As reported on R-help by Ming-Chung Li,
the cor() function has a new bug in R 1.8.0 when used with
matrix arguments (to give the Cor-Matrix) and the non-default     
      use = "pairwise.complete.obs"
argument (which can be abbreviated, e.g.   to  use = "pair").

A quite minimal example is

  > x <- cbind(1:3, c(0,4,5))
  > cor(x)[1,2]
  [1] 0.9449112
  > cor(x,use="pair")[1,2]
  [1] 0.8858796

This shouldn't have happened, has been my fault, and will be fixed shortly.

Martin Maechler <[EMAIL PROTECTED]>     http://stat.ethz.ch/~maechler/
Seminar fuer Statistik, ETH-Zentrum  LEO C16    Leonhardstr. 27
ETH (Federal Inst. Technology)  8092 Zurich     SWITZERLAND
phone: x-41-1-632-3408          fax: ...-1228                   <><

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