[Bioc-devel] installation errors with selected Bioconductor packages on Linux

Hello all-

 

I am currently trying to install Bioconductor on a Linux workstation.
Using either the biocLite or getBioC installation commands, most
packages install with no trouble (I've made use of limma already), but
11 packages have failed to install repeatedly.  I've appended an example
of the error message I'm getting, in this case for the affy package.
Any advice or insights would be greatly appreciated.

 

biocLite("affy")

 

Running bioCLite version 0.1  with R version  2.1.1

 

Running biocinstall version 1.2  with R version  2.1.1

trying URL
'http://www.bioconductor.org/packages/bioc/stable/src/contrib/affy_1.6.7
.tar.gz'

Content type 'application/x-gzip' length 1164993 bytes

opened URL

==================================================

downloaded 1137Kb

 

* 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/lib/R/include -DHAVE_ZLIB=1  -I/usr/local/include   -fPIC
-O2 -g -pipe -m32 -march=i686 -mtune=pentium4 -c chipbackground.c -o
chipbackground.o

gcc -I/usr/lib/R/include -DHAVE_ZLIB=1  -I/usr/local/include   -fPIC
-O2 -g -pipe -m32 -march=i686 -mtune=pentium4 -c getall_locations.c -o
getall_locations.o

gcc -I/usr/lib/R/include -DHAVE_ZLIB=1  -I/usr/local/include   -fPIC
-O2 -g -pipe -m32 -march=i686 -mtune=pentium4 -c mas5calls.c -o
mas5calls.o

gcc -I/usr/lib/R/include -DHAVE_ZLIB=1  -I/usr/local/include   -fPIC
-O2 -g -pipe -m32 -march=i686 -mtune=pentium4 -c qnorm.c -o qnorm.o

gcc -I/usr/lib/R/include -DHAVE_ZLIB=1  -I/usr/local/include   -fPIC
-O2 -g -pipe -m32 -march=i686 -mtune=pentium4 -c read_abatch.c -o
read_abatch.o

gcc -I/usr/lib/R/include -DHAVE_ZLIB=1  -I/usr/local/include   -fPIC
-O2 -g -pipe -m32 -march=i686 -mtune=pentium4 -c rma2.c -o rma2.o

gcc -I/usr/lib/R/include -DHAVE_ZLIB=1  -I/usr/local/include   -fPIC
-O2 -g -pipe -m32 -march=i686 -mtune=pentium4 -c rma_background2.c -o
rma_background2.o

gcc -I/usr/lib/R/include -DHAVE_ZLIB=1  -I/usr/local/include   -fPIC
-O2 -g -pipe -m32 -march=i686 -mtune=pentium4 -c rma_common.c -o
rma_common.o

gcc -shared -L/usr/local/lib -o affy.so chipbackground.o
getall_locations.o mas5calls.o qnorm.o read_abatch.o rma2.o
rma_background2.o rma_common.o -lz   -L/usr/lib/R/lib -lR

gcc -shared -L/usr/local/lib -o affy.so chipbackground.o
getall_locations.o mas5calls.o qnorm.o read_abatch.o rma2.o
rma_background2.o rma_common.o -lz   -L/usr/lib/R/lib -lR

/usr/bin/ld: skipping incompatible /usr/lib/R/lib/libR.so when searching
for -lR/usr/bin/ld: cannot find -lR

collect2: ld returned 1 exit status

make: *** [affy.so] Error 1

ERROR: compilation failed for package 'affy'

** Removing '/usr/lib/R/library/affy'

** Restoring previous '/usr/lib/R/library/affy'