[Bioc-devel] Help: package builder error messages

[Dan Tenenbaum]

----- Original Message -----
> From: "Li Shen" <shenli.sam at gmail.com>
> To: bioc-devel at 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/
> 
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