[R] meta-question about R

William Dunlap wdunlap at tibco.com
Thu Apr 24 05:22:01 CEST 2014

Aren't those files support for named semaphores (made with sem_open())?
Packages like BH and RSQLite contain calls to sem_open.   Is your long-running
R process using such a package?

I don't think you would want to delete those files, but perhaps you can look into
whatever R package creates them and see if you can modify the code to give
them better names and then add those names to rkhunter's whitelist.

Bill Dunlap
TIBCO Software
wdunlap tibco.com

> -----Original Message-----
> From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On Behalf
> Of Jim Lemon
> Sent: Wednesday, April 23, 2014 2:18 PM
> To: m.roth at 5-cent.us
> Cc: r-help at r-project.org
> Subject: Re: [R] meta-question about R
> 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
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