On Jul 19, 2012, at 12:13 PM, Paul Johnson wrote: > I've asked a question in the BioConductor list about package > management. My solution depends on your answer to the following > question. > > Are installed R packages "relocatable"? >
It depends on the platform and what you want to relocate (R or just the packages) and on the package itself. For example on OS X absolute paths are included in dylibs, so you can move packages that allow it and don't link to other packages but you can't relocate R or packages that link to other packages directly or libraries within the package (that should be rare, though). Whether a package allows relocation depends whether it hard-codes any paths it uses - typical packages use facilities like system.file to locate files so those are relocatable, but if a package determines paths at configure time it may not be relocatable. Since you didn't even specify the platform you're interested in, this is only a generic answer ... > I mean relocatable in the same sense that files in a RedHat RPM file > might be "relocatable" after compiling > (http://www.rpm.org/max-rpm/ch-rpm-reloc.html). This allows one to > build a package as the ordinary user and then the root user can take > the result and put it wherever it fits well in the path (say, > /usr/local/lib/R/library). > > Here is why I asked. I manage packages in our cluster and some users > have asked me to install some BioConductor packages. BioConductor > install documents expect me to run a script as root that does a bunch > of changes, and I'm just unwilling to do that. If I have to do > something as root, it has to be something more focused like running a > particular R command (install.packages(), for example). It seems > insane to me that they expect (http://www.bioconductor.org/install) a > root user to run > You can install BioC packages simply with install.packages() - there is no black magic involved, it's a regular repository just like CRAN ... Cheers, Simon > source("http://bioconductor.org/biocLite.R";) > biocLite("limma") > > If I could do the installs as me with their script, and then copy the > install folder into the system, then it would be OK, if the packages > would work. > > Or perhaps post-processing is required to fiddle some paths inside > package files? > > pj > -- > Paul E. Johnson > Professor, Political Science Assoc. Director > 1541 Lilac Lane, Room 504 Center for Research Methods > University of Kansas University of Kansas > http://pj.freefaculty.org http://quant.ku.edu > > ______________________________________________ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > > ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
