Hello everyone I have been trying to install bioconductor on ubuntu 7.10 gutsy using R version 2.5.1, and getting a lot of error messages: Here are a few: 1: package âxtableâ is not available in: install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... 2: dependency âsurvivalâ is not available in: install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... 3: installation of package 'affyio' had non-zero exit status in: install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... 4: installation of package 'lattice' had non-zero exit status in: install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... 5: installation of package 'KernSmooth' had non-zero exit status in: install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... I have installed r-base-core, build-essential, g77, reflas3, reflas3-dev, r-base-dev, and r-recommended. When I tried to install affyio by itself, I got the following error message: > biocLite(c("affyio")) Running biocinstall version 2.0.8 with R version 2.5.1 Your version of R requires version 2.0 of Bioconductor. Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : argument 'lib' is missing: using '/usr/local/lib/R/site- library' trying URL 'http://bioconductor.org/packages/2.0/bioc/src/contrib/affyio_1.4.1.ta r.gz' Content type 'application/x-gzip' length 59104 bytes opened URL ================================================== downloaded 57Kb * Installing *source* package 'affyio' ... creating cache ./config.cache checking how to run the C preprocessor... cc -E checking for main in -lz... no updating cache ./config.cache creating ./config.status creating src/Makevars ** libs gcc-4.2 -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include -fpic -g -O2 -c read_abatch.c -o read_abatch.o /bin/bash: gcc-4.2: command not found make: *** [read_abatch.o] Error 127 chmod: cannot access `/usr/local/lib/R/site-library/affyio/libs/*': No such file or directory ERROR: compilation failed for package 'affyio' ** Removing '/usr/local/lib/R/site-library/affyio' The downloaded packages are in /tmp/RtmpowXclV/downloaded_packages Warning message: installation of package 'affyio' had non-zero exit status in: install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, If anyone can offer suggestions or help, it would be appreciated. Thanks, R [[alternative HTML version deleted]]

Hi, On Jul 10, 2008, at 3:52 PM, Rebecca Griffiths wrote: > Hello everyone > > I have been trying to install bioconductor on ubuntu 7.10 gutsy > using R > version 2.5.1, and getting a lot of error messages: <snip> I'd suggest trying to install a newer version of R, the latest one is 2.7.1 Check out the instructions here: http://cran.r-project.org/bin/linux/ubuntu/README.html If you're still having problems installing the newest release, I think it would then be worth trying to figure out what's going wrong. -steve -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Cornell Medical College http://cbio.mskcc.org/~lianos

Dear Rebecca, please see below > I have been trying to install bioconductor on ubuntu 7.10 gutsy using R > version 2.5.1, and getting a lot of error messages: > > > > Here are a few: > > 1: package ?xtable? is not available in: install.packages(pkgs = pkgs, repos > = repos, dependencies = dependencies, ... > > 2: dependency ?survival? is not available in: install.packages(pkgs = pkgs, > repos = repos, dependencies = dependencies, ... > > 3: installation of package 'affyio' had non-zero exit status in: > install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, > ... > > 4: installation of package 'lattice' had non-zero exit status in: > install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, > ... > > 5: installation of package 'KernSmooth' had non-zero exit status in: > install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, > ... > > > > I have installed r-base-core, build-essential, g77, reflas3, reflas3-dev, > r-base-dev, and r-recommended. > > > > When I tried to install affyio by itself, I got the following error message: > >> biocLite(c("affyio")) > > Running biocinstall version 2.0.8 with R version 2.5.1 > > Your version of R requires version 2.0 of Bioconductor. > > Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = > dependencies, : > > argument 'lib' is missing: using '/usr/local/lib/R/site- library' > > trying URL > 'http://bioconductor.org/packages/2.0/bioc/src/contrib/affyio_1.4.1. tar.gz' > > Content type 'application/x-gzip' length 59104 bytes > > opened URL > > ================================================== > > downloaded 57Kb > > > > * Installing *source* package 'affyio' ... > > creating cache ./config.cache > > checking how to run the C preprocessor... cc -E > > checking for main in -lz... no > > updating cache ./config.cache > > creating ./config.status > > creating src/Makevars > > ** libs > > gcc-4.2 -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include -fpic > -g -O2 -c read_abatch.c -o read_abatch.o > > /bin/bash: gcc-4.2: command not found > ^^^^^^^^^^ This is the first problem. To install packages from source (which is the common thing to do in Linux) you will need to install various compilers and software development tools into your Ubuntu. Note that this is not a Bioconductor "problem" but a general property of R. MacOSX and Windows versions of R and Bioconductor make it a bit easier by offering "precompiled" packages, but in Linux you (and your computer) are expected to build "from source code". I am afraid that this will require some iterations and careful reading of the output of attempts at installation, in order to see which Ubuntu packages you need to add. As Steve pointed out, it is also recommendable that you install R 2.7 rather than 2.5.1, and you can do this on your "old" Ubuntu, just not with the Ubuntu package manager, but rather by also building R 2.7 "from source". Some general help can be found here: http://cran.r-project.org/doc/manuals/R-admin.html Hope this helps Wolfgang > make: *** [read_abatch.o] Error 127 > > chmod: cannot access `/usr/local/lib/R/site-library/affyio/libs/*': No such > file or directory > > ERROR: compilation failed for package 'affyio' > > ** Removing '/usr/local/lib/R/site-library/affyio' > > > > The downloaded packages are in > > /tmp/RtmpowXclV/downloaded_packages > > Warning message: > > installation of package 'affyio' had non-zero exit status in: > install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, > > > > > > If anyone can offer suggestions or help, it would be appreciated. > > > > Thanks, > > R > > > [[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 -- ---------------------------------------------------- Wolfgang Huber, EMBL-EBI, http://www.ebi.ac.uk/huber