Feature request: display file name in R CMD check warning
On 11-03-17 12:33 PM, Dan Tenenbaum wrote:
On Thu, Mar 17, 2011 at 2:36 AM, Duncan Murdoch <murdoch.duncan at 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