I am having problem installing affy package from source on my Debian system
with R-2.8.0. The earlier version (from bioc2.2) works fine with R-2.7.0 on
the same system.
Any idea of what is going wrong with the new version?


###################################################################
> sessionInfo()
R version 2.8.0 (2008-10-20)
i686-pc-linux-gnu

locale:
LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.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_2.8.0

##################################################################
> source("http://bioconductor.org/biocLite.R")
> biocLite("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 -std=gnu99 -I/usr/local/lib/R/include -DHAVE_ZLIB=1
-I/usr/local/include -I"/usr/local/lib/R/library/preprocessCore/include"
-fpic  -g -O2 -c chipbackground.c -o chipbackground.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DHAVE_ZLIB=1
-I/usr/local/include -I"/usr/local/lib/R/library/preprocessCore/include"
-fpic  -g -O2 -c getall_locations.c -o getall_locations.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DHAVE_ZLIB=1
-I/usr/local/include -I"/usr/local/lib/R/library/preprocessCore/include"
-fpic  -g -O2 -c mas5calls.c -o mas5calls.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DHAVE_ZLIB=1
-I/usr/local/include -I"/usr/local/lib/R/library/preprocessCore/include"
-fpic  -g -O2 -c rma2.c -o rma2.o
rma2.c:108:29: error: rma_background4.h: No such file or directory
rma2.c:119:45: error: preprocessCore_background_stubs.c: No such file or
directory
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 'do_RMA2':
rma2.c:133: warning: implicit declaration of function
'R_subColSummarize_medianpolish_log'
rma2.c:133: warning: assignment makes pointer from integer without a cast
rma2.c: In function 'rma_c_complete':
rma2.c:248: warning: implicit declaration of function 'rma_bg_correct'
make: *** [rma2.o] Error 1
chmod: cannot access `/usr/local/lib/R/site-library/affy/libs/*': No such
file or directory
ERROR: compilation failed for package 'affy'
** Removing '/usr/local/lib/R/site-library/affy'
** Restoring previous '/usr/local/lib/R/site-library/affy'

The downloaded packages are in
        /tmp/RtmprdJr3r/downloaded_packages
Warning message:
In install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies,  :
  installation of package 'affy' had non-zero exit status




-- 
Mizanur Khondoker
Division of Pathway Medicine (DPM)
The University of Edinburgh Medical School
The Chancellor's Building
49 Little France Crescent
Edinburgh EH16 4SB
United Kingdom

Tel:  +44 (0) 131 242 6287
Fax: +44 (0) 131 242 6244
http://www.pathwaymedicine.ed.ac.uk/

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