Le 20/07/2020 à 10:15, Abby Spurdle a écrit :
It's possible to run R (or a c parent process) as a background process
via a named pipe, and then write script files to the named pipe.
However, the details depend on what shell you use.
The last time I tried (which was a long time ago), I created a small c
program to run R, read from the named pipe from within c, then wrote
it's contents to R's standard in.
It might be possible to do it without the c program.
Haven't checked.
For testing purposes, you can do:
- in a shell 1:
mkfifo rpipe
exec 3>rpipe # without this trick, Rscript will end after the first
"echo" hereafter or at the end of your first script.
- in a shell 2:
Rscript rfifo
- in a shell 3:
echo "print('hello')" > rpipe
echo "print('hello again')" > rpipe
Then in the shell 2, you will see the output:
[1] "hello"
[1] "hello again"
etc.
If your R scripts contain "stop()" or "q('yes')" or any other error, it
will end the Rscript process. Kind of watch-dog can be set for automatic
relaunching if needed. Another way to stop the Rscript process is to
kill the "exec 3>rpipe" one. You can find its PID with "fuser rpipe"
Best,
Serguei.
On Mon, Jul 20, 2020 at 3:50 AM Mario Annau <mario.an...@gmail.com> wrote:
Dear all,
in our current setting we have our packages stored on a (rather slow)
network drive and need to invoke short R scripts (using RScript) in a
timely manner. Most of the script's runtime is spent with package loading
using library() (or loadNamespace to be precise).
Is there a way to cache the package namespaces as listed in
loadedNamespaces() and load them into memory before the script is executed?
My first simplistic attempt was to serialize the environment output
from loadNamespace() to a file and load it before the script is started.
However, loading the object automatically also loads all the referenced
namespaces (from the slow network share) which is undesirable for this use
case.
Cheers,
Mario
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Serguei Sokol
Ingenieur de recherche INRAE
Cellule mathématiques
TBI, INSA/INRAE UMR 792, INSA/CNRS UMR 5504
135 Avenue de Rangueil
31077 Toulouse Cedex 04
tel: +33 5 61 55 98 49
email: so...@insa-toulouse.fr
http://www.toulouse-biotechnology-institute.fr/
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