R help - Oct 2004 - Installing packages on Debian linux

Gorjanc Gregor wrote:
> same/similiar packaging system (dependencies, ...) as Debian. Is it wise
> to mix all three methods?
Mixing R CMD and install.packages() doesn't pose any problems, AFAIK, but
mixing any of them with apt-get does. The problem is that apt-get doesn't
know what you're doing with R CMD or install.packages() or
remove.packages(),
so you may end up with duplicate packages (possibly in different places, see
below). I generally try to leave as much package management up to the system,
so I choose apt-get whenever possible. However, not all CRAN packages are
available from Debian yet, so you may end up having to use install.packages()
to install some packages.

> Which method is prefered for installation of R packages under Debian linux?
> - apt-get install R-package_name
> - install.packages('R-package_name')
> 
> I actually never tried with install.packages under linux. Where does it put
> the filesm under /usr/local or standard path?
install.packages() will use /usr/local/lib/R/site-library as default, but you
can change that with the lib argument. apt-get will put them
in /usr/lib/R/site-library.

I have a question to add myself though: is it still necessary to add a line
like:

deb http://cran.r-project.org/bin/linux/debian woody main

to /etc/apt/sources.list, as indicated in the CRAN mirrors? This might be
redundant, as a lot of packages are already available through the Debian
mirrors anyway, but I haven't checked how the list compares with the one in
CRAN.

Dirk? (Dirk Eddelbuettel is the maintainer of R Debian packages)

-- 
Best wishes,
Sebastian

I run Debian, and I do a mix of two paths: install using apt-get and
install using install.packages() under R. Both work and it's safe to
use both together. However, as has been pointed out, you tend to get
dumped with multiple copies of some packages since the two channels
lead to two different directories (/usr/local/lib/R/site-library for
install.packages() and /usr/lib/R/site-library for Debian). I haven't
yet figured out whether R will automatically use the more-recent
version if there are two versions of a library that are installed.

The Debian path is superior since it involves automatic handling of
dependencies. But I believe that's changed significantly (for the
better) in R 2.0,which hasn't yet made it into Debian::testing.

I use a generic /etc/apt/sources.list with testing. Specifically, it
reads:
  deb http://http.us.debian.org/debian testing main contrib non-free
  deb http://non-us.debian.org/debian-non-US testing/non-US main contrib
non-free

So you don't need a line for cran.r-project.org in order to get the
stuff in testing. As you may know, Debian's policies involve a
two-week waiting period, and a lack of critical bugs reported, for a
package to make it into testing. So there's a certain innate lag in
what you see in testing. If you're a user of testing, it's because you
like that tradeoff between timelag and stability.

The Debian packages get updated automatically when one does 
  # apt-get update && apt-get dist-upgrade
from time to time. The stuff you get using install.packages()
doesn't. A few weeks ago I had asked Dirk how one might automate the
removal of packages that I put in, using install.packages(), which
later came out as Debian packages. I also asked how one might
automatically do an install.packages() on the stuff that is installed
on my machine but isn't yet out as a Debian package. He said this is a
bit harder than meets the eye. I haven't gone into mucking with this
yet...


On an unrelated note, here's the shell script that I use to "fetch me
everything connected with R" :

# ---------------------- snip snip snip
#!/bin/sh
apt-cache search '^r-' \
	| egrep -v -i '(biology|genetic|map|odbc|sql)' \
	| awk '/^r\-/ {print $1}' \
	| xargs apt-get install --yes
# ---------------------- snip snip snip

In order to run it, I say:

   # apt-get update && takeallR.sh

-- 
Ajay Shah                                                   Consultant
ajayshah at mayin.org                      Department of Economic Affairs
http://www.mayin.org/ajayshah           Ministry of Finance, New Delhi