[BioC] Affy Install

[Jason Skelton]

Hi

I'm having difficulty using the R CMD INSTALL command with the affy 
package, I can use it with any other package from Bioconductor except 
any of the affy package versions:



hoyle[jps]55: /usr/local/bin/R CMD INSTALL -l 
/nfs/team85/jps/R_dictyostelium/library 
/nfs/team85/jps/R_dictyostelium/affy_1.3.27.tar.gz
* 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 
-D__NO_MATH_INLINES -mieee-fp  -fPIC  -g -O2 -c chipbackground.c -o 
chipbackground.o
gcc -I/usr/local/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 -I/usr/local/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 -I/usr/local/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 -I/usr/local/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 -I/usr/local/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 -I/usr/local/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 rma2.o rma_background2.o 
rma_common.o -lz
** R
** data
** demo
** inst
** save image
[1] FALSE
Warning message:
There is no package called 'Biobase' in: library(package, character.only 
= TRUE, logical = TRUE, warn.conflicts = warn.conflicts,
[1] TRUE
[1] TRUE
Error in getClass(Class, where = topenv(parent.frame())) :
	"MIAME" is not a defined class
Execution halted
ERROR: execution of package source for 'affy' failed
** Removing 
'/.automount/babel/root/nfs/jps/R_dictyostelium/Jasonlibrary/affy'
** Restoring previous 
'/.automount/babel/root/nfs/jps/R_dictyostelium/Jasonlibrary/affy'

It's asking for Biobase, WHICH OF COURSE I HAVE ALREADY INSTALLED
and the correct version

I've tried all these versions with the same outcome

affy_1.3.23.tar.gz
affy_1.3.27.tar.gz
affy_1.4.4.tar.gz

currently have biobase version 1.4.1 installed

any ideas would greatfully be received

thanks

Jason





-- 
--------------------------------
Jason Skelton
Pathogen Microarrays
Wellcome Trust Sanger Institute
Hinxton
Cambridge
CB10 1SA

Tel +44(0)1223 834244 Ext 7123
Fax +44(0)1223 494919