From hpages at fhcrc.org  Wed Oct 19 23:25:25 2011
From: hpages at fhcrc.org (=?windows-1252?Q?Herv=E9_Pag=E8s?=)
Date: Wed, 19 Oct 2011 14:25:25 -0700
Subject: [Rd] warnings issued at installation time not reported by 'R CMD
	check'
Message-ID: <4E9F4045.1010700@fhcrc.org>

Hi,

Warnings issued at installation time are not reported by 'R CMD check'.

Some of them are really important and telling something very useful
to the developer. See for example this warning:

 
http://bioconductor.org/checkResults/2.9/bioc-LATEST/globaltest/wilson2-checksrc.html

Actually, there is no formal warning reported by 'R CMD check' for
this package but if you scroll down the report and look at the output
produced during installation (globaltest.Rcheck/00install.out), you'll
see this:

   * installing *source* package ?globaltest? ...
   ** R
   ** data
   ** inst
   ** preparing package for lazy loading
   Warning in .simpleDuplicateClass(def, prev) :
     A specification for class ?data.frameOrNULL? in package 
?globaltest? seems equivalent to one from package ?Biobase? and is not 
turning on duplicate class definitions for this class
   Creating a generic function for ?sort? from package ?base? in package 
?globaltest?
   Creating a generic function for ?model.matrix? from package ?stats? 
in package ?globaltest?
   Creating a generic function for ?coefficients? from package ?stats? 
in package ?globaltest?
   Creating a generic function for ?fitted.values? from package ?stats? 
in package ?globaltest?
   Creating a generic function for ?residuals? from package ?stats? in 
package ?globaltest?
   ** help
   *** installing help indices
   ** building package indices ...
   *** tangling vignette sources ...
    ?GlobalTest.Rnw?
    ?GlobalTest_deprecated.Rnw?
   ** testing if installed package can be loaded

   * DONE (globaltest)

Why isn't this warning reported by 'R CMD check'?

Also the output of 'R CMD build' is not saying anything:

 
http://bioconductor.org/checkResults/2.9/bioc-LATEST/globaltest/wilson2-buildsrc.html

even though the package was installed to re-build the vignettes.
'R CMD build' might not be the place for issuing this kind of warning
though but 'R CMD check' definitely is.

This is with 2.14.0 beta (2011-10-16 r57266) on 64-bit openSUSE 11.4.

Thanks,
H.

-- 
Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319



[Rd] warnings issued at installation time not reported by 'R CMD check'
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