From rgentlem at fhcrc.org  Thu Apr 20 20:21:51 2006
From: rgentlem at fhcrc.org (Robert Gentleman)
Date: Thu, 20 Apr 2006 11:21:51 -0700
Subject: [Rd] R CMD check: non source files in src on (2.3.0 RC
 (2006-04-19 r37860))
In-Reply-To: <Pine.LNX.4.64.0604200752001.14307@gannet.stats.ox.ac.uk>
References: <44472D38.80603@berkeley.edu>
	<Pine.LNX.4.64.0604200752001.14307@gannet.stats.ox.ac.uk>
Message-ID: <4447D13F.6020701@fhcrc.org>

I disagree, things like README files and other objects are important and 
should be included. I don't see the real advantage to such warnings, if 
someone wants them they could be turned on optionally.

If size is an issue then authors should be warned that their package is 
large (in the top 1% at CRAN would be useful to some). I also find it 
helpful to know whose packages take forever to build, which we don't do.

Just because someone put something in TFM doesn't mean it is either a 
good idea or sensible, in my experience.

best wishes
   Robert


Prof Brian Ripley wrote:
> On Wed, 19 Apr 2006, James Bullard wrote:
> 
> 
>>Hello, I am having an issue with R CMD check with the nightly build of
>>RC 2.3.0 (listed in the subject.)
> 
> 
> This is all explained in TFM, `Writing R Extensions'.
> 
> 
>>The problem is this warning:
>>
>>* checking if this is a source package ... WARNING
>>Subdirectory 'src' contains:
>>  README _Makefile
>>These are unlikely file names for src files.
>>
>>In fact, they are not source files, but I do not see any reason why they
>>cannot be there, or why I need to be warned of their presence.
>>Potentially I could be informed of their presence, but that is another
>>matter.
> 
> 
> Having unnecessary files in other people's packages just waste space and 
> download bandwidth for each one of the users.
> 
> 
>>Now, I only get this warning when I do:
>>
>>R CMD build affxparser
>>R CMD check -l ~/R-packages/ affxparser_1.3.3.tar.gz
>>
>>If I do:
>>
>>R CMD check -l ~/R-packages affxparser
>>
>>I do not get the warning. Is this inconsistent, or is there rationale
>>behind this? I think the warning is inappropriate, or at the least a
>>little restrictive. It seems as if I should be able to put whatever I
>>want in there, especially the _Makefile as I like to build test programs
>>directly and I want to be able to build exactly what I check out from
>>my source code repository without having to copy files in and out.
> 
> 
> All described in TFM, including how to set defaults for what is checked.
> 
> 
>>The output from R CMD check is below. Any insight would be appreciated.
>>As always thanks for your patience.
> 
> 
> [...]
> 
> 

-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org



[Rd] R CMD check: non source files in src on (2.3.0 RC (2006-04-19 r37860))
Robert Gentleman