Hi Hong, Seth is correct..! On Linux: Download: R-2.1.0.tar.gz $ tar xvfz R-2.1.0.tar.gz $ ./configure $ make $ make check-all Now login as super user or root to your Linux computer $ su $ make install $ exit $ R Your are good to go. Saurin --- Seth Falcon <sfalcon@fhcrc.org> wrote: > Hi Fangxin, > > On 6 Jun 2005, fhong@salk.edu wrote: > > I am trying to install Bioconductor under linux. > By following the > > manual, I first installed R 2.1.0 from > R-2.1.0.tar.gz downloaded > > from R website > > > > tar xvfz R-2.1.0.tar.gz > > > > Then I have successfully run > > ./configure > > make > > > > I met errors and wouldn't go through when I tried > > make check (or make check FORCE=FORCE or make > check-devel) > > If 'make check' reports errors, it is usually > prudent to resolve them > before proceeding. It may be that solving the issue > you report below > relating to X11 will also solve the make check > errors. > > > But it looks like R is installed. After I copied > shell-script 'R' to > > 'usr/local/bin/R', typing 'R' on the command line > invokes the R of > > current version. ( there is an old version R > installed, I just > > simple replace the old R at 'usr/local/bin' by the > new one) > > Why not just use: > make install > > > But when I tried to install Bioconductor, I met > the problem > >> source("http://www.bioconductor.org/getBioC.R") > > X connection to localhost:10.0 broken (explicit > kill or server > > shutdown). > > I'm assuming you are accessing the Linux server via > ssh (we'd need > more detail on exactly what your setup is and how > you are using it). > You may want to try a fresh ssh connection. The X11 > error is unlikely > to be related to R. > > An alternative is to unset the DISPLAY environment > variable. In bash > (default Linux shell): > > unset DISPLAY > > This will turn off the X11 capability for R (and > other apps), but > should avoid the error message you saw. > > > > This didn't happen when I used the old version R. > Any suggestion is > > greatly appreciated!! > > Lastly, you may want to install R in your home > directory instead of at > the system level. This way, you have the most > control over the > version and what packages are and are not installed. > > > Here's one way to accomplish this: > > mkdir ~/R-2.1.0 > mkdir ~/src > cd ~/src > tar xzvf ~/R-2.1.0.tar.gz > cd R-2.1.0 > ./configure --prefix=~/R-2.1.0 && make && make > install > > Then add ~/R-2.1.0/bin to your path. > > Many of us developers skip the install step and run > from the build > directory. I think some of the help may not get > built with this > approach, but it is a bit faster which can be useful > when one is often > recompiling R. > > Hope these suggestions are useful. > > Best, > > + seth > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >

Thank Seth >> But it looks like R is installed. After I copied shell-script 'R' to >> 'usr/local/bin/R', typing 'R' on the command line invokes the R of >> current version. ( there is an old version R installed, I just >> simple replace the old R at 'usr/local/bin' by the new one) > > Why not just use: > make install I tried this, it looks OK ( no error message). Then I copied shell- script 'R' to '/usr/local/bin/R'again. But it still gave me the same thing when I typed in R > source("http://www.bioconductor.org/getBioC.R") X connection to localhost:10.0 broken (explicit kill or server I also unset the DISPLAY environment variable using "unset DISPLAY", but the problem is still there. I am accessing the linux (at my laptop) via ssh as a super user. The linux machine information returned by "uname -a" is Linux qtlpc.salk.edu 2.4.20-31.9bigmem #1 SMP Tue Apr 13 17:11:51 EDT 2004 i686 i686 i386 GNU/Linux As I mentioned before, there was an old version R installed before, it didn't gave me that error when I typed "source("http://www.bioconductor.org/getBioC.R")", which make me think there may be something wrong with my installation. thanks for your help. Fangxin >> But when I tried to install Bioconductor, I met the problem >>> source("http://www.bioconductor.org/getBioC.R") >> X connection to localhost:10.0 broken (explicit kill or server >> shutdown). > > I'm assuming you are accessing the Linux server via ssh (we'd need > more detail on exactly what your setup is and how you are using it). > You may want to try a fresh ssh connection. The X11 error is unlikely > to be related to R. > > An alternative is to unset the DISPLAY environment variable. In bash > (default Linux shell): > > unset DISPLAY > > This will turn off the X11 capability for R (and other apps), but > should avoid the error message you saw. > > >> This didn't happen when I used the old version R. Any suggestion is >> greatly appreciated!! > > Lastly, you may want to install R in your home directory instead of at > the system level. This way, you have the most control over the > version and what packages are and are not installed. > > Here's one way to accomplish this: > > mkdir ~/R-2.1.0 > mkdir ~/src > cd ~/src > tar xzvf ~/R-2.1.0.tar.gz > cd R-2.1.0 > ./configure --prefix=~/R-2.1.0 && make && make install > > Then add ~/R-2.1.0/bin to your path. > > Many of us developers skip the install step and run from the build > directory. I think some of the help may not get built with this > approach, but it is a bit faster which can be useful when one is often > recompiling R. > > Hope these suggestions are useful. > > Best, > > + seth > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > -------------------- Fangxin Hong Ph.D. Plant Biology Laboratory The Salk Institute 10010 N. Torrey Pines Rd. La Jolla, CA 92037 E-mail: fhong@salk.edu (Phone): 858-453-4100 ext 1105