[R-SIG-Mac] bug in polychor with R 2.6.0
William Revelle
lists at revelle.net
Mon Sep 17 02:28:38 CEST 2007
Ok, I made it go away.
Following Ben's hint, I reinstalled mvtnorm from CRAN and polychor
works perfectly again.
For Rgraphviz, I had not loaded one of the dependencies for graph,
and although graph did not object, it just crashed.
With a reinstalled mvtnorm, and Rgraphviz and graph and ...,
everything works beautifully.
Thanks. I was unaccustomed to having such an ungraceful exit
compared to the normal set of warnings. But that is what happens
when you try out an alpha release.
Bill
At 6:51 PM -0500 9/16/07, William Revelle wrote:
>Ben,
>
>At 7:15 PM -0400 9/16/07, Ben Bolker wrote:
>> Has anyone noticed that the problem (whatever it is)
>>seems to occur in code from the included mvtnorm
>>package (specifically the guts of the
>>mvt() function), *not* the polycor package?
>>[cc'd to mvtnorm package maintainer]
>
>
> At least that solves the polychor problem. You are right.
>I tried it with just the mvtnorm package and the error occurs.
>
>Error trace follows:
>
>> sessionInfo()
>R version 2.6.0 alpha (2007-09-15 r42871)
>i386-apple-darwin8.10.1
>
>locale:
>en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
>attached base packages:
>[1] stats graphics grDevices utils datasets methods base
>
>other attached packages:
>[1] mvtnorm_0.8-1
>> example(pmvnorm)
>
>pmvnrm> n <- 5
>
>pmvnrm> mean <- rep(0, 5)
>
>pmvnrm> lower <- rep(-1, 5)
>
>pmvnrm> upper <- rep(3, 5)
>
>pmvnrm> corr <- diag(5)
>
>pmvnrm> corr[lower.tri(corr)] <- 0.5
>
>pmvnrm> corr[upper.tri(corr)] <- 0.5
>
>pmvnrm> prob <- pmvnorm(lower, upper, mean, corr)
>
> *** caught bus error ***
>address 0x0, cause 'non-existent physical address'
>
>Traceback:
> 1: .Fortran("mvtdst", N = as.integer(n), NU = as.integer(df), LOWER
>= as.double(lower), UPPER = as.double(upper), INFIN =
>as.integer(infin), CORREL = as.double(corrF), DELTA =
>as.double(delta), MAXPTS = as.integer(maxpts), ABSEPS =
>as.double(abseps), RELEPS = as.double(releps), error =
>as.double(error), value = as.double(value), inform =
>as.integer(inform), PACKAGE = "mvtnorm")
> 2: mvt(lower = lower, upper = upper, df = 0, corr = corr, delta =
>mean, maxpts = maxpts, abseps = abseps, releps = releps)
> 3: pmvnorm(lower, upper, mean, corr)
> 4: eval.with.vis(expr, envir, enclos)
> 5: eval.with.vis(ei, envir)
> 6: source(zfile, local, echo = echo, prompt.echo =
>paste(prompt.prefix, getOption("prompt"), sep = ""),
>continue.echo = paste(prompt.prefix, getOption("continue"), sep =
>""), verbose = verbose, max.deparse.length = Inf, encoding =
>encoding, skip.echo = skips)
> 7: example(pmvnorm)
>
>Bill
>
>
>
>>>On Sep 15, 2007, at 10:49 AM, William Revelle wrote:
>>>
>>>
>>>>John,
>>>> I have been testing out R2.6.0 alpha to see if my psych package
>>>>works. I am running the R Gui for the Mac.
>>>>
>>>>There seems to be a problem with the polychor function in your
>>>>polycor package. I think this might be a general problem with R
>>>>2.6.0 alpha but I am not sure. I am copying the R mac list to see
>>>>if this is a general problem with the alpha gui.
>>>>
>>>>Bill
>>>>
>>>>
>>>> From a clean start
>>>>
>>>>[Workspace restored from /Volumes/WR/bill/.RData]
>>>>
>>>>
>>>>> version
>>>>>
>>>> _
>>>>platform i386-apple-darwin8.10.1
>>>>arch i386
>>>>os darwin8.10.1
>>>>system i386, darwin8.10.1
>>>>status alpha
>>>>major 2
>>>>minor 6.0
>>>>year 2007
>>>>month 09
>>>>day 14
>>>>svn rev 42851
>>>>language R
>>>>version.string R version 2.6.0 alpha (2007-09-14 r42851)
>>>>
>>>>
>>>>
>>>>> library(polycor)
>>>>>
>>>>Loading required package: mvtnorm
>>>>
>>>>> ?polychor #to get the help file with the following demo
>>>>> set.seed(12345)
> >>>> data <- rmvnorm(1000, c(0, 0), matrix(c(1, .5, .5, 1), 2, 2))
>>>>> x <- data[,1]
>>>>> y <- data[,2]
>>>>> cor(x, y) # sample correlation
>>>>>
>>>>[1] 0.5285446
>>>>
>>>>> x <- cut(x, c(-Inf, .75, Inf))
>>>>> y <- cut(y, c(-Inf, -1, .5, 1.5, Inf))
>>>>> polychor(x, y) # 2-step estimate
>>>>>
>>>> *** caught bus error ***
>>>>address 0x0, cause 'non-existent physical address'
>>>>
>>>>Traceback:
>>>> 1: .Fortran("mvtdst", N = as.integer(n), NU = as.integer(df), LOWER
>>>>= as.double(lower), UPPER = as.double(upper), INFIN =
>>>>as.integer(infin), CORREL = as.double(corrF), DELTA =
>>>>as.double(delta), MAXPTS = as.integer(maxpts), ABSEPS =
>>>>as.double(abseps), RELEPS = as.double(releps), error =
>>>>as.double(error), value = as.double(value), inform =
>>>>as.integer(inform), PACKAGE = "mvtnorm")
>>>> 2: mvt(lower = lower, upper = upper, df = 0, corr = corr, delta =
>>>>mean, maxpts = maxpts, abseps = abseps, releps = releps)
>>>> 3: pmvnorm(lower = c(row.cuts[i], col.cuts[j]), upper = c(row.cuts[i
>>>>+ 1], col.cuts[j + 1]), corr = R)
>>>> 4: binBvn(rho, row.cuts, col.cuts)
>>>> 5: f(arg, ...)
>>>> 6: function (arg) f(arg, ...)(-0.23606797749979)
>>>> 7: optimise(f, interval = c(-1, 1))
>>>> 8: polychor(x, y)
>>>>
>
>
>--
>William Revelle http://personality-project.org/revelle.html
>Professor http://personality-project.org/personality.html
>Department of Psychology http://www.wcas.northwestern.edu/psych/
>Northwestern University http://www.northwestern.edu/
>Use R for statistics:
>http://personality-project.org/r
>
>_______________________________________________
>R-SIG-Mac mailing list
>R-SIG-Mac at stat.math.ethz.ch
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--
William Revelle http://personality-project.org/revelle.html
Professor http://personality-project.org/personality.html
Department of Psychology http://www.wcas.northwestern.edu/psych/
Northwestern University http://www.northwestern.edu/
Use R for statistics: http://personality-project.org/r
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