Dear Bioconductor Users:

I installed from source code the R 2.6.1 into a Linux redhat Enterprise
2.1, with no problems. It runs okay. 

Then, I installed R packages from source code also (*.tar.gz) files. I
do this sort of "manual" installation because this Linux box is not
connected to the internet due to "security" reasons from my IT folks. It
is a pain. Anyhow, I have successfully installed several R packages from
source code using this command:

 

R CMD INSTALL -l /home/software/R/library package_name.tar.gz

 

But to my surprise, I could not install the "affy_1.16.0.tar.gz"
package. I have tried several ways unsuccessfully. This is the error
message for this "affy" install:

 

[root@localhost R]# R CMD INSTALL -l /home/software/R/library
affy_1.16.0.tar.gz

/home/software/R/library

* 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 -I/usr/local/lib/R/include
-DHAVE_ZLIB=1  -I/usr/local/include    -fpi c  -g -O2 -c
chipbackground.c -o chipbackground.o

gcc -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/lib/R/include
-DHAVE_ZLIB=1  -I/usr/local/include    -fpi c  -g -O2 -c
getall_locations.c -o getall_locations.o

gcc -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/lib/R/include
-DHAVE_ZLIB=1  -I/usr/local/include    -fpi c  -g -O2 -c mas5calls.c -o
mas5calls.o

gcc -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/lib/R/include
-DHAVE_ZLIB=1  -I/usr/local/include    -fpi c  -g -O2 -c rma2.c -o
rma2.o

rma2.c:117:48: preprocessCore_normalization_stubs.c: No such file or
directory

rma2.c:118:48: preprocessCore_summarization_stubs.c: No such file or
directory

rma2.c: In function `do_RMA':

rma2.c:180: warning: implicit declaration of function `MedianPolish'

rma2.c: In function `rma_c_call':

rma2.c:260: warning: implicit declaration of function `qnorm_c'

make: *** [rma2.o] Error 1

chmod: failed to get attributes of
`/home/software/R/library/affy/libs/*': No such file or directory

ERROR: compilation failed for package 'affy'

** Removing '/home/software/R/library/affy'

[root@localhost R]#

 

Is the package defective? Or am I doing something wrong. Please, I will
appreciate very much your help on installing this "affy" package.

Roger

 

 

 

 

Roger L. Vallejo, Ph.D.

Computational Biologist & Geneticist

U.S. Department of Agriculture, ARS            

National Center for Cool & Cold Water Aquaculture

11861 Leetown Road

Kearneysville, WV 25430

Voice:    (304) 724-8340 Ext. 2141

Email:    roger.vallejo@ars.usda.gov <mailto:roger.vallejo@ars.usda.gov>


http://www.ars.usda.gov/pandp/people/people.htm?personid=37662

 

 


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