[R] meta-question about R

mark m.roth at 5-cent.us
Thu Apr 24 12:52:25 CEST 2014

On 04/23/14 23:22, William Dunlap wrote:
> 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.

You don't seem to understand what I'm asking. I have zero intention of 
deleting those files. I'm sure that my user's long-running job is creating 
them. What I'm asking is if ANYONE HERE knows if there is some configuration 
file, or command inside R, that would tell R, whatever package it's using (I 
assume that all packages inherit from the top-level process), when it creates 
files in /dev/shm, to name them something that I can use with wildcards in 
rkhunter's configuration file so that rkhunter ignores them.

>> -----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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>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.

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