[R-SIG-Mac] problem with some packages in R 2.6.0 alpha for Mac

[William Revelle]

Hi,

The packages polycor and Rgraphviz have a bus error (and R crash) 
when running their examples under 2.6.0 alpha.  They both work 
perfectly well with 2.5.1.


I have written John Fox about polycor and he reports that it works 
fine for Windows XP with R 2.6.0 alpha and suggests it is a Mac 2.6.0 
problem.

Good luck and thanks for such a wonderful interface to such a 
wonderful program.


Bill


Below are the two error logs:


   Using  a MacBook Pro:
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)


[Workspace restored from /Volumes/WR/bill/.RData]

>  library(polycor)
Loading required package: mvtnorm
>  ?polychor
>  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

---for polycor , running the  polychor demo


  *** 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)

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection: polychor(x, y, ML=TRUE, std.err=TRUE)  # ML estimate
Selection:


--------------------------
for Rgraphviz, running the graphviz demo
restarted R 2.6.0,
libary(Rgraphviz)
_____________________________________

>   V <- letters[1:10]
>    M <- 1:4
>    g1 <- randomGraph(V, M, .2)

  *** caught bus error ***
address 0xc, cause 'non-existent physical address'

Traceback:
  1: .Call("graph_is_adjacent", fromEdges, to, PACKAGE = "graph")
  2: isAdjacent(graph, from, to)
  3: isAdjacent(graph, from, to)
  4: graph:::.verifyEdges(graph, from, to)
  5: graph:::.getEdgeKeys(self, from, to)
  6: `edgeData<-`(`*tmp*`, from = from, to = to, attr = "weight", 
value = c(1, 2, 2, 1, 1, 2, 1, 2, 1, 1, 1, 1))
  7: `edgeData<-`(`*tmp*`, from = from, to = to, attr = "weight", 
value = c(1, 2, 2, 1, 1, 2, 1, 2, 1, 1, 1, 1))
  8: graphNEL_init_edgeL_weights(.Object)
  9: .local(.Object, ...)
10: initialize(value, ...)
11: initialize(value, ...)
12: new("graphNEL", nodes = V, edgeL = rval)
13: randomGraph(V, M, 0.2)


-- 
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