BUG: Pathnames are too long for MS Windows

[HenrikBengtsson]

Running R CMD check on Windows gives errors like:

Warning in gzfile(file, mode) :
  cannot open compressed file 'overlapScoreData/human,HAP1,unique,bin_size=100000,partition_by=cells_by_half,min_cell_size=2,window_size=5,fraction=0.100,mainseed=0xBEEF/human,HAP1,unique,chr=22,bin_size=100000,partition_by=cells_by_half,min_cell_size=2,window_size=5,fraction=0.100,seed=28e0e3fd,topdom.rds', probable reason 'No such file or directory'
Error in gzfile(file, mode) : cannot open the connection

There is a limit of 255 characters in the effective absolute pathname on Windows. The above relative pathname is 276 characters long by itself. To this should be added the length of the path to the working directory.

Action

For now, document that TopDomStudy will not work on MS Windows because of this.