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<TITLE>still having problems </TITLE>
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<P><FONT SIZE=2>Hi again!<BR>
<BR>
I have brought things down to the bones here. Still no luck.<BR>
<BR>
The files are /home/erin/R-2.9.0/bin/perm.short.R and /home/erin/R-2.9.0/bin/perm4.swift<BR>
<BR>
<BR>
[erin@tp-login2 bin]$ swift -tc.file tc.data perm4.swift<BR>
Swift svn swift-r2950 cog-r2406<BR>
<BR>
RunID: 20090615-1137-nbfujhb2<BR>
Progress:<BR>
Progress: Checking status:1<BR>
Progress: Stage in:1<BR>
Execution failed:<BR>
Exception in RInvoke:<BR>
Arguments: [perm.short.R, 0]<BR>
Host: localhost<BR>
Directory: perm4-20090615-1137-nbfujhb2/jobs/v/RInvoke-vti60bcj<BR>
stderr.txt:<BR>
stdout.txt:<BR>
----<BR>
<BR>
Caused by:<BR>
Exit code 1<BR>
[erin@tp-login2 bin]$ cat perm4.swift<BR>
type file{}<BR>
<BR>
(file procOut) permScript (file script, int batchSize){<BR>
app{<BR>
RInvoke @filename(script) batchSize ;<BR>
}<BR>
}<BR>
<BR>
<BR>
<BR>
<BR>
<BR>
<BR>
<BR>
int batchSize=0;<BR>
file script<"perm.short.R">;<BR>
file procOut<"a.txt">;<BR>
procOut=permScript(script, batchSize);<BR>
<BR>
[erin@tp-login2 bin]$ cat perm.short.R<BR>
# -- read data files that are hardcoded per analysis and get<BR>
vox_speech_vec <- as.matrix(read.table("origccf.txt"))<BR>
pm <- as.matrix(read.table("corr.perm.matrix.txt"))<BR>
allinputs <- Sys.getenv("R_SWIFT_ARGS")<BR>
print(allinputs)<BR>
permlength <- as.numeric(noquote(strsplit(allinputs," ")[[1]][1]))<BR>
# startrpermrow <- as.numeric(noquote(strsplit(allinputs," ")[[1]][1]))<BR>
startrpermrow <- 1<BR>
endpermrow <- permlength + startrpermrow<BR>
debug = 1<BR>
if (debug == 1) {<BR>
print(paste("start", startrpermrow, "end", endpermrow, sep=","))<BR>
}<BR>
# rotate across specified rows in permutation matrix<BR>
for (rr in startrpermrow:endpermrow){<BR>
permvec = pm[rr,]<BR>
# initialize a 'ccf' matrix for each permutation<BR>
ccf <- matrix(nrow=200, ncol=1)<BR>
mat_row = 0<BR>
for (vox in 1:200) {<BR>
mat_row = mat_row + 1<BR>
speechperm_ccf <- ccf(vox_speech_vec[vox,], permvec, lag.max = 6, type = c("correlation"), na.action=na.pass, plot = FALSE)<BR>
if (any(speechperm_ccf$acf[1:13] == "NaN")) {<BR>
# speechperm_ccf$acf[1:13] = 0<BR>
speechperm_ccf$acf[1:13] <- rep(0,13)<BR>
} else {<BR>
speechperm_ccf$acf[1:13] = speechperm_ccf$acf[1:13]<BR>
}<BR>
speechperm_ccf <- as.matrix(data.frame(speechperm_ccf$acf, speechperm_ccf$lag))[7:13,]<BR>
speechperm_cor <- speechperm_ccf[which.max(speechperm_ccf[,1]),]<BR>
ccf[mat_row, ] <- c(speechperm_cor[[1]])<BR>
}<BR>
write.table (ccf, file=paste("a.txt",sep=""), row.names=FALSE, col.names=FALSE)<BR>
if (debug == 1) {<BR>
print(paste("permrow finished", rr, sep=","))<BR>
print(date())<BR>
}<BR>
rm(ccf)<BR>
}<BR>
[erin@tp-login2 bin]$<BR>
<BR>
Any help appreciated.<BR>
<BR>
<BR>
<BR>
<BR>
Erin M. Hodgess, PhD<BR>
Associate Professor<BR>
Department of Computer and Mathematical Sciences<BR>
University of Houston - Downtown<BR>
mailto: hodgesse@uhd.edu<BR>
<BR>
</FONT>
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