Functions in the raster package create temporary files if the values of an output Raster* object cannot be stored in memory (RAM). This can happen when no filename is provided to a function and in functions where you cannot provide a filename (e.g. when using 'raster algebra').
Temporary files are automatically removed at the start of each session. During a session you can use showTmpFiles to see what is there and removeTmpFiles to delete all the temporary files. rasterTmpFile returns a temporary filename. These can be useful when developing your own functions. These filenames consist of prefix_date_time_pid_rn where pid is the process id returned by Sys.getpid and rn is a 5 digit random number. This should make tempfiles unique if created at different times and also when created in parallel processes (different pid) that use set.seed and call rasterTmpFile at the same time. It is possible, however, to create overlapping names (see the examples), which is undesirable and can be avoided by setting the prefix argument.