[BioC] how to install updated CDF package and probe package in R to run GCRMA?

[Yan Zhang]

Recently, I got a new CDF file which trimmed some probes out and 
rearrange probe to probeset. I also got new trimmed probesequence file. 
I could  use new cdf file to generate new cdf envirment and do RMA. I 
can also generate probe package and install it without any problem. But 
when I run gcrma, I got the following error message:

Error in compute.affinities(cdfName(object), verbose = verbose) :
       NAs are not allowed in subscripted assignments

Anyone know what cause this error and how to solve it?

best
yan