Hi Hans,
sorry for the delayed response.
Ok … I am working on 10.7.2 (so I already upgraded to lion – kind of regret it …)
R version 2.13.1 (2011-07-08).
So this is what I found in the first lines of the r_out-file:
WARNING: unknown option '--TMRdaemon'
ARGUMENT '2' __ignored__
[1] ".RProfile im User Order laedt:" [1] "Programmierung/R Arbeitsverzeichnis/eigene Funktionen/own.functions.R" > source("/Users/bath/Library/Application Support/Rdaemon/daemon/start.r") > sink('/Users/bath/Library/Application Support/Rdaemon/r_tmp');cat(geterrmessage());sink(file=NULL)
(the first two lines are just from a print-expression of the .Rprofile file that is loaded at the beginning of an R-session)
then my script seems to work fine till this point (line 177 in the original script) :
> x <- c(14, 17, 20, 23) > for(i in 1:length(x)) { prfor(i in 1:length(x)) { prfor(i in 1:length(x)) { prfor(i in 1:length(x)) { prfor(i i_reduced) Error: unexpected 'in' in "for(i in 1:length(x)) { prfor(i in" > full_matrix <- cbind(full_matrix, reduced_datfull_matrix <- cbind(full_matrix, reduced_datfull_matrix <- cbind(fse { final_matrix <- rbind(final_matrix, full_matrix) } Error: unexpected '{' in "full_matrix <- cbind(full_matrix, reduced_datfull_matrix <- cbind(full_matrix, reduced_datfull_matrix <- cbind(fse {"
the original code looks like this:
x <- c(12, 15, 18, 21) for(i in 1:length(x)) { prt_reduced[,x[i]] <- reorder(prt_reduced[,x[i]], c(3,4,1,2)) } x <- c(13, 16, 19, 22) for(i in 1:length(x)) { prt_reduced[,x[i]] <- reorder(prt_reduced[,x[i]], c(3,1,2)) } x <- c(14, 17, 20, 23) for(i in 1:length(x)) { prt_reduced[,x[i]] <- reorder(prt_reduced[,x[i]], c(2,1)) }
(the first two loops work without an error message only the last one is transformed in a strange way.
hope that helps ..?
On 14.10.2011, at 11:20, Hans-Jörg Bibiko wrote:
On 13 Oct 2011, at 23:23, Martin Batholdy wrote:
I start the Rdaemon with CMD+enter and then execute selected lines with the "execute selection" menu item. A small window pops up with a progress bar and the message "sending task to Rdaemon". After this is finished the selection converts to R-output.
I don't have a separate R-window open.
The script is actually not that large. It is just about 200 lines of code (8kb on disk).
But since I get this strange parsing-behavior always at the end of the script, I thought it has something to do with that.
Hi Martin,
ok, I got it [Rdaemon offers flexible workflows ;) ]
The point is that the output of the R console which runs in the background will be parsed by a Perl script to clean the output since it could contain many control characters etc. I guess that's the problem.
Important: Which MacOSX and R version do you running?
and
Please do the following:
- start a new Rdaemon session
- execute your R code in question
- go to the "R Console (Rdaemon)" menu > "Rdaemon Tools" > "Logfiles" > "Open console log file r_out" [short-cut ⌥⌘T]
- a new window should appear showing the RAW output of the current R session's output [don't be confused ;)]
- check the window's content for any confidential data and if you can send me the content please do this:
-- open Finder; go to ~/Library/Application Support/Rdaemon; and send me the file "r_out" [please do not copy/save the content file to another file since editors can "destroy" its content due to possible control characters]
With this I can check the Perl script. Maybe I missed some output sequences to catch.
Best, --Hans
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