[Rd] Embedded R Fails When Run on LSF Queue System
Dirk Eddelbuettel
edd at debian.org
Mon Nov 11 02:49:44 CET 2013
On 10 November 2013 at 16:32, Nigel Delaney wrote:
| I had a quick question I was hoping someone might be able to answer, as my journey through the source code so far has not been very profitable. I have a command line program that embeds R, and the program works just fine when run from the command line. However, when I run the program as a job in the LSF cluster at my institute, the following error occurs:
|
| Fatal error: you must specify '--save', '--no-save' or '--vanilla'
|
| This is confusing becasue I believe I have set this by changing the startup parameters so that the no-save option is in use. I initialize R with the following collection of function calls:
|
| 1-Rf_initialize_R
| 2-R_SetParams
| 3-setup_Rmainloop
|
| At step 2 I pass in a structure that specifies the no-save option (as well as interactive=true, verbose=false), so I would expect it to be okay, but I still receive this error. Again, not at the terminal but only when run as a separate process.
|
| I gathered from this thread that someone else has experienced this (https://stat.ethz.ch/pipermail/r-help/2008-March/155935.html), but am not sure how best to rectify it as I believe I have already changed the setting.
|
| Does anyone know what a good solution or work around might be?
As a first approximation, when the manual tells you do something a certain
way, you are in fact better off doing it that way.
I stand behind two projects embedding R: littler (with Jeff Horner), and
RInside (with Romain Francois). Both do this explicitly. From littler.c:
char *R_argv[] = {(char*)programName, "--gui=none", "--no-restore", "--no-save", "--no-readline", "--silent", "", ""};
char *R_argv_opt[] = {"--vanilla", "--slave"};
int R_argc = (sizeof(R_argv) - sizeof(R_argv_opt) ) / sizeof(R_argv[0]);
[...]
/* some logic to add R_argv_opt parts to R_argv omitted (/
[...]
Rf_initEmbeddedR(R_argc, R_argv); /* Initialize the embedded R interpreter */
Hope this helps, Dirk
--
Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com
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