Re: Failure to execute NONMEM from R
I believe the problem is actually that is cross referenced
http://discuss.go-isop.org/t/psn-execute-failed-to-start-when-called-from-rstudio/1119
It
is not a path issue
Mike and I have had a small amount of offline exploration and can confirm
it a pervasive issue with NM74 being called from Rstudio. This is not just
PsN, I also use a separate language (go) to manage the nmfe commands and
invoking that from Rstudio via system2/processx/sys all fails in the same
fashion. At this point, I believe it is likely a permissions issue, but I
am unsure of if the (primary) culprit is nonmem or Rstudio.
We will need to get Bob's input whether there was a change in the mechanics
of how nonmem is invoked from 73 --> 74 to hopefully narrow the surface
area of what could be causing the problem.
Quoted reply history
On Wed, Dec 20, 2017 at 10:47 PM HUI, Ka Ho <[email protected]>
wrote:
> Thanks for attending the problem, Bill.
>
>
>
> Exactly which path should I be looking for? Am I to check if the desired
> path exists in the list or not?
>
> I tried adding the paths for NONMEM, PsN, R and Rstudio into the list and
> executed commands in R again – nothing has changed so far. Any idea?
>
>
>
> Thanks,
>
> Matthew
>
>
>
> *From:* Bill Denney [mailto:[email protected]]
> *Sent:* Thursday, December 21, 2017 11:11 AM
> *To:* HUI, Ka Ho <[email protected]>
> *Cc:* [email protected]
> *Subject:* Re: [NMusers] Failure to execute NONMEM from R
>
>
>
> Hi Matthew,
>
>
>
> Since everything is working when run directly from the command line (cmd),
> I would guess that it's something like a path issue.
>
>
>
> Check your path at the command prompt (type "path") and in RStudio
> ("Sys.getenv("PATH")").
>
>
>
> Thanks,
>
>
>
> Bill
>
>
> On Dec 20, 2017, at 21:54, HUI, Ka Ho <[email protected]>
> wrote:
>
> Dear NMusers,
>
>
>
> Recently I need to execute NONMEM 7.4 from Rstudio terminal. I have tried
> the following scripts:
>
> 1. `system2(“execute FIT_01.mod”)` #Through
> PsN, using `system2`
> 2. `shell(“execute FIT_01.mod”)`
> #Through PsN, using `shell`
> 3. `write(“execute FIT_01.mod”, “FIT_01.bat”)`
> `shell(“FIT_01.bat”)`
> #Through PsN, using `shell` to call a batch file
> 4. `write(“execute FIT_01.mod”, “FIT_01.bat”)`
> `shell.exec(“FIT_01.bat”)`
> #Through PsN, using `shell.exec` to call a batch file
> 5. The above commands, but call through C:/nm74g64/run/nmfe74.bat
> directly
>
>
>
> The above were also tested using the test dataset `CONTROL5`
>
>
>
> Results:
>
> 1. gave me the `running command '"execute FIT_01.mod"' had status 127`
> warning without any execution
>
>
>
> (2)-(4) gave me the following messages:
>
> Starting 1 NONMEM executions. 1 in parallel.
> S:1 ..
> All executions started.
> Starting NMTRAN
> NMtran failed. There is no output for model 1. Contents of FMSG:
>
> Not restarting this model.
> F:1 ..
> execute done
>
> (5) similar to (1) but the status/error code became 107
>
>
>
> None of the above has led to a successful NONMEM run. But the above
> command lines work when outside R (i.e. through `cmd` +/- PsN)
>
> Is there anyone experiencing the same issue?
>
>
>
> System/software info:
>
> OS: Windows 10
>
> NONMEM v7.4
>
> R3.4.2
>
> Rstudio v1.1.383
>
>
>
> Best regards,
>
> *Matthew Hui*
>
> PhD Student
>
> School of Pharmacy
>
> *Faculty of Medicine*
>
> *The Chinese University of Hong Kong*
>
>
>
>