There have been some changes, up to svn revision 39037 at the moment,
but there will be some more. All reports are appreciated. Some are
easier for me to check out than others (I'm working from a home setup
that does not have all of CRAN available (!) so it takes time to test a
package with many dependencies in "CMD check"s view of things.)
John
Roger Bivand wrote:
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 at 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.
[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"
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=):
[1] "/home/rsb/topics/packages/sp-bundle/sp.Rcheck"
[2] "/home/rsb/topics/r_libs"
[3] "/home/rsb/topics/Rtobe240/lib/R/library"
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"
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:
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