[BioC] affy Package install

[Robert Gentleman]

A longer explanation might be helpful here:

Since you cannot use the recommended method you will basically need to 
figure out all the dependencies and install them first.
You can find the (direct) dependencies here:
http://bioconductor.org/packages/2.1/bioc/html/affy.html

and then you will need to download and install them first. If any of 
those packages have dependencies, you will need to resolve them in a 
similar manner.

best wishes
  Robert



Benilton Carvalho wrote:
> and now that I read that the machine is offline, just download all the 
> dependencies...
> 
> you don't seem to have "preprocessCore".
> 
> sorry for not reading your message completely, my bad.
> 
> 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]]
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: 
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
> 

-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org