Thanks a lot for all of you that have reply me about opening and
ending R workspaces in BATCH mode. However replies were a king general
and I?m afraid I could not take the entire message from them.
Therefore I chose to expose here a representative fraction of my work.
I have 50 Rdata files (F1,F2,F3,F4,
,F50) with objects inside.
I need to:
open F1:
- perform some simple operations with the objects
- export the solution with write.table
- end F1 session
open F2
repeat procedures as F1
open F50
repeat procedures as F1
My difficulty here is to end a workspace and open one from the scratch
to avoid mixing files from consecutive worksessions, and thus using R
memory unnecessarily. I could use rm() to delete objects from the
previous sessions but it seems not an efficient task.
Any suggestions on how to perform this in Batch Mode? An examplified
help would be nice!
Diogo Andr? Alagador
http://www.biochange-lab.eu/people/diogo-alagador
Biodiversity and Global Change Lab, Museo Nacional de Ciencias
Naturales, CSIC, Madrid, Espa?a
Forest Research Centre, Instituto Superior de Agronomia, UTL, Lisboa, Portugal
How to save R "clean" sessions in BATCH mode?
4 messages · Diogo André Alagador, Sarah Goslee, Douglas Bates +1 more
Would rm(list=ls()) not be an easier solution, if I understand your question correctly? Sarah
On Sat, May 16, 2009 at 11:21 AM, <mcnda839 at mncn.csic.es> wrote:
Thanks a lot for all of you that have reply me about opening and ending R workspaces in BATCH mode. However replies were a king general and I?m afraid I could not take the entire message from them. Therefore I chose to expose here a representative fraction of my work. I have 50 Rdata files (F1,F2,F3,F4,?,F50) with objects inside. I need to: open F1: ? - perform some simple operations with the objects ? - export the solution with write.table ? - end F1 session open F2 ? repeat procedures as F1 ? open F50 ? repeat procedures as F1 ? My difficulty here is to end a workspace and open one from the scratch to avoid mixing files from consecutive worksessions, and thus using R memory unnecessarily. I could use rm() to delete objects from the previous sessions but it seems not an efficient task. Any suggestions on how to perform this in Batch Mode? An examplified help would be nice! Diogo Andr? Alagador http://www.biochange-lab.eu/people/diogo-alagador Biodiversity and Global Change Lab, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Espa?a Forest Research Centre, Instituto Superior de Agronomia, UTL, Lisboa, Portugal
Sarah Goslee http://www.functionaldiversity.org
On Sat, May 16, 2009 at 10:21 AM, <mcnda839 at mncn.csic.es> wrote:
Thanks a lot for all of you that have reply me about opening and ending R workspaces in BATCH mode. However replies were a king general and I?m afraid I could not take the entire message from them. Therefore I chose to expose here a representative fraction of my work. I have 50 Rdata files (F1,F2,F3,F4,?,F50) with objects inside. I need to: open F1: ? - perform some simple operations with the objects ? - export the solution with write.table ? - end F1 session open F2 ? repeat procedures as F1 ? open F50 ? repeat procedures as F1 ? My difficulty here is to end a workspace and open one from the scratch to avoid mixing files from consecutive worksessions, and thus using R memory unnecessarily. I could use rm() to delete objects from the previous sessions but it seems not an efficient task. Any suggestions on how to perform this in Batch Mode? An examplified help would be nice!
First try either Rcmd BATCH --help # for Windows or R CMD BATCH --help # for Mac OS X or for Linux and note that there are optional arguments --no-save and --no-restore. Use them.
Diogo Andr? Alagador http://www.biochange-lab.eu/people/diogo-alagador Biodiversity and Global Change Lab, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Espa?a Forest Research Centre, Instituto Superior de Agronomia, UTL, Lisboa, Portugal
______________________________________________ R-help at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
1 day later
Le samedi 16 mai 2009 ? 17:21 +0200, mcnda839 at mncn.csic.es a ?crit :
Thanks a lot for all of you that have reply me about opening and ending R workspaces in BATCH mode. However replies were a king general and I?m afraid I could not take the entire message from them. Therefore I chose to expose here a representative fraction of my work. I have 50 Rdata files (F1,F2,F3,F4,
,F50) with objects inside.
I need to:
open F1:
- perform some simple operations with the objects
- export the solution with write.table
- end F1 session
open F2
repeat procedures as F1
open F50
repeat procedures as F1
My difficulty here is to end a workspace and open one from the scratch to avoid mixing files from consecutive worksessions, and thus using R memory unnecessarily. I could use rm() to delete objects from the previous sessions but it seems not an efficient task.
And re-loading R, rebuilding a whole process context, re-allocating memory is an efficient one ? Hah !
Any suggestions on how to perform this in Batch Mode? An examplified help would be nice!
Why not encapsulate your procedures in a function taking the filename as its argument and loop?ng on the filenames list ? Anything created in the function, being local to the function, will be (efficiently) cleaned up at the function exit. Magic... Exemple :
ls()
character(0)
Foo<-runif(10,0,1) ls()
[1] "Foo"
?save.image
save.image("Foo1.RData")
ls()
[1] "Foo"
rm(list=ls()) Foo<-letters[round(runif(10,min=1,max=26))] Foo
[1] "v" "m" "b" "y" "g" "u" "r" "f" "y" "q"
save.image("Foo2.RData")
rm(list=ls())
bar<-edit()
bar<-edit() Waiting for Emacs...
bar
function(filename) {
load(file=filename)
print(ls())
print(Foo)
invisible(NULL)
}
ls()
[1] "bar"
bar("Foo1.RData")
[1] "filename" "Foo" # Note : by default, ls() list the function's # environment, not the global one... **> no "bar" here... [1] 0.8030422 0.6326055 0.8188481 0.6161665 0.5917206 0.6631358 0.7290200 [8] 0.2970315 0.2016259 0.4473244
ls()
[1] "bar" # Bar is still in the global environment...
bar("Foo2.RData")
[1] "filename" "Foo" [1] "v" "m" "b" "y" "g" "u" "r" "f" "y" "q"
ls()
[1] "bar"
Good enough for you ? HTH, Emmanuel Charpentier