R devel - Oct 2011 - .onLoad failing because could not find function "loadMethod"

Hi,

This strange warning happen sometimes when running 'R CMD check':

   * checking whether the package can be loaded with stated dependencies 
... WARNING

   Error : .onLoad failed in loadNamespace() for ?pkgB?, details:
     call: length(new("A"))
     error: could not find function "loadMethod"
   Error: package/namespace load failed for ?pkgB?
   Execution halted

   It looks like this package (or one of its dependent packages) has an
   unstated dependence on a standard package.  All dependencies must be
   declared in DESCRIPTION.
   See the information on DESCRIPTION files in the chapter ?Creating R
   packages? of the ?Writing R Extensions? manual.

The same warning is reported during the 2 next checks:

   * checking whether the package can be unloaded cleanly ... WARNING
   <same error here>
   * checking whether the namespace can be loaded with stated 
dependencies ... WARNING
   <same error here>

It seems to happen when pkgB has code in its .onLoad hook that
tries to call a method defined in pkgA (pkgB imports pkgA) on an object
'x' that is an instance of a class defined in pkgA. For some obscure
reason it seems that, at the time the .onLoad hook is executed, the
methods package (which is imported in both packages) is not working
properly.

I've put 2 toy packages here that illustrate the problem:

   https://rapidshare.com/files/4043144391/pkgA_1.0.tar.gz

   https://rapidshare.com/files/1959508331/pkgB_1.0.tar.gz

I'm using R version 2.14.0 alpha (2011-10-10 r57211).

The .onLoad hook in pkgB is:

.onLoad <- function(libname, pkgname)
{
     showMethods("length")
     length(new("A"))
}

Class A and the length method for this class is defined in pkgA.

Because of the showMethods("length") statement, you should see this
when running R CMD check pkgB_1.0.tar.gz:

   * checking whether the package can be loaded with stated dependencies 
... WARNING
   Function: length (package base)
   x="A"

   Error : .onLoad failed in loadNamespace() for ?pkgB?, details:
     call: length(new("A"))
     error: could not find function "loadMethod"
   Error: package/namespace load failed for ?pkgB?
   Execution halted

Any insight on this would be appreciated.

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

On 11-10-14 05:46 PM, Herv? Pag?s wrote:
[...]
>
> I've put 2 toy packages here that illustrate the problem:
>
> https://rapidshare.com/files/4043144391/pkgA_1.0.tar.gz
>
> https://rapidshare.com/files/1959508331/pkgB_1.0.tar.gz
arghh, sorry for the broken links. I'll try to put those packages
somewhere else.

H.

The thing that happens during the check is that the methods package is 
not among the automatically loaded and attached packages.

When the pkgB packages is attached, the Namespaces of pkgA and methods 
are loaded but not attached.

Note that one of the checks tells you:

"A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start."


If you like to see into the details more easily, just start R with

R  R_DEFAULT_PACKAGES=NULL
and then try to
  library("pkgB")
and you are able to reproduce the check messages.

You can avoid n-1 Warnings/Errors in the checks by adding
library("methods")
in your .onLoad function, but of course you cannot get rid of the check 
that checks that the package can be loaded with the base namespace only.

Best,
Uwe Ligges








On 15.10.2011 02:46, Herv? Pag?s wrote:
> Hi,
>
> This strange warning happen sometimes when running 'R CMD check':
>
> * checking whether the package can be loaded with stated dependencies
> ... WARNING
>
> Error : .onLoad failed in loadNamespace() for ?pkgB?, details:
> call: length(new("A"))
> error: could not find function "loadMethod"
> Error: package/namespace load failed for ?pkgB?
> Execution halted
>
> It looks like this package (or one of its dependent packages) has an
> unstated dependence on a standard package. All dependencies must be
> declared in DESCRIPTION.
> See the information on DESCRIPTION files in the chapter ?Creating R
> packages? of the ?Writing R Extensions? manual.
>
> The same warning is reported during the 2 next checks:
>
> * checking whether the package can be unloaded cleanly ... WARNING
> <same error here>
> * checking whether the namespace can be loaded with stated dependencies
> ... WARNING
> <same error here>
>
> It seems to happen when pkgB has code in its .onLoad hook that
> tries to call a method defined in pkgA (pkgB imports pkgA) on an object
> 'x' that is an instance of a class defined in pkgA. For some
obscure
> reason it seems that, at the time the .onLoad hook is executed, the
> methods package (which is imported in both packages) is not working
> properly.
>
> I've put 2 toy packages here that illustrate the problem:
>
> https://rapidshare.com/files/4043144391/pkgA_1.0.tar.gz
>
> https://rapidshare.com/files/1959508331/pkgB_1.0.tar.gz
>
> I'm using R version 2.14.0 alpha (2011-10-10 r57211).
>
> The .onLoad hook in pkgB is:
>
> .onLoad <- function(libname, pkgname)
> {
> showMethods("length")
> length(new("A"))
> }
>
> Class A and the length method for this class is defined in pkgA.
>
> Because of the showMethods("length") statement, you should see
this
> when running R CMD check pkgB_1.0.tar.gz:
>
> * checking whether the package can be loaded with stated dependencies
> ... WARNING
> Function: length (package base)
> x="A"
>
> Error : .onLoad failed in loadNamespace() for ?pkgB?, details:
> call: length(new("A"))
> error: could not find function "loadMethod"
> Error: package/namespace load failed for ?pkgB?
> Execution halted
>
> Any insight on this would be appreciated.
>
> Thanks,
> H.
>