It looks like on my computer, if I remove "\bibliographystyle{apalike}",
the pdf simply cannot be built from Rnw. So I followed Dan's suggestion.
This time, I passed building on Mac but still failed Windows with the same
error message.

My understanding is that the pdf was not generated from the tex file. But
what happened? Does anyone know?

Thanks,

- Li


On Wed, Nov 20, 2013 at 2:08 PM, Kasper Daniel Hansen <
kasperdanielhansen@gmail.com> wrote:

> Assuming you have just copied the Sweave template from someone else, you
> probably don't want to follow Dan's suggestion.  Instead search for apalike
> in the document and delete the line containing it.  It is probably (from
> memory)
>   \bibliographystyle{apalike}
>
> Kasper
>
>
> On Wed, Nov 20, 2013 at 2:05 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote:
>
>>
>>
>> ----- Original Message -----
>> > From: "Li Shen" <shenli.sam@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
>>
>
>


-- 
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]]

