[BioC] bioconductor affy lib with R 2.0.1

[Susan J. Miller]

I have just installed R 2.0.1 on our Solaris8 system, and when I try to 
run getBioC, the following errors occur.  Can someone suggest a solution 
to this problem?


 > source("http://www.bioconductor.org/getBioC.R")
 > getBioC()
Running getBioC version 1.2.69....
If you encounter problems, first make sure that
you are running the latest version of getBioC()
which can be found at: www.bioconductor.org/getBioC.R

Please direct any concerns or questions to bioconductor at stat.math.ethz.ch.

[1] "Attempting to download affy from 
http://www.bioconductor.org/repository/release1.5/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 -I/usr/local/lib/R/include -DHAVE_ZLIB=1  -I/usr/local/include 
-fPIC  -g -O2 -c chipbackground.c -o chipbackground.o
gcc -I/usr/local/lib/R/include -DHAVE_ZLIB=1  -I/usr/local/include 
-fPIC  -g -O2 -c getall_locations.c -o getall_locations.o
gcc -I/usr/local/lib/R/include -DHAVE_ZLIB=1  -I/usr/local/include 
-fPIC  -g -O2 -c mas5calls.c -o mas5calls.o
gcc -I/usr/local/lib/R/include -DHAVE_ZLIB=1  -I/usr/local/include 
-fPIC  -g -O2 -c qnorm.c -o qnorm.o
gcc -I/usr/local/lib/R/include -DHAVE_ZLIB=1  -I/usr/local/include 
-fPIC  -g -O2 -c read_abatch.c -o read_abatch.o
gcc -I/usr/local/lib/R/include -DHAVE_ZLIB=1  -I/usr/local/include 
-fPIC  -g -O2 -c rma2.c -o rma2.o
gcc -I/usr/local/lib/R/include -DHAVE_ZLIB=1  -I/usr/local/include 
-fPIC  -g -O2 -c rma_background2.c -o rma_background2.o
gcc -I/usr/local/lib/R/include -DHAVE_ZLIB=1  -I/usr/local/include 
-fPIC  -g -O2 -c rma_common.c -o rma_common.o
gcc -G -L/usr/local/lib -o affy.so chipbackground.o getall_locations.o 
mas5calls.o qnorm.o read_abatch.o rma2.o rma_background2.o rma_common.o 
-lz
** R
** data
** demo
** inst
** save image
[1] TRUE
[1] TRUE
Error in library(package, character.only = TRUE, logical = TRUE, 
warn.conflicts = warn.conflicts,  :
         'Biobase' is not a valid package -- installed < 2.0.0?
Execution halted
Broken Pipe
ERROR: execution of package source for 'affy' failed
** Removing '/usr/local/lib/R/library/affy'
** Restoring previous '/usr/local/lib/R/library/affy'



-- 
Thanks,
-susan

Susan J. Miller
Biotechnology Computing Facility
Arizona Research Laboratories
Bio West 228
University of Arizona
Tucson, AZ  85721
(520) 626-2597