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RE: [NMusers] Rcpp alongside NONMEM

From: Bauer, Robert <>
Date: Thu, 3 Nov 2016 18:11:07 +0000

If you have nonmem7.3 or greater, then you can fill in nmloc or nmloc.bat in the root nonmem installation directory with the gfortran path.
Then nonmem executions will rely on the location of gfortran specified in the nmloc file.
Please see section I.5 of nm730.pdf for details.

Robert J. Bauer, Ph.D.
Pharmacometrics R&D
ICON Early Phase
820 W. Diamond Avenue
Suite 100
Gaithersburg, MD 20878
Office: (215) 616-6428
Mobile: (925) 286-0769<><>

From: [] On Behalf Of Itziar Irurzun Arana
Sent: Thursday, November 03, 2016 10:49 AM
To: Smith, Mike K
Subject: Re: [NMusers] Rcpp alongside NONMEM

Hi Mike,

I had the same problem some months ago and what I finally did was to update the path environment variable for the current R session only with the following code:

    path <- "C:\\RBuildTools" #Write the path to your Rtools or RBuildTools folder
    rtools <- paste(path, "\\bin<file:///\\bin>", sep = "")
    gcc <- paste(path, "\\gcc-4.6.3\\bin<file:///\\gcc-4.6.3\bin>", sep = "")
    path <- strsplit(Sys.getenv("PATH"), ";")[[1]]
    new_path <- c(rtools, gcc, path)
    new_path <- new_path[!duplicated(tolower(new_path))]
    Sys.setenv(PATH = paste(new_path, collapse = ";"))

I always run this before using simulation tools which rely on Rcpp and it works. When you close your R session this information is lost, so you wouldn't have problems with other compilers. Then you can leave the NONMEM gfortran compiler in the first place on the PATH.

If you have more questions, don't hesitate to ask.

Itziar Irurzun

2016-11-03 17:42 GMT+01:00 Smith, Mike K <<>>:

My colleagues and I are running into problems using modelling and simulation tools which rely on Rcpp (e.g. Stan, mrgsolve, PKPDsim) alongside an existing NONMEM installation. The problem is that we have TWO versions of compilers installed – one for NONMEM and one from the Rtools set.

For NONMEM we’re using gfortran 4.5.0 installed in C:\Program Files (x86)\gfortran\libexec\gcc\i586-pc-mingw32\4.5.0. (Running Windows 8).

When Rtools installs it allows me to configure where the RBuildTools sits on the PATH, but if I put it first (as recommended) then it stops NONMEM picking up the gfortran compiler above, and NONMEM doesn’t run successfully. But if I put the RBuildTools further down the path, then it doesn’t set up c++ as a command line executable.

If anyone has experience at making these play nicely together without having to hack the PATH, I’d be really interested to hear from you. While hacking PATH variables is fine individually, it’s not a recipe that’s easily rolled out and supported across an organisation… (Although I’d still like to know how you might hack the PATH info to get this to work!).

Mike K. Smith
Pfizer WRD, Sandwich (IPC 096)
Tel: +44 (0)1304 643561<tel:%2B44%20%280%291304%20643561>
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Itziar Irurzun Arana, PhD Student
Department of Pharmacy and Pharmaceutical Technology
School of Pharmacy, University of Navarra
Pamplona, Spain
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Received on Thu Nov 03 2016 - 14:11:07 EDT

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