From dtenenba at fhcrc.org  Thu Mar 17 17:33:42 2011
From: dtenenba at fhcrc.org (Dan Tenenbaum)
Date: Thu, 17 Mar 2011 09:33:42 -0700
Subject: [Rd] Feature request: display file name in R CMD check warning
In-Reply-To: <4D81D636.2060209@gmail.com>
References: <AANLkTi=D483mk=SVgM5w4bd9gazMA2XeFS_ufLNHOTyL@mail.gmail.com>
	<4D81D636.2060209@gmail.com>
Message-ID: <AANLkTinuKBHZJoH5MKwqy91qoxKth3AK=T+ZxNkYuena@mail.gmail.com>

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.

Thanks
Dan


> Duncan Murdoch
>



[Rd] Feature request: display file name in R CMD check warning
Dan Tenenbaum