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