On Tue, 25 Nov 2003, michael watson (IAH-C) wrote:
Hi
I am using R as a back-end to some CGI scripts, written in Perl. My platform is
Suse Linux 8.2, Apache 1.3.7. So the CGI script takes some form parameters, opens a
pipe to an R process, loads up some Bioconductor libraries, executes some R commands
and takes the ouput and creates a web page. It is all very neat and works well.
I am trying to make my cgi scripts quicker and it turns out that the bottle-neck is
the loading of the libraries into R - for example loading up marrayPlots into R
takes 10-20 seconds, which although not long, is long enough for users to imagine it
is not working and start clicking reload
So I just wondered if anyone had a neat solution whereby I could somehow have the
required libraries permanently loaded into R - perhaps I need a persistent R process
with the libraries in memory that I can pipe commands to? Is this possible?
Thanks
Mick
One option we have been experimenting with is to process the contents
of packages into a simple data base and then use lazy loading. This
means that loading a package will load only a small amount of
information, basically the names of the variables defined. The actual
values are only loaded from the data base on demand. An experimental
package that implements this is available at
http://www.stat.uiowa.edu/~luke/R/serialize/lazyload.tar.gz
I believe `make check-all' passes with all base and recommended
packages set up for lazy loading. Lazy laoding has not been tested
much with packages using S4 methods or with anything in Bioconductor
as far as I know. So this may or may not do anything useful for you.
[WARNING: Since this messes with the installed packages in your R
system you should only experiment with it in an R installation you can
afford to mess up.]
The README file from the package is attached below.
Best,
luke
(README)---
This package provides tools to set up packages for lazy loading from a
data base. If you want to try this out, here are the steps:
1) Install the current version of package lazyload from
http://www.stat.uiowa.edu/~luke/R/serialize/.
2) To make base use lazy loading, start R with something like
env R_DEFAULT_PACKAGES=NULL R
to make sure no packages are loaded. Then do
source(file.path(.find.package(lazyload),makebasedb.R))
library(lazyload)
makeLazyLoading(base)
Make sure to do the source first, then the library call.
3) To make package foo use lazy loading use makeLazyLoading(foo).
You can make all base packages use lazy loading with
for (p in rev(installed.packages(priority=base)[,Package])) {
cat(paste(converting, p, ...))
makeLazyLoading(p)
cat(done\n)
}
The rev() is a quick and dirty way to get stepfun done before modreg,
since modreg imports from stepfun.
--
Luke Tierney
University of Iowa Phone: 319-335-3386
Department of Statistics andFax: 319-335-3017
Actuarial Science
241 Schaeffer Hall email: [EMAIL PROTECTED]
Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu
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