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

[James MacDonald]

It's probably not on your end. I don't think affy 1.3.14 and R-1.8.0 are
fully compatible yet. R-1.8.0 just recently went into feature freeze, so
I think it will take a little bit for the affy maintainers to get
everything squared away.

Jim



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623

>>> "Nicholas Lewin-Koh" <nikko at hailmail.net> 10/02/03 03:34AM >>>
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

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