From ripley at stats.ox.ac.uk  Fri Sep  1 10:28:08 2006
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Fri, 1 Sep 2006 09:28:08 +0100 (BST)
Subject: [Rd] S4 changes - sp fails
In-Reply-To: <Pine.LNX.4.44.0609010931490.5844-100000@reclus.nhh.no>
References: <Pine.LNX.4.44.0609010931490.5844-100000@reclus.nhh.no>
Message-ID: <Pine.LNX.4.64.0609010925120.26402@gannet.stats.ox.ac.uk>

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.)

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
> > > 
> > > 
> > 
> > 
> 
> 

-- 
Brian D. Ripley,                  ripley at 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




[Rd] S4 changes - sp fails
Prof Brian Ripley