Function completely locks up my computer if the input is too big

Hi all,

Thanks for the suggestions. Updating the function as below to break the
problem into chunks seemed to do the trick - perhaps there is a relatively
small limit to the size of a vector that R can work with?

Best

rotate <- function(x,y,tilt,threshold){

df.main<-data.frame(x,y)

 if(length(x)> threshold){
l <- round(length(x)/ threshold, 0)
dfchunk <- split(df.main, factor(sort(rank(row.names(df.main))%%l)))
 n<-length(summary(dfchunk)[,1])
xy<-vector("list", n)
for (i in 1:n){
wk.df <- dfchunk[[i]]
x <- wk.df$x
y <- wk.df$y
d2 <- x^2+y^2
rotate.dis<-sqrt(d2)
or.rad <- atan(x/y)
or.deg <- Rad2Deg(or.rad)

 or.deg[is.na(or.deg)] <- 0
 tilt.in <- tilt + or.deg
xy[[i]]<-data.frame(Pol2Car(distance=rotate.dis, deg=tilt.in))
}
 xy<-do.call("rbind", xy[1:n])
  } else {
 d2 <- x^2+y^2
rotate.dis<-sqrt(d2)
or.rad <- atan(x/y)
or.deg <- Rad2Deg(or.rad)

n <- length(or.deg)
for(i in 1:n){
if(is.na(or.deg[i])==TRUE) {or.deg[i] <- 0}
}
 tilt.in <- tilt + or.deg

xy<-data.frame(Pol2Car (distance=rotate.dis, deg=tilt.in))
}

xy
}

*Ben Caldwell*

Graduate Fellow
University of California, Berkeley
130 Mulford Hall #3114
Berkeley, CA 94720
Office 223 Mulford Hall
(510)859-3358


On Tue, Mar 5, 2013 at 1:44 PM, Peter Alspach <
Peter.Alspach at plantandfood.co.nz> wrote:

Tena koe Benjamin

I haven't looked at you code in detail, but in general ifelse is slow and
can generally be avoided.  For example,

ben <- 1:10^7
system.time(BEN <- ifelse(ben<10, NA, -ben))
   user  system elapsed
   1.31    0.24    1.56
system.time({BEN1 <- -ben; BEN1[BEN1> -10] <- NA})
   user  system elapsed
   0.17    0.03    0.20
all.equal(BEN, BEN1)
[1] TRUE

HTH ...

Peter Alspach

-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org]
On Behalf Of Benjamin Caldwell
Sent: Wednesday, 6 March 2013 10:18 a.m.
To: r-help
Subject: [R] Function completely locks up my computer if the input is too
big

Dear r-help,


Somewhere in my innocuous function to rotate an object in Cartesian space
I've created a monster that completely locks up my computer (requires a
hard reset every time). I don't know if this is useful description to
anyone - the mouse still responds, but not the keyboard and not windows
explorer.

The script only does this when the input matrix is large, and so my
initial runs didn't catch it as I used a smaller matrix to speed up the
test runs.
When I tried an input matrix with a number of dimensions in the same order
of magnitude as the data I want to read in, R and my computer choked. This
was a surprise for me, as I've always been able to break execution in the
past or do other tasks. So i tried it again, and still no dice.

Now I need the function to work as subsequent functions/functionality are
dependent, and I can't see anything on the face of it that would likely
cause the issue.

Any insight on why this happens in general or specifically in my case are
appreciated. Running R 15.2, Platform: x86_64-w64-mingw32/x64 (64-bit) on a
windows 7 machine with 4 mb RAM. In the meantime I suppose I'll write a
loop to do this function piece-wise for larger data and see if that helps.

Script is attached and appended below.

Thanks

Ben Caldwell



#compass to polar coordinates

compass2polar <- function(x) {-x+90}



#degrees (polar) to radians

Deg2Rad <- function(x) {(x*pi)/180}



# radians to degrees

Rad2Deg <- function (rad) (rad/pi)*180



# polar to cartesian coordinates - assumes degrees those from a compass.
output is a list, x & y of equal length

Pol2Car <- function(distance,deg) {


rad <- Deg2Rad(compass2polar(deg))

rad <- rep(rad, length(distance))


x <- ifelse(is.na(distance), NA, distance * cos(rad))

y <- ifelse(is.na(distance), NA, distance * sin(rad))


x<-round(x,2)

y<-round(y,2)


cartes<- list(x,y)

name<-c('x','y')

names(cartes)<-name

cartes

}





#rotate an object, with assumed origin at 0,0, in any number of degrees

rotate <- function(x,y,tilt){ 8


d2 <- x^2+y^2

rotate.dis<-sqrt(d2)

or.rad <- atan(x/y)

or.deg <- Rad2Deg(or.rad)


n <- length(or.deg)

for(i in 1:n){

if(is.na(or.deg[i])==TRUE) {or.deg[i] <- 0}

}

# browser()

tilt.in <- tilt + or.deg


xy<-Pol2Car (distance=rotate.dis, deg=tilt.in)

 # if(abs(tilt) >= 0) {

 # shift.frame <- cbind(xy$x, xy$y)

# shift.frame.val <- shift.frame[shift.frame[,2]==min(shift.frame[,2]),]

# shift.x<- shift.frame.val[1] * -1

# shift.y<- shift.frame.val[2] * -1

# x<-xy$x + shift.x

# y<-xy$y + shift.y

# }

# name <- c('x', 'y')

# xy<-list(x,y)

# names(xy)<-name

 xy

}


x <- seq(0,5, .5)

y <- seq(0,5, .5)

z <- seq(0,5, .5)

dquad<-expand.grid(x,y,z)

name<-c("y","x","z")

names(dquad)<-name


plot(dquad$x, dquad$y, xlim=c(-25,25), ylim=c(-25,25))


#this works fine

rotated<-rotate(dquad$x, dquad$y, 45)



points(rotated$x, rotated$y, col='green')


# profiling of both time and memory

Rprof("myFunction.out", memory.profiling=T)

y <- myFunction(x)

Rprof(NULL)

summaryRprof("myFunction.out", memory="both")



#############

x <- seq(0,5, .1)

y <- seq(0,5, .1)

z <- seq(0,5, .1)

dquad<-expand.grid(x,y,z)

name<-c("y","x","z")

names(dquad)<-name

# running the below locks up my machine (commented out to avoid accidental
run)

# rotated<-rotate(dquad$x, dquad$y, 45)

The contents of this e-mail are confidential and may be subject to legal
privilege.
 If you are not the intended recipient you must not use, disseminate,
distribute or
 reproduce all or any part of this e-mail or attachments.  If you have
received this
 e-mail in error, please notify the sender and delete all material
pertaining to this
 e-mail.  Any opinion or views expressed in this e-mail are those of the
individual
 sender and may not represent those of The New Zealand Institute for Plant
and
 Food Research Limited.

	[[alternative HTML version deleted]]