[BioC] affy devel fails to install with getBioC and Rbeta1.8.0

[Nicholas Lewin-Koh]

Hi,
Not sure if this is on my end or not. Using todays R-1.8.0 beta release
and RH linux 9.0:

> getBioC(relLevel = "devel",destdir="test/testlibs")
    .......

[1] "Attempting to download affy from
http://www.bioconductor.org/repository/devel/package/Source"
[1] "Download complete."
[1] "Installing affy"
* Installing *source* package 'affy' ...
creating cache ./config.cache
checking how to run the C preprocessor... cc -E
checking for main in -lz... yes
checking for zlib.h... yes
checking if zlib version >= 1.1.3... yes
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
gcc -Itest/lib/R/include -DHAVE_ZLIB=1  -I/usr/local/include
-D__NO_MATH_INLINES -mieee-fp  -fPIC  -g -O2 -c chipbackground.c -o
chipbackground.o
gcc -Itest/lib/R/include -DHAVE_ZLIB=1  -I/usr/local/include
-D__NO_MATH_INLINES -mieee-fp  -fPIC  -g -O2 -c getall_locations.c -o
getall_locations.o
gcc -Itest/lib/R/include -DHAVE_ZLIB=1  -I/usr/local/include
-D__NO_MATH_INLINES -mieee-fp  -fPIC  -g -O2 -c qnorm.c -o qnorm.o
gcc -Itest/lib/R/include -DHAVE_ZLIB=1  -I/usr/local/include
-D__NO_MATH_INLINES -mieee-fp  -fPIC  -g -O2 -c read_abatch.c -o
read_abatch.o
gcc -Itest/lib/R/include -DHAVE_ZLIB=1  -I/usr/local/include
-D__NO_MATH_INLINES -mieee-fp  -fPIC  -g -O2 -c read_cdffile.c -o
read_cdffile.o
gcc -Itest/lib/R/include -DHAVE_ZLIB=1  -I/usr/local/include
-D__NO_MATH_INLINES -mieee-fp  -fPIC  -g -O2 -c rma2.c -o rma2.o
gcc --Itest/lib/R/include -DHAVE_ZLIB=1  -I/usr/local/include
-D__NO_MATH_INLINES -mieee-fp  -fPIC  -g -O2 -c rma_background2.c -o
rma_background2.o
gcc -Itest/lib/R/include -DHAVE_ZLIB=1  -I/usr/local/include
-D__NO_MATH_INLINES -mieee-fp  -fPIC  -g -O2 -c rma_common.c -o
rma_common.o
gcc -shared -L/usr/local/lib -o affy.so chipbackground.o
getall_locations.o qnorm.o read_abatch.o read_cdffile.o rma2.o
rma_background2.o rma_common.o -lz   
-L/test/lib/R/bin -lR
** R
** data
** demo
** inst
** save image
Welcome to Bioconductor
         Vignettes contain introductory material.  To view,
         simply type: openVignette()
         For details on reading vignettes, see
         the openVignette help page.
[1] TRUE
[1] TRUE
[1] TRUE
[1] "Cdf"
[1] "name.levels"
[1] "name.levels"
[1] "name.levels<-"
[1] "name.levels<-"
[1] "pbase"
[1] "pbase"
[1] "pbase<-"
[1] "pbase<-"
[1] "pbase.levels"
[1] "pbase.levels"
[1] "pbase.levels<-"
[1] "pbase.levels<-"
[1] "tbase"
[1] "tbase"
[1] "tbase<-"
[1] "tbase<-"
[1] "tbase.levels"
[1] "tbase.levels"
[1] "tbase.levels<-"
[1] "tbase.levels<-"
[1] "atom"
[1] "atom"
[1] "atom<-"
[1] "atom<-"
[1] "probeNames"
[1] "probeNames"
[1] "probeNames<-"
[1] "probeNames<-"
[1] "show"
[1] "AffyBatch"
[1] "intensity"
[1] "intensity"
[1] "intensity<-"
[1] "intensity<-"
[1] "length"
[1] "ncol"
[1] "ncol"
[1] "nrow"
[1] "nrow"
[1] "getCdfInfo"
[1] "getCdfInfo"
Error in getMethodsForDispatch(f, fdef) : Trying to get slot ".Methods"
from an
object whose class ("genericMethods") is not defined
Execution halted
test/lib/R/bin/INSTALL: line 1: 15051 Broken pipe             cat
"test/testlibs/affy/R/affy"
ERROR: execution of package source for 'affy' failed
** Removing 'test/testlibs/affy'
Warning message:
Installation of package affy had non-zero exit status in:
installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce)
[1] "Attempting to download affycomp from
http://www.bioconductor.org/repository/devel/package/Source"
 

Note if some of the paths look funny I had to take them out becuase of
company security.

Nicholas