[BioC] affy Package install

[Benilton Carvalho]

just use the recommended method of installation:

source("http://www.bioconductor.org/biocLite.R")
biocLite("affy")

that will take care of all dependencies (the problem you're having).

b

On Dec 27, 2007, at 5:24 PM, Vallejo, Roger wrote:

> 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 at 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 at 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 at ars.usda.gov 
> <mailto:roger.vallejo at ars.usda.gov>
>
>
> http://www.ars.usda.gov/pandp/people/people.htm?personid=37662
>
>
>
>
>
>
> 	[[alternative HTML version deleted]]
>
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