Thanks for the quick reply!
In answer to your questions, I believe that I was using the most recent version of mosaics, even though I had an older version of R. Unfortunately, I can't double-check, because I had to reinstall it after my R got updated.
The chromosome names do coincide among all the files. However, they aren't in the same order in all the files - would that cause a problem?
Here are the command lines I'm using. I first built the bins from bed files (I've tried using the bin data that I made before and making new bin data; constructBins() works, but I still get an error after calling readBins()):
constructBins(infile="../Density/Stage_9_1.ext300.bed", fileFormat="bed", outfileLoc="./", byChr=FALSE, useChrfile=FALSE, chrfile=NULL, PET=FALSE, fragLen=300, binSize=50)
binData <- readBins(type=c("chip", "M", "GC", "N"), fileName=c("./Stage_9_1.ext300.bed_fragL300_bin50.txt", "./dp3_map_fragL300_bin50.txt", "./dp3_GC_fragL300_bin50.txt", "./dp3_N_fragL300_bin50.txt"))