[Bioc-devel] BiocCheck

Dan Tenenbaum dtenenba at fhcrc.org
Thu May 29 17:07:32 CEST 2014

Hi Kasper,

----- Original Message -----
> From: "Kasper Daniel Hansen" <kasperdanielhansen at gmail.com>
> To: bioc-devel at r-project.org
> Sent: Wednesday, May 28, 2014 7:20:00 AM
> Subject: [Bioc-devel] BiocCheck
> 1) The hash bang in the BiocCheck script currently requires
> intervention at
> install time.

Only if you don't have permission to write the script to $R_HOME/bin. Otherwise it is handled for you.

I would prefer to use

#!/usr/bin/env Rscript

but the problem with that is you can't add an argument like:

#!/usr/bin/env Rscript --vanilla

env doesn't support that.

> It would be much more convenient if the script could read of the
> location
> of R, in the same way as (say) the Sweave script can.  In fact, I
> modified
> the BiocCheck script as per the Sweave script but ran into problems
> with
> .BiocCheckFromCommandLine, and figured I better stop.

What does Sweave do? What problem did you run into?

> 2) Re. the checks for coding style: it would be convenient if there
> was an
> option (perhaps disabled by default, perhaps not) which lists the
> offending
> files for each "issue".

I think this would need to be disabled by default; in practice I see that many many files per package are "offending". 

I can't get to this right away but I've added



> Best,
> Kasper
> 	[[alternative HTML version deleted]]
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