[R-SIG-Mac] bug in polychor with R 2.6.0

[William Revelle]

Jan and Kasper,


I am running Mac OS X 10.4.10

R  framework  installed directly from  CRAN (ucla mirror) (i.e., I 
did not compile it, I just installed the framework and GUI).

polycor reinstalled from CRAN   (version 0.7.3)
also similar failure when using Rgraphviz  1.15.9
Rgraphviz installed from bioconductor using the  commands

source("http://bioconductor.org/getBioC.R")
biocLite <- function(pkgs, groupName="lite", ...)
     if (missing(pkgs))
         biocinstall(groupName=groupName, ...)
     else
         biocinstall(pkgs=pkgs, groupName=groupName, ...)
}
biocLite("Rgraphviz")
Running biocinstall version 2.1.7 with R version 2.6.0 (under development)
Your version of R requires version 2.1 of Bioconductor.
trying URL 
'http://bioconductor.org/packages/2.1/bioc/bin/macosx/universal/contrib/2.6/Rgraphviz_1.15.9.tgz'

Before the Rgraphviz crash, here is the sessionInfo:
>  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] Rgraphviz_1.15.9 graph_1.14.2   

loaded via a namespace (and not attached):
[1] cluster_1.11.8 tools_2.6.0

The presumption is this is not polychor but something  about R 2.6.0 for Mac

version information:

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            15                                      
svn rev        42871                                   
language       R                                       
version.string R version 2.6.0 alpha (2007-09-15 r42871)

Crash is reliable.  I am happy to send any more dump information you 
want.  Here is the R traceback

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] polycor_0.7-3 mvtnorm_0.8-1
>  example(polychor)

plychr> set.seed(12345)

plychr> data <- rmvnorm(1000, c(0, 0), matrix(c(1, .5, .5, 1), 2, 2))

plychr> x <- data[,1]

plychr> y <- data[,2]

plychr> cor(x, y)  # sample correlation
[1] 0.5285446

plychr> x <- cut(x, c(-Inf, .75, Inf))

plychr> y <- cut(y, c(-Inf, -1, .5, 1.5, Inf))

plychr> 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)
  9: eval.with.vis(expr, envir, enclos)
10: eval.with.vis(ei, envir)
11: 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)
12: example(polychor)



Bill



At 3:34 PM -0700 9/16/07, Jan de Leeuw wrote:
>Works fine with R-devel on OS X 10.4.11, R compiled with icc/ifort,
>2 x 3 Ghz Quad-Core Xeon. Also on OS X 10.5. Could be gnu fortran
>problem.
>
>
>===
>Jan de Leeuw; Distinguished Professor and Chair, UCLA Department of 
>Statistics;
>Director: UCLA Center for Environmental Statistics (CES);
>Editor: Journal of Multivariate Analysis, Journal of Statistical Software;
>US mail: 8125 Math Sciences Bldg, Box 951554, Los Angeles, CA 90095-1554
>phone (310)-825-9550;  fax (310)-206-5658;  email: 
><mailto:deleeuw at stat.ucla.edu>deleeuw at stat.ucla.edu
>
>.mac: jdeleeuw +++ skype: j_deleeuw +++ homepage: 
><http://www.cuddyvalley.org>http://www.cuddyvalley.org
> 
>-------------------------------------------------------------------------------------------------
>           No matter where you go, there you are. --- Buckaroo Banzai
> 
>  <http://gifi.stat.ucla.edu/sounds/nomatter.au>http://gifi.stat.ucla.edu/sounds/nomatter.au 
> 
> 
>------------------------------------------------------------------------------------------------- 
>


-- 
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