[Bioc-devel] BiocCheck crash with package vignette?

[Leo Lahti]

Thanks Dan, this solved the problem !

/ Leo

On Mon, Sep 15, 2014 at 6:42 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:

> Hi Leo,
>
> ----- Original Message -----
> > From: "Leo Lahti" <leo.lahti at iki.fi>
> > To: bioc-devel at r-project.org
> > Sent: Monday, September 15, 2014 10:19:55 AM
> > Subject: [Bioc-devel] BiocCheck crash with package vignette?
> >
> > Dear Bioc developers,
> >
> > The BioC guidelines request that package authors run BiocCheck
> > successfully
> > before package submission. To get this working in Linux, I copied the
> > BiocCheck script to /usr/lib/R/bin as adviced and it seemed to work.
> > However, I am now bumping into problems with BiocCheck related to
> > vignette.
> >
> > Specifically, after successfully building package tarball without
> > errors/warnings in R version 3.1.1 the BiocCheck generates the
> > following
> > error. This error is not solved by adding the argument
> > --no-check-vignettes
> > nor by running BiocCheck from R:
> >
> > > R CMD BiocCheck -mypackage_0.99.0.tar.gz
> >
> > * This is BiocCheck, version 1.0.2.
> > * BiocCheck is a work in progress. Output and severity of issues may
> >   change.
> > * Installing package...
> > * This is a software package, checking vignette directories...
> > * # of chunks: 4, # of eval=FALSE: 1 (25%)
> > * Checking version number...
> >     * RECOMMENDED: y of x.y.z version should be even in release
> > * Checking biocViews...
> > * Checking build system compatibility...
> > * Checking unit tests...
> > Warning in file(filename, "r") :
> >   cannot open file '/tmp/RtmpGXbMdl/vignette.Rmd': No such file or
> >   directory
> > Error in file(filename, "r") : cannot open the connection
> > Calls: <Anonymous> ... BiocCheck -> parseFiles -> parseFile -> parse
> > -> file
> > Execution halted
> >
> >
> > My package contains the file vignettes/vignette.Rmd and I can convert
> > this
> > with knitr without problems. I have not been able solve this after
> > considerable searching of hints from the web.
> >
> > Any ideas on what is causing this failure, and how to solve it ?
> >
> > The source code for my problematic package is here, if it is of any
> > help:
> > https://github.com/microbiome/microbiome/
> >
>
> This is a bug in BiocCheck, it's trying to figure out how to extract the R
> code from your vignette and since it didn't find
> VignetteBuilder: knitr
> in your DESCRIPTION file, it tries to Stangle a non-existent .Rnw file.
>
> I'll fix this but you can avoid the problem by adding
> VignetteBuilder: knitr
>
> to your DESCRIPTION file. Perhaps BiocCheck can detect this situation as
> well.
>
> Dan
>
> > best regards
> > Leo Lahti
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>

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