[BioC] affy Package install

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Hi Roger,

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.

What a pain really! Maybe you can convince your IT folks to setup internal
mirrors of the CRAN and Bioconductor package repositories. Then you would
need to convince them to agree to update these repositories on a regular
basis (once a week is reasonable, once a month is still better than nothing,
but less than that can be a problem).
This is the CRAN Mirror HOWTO:
  http://cran.fhcrc.org/mirror-howto.html
and this is the BioC Mirror Howto:
  http://bioconductor.org/download/mirrors/mirror-howto.html
It doesn't give a lot of details but generally speaking setting up a mirror
is not complicated if you are already familiar with rsync and http server
administration/configuration (using Unix/Linux + Apache for this is a very
common choice: it's cheap, reliable, easy and very well documented).
Finally you would need to modify the biocLite.R script a little bit (I, or
other people on this list who have done this before, can help with this).

Let me know if you are interested, I can provide more details.

Cheers,
H.


> 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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