For the bibtex error you seem to be using two different styles files. I
think we need to see the preamble (header) of the vignette.
Inside BiocStyle there is a template_sweave.Rnw file which you could have a
look at.
Kasper
On Wed, Nov 20, 2013 at 1:54 PM, Li Shen <shenli....@gmail.com> wrote:
> 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?
>
> 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/
>
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>
> _______________________________________________
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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