On 21/04/2012 14:18, Whit Armstrong wrote:
I'm trying to R CMD check a package, and I'm getting the 'checking S3
generic/method consistency' warning.
I have written a function 'gamma.dist' which is _not_ an S3 method,
but happens to collide with the 'gamma' function from the R::base
namespace.
Is there a way of telling CMD check that the name is intentional and
is not meant to be an S3 method?
More importantly, there is no way to tell the generic, and there is a
"dist" class in use in the 'stats' package.
My function is defined as follows:
gamma.dist<- function(x,alpha,beta,observed=FALSE) {
attr(x,"distributed")<- "gamma"
attr(x,"alpha")<- substitute(alpha)
attr(x,"beta")<- substitute(beta)
attr(x,"observed")<- observed
attr(x,"env")<- new.env()
class(x)<- "mcmc.object"
x
}
with corresponding man page:
\name{normal.dist}
\alias{normal.dist}
\alias{uniform.dist}
\alias{gamma.dist}
\alias{bernoulli.dist}
\alias{binomial.dist}
...
...
\usage{
normal.dist(x, mu, tau, observed = FALSE)
uniform.dist(x, lower, upper, observed = FALSE)
gamma.dist(x, alpha, beta, observed = FALSE)
bernoulli.dist(x, p, observed = FALSE)
binomial.dist(x, n, p, observed = FALSE)
}
I am reluctant to change the name of the function b/c all my
distribution methods use the same convention of 'distribution
type'.dist.
Do CRAN maintainers view this warning as a blocker for the package
(full make check output below, which includes a few additional
warnings I'm in the process of fixing)?
That's a question for them, not R-devel, isn't it?
Thanks,
Whit
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building ‘rcppbugs_0.0.1.tar.gz’
* using log directory ‘/home/warmstrong/dvl/R.packages/rcppbugs.Rcheck’
* using R version 2.15.0 (2012-03-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘rcppbugs/DESCRIPTION’ ... OK
* this is package ‘rcppbugs’ version ‘0.0.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking whether package ‘rcppbugs’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 8.4Mb
sub-directories of 1Mb or more:
libs 8.1Mb
* 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 non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... WARNING
gamma:
function(x)
gamma.dist:
function(x, alpha, beta, observed)
See section ‘Generic functions and methods’ of the ‘Writing R
Extensions’ manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
S3 methods shown with full name in documentation object 'normal.dist':
‘gamma.dist’
The \usage entries for S3 methods should use the \method markup and
not their full name.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... WARNING
Non-portable flags in variable ‘PKG_CXXFLAGS’:
-Wall -std=c++0x
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking examples ... OK
* checking PDF version of manual ... OK
WARNING: There were 2 warnings.
NOTE: There were 2 notes.
See
‘/home/warmstrong/dvl/R.packages/rcppbugs.Rcheck/00check.log’
for details.
warmstrong@krypton:~/dvl/R.packages$ R
gamma
function (x) .Primitive("gamma")
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--
Brian D. Ripley, rip...@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
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