[R] R environment

[Henrik Bengtsson]

Unfortunately Duncan's suggestion to restart is probably the only way to 
go here.  I've done similar thing myself too.  What I've learned was 
that it is clever to include a so called hot-patch mechanism in your 
code, which will load R source code found in a certain directory, say, 
"hot/", once in a while (easy if you have do interations) and at the end 
of the batch code. Here is the idea (typed out of my head):

patchCode <- function(path="hot", pattern="[.]R$", removeAfter=FALSE, ...) {
   files <- list.files(pattern=pattern, path=path, full.names=TRUE);
   for (file in files) {
     tryCatch({
       # You don't want you patch code to kill you batch job,
       # if you for instance have a typo.
       cat("Hot-path file: ", file, "\n");
       source(file);
       # Remove the file afterwards? Especially useful if you only
       # want to redefine functions, and patch once.  This way you
       # can also see what files has successfully been source():ed.
       if (removeAfter)
         file.remove(file);
     }, error = function(ex) {
       cat("Ignored error when sourcing:\n");
       print(ex);
     })
   }
} # patchCode()

Then in your batch code something like this:

while (!converged) {
   # Patch the code every iteration.
   patchCode(path="hot/", removeAfter=TRUE)
   # The rest of your code here
}

# Put the code you want to call at the end, in a directory
# of its own.
patchCode(path="hot/onFinally/", removeAfter=TRUE)
# End of your batch code

Cheers

Henrik


Duncan Murdoch wrote:
> Jean Eid wrote:
> 
>>This is probably a weird question but I need to know if there is a way...
>>
>>I run an R batch job without saving the variables at each step to the
>>disk.   Is there a way to invoke another session of R and link it to the
>>same environment for read only.
>>
>>The problem is that I am running optim with every step getting the
>>parameters into the global env using <<- However, I forgot to issue a
>>save(list=ls(),...) right after so I can load and see how the parameters
>>are changing. It's been couple of days and it is still running so I am
>>hoping that I can invoke another session of R and link it to the
>>environment of the batch session. Does this sound totally ridiculous ?
>>
>>it is a debian machine with R 2.1.1
> 
> 
> If you happened to have compiled R with debug information, you might be 
> able to use gdb or another debugger to examine variables in the running 
> process, but you probably didn't, and it's probably easier to kill the 
> job, fix it, and start it again, than it would be to learn how to see 
> the active variables using gdb.
> 
> Duncan Murdoch
> 
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