
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

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