On 11-03-17 12:33 PM, Dan Tenenbaum wrote:
On Thu, Mar 17, 2011 at 2:36 AM, Duncan Murdoch
<murdoch.dun...@gmail.com> wrote:
On 16/03/2011 7:55 PM, Dan Tenenbaum wrote:
Hi,
I came across the following warning in R CMD check (it only occurred on
Windows):
The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
The package I'm looking at is one that I did not write which has 34 .Rd
files. This warning does not tell me which file to look in. It would be
very
helpful if it did. Same goes for other warnings/errors produced by R CMD
check.
I was unable to duplicate this. When I tried it by messing up one of the
man pages in the ellipse package, I got this:
S3 methods shown with full name in documentation object 'ellipse.glm':
ellipse.glm
The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
"Documentation object 'ellipse.glm'" tells me the \name{} inside the .Rd
file, which is enough to uniquely identify the file. Are you not seeing
this part of the message?
No, I'm not.
I still can't identify the offending file, but you can download the
whole package:
svn --username readonly --password readonly export
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/affyILM/
Then run R CMD check on this package. You may need to install dependencies.
I installed a lot of dependencies, but couldn't trust check because of
this warning:
Found the following significant warnings:
Warning: running command 'C:\WINDOWS\system32\cmd.exe /c ftype perl'
had status 2
I'm not sure where this comes from; I don't think bgafun uses perl, so
it's from one of the dependencies. But I think the error message you
are seeing is spurious: something else is going wrong when check tries
to check \usage sections, and so it reports that there was an error.
As a sort of confirmation of this, I removed the dependencies from the
DESCRIPTION file and tried to run check; I got lots of errors because of
the missing dependencies now, but the one about S3 methods went away.
Not sure what to suggest to diagnose this; I'm not familiar with most of
those packages I just installed as dependencies. But I think it's safe
to say that you shouldn't worry about the \usage sections.
If you do figure out what's going wrong, please let us know because it
would probably be a good idea to fix the usage checks so they give the
right message.
Duncan Murdoch
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