R SIG Fedora - Feb 2010 - Improving RPM packaging for R; ideas gathered from the Debian folks

Hi, everybody.

I've got some Centos Linux systems and some Ubuntu Linux systems.  R's
basically the same in either place, but the packaging of R for Debian
systems seems better to me than it is on Fedora/Redhat/Centos.

I joined R-sig-debian and we talk about package management issues
there sometimes. One of the really handy R packaging ideas they have
is to customize R environment so that there are several directories in
the package path.

It adjusts the etc/Renviron file so that it has:

R_LIBS_USER=${R_LIBS_USER-'~/R/i486-pc-linux-gnu-library/2.10'}
R_LIBS_SITE=${R_LIBS_SITE-'/usr/local/lib/R/site-library:/usr/lib/R/site-library:/usr/lib/R/library'}

That would be pretty easy to add into the R packaging for RPM systems.
The benefit is as follows.

If an unprivileged user tries to install an R package, there's no
error, but rather it installs the rpm under $HOME/R/i386.
If a privileged user installs a package in R, that goes into /usr/local/lib/R.
If the privileged user installs an RPM that with packages that come
from R itself, the package is supposed to be built so it goes into
/usr/lib/R/, and if a package is built for circulation, it would
deposit into /usr/lib/R/site-libarary. In this way, one can have
several non-conflicting versions of a package, and users can
experiment with packages in their personal space and not destroy the
system package.

That's pretty handy, I think. Its a significant convenience for
Debian-based users of R.

"Over there" in r-sig-deb, I learned that Dirk Eddelbuettel and
Charles Blundell developed a thing called "cran2deb".

http://www.mail-archive.com/debian-science at lists.debian.org/msg03306.html

That has debian packages of almost every R package you can get on CRAN.

I wonder if we couldn't do something like that for RPM users. There
are SOME R packages you can get in rpm, but not a comprehensive
collection.  I'm not entirely sure we should do it, as it may just
generate more user dependency.  But sometimes I think it would be
handy.

Dirk also has a neat RSS service announcing new R packages.
http://dirk.eddelbuettel.com/cranberries/

I've been building RPMs for about 10 years and Debian packages for
about 2 years.  It seems to me the RPM system is simpler and more
straightforward, but it is hard to argue with the success of the
Debian folks in creating packages that have handy features.

What do you think?

-- 
Paul E. Johnson
Professor, Political Science
1541 Lilac Lane, Room 504
University of Kansas

On 02/03/2010 09:12 PM, Paul Johnson wrote:
> One of the really handy R packaging ideas they have
> is to customize R environment so that there are several directories in
> the package path.
> 
> It adjusts the etc/Renviron file so that it has:
> 
> R_LIBS_USER=${R_LIBS_USER-'~/R/i486-pc-linux-gnu-library/2.10'}
>
R_LIBS_SITE=${R_LIBS_SITE-'/usr/local/lib/R/site-library:/usr/lib/R/site-library:/usr/lib/R/library'}
> 
> That would be pretty easy to add into the R packaging for RPM systems.
>
> The benefit is as follows.
> 
> If an unprivileged user tries to install an R package, there's no
> error, but rather it installs the rpm under $HOME/R/i386.
Well, I don't think a standard setup will permit an unprivileged user to
install rpm packages, but this should work when building things from
CRAN, I suppose.

My only concerns are:

1) Users shouldn't be assuming that /usr/local/lib/R exists. Fedora
packages can't create that directory, and we don't really want the first
user to hit that directory to create it with their own ownership privs.
2) Right now, we have two locations for R packages from Fedora:
%{_libdir}/R/library/* and %{_datadir}/R/library/* (arch vs noarch). I'm
not sure it is worth making another set of separate directories.

Or to sum it up, I think the R_LIBS_USER setting makes some sense, but
I'm not sure the additional complexity of R_LIBS_SITE adds any value.

Also, I'm not sure why there is so much hierarchy in the proposed
setting for R_LIBS_USER. The R version, perhaps is understandable, but
the target architecture?
> "Over there" in r-sig-deb, I learned that Dirk Eddelbuettel and
> Charles Blundell developed a thing called "cran2deb".
> 
> http://www.mail-archive.com/debian-science at
lists.debian.org/msg03306.html
> 
> That has debian packages of almost every R package you can get on CRAN.
I'm not personally a fan of autogenerated packages. If people are
interested in a CRAN package, we can get it added to Fedora and properly
maintained. The number of times that RScaLAPACK has broken has convinced
me of the value of having someone responsible for keeping these bits
alive. :)

With that said, various folks have made some good tools for making quick
and easy R module RPM packages, and those are an excellent first step
for getting those packages into Fedora.

~spot