Hi, Bioconductor: I was trying to install some new packages in R, but for no obvious reason, it gave me the following error info. Any suggestions what was going on? Thanks, Jacob The error info was: ################################################################### install.packages("affyio_0.99.3.tar.gz", repos=NULL) * Installing *source* package 'affyio' ... 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 -I/usr/home/jacob/R-2.2.1/include -DHAVE_ZLIB=1 -I/usr/local/include -fPIC -g -O2 -c read_abatch.c -o read_abatch.o gcc -I/usr/home/jacob/R-2.2.1/include -DHAVE_ZLIB=1 -I/usr/local/include -fPIC -g -O2 -c read_bpmap.c -o read_bpmap.o gcc -I/usr/home/jacob/R-2.2.1/include -DHAVE_ZLIB=1 -I/usr/local/include -fPIC -g -O2 -c read_cdffile2.c -o read_cdffile2.o gcc -I/usr/home/jacob/R-2.2.1/include -DHAVE_ZLIB=1 -I/usr/local/include -fPIC -g -O2 -c read_cdf_xda.c -o read_cdf_xda.o gcc -shared -L/usr/local/lib64 -o affyio.so read_abatch.o read_bpmap.o read_cdffile2.o read_cdf_xda.o -lz -L/usr/home/jacob/R-2.2.1/lib -lR /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.3/../../../../x86_64-suse- linux /bin/ld: cannot find -lR collect2: ld returned 1 exit status make: *** [affyio.so] Error 1 ERROR: compilation failed for package 'affyio' ** Removing '/usr/home/jacob/R-2.2.1/library/affyio' Warning message: installation of package 'affyio_0.99.3.tar.gz' had non-zero exit status in: install.packages("affyio_0.99.3.tar.gz", repos = NULL) This email message, including any attachments, is for the so...{{dropped}}

Hi Jacob, The package you are trying to install belongs to Bioconductor 1.8 hence it's aimed to work with R-2.3 only. I can see that you are using R-2.2.1 so only Bioconductor 1.7 packages are guaranteed to work for you. The easiest way to install a Bioconductor package is to use the biocLite() function: > source('http://bioconductor.org/biocLite.R') > biocLite('affyio') Running bioCLite version 0.1 with R version 2.2.1 Running biocinstall version 1.1 with R version 2.2.1 dependency '?affyio?' is not available which means that there is no affyio package for your version of R (affyio is new in Bioconductor 1.8). But with R-2.3: > biocLite('affyio') Running bioCLite version 0.1 with R version 2.3.0 Running biocinstall version 1.3 with R version 2.3.0 trying URL 'http://www.bioconductor.org/packages/bioc/1.8/src/contrib/affyio_0.99 .3.tar.gz' Content type 'application/x-gzip' length 55561 bytes opened URL ================================================== downloaded 54Kb * Installing *source* package 'affyio' ... ... * DONE (affyio) The downloaded packages are in /tmp/RtmpqYhmFO/downloaded_packages > Regards, H.