Hi Joseph -- Wolfgang Huber <[email protected]> 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, 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 -- 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 _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
