[BioC] Installing affy package

Keith Satterley keith at wehi.EDU.AU
Wed Nov 25 02:20:13 CET 2009


Hi Dorothy,

I'm not sure about the smootScatter error. Sometimes these sort of 
things are sorted out by having compatible versions. Have you tried 
using biocLite? Do the following:

source("http://bioconductor.org/biocLite.R")
biocLite("affy",dependencies=TRUE)

This will ensure you get the correct version of affy for your version of R.

If you provide the output from the sessionInfo() function, people can 
tell what versions of software you have and whether they match or not.

If possible install the latest R, (currently version 2.10.0) and use 
biocLite, as described above and also at the bioconductor website:

http://www.bioconductor.org/docs/install/

hope that helps,

Keith.

dorothyc wrote:
> Hi,
>
> I've been experiencing problems installing the affy package (please  
> see output below).  I've installed the latest versions of Biobase and  
> affyio already.
>
> Thanks very much!!
>
> Regards,
> Dorothy
>
> #############
> ~/% R CMD INSTALL affy_1.24.2.tar.gz
> * Installing to library '/home/dorothyc/R/x86_64-unknown-linux-gnu- 
> library/2.8'
> * 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 -std=gnu99 -I/projects/tab/linux/x86_64/lib64/R/include - 
> DHAVE_ZLIB=1  -I/usr/local/include -I"/home/dorothyc/R/x86_64-unknown- 
> linux-gnu-library/2.8/pr
> eprocessCore/include"   -fpic  -g -O2 -c chipbackground.c -o  
> chipbackground.o
> gcc -std=gnu99 -I/projects/tab/linux/x86_64/lib64/R/include - 
> DHAVE_ZLIB=1  -I/usr/local/include -I"/home/dorothyc/R/x86_64-unknown- 
> linux-gnu-library/2.8/pr
> eprocessCore/include"   -fpic  -g -O2 -c getall_locations.c -o  
> getall_locations.o
> gcc -std=gnu99 -I/projects/tab/linux/x86_64/lib64/R/include - 
> DHAVE_ZLIB=1  -I/usr/local/include -I"/home/dorothyc/R/x86_64-unknown- 
> linux-gnu-library/2.8/pr
> eprocessCore/include"   -fpic  -g -O2 -c mas5calls.c -o mas5calls.o
> gcc -std=gnu99 -I/projects/tab/linux/x86_64/lib64/R/include - 
> DHAVE_ZLIB=1  -I/usr/local/include -I"/home/dorothyc/R/x86_64-unknown- 
> linux-gnu-library/2.8/pr
> eprocessCore/include"   -fpic  -g -O2 -c rma2.c -o rma2.o
> gcc -std=gnu99 -I/projects/tab/linux/x86_64/lib64/R/include - 
> DHAVE_ZLIB=1  -I/usr/local/include -I"/home/dorothyc/R/x86_64-unknown- 
> linux-gnu-library/2.8/pr
> eprocessCore/include"   -fpic  -g -O2 -c rma_common.c -o rma_common.o
> gcc -std=gnu99 -shared -L/usr/local/lib64 -o affy.so chipbackground.o  
> getall_locations.o mas5calls.o rma2.o rma_common.o -lz
> ** R
> ** data
> ** demo
> ** inst
> ** preparing package for lazy loading
>
> Loading required package: Biobase
>
> Welcome to Bioconductor
>
>    Vignettes contain introductory material. To view, type
>    'openVignette()'. To cite Bioconductor, see
>    'citation("Biobase")' and for packages 'citation(pkgname)'.
>
> Error in importIntoEnv(impenv, impnames, ns, impvars) :
>    object ''smoothScatter'' is not exported by 'namespace:graphics'
> Calls: <Anonymous> ... loadNamespace -> namespaceImportFrom ->  
> importIntoEnv
> Execution halted
> ERROR: lazy loading failed for package 'affy'
> ** Removing '/home/dorothyc/R/x86_64-unknown-linux-gnu-library/2.8/affy'
> ** Restoring previous '/home/dorothyc/R/x86_64-unknown-linux-gnu- 
> library/2.8/affy'
> 	[[alternative HTML version deleted]]
>
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