From dtenenba at fhcrc.org  Thu Mar 17 17:35:23 2011
From: dtenenba at fhcrc.org (Dan Tenenbaum)
Date: Thu, 17 Mar 2011 09:35:23 -0700
Subject: [Rd] Feature request: display file name in R CMD check warning
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References: <AANLkTi=D483mk=SVgM5w4bd9gazMA2XeFS_ufLNHOTyL@mail.gmail.com>
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Message-ID: <AANLkTi=nRmV58+tjH5XNtEruGP5=s2dxnGWpDUnzpZob@mail.gmail.com>

On Thu, Mar 17, 2011 at 9:33 AM, Dan Tenenbaum <dtenenba at fhcrc.org> 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.
>

Oops, sorry, this is the wrong package.
The one that produces this warning is:

svn --username readonly --password readonly export
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bgafun

This warning only occurs under windows.

Dan


> Thanks
> Dan
>
>
>> Duncan Murdoch
>>
>



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