Re: [Rd] S4 changes - sp fails

From: Roger Bivand <Roger.Bivand_at_nhh.no>
Date: Fri 01 Sep 2006 - 11:30:32 GMT


On Fri, 1 Sep 2006, Roger Bivand wrote:

> On Fri, 1 Sep 2006, Prof Brian Ripley wrote:
>
> > 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.)

On a different RHEL 4 i386 with R version 2.4.0 (2006-09-01 r39049), and fully updated sp CVS from

cvs -z3 -d:pserver:anonymous@r-spatial.cvs.sourceforge.net:/cvsroot/r-spatial checkout sp

CND check sp passes with no error (with RColorBrewer the only installed package in a test library).

I'll try again on the first machine (which is also RHEL 4 i386, but where R was at 2006-08-31 r39045, and where there may have been configuration issues (wrong library path?).

Roger

>
> Thanks.
>
> I reran the interactive test:
>
> library(sp, lib.loc="sp.Rcheck")
> example("DMS-class")
>
> which ran without problems.
>
> > .libPaths()
> [1] "/home/rsb/topics/r_libs"
> [2] "/home/rsb/topics/Rtobe240/lib/R/library"
> > list.files(.libPaths()[1])
> [1] "abind" "maptools" "pixmap" "RColorBrewer" "R.css"
> [6] "rgdal" "SparseM" "spdep" "tripack"
> > 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"
>
> >
> > I now suspect there is a protection problem in the new S4 dispatch code.
> > Using gctorture/valgrind may help locate it.
>
> Running check --use-gct sp now.
>
> Roger
>
> >
> > 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
> > > > >
> > > > >
> > > >
> > > >
> > >
> > >
> >
> >
>
>

-- 
Roger Bivand
Economic Geography Section, Department of Economics, Norwegian School of
Economics and Business Administration, Helleveien 30, N-5045 Bergen,
Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43
e-mail: Roger.Bivand@nhh.no

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