[Bioc-devel] Strange error during package check (pcaMethods package)

I am the maintainer of the pcaMethods package. During the automated
package checks I receive the following error message on
/wellington/ Linux (SUSE 9.2) and on /derby/ Mac OS X (10.4.8) (see below).
Build is fine for all packages.
I guess that has something to do with the upgrade to R-2.5.0, but I really
cannot interpret the error message.

It builds and checks fine on my (Mac OS) desktop and Linux laptop with 
R-2.5.0.

Hi Wolfram,

Wolfram Stacklies <wolfram.stacklies at gmail.com> writes:
  

I am the maintainer of the pcaMethods package. During the automated
package checks I receive the following error message on
/wellington/ Linux (SUSE 9.2) and on /derby/ Mac OS X (10.4.8) (see below).
Build is fine for all packages.
I guess that has something to do with the upgrade to R-2.5.0, but I really
cannot interpret the error message.
    

It is not one I've seen before either.  The "could not find function"
part appears to be coming from findFun in envir.c and this gets used
by the methods package (among others).

I don't know if it will solve the issue, but two things you should do:

1. Since you define S4 classes and methods and have a NAMESPACE file,
   you need to add a .onLoad function to your package as described in
   the Writing R Extensions manual:

     .onLoad <- function(libname, pkgname) require("methods")

2. You have 'SaveImage: no' in the DESCERIPTION file and this is not
   recommended for packages that use S4.  Can you try setting this to
   yes?

  

It builds and checks fine on my (Mac OS) desktop and Linux laptop with 
R-2.5.0.
    

It builds and checks for me using an R-2.5.0 beta.  The build
(vignette) and the check (examples + vignette) take a looong time.  If
it were my package, I would see about trimming down the example data
so that checking the package takes less time.

Another comment: in the example for svdImpute, you demonstrate
extracting components from the result object using direct slot access
via '@'.  You might consider using accessor methods instead.  So
instead of result at scores you would do scores(result).  When you want
to reorganize how the result is structured you will be very glad for
such an interface layer.

+ seth

Hi Wolfram,

Wolfram Stacklies <wolfram.stacklies at gmail.com> writes:
  

I am the maintainer of the pcaMethods package. During the automated
package checks I receive the following error message on
/wellington/ Linux (SUSE 9.2) and on /derby/ Mac OS X (10.4.8) (see below).
Build is fine for all packages.
I guess that has something to do with the upgrade to R-2.5.0, but I really
cannot interpret the error message.
    

It is not one I've seen before either.  The "could not find function"
part appears to be coming from findFun in envir.c and this gets used
by the methods package (among others).

I don't know if it will solve the issue, but two things you should do:

1. Since you define S4 classes and methods and have a NAMESPACE file,
   you need to add a .onLoad function to your package as described in
   the Writing R Extensions manual:

     .onLoad <- function(libname, pkgname) require("methods")

2. You have 'SaveImage: no' in the DESCERIPTION file and this is not
   recommended for packages that use S4.  Can you try setting this to
   yes?

  

It builds and checks fine on my (Mac OS) desktop and Linux laptop with 
R-2.5.0.
    

It builds and checks for me using an R-2.5.0 beta.  The build
(vignette) and the check (examples + vignette) take a looong time.  If
it were my package, I would see about trimming down the example data
so that checking the package takes less time.

Another comment: in the example for svdImpute, you demonstrate
extracting components from the result object using direct slot access
via '@'.  You might consider using accessor methods instead.  So
instead of result at scores you would do scores(result).  When you want
to reorganize how the result is structured you will be very glad for
such an interface layer.

+ seth