From khansen at stat.Berkeley.EDU  Thu Apr 20 22:06:00 2006
From: khansen at stat.Berkeley.EDU (Kasper Daniel Hansen)
Date: Thu, 20 Apr 2006 13:06:00 -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.4.64.0604202023190.487@gannet.stats.ox.ac.uk>
References: <Pine.LNX.4.44.0604202050330.4886-100000@reclus.nhh.no>
	<4447DE41.9000402@fhcrc.org>
	<Pine.LNX.4.64.0604202023190.487@gannet.stats.ox.ac.uk>
Message-ID: <3DD79D88-B705-4598-A3B7-4C592F0C6218@stat.berkeley.edu>

One thing which I personally disagree with is that the procedure for  
the check is different when run on a directory than on a tarball (I  
am talking about the defaults here, I now know I can change it  
locally). I could understand the difference if the check resulted in  
an _error_ such that I would be unable to install the package if I  
have eg. object files in the src directory.

I did the original checking for the package Jim (the OP) referred to,  
and I did expect that since it passed R CMD check (on my svn checkout  
directory), everything would be fine (this was with R-beta from  
Sunday). It was a bit of a surprise for me to learn that there was  
differences.

This is a case where I fail to see the advantage of the default  
settings, and I do see some disadvantages. But probably not important  
enough for R-2.3.0.

/Kasper

On Apr 20, 2006, at 12:40 PM, Prof Brian Ripley wrote:

> 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
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel



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