When I load and work with large (1GB) data files in R copies of these files seem to be saved somewhere on my hard drive. Now my hard drive is almost completely full and I am unable to use R for fear of running out of space. I've tried deleting temporary directories associated with R, restarting, looking for large files, reinstalling R, but I can't seem to free up the bulk of the space or figure out where these files are being stored.
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That sounds really strange. What analysis have you done on hard disk utilization?
From your home directory, I would look at invisible directories, especially the hidden Library directory for R cache files. Press Shift + Command + . (or Shift + Command + the period key) to make invisible directories visible.
Then select all directories in your Home directory and using the inspector to find large size volumes. Assuming you have only maybe 30 directories in your home, select all directories by pressing Command + A, then press Command + I. Note each directory file size.
Anything in the 90GB mark should stand out. Once you find it, drill down into the sub-directories.
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