[BioC] How to include external applications in package vignette code?

Sean Davis sdavis2 at mail.nih.gov
Thu Mar 1 20:32:06 CET 2012

On Thu, Mar 1, 2012 at 9:05 AM, Dave Gerrard [guest]
<guest at bioconductor.org> wrote:
> Hi,
> I have created an R package that makes extensive use of external applications (BLAST and MUSCLE) in a typical workflow. I have written a sweave document that could be used as a vignette but which I currently 'build' separately because it makes use of local installations of the two external applications. Is there any way that I could get this package into Bioconductor with a vignette that won't build until the user installs these applications? Or should I just sent it to CRAN?

You might just add an eval=false to the appropriate chunks.  That may
mean that you need to include some small example MUSCLE and BLAST
outputs so that the rest of your code can work from that instead.


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