[BioC] Problem with affy mas5 on Linux but not Windows...

[James Carman]

If I try to run this code on Linux, it fails, but it works on Windows:

> library(affy)
> aff <- ReadAffy()
> m5 <- mas5(aff)
background correction: mas
PM/MM correction : mas
expression values: mas
background correcting...Error in as.vector(data) : NAs in foreign
function call (arg 2)

Here's the result of sessionInfo():
> sessionInfo()
R version 2.12.1 (2010-12-16)
Platform: x86_64-redhat-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C
 [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8
 [5] LC_MONETARY=C             LC_MESSAGES=en_US.utf8
 [7] LC_PAPER=en_US.utf8       LC_NAME=C
 [9] LC_ADDRESS=C              LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] hgu133a2cdf_2.7.0 affy_1.28.0       Biobase_2.10.0

loaded via a namespace (and not attached):
[1] affyio_1.16.0         preprocessCore_1.10.0 tools_2.12.1

Here's my platform:

> uname -a
Linux carman-op755 2.6.35.10-74.fc14.x86_64 #1 SMP Thu Dec 23 16:04:50
UTC 2010 x86_64 x86_64 x86_64 GNU/Linux

Here's the version of R that I'm running:

> rpm -qa | grep R-
R-core-2.12.1-1.fc14.x86_64
R-devel-2.12.1-1.fc14.x86_64
R-2.12.1-1.fc14.x86_64


We have used this process in the past and it has worked fine.  I got a
new computer and installed the latest Bioconductor package(s) on it
and now I'm getting this failure.  Any ideas?

Thank you,

James Carman