[R] R crashing oddly

[Joshua Wiley]

Michael,

Good news (relatively speaking).  I ran your code again, but this time
I actually looked at what I pasted in and noticed some errors.  When I
actually pulled your code into a text editor, there was an issue with
one of the comments wrapping to the next line without a new #
(probably an email issue).

For others if "## BEGIN" is line 1; the comment issue is on line 44 (#
nugget for space is (then the line break) determined by the nugget for
time).

Once I fixed that, I got slightly different results.

########From Rterm########

Browse[6]>
debug: space.nug <- temp[2]
Browse[6]>
debug: cor.time <- lapply(attr(object[["time"]], "covariate"), function(mat) (1
-
    time.nug) * exp(-mat/time.rng))
Browse[6]>

Traceback:
 1: FUN(X[[5L]], ...)
 2: lapply(attr(object[["time"]], "covariate"), function(mat) (1 -     time.nug)
 * exp(-mat/time.rng))
 3: corMatrix.corSPT(object)
 4: corMatrix(object)
 5: unlist(corMatrix(object))
 6: corFactor.corSPT(object)
 7: corFactor(object)
 8: `coef<-.corSPT`(`*tmp*`, value = c(0, 0, 1.49011611938477e-08))
 9: `coef<-`(`*tmp*`, value = c(0, 0, 1.49011611938477e-08))
10: `coef<-.modelStruct`(`*tmp*`, value = c(0.375881355354461, 0, 0, 1.490116119
38477e-08))
11: `coef<-`(`*tmp*`, value = c(0.375881355354461, 0, 0, 1.49011611938477e-08))
12: logLik.lmeStruct(lmeSt, lmePars)
13: logLik(lmeSt, lmePars)
14: objective(.par, ...)
15: .Call(R_port_nlminb, obj, grad, hess, rho, low, upp, d = rep(as.double(scale
),     length.out = length(par)), iv, v)
16: nlminb(c(coef(lmeSt)), function(lmePars) -logLik(lmeSt, lmePars),     contro
l = list(iter.max = controlvals$msMaxIter, eval.max = controlvals$msMaxEval,
     trace = controlvals$msVerbose))
17: lme.formula(fixed = e ~ a, random = ~1 | g, data = df, correlation = corSPT(
corExp(c(1,     0.5), form = ~t | g, nugget = TRUE), corExp(c(1, 0.5), form = ~x
 +     y | g, nugget = TRUE)), control = list(msVerbose = TRUE,     opt = "nlmin
b"))
18: lme(fixed = e ~ a, random = ~1 | g, data = df, correlation = corSPT(corExp(c
(1,     0.5), form = ~t | g, nugget = TRUE), corExp(c(1, 0.5), form = ~x +     y
 | g, nugget = TRUE)), control = list(msVerbose = TRUE,     opt = "nlminb"))
Error in FUN(X[[5L]], ...) : caught access violation - continue with care
>


########From Rterm (again, but this time running the code from Xemacs)########

Browse[3]>
debug: coef(object[[i]]) <- value[parMap[, i]]
Browse[3]>

Traceback:
 1: `coef<-.modelStruct`(`*tmp*`, value = c(0.47054905560461, 0,
1.49011611938477e-08, 0))
 2: `coef<-`(`*tmp*`, value = c(0.47054905560461, 0, 1.49011611938477e-08, 0))
 3: logLik.lmeStruct(lmeSt, lmePars)
 4: logLik(lmeSt, lmePars)
 5: objective(.par, ...)
 6: .Call(R_port_nlminb, obj, grad, hess, rho, low, upp, d =
rep(as.double(scale),     length.out = length(par)), iv, v)
 7: nlminb(c(coef(lmeSt)), function(lmePars) -logLik(lmeSt, lmePars),
   control = list(iter.max = controlvals$msMaxIter, eval.max =
controlvals$msMaxEval,         trace = controlvals$msVerbose))
 8: lme.formula(fixed = e ~ a, random = ~1 | g, data = df, correlation
= corSPT(corExp(c(1,     0.5), form = ~t | g, nugget = TRUE),
corExp(c(1, 0.5), form = ~x +     y | g, nugget = TRUE)), control =
list(msVerbose = TRUE,     opt = "nlminb"))
 9: lme(fixed = e ~ a, random = ~1 | g, data = df, correlation =
corSPT(corExp(c(1,     0.5), form = ~t | g, nugget = TRUE),
corExp(c(1, 0.5), form = ~x +     y | g, nugget = TRUE)), control =
list(msVerbose = TRUE,     opt = "nlminb"))
Error in coef(object[[i]]) <- value[parMap[, i]] :
  caught access violation - continue with care
>

Then it occurred to me that RGui sometimes behaves slightly
differently, and that you might be using the Gui so I ran it again
there and it crashed, froze, and I had to manually kill the process.

I don't know if that really helps, but at least I (sort of?)
replicated your crashing.

Josh


<snipped a bunch of stuff because I already included a lot of output>


-- 
Joshua Wiley
Senior in Psychology
University of California, Riverside
http://www.joshuawiley.com/