Liaw, Andy wrote: >/usr/lib/R/library is the default place where packages are installed, but by >no means the only place where they can be installed. Where R searches for >packages when asked is defined by the environment variable R_LIBS, which can >be defined in several possible places. See the `Details' section of >?Startup (type that at the R prompt). > > Using R_LIBS, the user simply uses install.packages() in R to install a package and R and R_LIBS takes care of the rest. We added the following to each users shell-startup script to manage many users on a heterogeneous system: if test "${R_LIBS}" = ""; then # Get the OS type in lower case ostype=`uname -s | tr '[A-Z]' '[a-z]'` export R_LIBS=${HOME}/R/R_LIBS/${ostype}/library/ if ! test -d "${R_LIBS}"; then mkdir -p ${R_LIBS} fi fi This was needed because some packages build native code and therefore had to be installed in seperate locations depending on platform. Plain R packages would take up unecessary space this way, but we could live with that. Note that R_LIBS may hold more than one directory, so you could include a R_LIBS=${HOME}/R/R_LIBS/cross-platform/library/ directory, but then the user has to specify this directory explicitly when calling install.packages(). /Henrik >BTW, R-help is probably the more appropriate place for a non-BioC specific >question like this. You're likely to get more useful help there. > >Cheers, >Andy > > > > > >>From: Michael Green >> >>New to the list, first post! >> >>I'm doing sysadmin work for our Bioinformatics department where I >>manage a couple of IBM BladeCenter based clusters. Systems are running >>SLES9 SP1 i586 (dual Xeon 32bit). >>Before I'm going to ask my question I must admit that I'm complete >>novice to R, and since I won't use it myself I didn't read much of the >>documentation supplied with the package. My question is more related >>to system administration + R, rather then to R itself. >> >>So here it is: >>Some time ago I received a request from our users to install R on one >>of the clusters. >>I went ahead and installed R-base-2.1.0-1 supplied by the >>vendor (SuSE/Novell). >>After that following the request of the users, I installed the >>Bioconductor packages using the standard procedure described at >><http: www.bioconductor.org="" download="">: >>source("http://www.bioconductor.org/biocLite.R") >>biocLite() >> >>Soon thereafter it became apparent that during their work with R, our >>users need to install/uninstall or otherwise change the hierarchy >>under /usr/lib/R which is of course not writable by any user other >>than root. As you surely know that's the case for almost every >>directory under /usr. From talking to one of my users I've learned >>that R routinely downloads/installs/updates itself and the changes go >>into /usr/lib/R exclusively (or almost exclusively?). >>Now I'm faced with dilemma of how to allow users to write to >>/usr/lib/R, which is not a big deal on itself as there are at least a >>couple of ways doing that: >>1. Play with standard unix permissions: create a new group for R >>users; chgrp <that_group> /usr/lib/R. etc... >>2. Create ACL for /usr/lib/R >> >>But my question is not about how to make /usrlib/R writable, but this: >>since /usr and everything under it is not traditionally writable by >>regular users what's the official stance of R developers on this? Is >>it assumed that all R users should have root access to the system >>where R installed to be able to change contents of /usr/lib/R and >>actually do any useful work? >> >>About our R installation: >>bioinfo4:/usr/lib/R # R >> >>R : Copyright 2005, The R Foundation for Statistical Computing >>Version 2.1.0 (2005-04-18), ISBN 3-900051-07-0 >> >> >> >>>sessionInfo() >>> >>> >>R version 2.1.0, 2005-04-18, i686-pc-linux-gnu >> >>attached base packages: >>[1] "methods" "stats" "graphics" "grDevices" "utils" >> "datasets" >>[7] "base" >> >>-- >>Warm regards, >>Michael Green >> >>_______________________________________________ >>Bioconductor mailing list >>Bioconductor at stat.math.ethz.ch >>https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> >> >> > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor > > > >

