OK, now it sounds like the behavior is exactly the same for both of us. I
think Gmail sometimes gobbles up newline characters, and that must have
messed up the code I sent out before.

Someone pointed out to me that a similar problem was identified before:

https://stat.ethz.ch/pipermail/r-sig-mixed-models/2008q3/001425.html
http://www.mail-archive.com/r-devel@r-project.org/msg13913.html

Does anyone know a strategy for dealing with this or isolating the problem?

Thanks again Josh for your help.

On Fri, Apr 23, 2010 at 9:44 AM, Joshua Wiley <jwiley.psych@gmail.com>wrote:

> 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/
>

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