[R] Unusual slowing of R matrix multiplication version 2.12.1 (2010-10-15) vs 2.12.0

[Joseph Kunkel]

R Version  2.12.1 (2010-10-15) vs 2.12.0 has slowed down 8 fold for dual core and 17 fold for dual-core-dual-processor Macs.  I have checked this result on 3 different macs using the following R-script:

Using Version 2.12.0 on a dual core dual processor Mac:
> source("http://www.bio.umass.edu/biology/kunkel/pub/R/CuriousResult.R")
matrix multiplication      43.543   1.308  14.788 
tcrossprod                 41.147   1.286  11.9 
transposition and reuse    40.407   3.525  43.606 
elementwise after reshape  21.474   1.828  23.124 
columnwise sapply          34.695   32.35  66.592 
for loop over columns      37.237   29.471 67.2 

On the same day upgrading to 2.12.1 on the same dual core dual processor Mac:

> source("http://www.bio.umass.edu/biology/kunkel/pub/R/CuriousResult.R")
matrix multiplication     256.775   2.178 256.919 
tcrossprod                246.609   1.987 247.075 
transposition and reuse    39.622   4.602  43.883 
elementwise after reshape  21.017   2.343  23.258 
columnwise sapply    39.393  37.069  75.834 
for loop over columns      35.461  33.155  68.165 

It seems clear that the upgrade to 2.12.1 has resulted in matrix multiplication using only one core.  Notice that the other techniques that avoid matrix multiplication seem to stay the same but the two approaches that use matrix multiply have degraded worse than the expected loss of just 4 fold.  Is it possible that a different matrix multiply library was used in changing from version 2.12.0 to 2.12.1?

Joe Kunkel