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

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Hi Richard,

Could you provide the information from sessionInfo()?  It will help us 
understand your system more so that we can have a better idea about what 
happened.  

Thanks,
Ting-Yaun

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'

_____________________________

Richard Wang

Biostatistician

UCSF - Immune Tolerance Network

4800 Montgomery Lane, Suite 300

Bethesda, MD 20814

(240) 235-6177

(240) 497-0351 fax

rwang at immunetolerance.org

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Hi Richard,
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.

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
The error message suggests an R installation/system configuration
issue.  How did you install R? 

The problem seems to be that the build is trying to link to libR.so,
but no such library is available.  When you build R from source, you
have a choice of building libR.so or not.  The default is not to build
it.  

When I install the affy package on one of our Linux systems, here's
the call to the linker that I see:

gcc -shared -L/usr/local/lib64 -o affy.so chipbackground.o
getall_locations.o mas5calls.o qnorm.o read_abatch.o rma2.o
rma_background2.o rma_common.o -lz

Notice that there is no -lR.  So I don't have an answer for you, but
perhaps the above gives you some hints of where to look (R site config
stuff --- see the admin manual).  You could also try building R from
source and seeing if that changes anything.

+ seth