From murdoch.duncan at gmail.com  Fri Mar 18 02:49:56 2011
From: murdoch.duncan at gmail.com (Duncan Murdoch)
Date: Thu, 17 Mar 2011 21:49:56 -0400
Subject: [Rd] Feature request: display file name in R CMD check warning
In-Reply-To: <AANLkTinuKBHZJoH5MKwqy91qoxKth3AK=T+ZxNkYuena@mail.gmail.com>
References: <AANLkTi=D483mk=SVgM5w4bd9gazMA2XeFS_ufLNHOTyL@mail.gmail.com>	<4D81D636.2060209@gmail.com>
	<AANLkTinuKBHZJoH5MKwqy91qoxKth3AK=T+ZxNkYuena@mail.gmail.com>
Message-ID: <4D82BA44.5000002@gmail.com>

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



[Rd] Feature request: display file name in R CMD check warning
Duncan Murdoch