Changes to the annotate package is expected to take place in two weeks that will involve removing all the data files for Affymetrix chips that are currectly in the data subdirectory of annotate. If your code relies on those data files, please consider using the data packages that can be downloaded from Bioconductor under Downloads and then Data where you will find annotation data for various Affymetrix chips in the format of data packages and XML files. A data package can be installed and loaded as any R packages. Typing packageName() (e. g. hgu95a()) after the package has been loaded will list all the rda files for that data package. Each rda file in the data subdirectory of a given data package is an R environment with key and value pairs. Data in each rda file can be accessed using operations that are applicable to an R environment object. The current version of annotate will be made available afterwards but the data files will not be updated. Please contact me if you have any concern.