Error in example due to incompatibility with macOS sandboxing

[barracuda156]

* checking examples ... ERROR
Running examples in ‘sfsmisc-Ex.R’ failed
The error most likely occurred in:

> ### Name: Sys.ps
> ### Title: Return Process Status (Unix 'ps') Information
> ### Aliases: Sys.ps Sys.sizes
> ### Keywords: utilities
> 
> ### ** Examples
> 
> (.pid <- Sys.getpid()) ## process ID of current process
[1] 89213
> Sys.sizes(.pid)
Warning in Sys.ps.cmd() :
  Unknown OS [Operating System]; 'ps' may not be compatible
Warning in Sys.ps.cmd() :
  Unknown OS [Operating System]; 'ps' may not be compatible
Warning in Sys.ps(process, c("rss", "vsz")) :
  Dropping invalid field names rss
sh: /bin/ps: Operation not permitted
Warning in system(cmd, intern = !usefile) :
  running command 'ps -p 89213 -o vsz ' had status 126
Error in Sys.ps(process, c("rss", "vsz")) : 
  call returned less than two lines:
Calls: Sys.sizes -> Sys.ps
Execution halted

[barracuda156]

This happens because macOS sandboxing forbids execution of /bin/ps.

[mmaechler]

I don't have direct access to a Mac and the Macbuilder does I think work, i.e., is not "sandboxing".
Do you know on how to find out in R if it is running "sandboxed" in this way?

What does

file.access(mode = 1, Sys.which("ps"))

give you on such a sandboxed mac ?

[barracuda156]

@mmaechler

> file.access(mode = 1, Sys.which("ps"))
/bin/ps 
      0

We have a solution in Macports for such cases, and it works for sfsmisc, but it is Macports-specific (added into portfile, solves the problem):

pre-test {
    # Example uses /bin/ps, which is forbidden by sandboxing.
    append portsandbox_profile " (allow process-exec (literal \"/bin/ps\") (with no-profile))"
}

[mmaechler]

> file.access(mode = 1, Sys.which("ps"))
/bin/ps 
      0

Hmm, the above says that /bin/ps does have execute permission...
So it seems to me that macOS is "lying" because you tell me the later /bin/ps is not allowed to execute.

Can you think of another way I can check on macOS, using R's system() or system2() if necessary,
if Sys.which("ps") will be working?

Of course, in the worst case, I probably should use something like try(system(....)) and see if it gives an error or not.
?

[mmaechler]

@barracuda156 : Can you tell me how this (replacing the current function in pkg sfsmisc) works:

Sys.ps.cmd <- function() {
  sys <- (si <- Sys.info())[["sysname"]]
  if(sys == "Linux") {
    s.rel <- si[["release"]] ## 2013-7: Kurt sees s.rel <- "3.9-1-amd64"
    rel <- c(as.integer(strsplit(s.rel,"[[:punct:]]")[[1]][1:2]) %*% c(1000,1))
    if(is.na(rel)) rel <- 3000
    if(rel >= 2006) "/bin/ps w" ## Linux kernel >= 2.6 (this is true for Ubuntu!)
    else if(rel >= 2002) "/bin/ps --width 1000" ## Linux >= 2.2
    else struct("/bin/ps w", type="BSD")
  }
  else if(sys == "SunOS") "/usr/bin/ps"
  else if(sys == "Darwin") { # macOS
    cmd <- struct("/bin/ps w", type="Darwin/macOS")
    ## test if it *works* (to some extent) {"sandboxed" did not allow /bin/ps to run}
    tmp <- tryCatch(u.sys(cmd, " | grep 'grep'"), error=identity)
    if(!inherits(tmp, "error"))
        cmd
    else
        stop(cmd," is not working: ", conditionMessage(tmp))
  }
  else {
    warning("Unknown OS [Operating System]; 'ps' may not be compatible")
    "ps"
  }
}

[mmaechler]

I will close this as "fixed" soon, as I did not get any reply from @barracuda156 about the above fix.