Dear All:

I have upgraded our R to 2.8.1 version and attempted to reinstall the affy package from bioconductor.  The installation attempt failed (the R output is below my signature).  During the installation I was running R as root.

Any suggestion you may have about this issue would be greatly appreciated.  Thank you in advance for your help.


Sincerely,


Boris Umylny

The R session log:

>  source("http://bioconductor.org/biocLite.R")
> biocLite("affy")
Running biocinstall version 2.3.10 with R version 2.8.1 
Your version of R requires version 2.3 of Bioconductor.
trying URL 'http://bioconductor.org/packages/2.3/bioc/src/contrib/affy_1.20.2.tar.gz'
Content type 'application/x-gzip' length 1136034 bytes (1.1 Mb)
opened URL
==================================================
downloaded 1.1 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 -std=gnu99 -I/usr/local/lib64/R/include -DHAVE_ZLIB=1  -I/usr/local/include -I"/usr/local/lib64/R/library/preprocessCore/include"   -fpic  -g -O2 -c chipbackground.c -o chipbackground.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -DHAVE_ZLIB=1  -I/usr/local/include -I"/usr/local/lib64/R/library/preprocessCore/include"   -fpic  -g -O2 -c getall_locations.c -o getall_locations.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -DHAVE_ZLIB=1  -I/usr/local/include -I"/usr/local/lib64/R/library/preprocessCore/include"   -fpic  -g -O2 -c mas5calls.c -o mas5calls.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -DHAVE_ZLIB=1  -I/usr/local/include -I"/usr/local/lib64/R/library/preprocessCore/include"   -fpic  -g -O2 -c rma2.c -o rma2.o
rma2.c:123:31: error: R_subColSummarize.h: No such file or directory
rma2.c:124:37: error: R_subColSummarize_stubs.c: No such file or directory
rma2.c: In function ādo_RMA2ā:
rma2.c:133: warning: implicit declaration of function āR_subColSummarize_medianpolish_logā
rma2.c:133: warning: assignment makes pointer from integer without a cast
make: *** [rma2.o] Error 1
chmod: cannot access `/usr/local/lib64/R/library/affy/libs/*': No such file or directory
ERROR: compilation failed for package 'affy'
** Removing '/usr/local/lib64/R/library/affy'

The downloaded packages are in
        /tmp/Rtmpgb8Bd0/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
> sessionInfo()
R version 2.8.1 (2008-12-22) 
x86_64-unknown-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_2.8.1
> 

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