[Bioc-devel] BiocCheck crash with package vignette?

[Dan Tenenbaum]

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
> 
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> 
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