[Rd] Two R editiosn in Unix cluster systems

Ista Zahn istazahn at gmail.com
Wed Oct 16 02:09:48 CEST 2013

OpenMx does install on R 3.01. I haven't tested extensively, but after
installing with

                 dependencies = TRUE,
                 repos = c(getOption("repos"),

the demos appear to run correctly.


On Tue, Oct 15, 2013 at 4:15 PM, Paul Johnson <pauljohn32 at gmail.com> wrote:
> Dear R Devel
> Some of our R users are still insisting we run R-2.15.3 because of
> difficulties with a package called OpenMX.  It can't cooperate with new R,
> oh well.
> Other users need to run R-3.0.1. I'm looking for the most direct route to
> install both, and allow users to choose at runtime.
> In the cluster, things run faster if I install RPMs to each node, rather
> than putting R itself on the NFS share (but I could do that if you think
> it's really better....)
> In the past, I've used the SRPM packaging from EPEL repository to make a
> few little path changes and build R RPM for our cluster nodes. Now I face
> the problem of building 2 RPMS, one for R-2.15.3 and one for R-newest, and
> somehow keeping them separate.
> If you were me, how would you approach this?
> Here's my guess
> First, The RPM packages need unique names, of course.
> Second, leave the RPM packaging for R-newest exactly the same as it always
> was.  R is in the path, the R script and references among all the bits will
> be fine, no need to fight. It will find what it needs in /usr/lib64/R or
> whatnot.
> For the legacy R, I'm considering 2 ideas.  I could install R with the same
> prefix, /usr, but very careful so the R bits are installed into separate
> places. I just made a fresh build of R and on RedHat 6, it appears to me R
> installs these directories:
> bin
> libdir
> share.
> So what if the configure line has the magic bindir=/usr/bin-R-2.15.3
> libdir = /usr/lib64/R-2.15.3, and whatnot. If I were doing Debian
> packaging, I suppose I'd be obligated (by the file system standard) to do
> that kind of thing. But it looks like a headache.
> The easy road is to set the prefix at some out of the way place, like
> /opt/R-2.15.3, and then use a post-install script to link
> /opt/R-2/15.3/bin/R to /usr/bin/R-2.15.3.  When I tried that, it surprised
> me because R did not complain about lack access to devel headers. It
> configures and builds fine.
> R is now configured for x86_64-unknown-linux-gnu
>   Source directory:          .
>   Installation directory:    /tmp/R
>   C compiler:                gcc -std=gnu99  -g -O2
>   Fortran 77 compiler:       gfortran  -g -O2
>   C++ compiler:              g++  -g -O2
>   Fortran 90/95 compiler:    gfortran -g -O2
>   Obj-C compiler:            gcc -g -O2 -fobjc-exceptions
>   Interfaces supported:      X11, tcltk
>   External libraries:        readline, ICU, lzma
>   Additional capabilities:   PNG, JPEG, TIFF, NLS, cairo
>   Options enabled:           shared BLAS, R profiling, Java
>   Recommended packages:      yes
> Should I worry about any runtime complications of this older R finding its
> of the newer R in the PATH ahead of it? I worry I'm making lazy
> assumptions?
> After that, I need to do some dancing with the RPM packaging.
> I suppose there'd be some comfort if I could get the users to define R_HOME
> in their user environment before launching jobs, I think that would
> eliminate the danger of confusion between versions, wouldn't it?
> 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
>         [[alternative HTML version deleted]]
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