From ripley at stats.ox.ac.uk  Thu Apr 20 21:40:48 2006
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Thu, 20 Apr 2006 20:40:48 +0100 (BST)
Subject: [Rd] R CMD check: non source files in src on (2.3.0 RC
 (2006-04-19 r37860))
In-Reply-To: <4447DE41.9000402@fhcrc.org>
References: <Pine.LNX.4.44.0604202050330.4886-100000@reclus.nhh.no>
	<4447DE41.9000402@fhcrc.org>
Message-ID: <Pine.LNX.4.64.0604202023190.487@gannet.stats.ox.ac.uk>

On Thu, 20 Apr 2006, Robert Gentleman wrote:

> Hi,
>
> Well, I guess if someone thinks they know how I am going to configure and 
> build the sources needed to construct appropriate dynamic libraries so well 
> that they can feel free to exclude files at their whim at install time, 
> perhaps they could feel just as free to exclude them at build time?

The checks are different if there is a configure file:

   Further, the check on the @file{src} directory is only run if the
   package/bundle does not contain a @file{configure} script (which
   corresponds to the value @samp{yes-maybe}) and there is no
   @file{src/Makefile} or @file{src/Makefile.in}.

> This makes no sense to me and certainly does not solve the size problem 
> mentioned by Brian. If there is a single example of something that was better 
> this way, I would be interested to hear it. I can think of several things 
> that are worse.

We found several examples with large and unnecessary files in the src 
directory via this check, as well as files in directories other than the 
ones the package author had intended.

It `makes no sense to me' to discuss situations that are not as 
implemented.  This was discussed some months ago, ideas trialled and those 
that were found worthwhile retained.  And now we are in code freeze.

>
> best wishes
>  Robert
>
>
> Roger Bivand wrote:
>> On Thu, 20 Apr 2006, Robert Gentleman wrote:
>> 
>> 
>>> 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.

Well, they are turned on optionally, but as the CRAN maintainers 
want them, submitters to CRAN ought to be aware that they will be run.


>> Isn't the point at least partly that all those files are lost on 
>> installation? If the README is to be accessible after installation, it can 
>> be placed under inst/, so that both users reading the source and installed 
>> versions can access it. So maybe the warning could be re-phrased to suggest 
>> use of the inst/ tree for files with important content?
>> 
>> Best wishes,
>> 
>> Roger
>> 
>> 
>>> 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.
>>>> 
>>>> 
>>>> [...]
>>>> 
>>>> 
>>> 
>>> 
>> 
>
>

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595



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