R devel - Apr 2006 - R CMD check: non source files in src on (2.3.0 RC (2006-04-19 r37860))

Hello, I am having an issue with R CMD check with the nightly build of 
RC 2.3.0 (listed in the subject.)

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.

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.

The output from R CMD check is below. Any insight would be appreciated. 
As always thanks for your patience.

jim




****************************************************************
**************** Directly on directory *************************
****************************************************************

bullard at sam:~/projects/bioc$ R CMD check -l ~/R-packages affxparser
* checking for working latex ... OK
* using log directory '/home/bullard/projects/bioc/affxparser.Rcheck'
* using Version 2.3.0 RC (2006-04-19 r37860)
* checking for file 'affxparser/DESCRIPTION' ... OK
* this is package 'affxparser' version '1.3.3'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'affxparser' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for syntax errors ... OK
* checking R files for library.dynam ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking Rd files ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking for CRLF line endings in C/C++/Fortran sources/headers ... OK
* checking for portable compilation flags in Makevars ... OK
* creating affxparser-Ex.R ... OK
* checking examples ... OK
* creating affxparser-manual.tex ... OK
* checking affxparser-manual.tex ... OK

****************************************************************
*************** On the R CMD build version *********************
****************************************************************

bullard at sam:~/projects/bioc$ R CMD check -l ~/R-packages/ 
affxparser_1.3.3.tar.gz
* checking for working latex ... OK
* using log directory '/home/bullard/projects/bioc/affxparser.Rcheck'
* using Version 2.3.0 RC (2006-04-19 r37860)
* checking for file 'affxparser/DESCRIPTION' ... OK
* this is package 'affxparser' version '1.3.3'
* checking package dependencies ... OK
* checking if this is a source package ... WARNING
Subdirectory 'src' contains:
   README _Makefile
These are unlikely file names for src files.
* checking whether package 'affxparser' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for syntax errors ... OK
* checking R files for library.dynam ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking Rd files ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking for CRLF line endings in C/C++/Fortran sources/headers ... OK
* checking for portable compilation flags in Makevars ... OK
* creating affxparser-Ex.R ... OK
* checking examples ... OK
* creating affxparser-manual.tex ... OK
* checking affxparser-manual.tex ... OK

WARNING: There was 1 warning, see
   /home/bullard/projects/bioc/affxparser.Rcheck/00check.log
for details

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