false warning - tools:::.get_S4_methods_list

[Yohan Chalabi]

>>>> "ULPO" == Uwe.Ligges at r-project.org
>>>> on Sun, 03 Jan 2010 03:05:52 +0100

   ULPO> Dear package maintainer,
   ULPO>
   ULPO> this notification has been generated automatically.
   ULPO> Your package fRegression_2100.76.tar.gz did pass 'R CMD check'
   ULPO> only with WARNING(s).
   ULPO> It has been built for Windows and
   ULPO> will be published within 24 hours in the corresponding
   ULPO> CRAN directory
   ULPO> (CRAN/bin/windows/contrib/2.10/).
   ULPO>
   ULPO> Please consider to submit a fixed version without any WARNING
   ULPO> until January 15.
   ULPO> For details (and for results on other platforms) see
   ULPO> http://cran.r-project.org/web/checks/check_summary.html
   ULPO> R version 2.10.1 (2009-12-14)
   ULPO>
   ULPO> All the best,
   ULPO> Uwe Ligges
   ULPO> (Maintainer of binary packages for Windows)
   ULPO>
   ULPO> * using log directory
   ULPO> 'd:/Rcompile/CRANpkg/local/2.10/fRegression.Rcheck'
   ULPO> * using R version 2.10.1 (2009-12-14)
   ULPO> * using session charset: ISO8859-1
   ULPO> * checking for file 'fRegression/DESCRIPTION' ... OK
   ULPO> * this is package 'fRegression' version '2100.76'
   ULPO> * checking package dependencies ... OK
   ULPO> * checking if this is a source package ... OK
   ULPO> * checking whether package 'fRegression' can be installed
   ULPO> ... OK
   ULPO> * checking package directory ... OK
   ULPO> * checking for portable file names ... OK
   ULPO> * checking DESCRIPTION meta-information ... OK
   ULPO> * checking top-level files ... OK
   ULPO> * checking index information ... OK
   ULPO> * checking package subdirectories ... OK
   ULPO> * checking R files for non-ASCII characters ... OK
   ULPO> * checking R files for syntax errors ... OK
   ULPO> * checking whether the package can be loaded ... OK
   ULPO> * checking whether the package can be loaded with stated
   ULPO> dependencies ... OK
   ULPO> * checking for unstated dependencies in R code ... OK
   ULPO> * checking S3 generic/method consistency ... OK
   ULPO> * checking replacement functions ... OK
   ULPO> * checking foreign function calls ... OK
   ULPO> * checking R code for possible problems ... OK
   ULPO> * checking Rd files ... OK
   ULPO> * checking Rd metadata ... OK
   ULPO> * checking Rd cross-references ... OK
   ULPO> * checking for missing documentation entries ... WARNING
   ULPO> Undocumented S4 methods:
   ULPO> generic 'summary' and siglist 'sparseMatrix'
   ULPO> All user-level objects in a package (including S4 classes
   ULPO> and methods)
   ULPO> should have documentation entries.
   ULPO> See the chapter 'Writing R documentation files' in manual
   ULPO> 'Writing R
   ULPO> Extensions'.
   ULPO> * checking for code/documentation mismatches ... OK
   ULPO> * checking Rd \usage sections ... OK
   ULPO> * checking line endings in C/C++/Fortran sources/headers
   ULPO> ... OK
   ULPO> * checking line endings in Makefiles ... OK
   ULPO> * checking for portable compilation flags in Makevars ... OK
   ULPO> * checking for portable use of ... OK
   ULPO> * checking examples ... OK
   ULPO> * checking tests ... OK
   ULPO> * checking PDF version of manual ... OK

Hi Uwe, 

It looks like undoc() produces a false warning with packages
that have no namespace and are using S4 methods.

I could track the problem down to tools:::.get_S4_methods_list which
returns the summary,sparseMatrix-method as a method defined in
"fRegression" which is obviously not the case.


Regards,
Yohan