Why no make install ? If you supplied the prefix command during configure everything goes fine. My usual bi-annual jig is : wget http://www.cran.r-project.org/src/base/R-2/R-2.2.0.tar.gz # varies tar xvfz R-2.2.0.tar.gz # varies cd R-2.2.0 # varies ./configure --prefix=/home/adai/R make make check make install Then I install most of R and BioConductor packages which takes a couple of hours to download and install. This currently requires about 1.3 GB in hard disk but most users would only require a handful of packages in which case this size will be substantially smaller. I find this is often the best solution as system administrators are usually very busy people and get annoyed when I ask them to update R/BioConductor on frequent basis. But as James pointed out, this depends on the number of people using R, how cutting edge they like to be and if they know how to install R as well as space and internet speed. Regards, Adai On Tue, 2005-11-08 at 08:58 -0500, James W. MacDonald wrote: > Hi Michael, > > Note that this question is more applicable to R-help > <r-help at="" stat.math.ethz.ch=""> rather than BioC, since it concerns > R-administration rather than a particular BioC package. > > Anyway, there are (at least) two ways around this problem that don't > involve making /usr/local writable by normal users. > > First, if there are not that many users, they can always install R in > their /home/username directory (e.g., ./configure and make, but no make > install). This is preferable in many ways due to the fact that R and > BioC are released semi-annually, which can make your job a pain if the > end users are constantly wanting the latest version. Of course this will > require that each user have enough disk space allotted to them. I think > this is probably the most common way to do things. > > Second, you could simply install R in the same fashion to a directory > where everybody has write privileges. This has the advantage of using > less disk space, but you then run the risk of people changing the > installation in ways that adversely affect other users. > > HTH, > > Jim > > > > Michael Green wrote: > > New to the list, first post! > > > > I'm doing sysadmin work for our Bioinformatics department where I > > manage a couple of IBM BladeCenter based clusters. Systems are running > > SLES9 SP1 i586 (dual Xeon 32bit). > > Before I'm going to ask my question I must admit that I'm complete > > novice to R, and since I won't use it myself I didn't read much of the > > documentation supplied with the package. My question is more related > > to system administration + R, rather then to R itself. > > > > So here it is: > > Some time ago I received a request from our users to install R on one > > of the clusters. > > I went ahead and installed R-base-2.1.0-1 supplied by the vendor (SuSE/Novell). > > After that following the request of the users, I installed the > > Bioconductor packages using the standard procedure described at > > <http: www.bioconductor.org="" download="">: > > source("http://www.bioconductor.org/biocLite.R") > > biocLite() > > > > Soon thereafter it became apparent that during their work with R, our > > users need to install/uninstall or otherwise change the hierarchy > > under /usr/lib/R which is of course not writable by any user other > > than root. As you surely know that's the case for almost every > > directory under /usr. From talking to one of my users I've learned > > that R routinely downloads/installs/updates itself and the changes go > > into /usr/lib/R exclusively (or almost exclusively?). > > Now I'm faced with dilemma of how to allow users to write to > > /usr/lib/R, which is not a big deal on itself as there are at least a > > couple of ways doing that: > > 1. Play with standard unix permissions: create a new group for R > > users; chgrp <that_group> /usr/lib/R. etc... > > 2. Create ACL for /usr/lib/R > > > > But my question is not about how to make /usrlib/R writable, but this: > > since /usr and everything under it is not traditionally writable by > > regular users what's the official stance of R developers on this? Is > > it assumed that all R users should have root access to the system > > where R installed to be able to change contents of /usr/lib/R and > > actually do any useful work? > > > > About our R installation: > > bioinfo4:/usr/lib/R # R > > > > R : Copyright 2005, The R Foundation for Statistical Computing > > Version 2.1.0 (2005-04-18), ISBN 3-900051-07-0 > > > > > >>sessionInfo() > > > > R version 2.1.0, 2005-04-18, i686-pc-linux-gnu > > > > attached base packages: > > [1] "methods" "stats" "graphics" "grDevices" "utils" "datasets" > > [7] "base" > > > > -- > > Warm regards, > > Michael Green > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > >