[R] meta-question about R

[Jim Lemon]

On 04/23/2014 11:58 PM, m.roth at 5-cent.us wrote:
> This really isn't about R, but configuring R. We're running R 3.0.2-1, the
> current default package, on CentOS 6.5 On a long-running job, R is
> creating files in /dev/shm: each set of three files are named (8 hex
> digits)-(4 hex digits)-(4 hex digits)-(4 hex digits)-(12 hex digits), and
> then sem.(same as the name)_counter_mutex, and (same as the name)_counter.
>
> For example,
> 156d23b0-9e67-46e2-afab-14a648252890
> 156d23b0-9e67-46e2-afab-14a648252890_counter
> sem.156d23b0-9e67-46e2-afab-14a648252890_counter_mutex
>
> Is there some way to configure R to add a prefix, say, to each of these
> files? We're running rkhunter (rootkit hunter) for security, and it
> complains about suspicious files, and I'd like some way to be able to tell
> it to, say, ignore R_temp.whatever....
>
Hi mark,
I assume that the problem is to identify the files in /dev/shm, not to 
simply change your R code to tack the prefix onto the files as it 
produces them. As your hexadecimal digits are probably randomly 
generated, the solution may be to identify all the files that have 
"_counter_mutex" in the name, then chip off the appropriate bits to get 
the troublesome first name.

filenames<-list.files(pattern="_counter_mutex")
# function to return the two other filenames
strip_fn<-function(x) {
  f2<-substr(x,5,nchar(x)-6)
  f1<-substr(f2,1,nchar(f2)-8)
  return(c(f1,f2))
}
# get all the filenames
filenames<-c(filenames,unlist(sapply(filenames,strip_fn)))
# stick on the prefix
newfilenames<-paste("R_temp",filenames,sep=".")
# create the commands
fnmove<-paste("mv",filenames,newfilenames)
# move the filenames
for(fn in 1:length(fnmove)) system(fnmove[fn])

Warning - I haven't tested the last bit of this, but it should work. 
There is probably some really neat string of heiroglyphs in a regular 
expression that will do this as well.

Jim