S4 changes - sp fails

Since writing that, I have found that there is a similar problem with 
testing mvoutliers (which does load sp), and it depends on exactly what 
has been done in what order.  (I'll forward to you the exact description.)

.libPaths()

list.files(.libPaths()[1])

sessionInfo()

I now suspect there is a protection problem in the new S4 dispatch code.
Using gctorture/valgrind may help locate it.

Brian

On Fri, 1 Sep 2006, Roger Bivand wrote:

On Fri, 1 Sep 2006, Prof Brian Ripley wrote:

Roger,

I had managed to run R CMD check on sp successfully on r39021 and r39043 
(current) in my nightly checks.  (There are a couple of tests where the 
show/print method is not being invoked, but that is not new.)

All I can suggest is to install R from scratch (make distclean), and then 
reinstall all relevant packages.  At a guess, your interactive use and R 
CMD check are picking up different libraries.

Brian,

I added .libPaths() and sessionInfo() to the offending example, and tried
with a fresh svn checkout built in a fresh directory and installed in a
fresh directory (no sp or methods in /home/rsb/topics/r_libs, which was
set with export R_LIBS=):

data(state)
.libPaths()

[1] "/home/rsb/topics/packages/sp-bundle/sp.Rcheck"
[2] "/home/rsb/topics/r_libs"                      
[3] "/home/rsb/topics/Rtobe240/lib/R/library"      

sessionInfo()

R version 2.4.0 Under development (unstable) (2006-08-31 r39045) 
i686-pc-linux-gnu 

locale:
LC_CTYPE=en_GB;LC_NUMERIC=C;LC_TIME=en_GB;LC_COLLATE=en_GB;LC_MONETARY=en_GB;LC_
MESSAGES=en_GB;LC_PAPER=en_GB;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREME
NT=en_GB;LC_IDENTIFICATION=C

attached base packages:
[1] "methods"   "stats"     "graphics"  "grDevices" "utils"     "datasets" 
[7] "base"     

other attached packages:
      sp 
"0.8-19" 

dd2dms(state.center$x)

Error in function (classes, fdef, mtable)  : 
        unable to find an inherited method for function "initialize", for 
signature "integer"
Execution halted

I also tried to replicate the problem by making a new, very small, package 
with just the apparently offending files:

spS4:
DESCRIPTION  man/  NAMESPACE  R/

spS4/man:
char2dms.Rd  DMS-class.Rd

spS4/R:
AAA.R  dms.R

and edited DESCRIPTION, NAMESPACE, and AAA.R to suit. In this setting 
there was no problem. I'll carry on looking. None of these files has 
changed between released 0.8-18 and CVS 0.8-19. 

Roger

There are around a dozen S4-using packages on CRAN that are currently 
failing their checks: some look like newly-discovered bugs but some look 
like problems in S4 dispatch (even of S3 dispatch for S3 generics turned 
into S4 generics).  More are producing apparently incorrect warnings.

Brian


On Thu, 31 Aug 2006, Roger Bivand wrote:

Under R version 2.4.0 (2006-08-30 r39024), sp fails CMD check following
the latest changes in methods.

The failures are in running examples and occur in CMD check:

data(state)
dd2dms(state.center$x)

Error in function (classes, fdef, mtable)  : 
        unable to find an inherited method for function "initialize", for 
signature "integer"

Offending code:

	deg <- as(floor(dd), "integer") 

After replacing by as.integer(floor(dd)), it fails on the local class 
definition:

dd2dms(state.center$x)

Error in function (classes, fdef, mtable)  : 
        unable to find an inherited method for function "initialize", for 
signature "DMS"

Installing sp, example("DMS-class") runs successfully interactively 
(other examples do too).

The methods package is declared as Depends: in DESCRIPTION, and
import(methods) in NAMESPACE; 

.onLoad <- function(lib, pkg) require(methods) is in the first R source 
file in Collate: order.

Should the methods package be being invoked in some other way, is there a 
reason why the installed package appears to run examples successfully that 
fail under CMD check?

Roger