bioc-sig-seq] report error 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 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 > > > [[alternative HTML version deleted]] > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing -- ---------------------------------------------------- Wolfgang Huber EMBL-EBI http://www.ebi.ac.uk/huber [[alternative HTML version deleted]]
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