[Debian-med-packaging] [devteam-bioc] How to create the documentation of BiocParallel

[Martin Morgan]

Hi Andreas

That's the reference manual, created from the files in man/ as part of the  R 
CMD build process with the command R CMD Rd2pdf BiocParallel/man/.

Usually  this file is removed by the build process. Here it seems to be a bug in 
R, where the package build process fails to remove the file when a package man 
page uses an \Sexpr{} markup tag.

Packages exercising this bug are

BiocParallel
genefu
predictionet
RamiGO
rTRM

I'll try to identify the underlying problem and forward to the R bug reporting 
system.

It would be appropriate to remove this file in your down-stream processing.

Martin

On 06/30/2014 12:30 AM, Maintainer wrote:
> Hello,
>
> as you might have realised the Debian Med team tries to package
> BioConductor modules for official Debian.  When looking at
> BiocParallel I realised that the tarball contains a PDF
>
>     BiocParallel/build/BiocParallel.pdf
>
> which has no obvious source and rule how it was created.  Debian
> ftpmaster is considering PDFs as "binary without source" and I would
> probably need to remove the file which is not in the interest of our
> users.  Could you give me some hint how to create this PDF?
>
> Thanks for providing BioConductor as Free Software
>
>       Andreas.
>
>


-- 
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793