[Bioc-devel] BiocCheck
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 https://github.com/Bioconductor/BiocCheck/issues/13 Dan
Best, Kasper [[alternative HTML version deleted]]
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