[BioC] install new bioconductor packages R2.7.0 - affy

[Martin Morgan]

Hi Peter-Bram --

I guess you are 'updating' an existing installation, in which case the
best bet is to follow the instructions on

http://bioconductor.org/download

and do something like

source("http://bioconductor.org/biocLite.R")
update.packages(repos=biocinstallRepos(), ask=FALSE)

(remove ask=FALSE if you want to be more selective about which
packages are updated). The underlying problem is that affy depends on
a pacakge called preprocessCore, and your version of preprocessCore is
out of date.

Martin

<P.A.C._t_Hoen at lumc.nl> writes:

> Dear list,
> We have updated to R2.7.0.
> I was using biocLite to also install the bioconductor 2.2 packages.
> Some of them were correctly installed, others not, amongst which affy 1.18.0
> I paste sessionInfo and logs below. Any idea what the problem is?
> Thanks for your advice,
> Peter-Bram
>
>> sessionInfo()
> R version 2.7.0 (2008-04-22) 
> x86_64-redhat-linux-gnu 
>
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base     
>
> loaded via a namespace (and not attached):
> [1] tools_2.7.0
>
>> source("http://bioconductor.org/biocLite.R")
>> biocLite("affy")
> Running biocinstall version 2.2.9 with R version 2.7.0 
> Your version of R requires version 2.2 of BioConductor.
> trying URL 'http://bioconductor.org/packages/2.2/bioc/src/contrib/affy_1.18.0.tar.gz'
> Content type 'application/x-gzip' length 1375563 bytes (1.3 Mb)
> opened URL
> ==================================================
> downloaded 1.3 Mb
>
> * 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/lib64/R/include -DHAVE_ZLIB=1  -I/usr/local/include -I"/usr/lib64/R/library/preprocessCore/include"   -fpic  -O2 -g -std=gnu99 -c chipbackground.c -o chipbackground.o
> gcc -I/usr/lib64/R/include -DHAVE_ZLIB=1  -I/usr/local/include -I"/usr/lib64/R/library/preprocessCore/include"   -fpic  -O2 -g -std=gnu99 -c getall_locations.c -o getall_locations.o
> gcc -I/usr/lib64/R/include -DHAVE_ZLIB=1  -I/usr/local/include -I"/usr/lib64/R/library/preprocessCore/include"   -fpic  -O2 -g -std=gnu99 -c mas5calls.c -o mas5calls.o
> gcc -I/usr/lib64/R/include -DHAVE_ZLIB=1  -I/usr/local/include -I"/usr/lib64/R/library/preprocessCore/include"   -fpic  -O2 -g -std=gnu99 -c rma2.c -o rma2.o
> rma2.c:107:29: error: rma_background4.h: No such file or directory
> rma2.c:118:45: error: preprocessCore_background_stubs.c: No such file or directory
> rma2.c: In function rma_c_complete:
> rma2.c:348: warning: implicit declaration of function rma_bg_correct
> make: *** [rma2.o] Error 1
> chmod: cannot access `/usr/lib64/R/library/affy/libs/*': No such file or directory
> ERROR: compilation failed for package 'affy'
> ** Removing '/usr/lib64/R/library/affy'
> ** Restoring previous '/usr/lib64/R/library/affy'
>
> The downloaded packages are in
>         /tmp/RtmpXSEp8l/downloaded_packages
> Updating HTML index of packages in '.Library'
> Warning message:
> In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,  :
>   installation of package 'affy' had non-zero exit status
>
> 	[[alternative HTML version deleted]]
>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

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