[Swift-user] still having problems

[Ben Clifford]

based on previous messages, its still unclear to me that you have the 
program working outside of Swift.

Pretty much you need to be able to run rInvoke perm.short.R 0 from the 
commandline successfully before attempting to run that command inside 
Swift.

On Mon, 15 Jun 2009, Hodgess, Erin wrote:

> Hi again!
> 
> I have brought things down to the bones here.  Still no luck.
> 
> The files are /home/erin/R-2.9.0/bin/perm.short.R and /home/erin/R-2.9.0/bin/perm4.swift
> 
> 
> [erin at tp-login2 bin]$ swift -tc.file tc.data perm4.swift
> Swift svn swift-r2950 cog-r2406
> 
> RunID: 20090615-1137-nbfujhb2
> Progress:
> Progress:  Checking status:1
> Progress:  Stage in:1
> Execution failed:
> 	Exception in RInvoke:
> Arguments: [perm.short.R, 0]
> Host: localhost
> Directory: perm4-20090615-1137-nbfujhb2/jobs/v/RInvoke-vti60bcj
> stderr.txt: 
> stdout.txt: 
> ----
> 
> Caused by:
> 	Exit code 1
> [erin at tp-login2 bin]$ cat perm4.swift
> type file{}
> 
> (file procOut) permScript (file script, int batchSize){
> 	        app{
> 	                RInvoke @filename(script) batchSize ;
> 	        }
> 	}
> 
> 
> 
> 
> 
> 
> 
> 	        int batchSize=0;
> 		        file script<"perm.short.R">;
> 	                file procOut<"a.txt">;
> 	                procOut=permScript(script, batchSize);
> 
> [erin at tp-login2 bin]$ cat perm.short.R
> 	# -- read data files that are hardcoded per analysis and get
> 	vox_speech_vec <- as.matrix(read.table("origccf.txt"))
> 	pm <- as.matrix(read.table("corr.perm.matrix.txt"))
> 	allinputs <- Sys.getenv("R_SWIFT_ARGS")
> 	print(allinputs)
> 	permlength <-  as.numeric(noquote(strsplit(allinputs," ")[[1]][1]))
> #	startrpermrow <- as.numeric(noquote(strsplit(allinputs," ")[[1]][1]))
> 	startrpermrow <- 1
> 	endpermrow <- permlength + startrpermrow
> 	debug = 1
> 	if (debug == 1) {
> 	        print(paste("start", startrpermrow, "end", endpermrow, sep=","))
> 	}
> 	 # rotate across specified rows in permutation matrix
> 	for (rr in startrpermrow:endpermrow){
> 	        permvec = pm[rr,]
> 	        # initialize a 'ccf' matrix for each permutation
> 	        ccf <- matrix(nrow=200, ncol=1)
> 	        mat_row = 0
> 	        for (vox in 1:200) {
> 	                mat_row = mat_row + 1
> 	                speechperm_ccf <- ccf(vox_speech_vec[vox,], permvec, lag.max = 6, type = c("correlation"), na.action=na.pass, plot = FALSE)
> 	                if (any(speechperm_ccf$acf[1:13] == "NaN")) {
> #	                        speechperm_ccf$acf[1:13] = 0
> 				speechperm_ccf$acf[1:13] <- rep(0,13)
> 	                        } else {
> 	                        speechperm_ccf$acf[1:13] = speechperm_ccf$acf[1:13]
> 	                }
> 	        speechperm_ccf <- as.matrix(data.frame(speechperm_ccf$acf, speechperm_ccf$lag))[7:13,]
> 	        speechperm_cor <- speechperm_ccf[which.max(speechperm_ccf[,1]),]
> 	        ccf[mat_row, ] <- c(speechperm_cor[[1]])
> 	        }
> 	        write.table (ccf, file=paste("a.txt",sep=""), row.names=FALSE, col.names=FALSE)
> 	        if (debug == 1) {
> 	                print(paste("permrow finished", rr, sep=","))
> 	                print(date())
> 	        }
> 	        rm(ccf)
> 	}
> [erin at tp-login2 bin]$ 
> 
> Any help appreciated.
> 
> 
> 
> 
> Erin M. Hodgess, PhD
> Associate Professor
> Department of Computer and Mathematical Sciences
> University of Houston - Downtown
> mailto: hodgesse at uhd.edu
> 
>