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RE: Failure to execute NONMEM from R

From: HUI, Ka Ho <matthew.hui>
Date: Thu, 21 Dec 2017 03:41:51 +0000

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?


From: Bill Denney [mailto:bill
Sent: Thursday, December 21, 2017 11:11 AM
To: HUI, Ka Ho <matthew.hui
Cc: nmusers
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")").



On Dec 20, 2017, at 21:54, HUI, Ka Ho <matthew.hui
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`


  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
Rstudio v1.1.383

Best regards,
Matthew Hui
PhD Student
School of Pharmacy
Faculty of Medicine
The Chinese University of Hong Kong

Received on Wed Dec 20 2017 - 22:41:51 EST

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