[Bioc-devel] Help: package builder error messages

[Dan Tenenbaum]

----- Original Message -----
> From: "Li Shen" <shenli.sam at gmail.com>
> To: "Dan Tenenbaum" <dtenenba at fhcrc.org>
> Cc: bioc-devel at r-project.org, "Kasper Daniel Hansen" <kasperdanielhansen at gmail.com>
> Sent: Wednesday, November 20, 2013 1:28:54 PM
> Subject: Re: [Bioc-devel] Help: package builder error messages
> 
> 
> Thanks, Dan! Will you remove the error message for me? Is there
> anything else I need to do?
> 
> 

The issue is resolved now. So you just need to wait to hear from the person who is assigned to review your package.
Dan


> 
> 
> 
> On Wed, Nov 20, 2013 at 4:14 PM, Dan Tenenbaum < dtenenba at fhcrc.org >
> wrote:
> 
> 
> 
> 
> 
> ----- Original Message -----
> > From: "Li Shen" < shenli.sam at gmail.com >
> 
> > To: "Kasper Daniel Hansen" < kasperdanielhansen at gmail.com >
> > Cc: "Dan Tenenbaum" < dtenenba at fhcrc.org >,
> > bioc-devel at r-project.org
> > Sent: Wednesday, November 20, 2013 1:06:47 PM
> > Subject: Re: [Bioc-devel] Help: package builder error messages
> > 
> > 
> > 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?
> > 
> 
> I think it's a bug with the single package builder. I will look into
> it and get back to you.
> 
> Thanks,
> Dan
> 
> 
> 
> 
> > 
> > Thanks,
> > 
> > 
> > - Li
> > 
> > 
> > 
> > On Wed, Nov 20, 2013 at 2:08 PM, Kasper Daniel Hansen <
> > kasperdanielhansen at 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 at fhcrc.org
> > >
> > wrote:
> > 
> > 
> > 
> > 
> > 
> > 
> > ----- 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/
> > > 
> > > [[alternative HTML version deleted]]
> > > 
> > > _______________________________________________
> > > Bioc-devel at r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > > 
> > 
> > _______________________________________________
> > Bioc-devel at 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/
> 
> 
> 
> 
> --
> 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/