RE: [NMusers] Failure to execute NONMEM from R

From: Bauer, Robert <Robert.Bauer_at_iconplc.com>
Date: Tue, 2 Jan 2018 18:58:49 +0000

I’ll be happy to determine if there is a difference between nm7.3 and nm7.4 in this matter. I am unable to replicate the issues in my environment, so I would like to know from Devin if the exact same gfortran (and which version) and R were used in comparing nonmem 7.3 versus nonmem 7.4?

Robert J. Bauer, Ph.D.
Senior Director
Pharmacometrics R&D
ICON Early Phase
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Robert.Bauer_at_iconplc.com<mailto:Robert.Bauer_at_iconplc.com>
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From: owner-nmusers_at_globomaxnm.com<mailto:owner-nmusers_at_globomaxnm.com> [mailto:owner-nmusers_at_globomaxnm.com] On Behalf Of Smith, Mike K
Sent: Tuesday, January 02, 2018 2:52 AM
To: HUI, Ka Ho; Tarj Sahota; Devin Pastoor
Cc: Bill Denney; nmusers_at_globomaxnm.com<mailto:nmusers_at_globomaxnm.com>
Subject: RE: [NMusers] Failure to execute NONMEM from R

Likewise, glad to report that Sys.unsetenv("GFORTRAN_STDOUT_UNIT") works. You need to submit this command (preferably at the top of an R script) each time you start R. The question remains *WHY*??? And what is different between NONMEM-7.3 and NONMEM-7.4 (to Devin's point).

I've managed to get NONMEM-7.4 to run using system, system2 and shell.
system2(command = 'c:/nm74g64/run/nmfe74.bat',
args = c('run1.mod',
'run1.lst'),
stdout = TRUE, stderr = TRUE,wait = TRUE)

cmd <- paste("c:/nm74g64/run/nmfe74.bat run1.mod run1.lst")
system( command = cmd)

or using PsN Execute:
system2(command = 'c:/strawberry/perl/bin/execute-4.7.9.bat',
args = c('run1.mod', '-nm_version="nonmem-7.4"'),
stdout = TRUE, stderr = TRUE,wait = TRUE)

-----Original Message-----
From: owner-nmusers_at_globomaxnm.com<mailto:owner-nmusers_at_globomaxnm.com> [mailto:owner-nmusers_at_globomaxnm.com] On Behalf Of HUI, Ka Ho
Sent: 22 December 2017 02:27
To: Tarj Sahota; Devin Pastoor
Cc: Bill Denney; nmusers_at_globomaxnm.com<mailto:nmusers_at_globomaxnm.com>
Subject: [EXTERNAL] RE: [NMusers] Failure to execute NONMEM from R

Thanks Tarj for your advice and it works!

sys.unsetenv("GFORTRAN_STDOUT_UNIT") is the line that is needed.

Matthew

-----Original Message-----
From: Tarj Sahota [mailto:t.sahota0_at_gmail.com]
Sent: Thursday, December 21, 2017 10:18 PM
To: Devin Pastoor <devin.pastoor_at_gmail.com<mailto:devin.pastoor_at_gmail.com>>
Cc: HUI, Ka Ho <matthew.hui_at_link.cuhk.edu.hk<mailto:matthew.hui_at_link.cuhk.edu.hk>>; Bill Denney <bill_at_denney.ws<mailto:bill_at_denney.ws>>; nmusers_at_globomaxnm.com<mailto:nmusers_at_globomaxnm.com>
Subject: Re: [NMusers] Failure to execute NONMEM from R

I get the same errors as Matthew (with NM 7.4.1+gfortran on windows) - I forgot to mention that in order to get it working on my machine I also need to use shell() rather than system()/system2()/... along with Sys.unsetenv("GFORTRAN_STDOUT_UNIT"). Not sure if that helps you, but it fixes the issue with my windows machine.

Tarj.

On Thu, Dec 21, 2017 at 11:49 AM, Devin Pastoor <devin.pastoor_at_gmail.com<mailto:devin.pastoor_at_gmail.com>> wrote:
> I believe the problem is actually that is cross referenced
> http://discuss.go-isop.org/t/psn-execute-failed-to-start-when-called-f<http://discuss.go-isop.org/t/psn-execute-failed-to-start-when-called-f>
> rom-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.
>
> On Wed, Dec 20, 2017 at 10:47 PM HUI, Ka Ho
> <matthew.hui_at_link.cuhk.edu.hk<mailto:matthew.hui_at_link.cuhk.edu.hk>>
> 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:bill_at_denney.ws]
>> Sent: Thursday, December 21, 2017 11:11 AM
>> To: HUI, Ka Ho <matthew.hui_at_link.cuhk.edu.hk<mailto:matthew.hui_at_link.cuhk.edu.hk>>
>> Cc: nmusers_at_globomaxnm.com<mailto:nmusers_at_globomaxnm.com>
>> 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 <matthew.hui_at_link.cuhk.edu.hk<mailto:matthew.hui_at_link.cuhk.edu.hk>>
>> wrote:
>>
>> Dear NMusers,
>>
>>
>>
>> Recently I need to execute NONMEM 7.4 from Rstudio terminal. I have
>> tried the following scripts:
>>
>> `system2(“execute FIT_01.mod”)` #Through PsN,
>> using `system2`
>> `shell(“execute FIT_01.mod”)` #Through
>> PsN, using `shell`
>> `write(“execute FIT_01.mod”, “FIT_01.bat”)` `shell(“FIT_01.bat”)`
>> #Through PsN, using `shell` to call a batch file `write(“execute
>> FIT_01.mod”, “FIT_01.bat”)` `shell.exec(“FIT_01.bat”)` #Through PsN,
>> using `shell.exec` to call a batch file The above commands, but call
>> through C:/nm74g64/run/nmfe74.bat directly
>>
>>
>>
>> The above were also tested using the test dataset `CONTROL5`
>>
>>
>>
>> Results:
>>
>> 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
>>
>>
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Received on Tue Jan 02 2018 - 13:58:49 EST

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