----- Original Message ----- > From: "Li Shen" <shenli....@gmail.com> > To: bioc-devel@r-project.org > Sent: Wednesday, November 20, 2013 10:54:14 AM > Subject: [Bioc-devel] Help: package builder error messages > > Hi, > > I'm trying to submit a new package to Bioc. Using the automated > package > builder, two out of three machines did not finish nicely. More > specific, my > package passed Linux but failed Windows and Mac. > > Here is the error messages for Windows: > ================================ > * checking for file 'GeneOverlap/DESCRIPTION' ... OK > * preparing 'GeneOverlap': > * checking DESCRIPTION meta-information ... OK > * installing the package to build vignettes > * creating vignettes ... ERROR > KernSmooth 2.23 loaded > Copyright M. P. Wand 1997-2009 > Warning: running command > '"C:\PROGRA~2\MIKTEX~1.9\miktex\bin\texi2dvi.exe" > --quiet --pdf "GeneOverlap.tex" -I > "E:/packagebuilder/R/share/texmf/tex/latex" -I > "E:/packagebuilder/R/share/texmf/bibtex/bst"' had status 1 > Error in find_vignette_product(name, by = "texi2pdf", engine = > engine) : > Failed to locate the 'texi2pdf' output file (by engine > 'utils::Sweave') > for vignette with name 'GeneOverlap'. The following files exists in > directory '.': 'GeneOverlap-013.pdf', 'GeneOverlap-019.pdf', > 'GeneOverlap-020.pdf', 'GeneOverlap-concordance.tex', > 'GeneOverlap.Rnw', > 'GeneOverlap.bib', 'GeneOverlap.synctex.gz', 'GeneOverlap.tex', > 'Rplots.pdf' > Calls: <Anonymous> -> find_vignette_product > Execution halted > > It looks like the PDF file was not built but can it be more specific > what > is wrong with the TEX file? How can I proceed from here? > > > Here is the error messages for Mac: > =========================== > * checking for file 'GeneOverlap/DESCRIPTION' ... OK > * preparing 'GeneOverlap': > * checking DESCRIPTION meta-information ... OK > * installing the package to build vignettes > * creating vignettes ... ERROR > KernSmooth 2.23 loaded > Copyright M. P. Wand 1997-2009 > Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = > quiet, : > Running 'texi2dvi' on 'GeneOverlap.tex' failed. > BibTeX errors: > The top-level auxiliary file: GeneOverlap.aux > The style file: > /Library/Frameworks/R.framework/Versions/3.1/Resources/library/BiocStyle/sty/unsrturl.bst > Illegal, another \bibstyle command---line 31 of file GeneOverlap.aux > : \bibstyle > : {apalike} > I'm skipping whatever remains of this command > Reallocated glb_str_ptr (elt_size=4) to 20 items from 10. > Reallocated global_strs (elt_size=20001) to 20 items from 10. > Reallocated glb_str_end (elt_size=4) to 20 items from 10. > Reallocated singl_function (elt_size=4) to 100 items from 50. > Database file #1: GeneOverlap.bib > Calls: <Anonymous> -> texi2pdf -> texi2dvi > Execution halted > > I'm using the new BiocStyle package for vignette styling. However, > the > package builder declared that one of its style files was illegal. > > Both error messages are confusing and there is a lack of specifics > for me > to diagnose what went wrong. Does anybody have similar experience? >
Since you are using a bibliographystyle, you need to tell BiocStyle NOT to use one, so in your vignette change BiocStyle::latex() to BiocStyle::latex(use.unsrturl=FALSE) Dan > Thanks, > > -- > Li Shen, Ph.D. Computer Science > Assistant Professor > Department of Neuroscience > Icahn School of Medicine at Mount Sinai > New York, NY 10029 > ################# > Want ChIP-seq differential analysis? Use: > https://code.google.com/p/diffreps/ > Test biological hypotheses with NGS data: > https://code.google.com/p/ngsplot/ > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel