[BioC] Install details for root level administrators

[Paul Johnson]

Greetings, BioConductor users.

Can  you share your sysadmin experience with me?

I administer R on a cluster computer system on which we use R with
about 250 packages from CRAN.  Now users ask me to install some
BioConductor packages, which I am willing to do.  However, for
security reasons, I am unwilling to log in as root and run your
scripts.

You see what I mean, don't you?  Nobody should as root run a script
from a website.

source("http://bioconductor.org/biocLite.R")

I can't run any script as root unless I understand all of the
implications, and the chaining together of scripts from biocLite to,
well, I can't tell exactly what, causes me too much concern.  Even
after downloading biocLite.R and trying to trace through its
implications, it is still an unworkable situation. I can't start R as
root and then run the biocLite program to install packages.

So, what to do?

Option 1. Tell all the users to install their own versions of the
BioConductor packages.  That would be OK, but maybe it is
inconsiderate to the ones who are not familiar with trouble in
compiling software.  If  they are missing the development headers,
then they will be dismayed & unhappy with me.


Option 2. Are installed R packages "relocatable" without danger of
breakage?  As non-root user, I could run the install using the
BioConductor scripts.  Then move the install directory into someplace
under /usr/local.  Would I have a valid, working install for all
users?

Here's what I mean

source("http://bioconductor.org/biocLite.R")
biocLite("limma", lib="/tmp/R/bioconductor")

trying URL 'http://www.bioconductor.org/packages/2.10/bioc/src/contrib/limma_3.12.1.tar.gz'
Content type 'application/x-gzip' length 1025822 bytes (1001 Kb)
opened URL
==================================================
downloaded 1001 Kb

* installing *source* package ‘limma’ ...
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -O3 -pipe
-g  -c normexp.c -o normexp.o
normexp.c: In function ‘fit_saddle_nelder_mead’:
normexp.c:153:3: warning: floating constant exceeds range of ‘double’
[-Woverflow]
gcc -std=gnu99 -shared -o limma.so normexp.o -L/usr/lib64/R/lib -lR
installing to /tmp/R/bioconductor/limma/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘limma.Rnw’
** testing if installed package can be loaded

* DONE (limma)

The downloaded source packages are in
	‘/tmp/Rtmp3c5pos/downloaded_packages’
exiting from: install.packages(pkgs = pkgs, lib = lib, repos = repos, ...)
Old packages: 'irr', 'mirt'
Update all/some/none? [a/s/n]: n
Warning message:
installed directory not writable, cannot update packages 'statnet'

Here's an example of why I can't run the BioConductor scripts as root.
 Note it asks me for  permission to update "irr" and "mirt", and then
I say no, and yet it says it can't write in the directory of
"statnet".  Huh? Luckily for me, statnet is in a place where I don't
have permission to damage it.

Nevertheless, I do end up with an install of the BioConductor package
limma in /tmp/R/bioconductor. Copy that to
"/usr/local/share/R/bioconductor" and then in the Renviron file do
something like

R_LIBS_SITE=${R_LIBS_SITE-'/usr/local/lib/R/site-library:/usr/lib/R/site-library:/usr/lib/R/library:/usr/local/share/R/bioconductor'}


But it only does any good if limma (or any other package) will work
after being relocated from /tmp/R/bioconductor  to
/usr/local/share/R/bioconductor.  Are there any paths or references
among package files that will fail after moving whole folders?

Option 3. Figure out the "old fashioned" R instructions to install
BioConductor packages without using  your scripts.  For example, am I
correct that the first step is to do this (with R-2.15.1):

install.packages("BiocInstaller", repos =
"http://www.bioconductor.org/packages/2.10/bioc",
lib="/usr/local/share/R/bioconductor")

That finishes the work of the biocLite.R script.

Installation of particular packages does not require "biocLite", does
it? This seems to work:

install.packages("limma", repos =
"http://www.bioconductor.org/packages/2.10/bioc",
lib="/usr/local/share/R/bioconductor")


If the install of "limma" or some other package fails because a
prerequisite is needed, I don't mind installing the prerequisites and
trying again.

I'll have to stay alert to version changes in BioConductor, and the
location of your repository.  That's a bad part of this.

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