We have just uploaded a bug fix to the release branch of affxparser, it may take some time before binaries etc. are available. The new version is 1.4.1 The fix deals with two issues: 1) Compilation fails using Gcc-4.0.3 shipped with R-2.3.0 under Mac OS X. It should work now. 2) On some platforms, reading a cel file resulted in zero (or very close to zero like 10^-30) for all returned intensities. We believe this is due to compiling with -O2 (and greater) using Gcc-4.0.x+ although a bug report obtained today indicates that this may also be a problem for Gcc-3.4.4 - something that mystifies us a bit. If the update does not resolve your difficulties, please email me directly. /Kasper