Question Re Calling nmfe7 from R

Dear NONMEM users, I recently have NONMEM 7.1.0 upgraded to 7.1.2, which only worked in Intel Fortran compiler, but not in DOS. When I tried to call nmfe7 from R, it apparently called DOS command and failed to run. Is there a way to link nmfe7 to Intel, instead of DOS? I've been waiting for an answer for my IT rep for two weeks and am wondering if I can get some guidance from our discussion group. Best regards, Shelley ======================================== Xiao Hu (Shelley), Ph.D. Senior Scientist, Clinical Pharmacology and Pharmacometrics Biogen Idec, Inc. 14 Cambridge Center Cambridge, MA 02142

Shelley, You may want to consider the R package (MIfuns), developed and released by Metrum Institute. It is available on CRAN (R package repository) and via googlecode ( http://code.google.com/p/mifuns/). Using this package along with the free NONMEM installer (NMQual), also available via googlecode ( http://code.google.com/p/nmqual/) , will allow you to call nonmem from R and also provides a complete set of R functions for performing analyses, preparing data sets, generating and analyzing bootstraps, and generating post analyses tables and figures. It is more than just running NONMEM from R so you will likely find it helpful in the other aspects of data prep and modeling I just mentioned. Regards, Bill

I think the real underlying issue is that the system environment variables have not been set for Intel Fortran and Microsoft Visual Studio. The Intel build environment window is being used to run NONMEM so R cannot call NONMEM (whether it is just a run or any function of MIfuns). The NONMEM release CD contains a document that describes how to set environment variables for Intel Fortran and Microsoft Visual Studio (NONMEM-PDx-Pop-Support.pdf). Then R or R/MIfuns will be able to call NONMEM. William J. Bachman, Ph.D. Director, Pharmacometrics R&D Icon Development Solutions 6031 University Blvd., Suite 300 Ellicott City, MD 21043 Office 215-616-8699 [email protected]

Shelley, Your question is not very clear. If you run NONMEM using Intel Software Development Tools -> Intel Fortran Compiler -> Fortran Build Environment .. window, this window has all necessary environment variables set. You need to have those variables set globally to be able to run NONMEM from R. Assuming you work on Windows, you can use Control Panel -> System -> Advanced System Settings -> Enviroment Variables to see and set environment variables globally. To see all environment variables that are set in Fortran Build Environment window, type SET in that window, or type SET > temp.txt to have all the variables be printed to the file temp.txt. Regards, Katya Ekaterina Gibiansky, Ph.D. CEO&CSO, QuantPharm LLC Web: www.quantpharm.com Email: EGibiansky at quantpharm.com Tel: (301)-717-7032 On May 4, 2011, at 11:50 AM, Xiao Hu wrote: Dear NONMEM users, I recently have NONMEM 7.1.0 upgraded to 7.1.2, which only worked in Intel Fortran compiler, but not in DOS. When I tried to call nmfe7 from R, it apparently called DOS command and failed to run. Is there a way to link nmfe7 to Intel, instead of DOS? I've been waiting for an answer for my IT rep for two weeks and am wondering if I can get some guidance from our discussion group. Best regards, Shelley ======================================== Xiao Hu (Shelley), Ph.D. Senior Scientist, Clinical Pharmacology and Pharmacometrics Biogen Idec, Inc. 14 Cambridge Center Cambridge, MA 02142

Dear all, thank you all for your valuable input! I'm gladly reporting back that the problem was resolved. I'd like to give more background information since I wasn't clear on what I was doing and what type of error message I received. Here's more details. Background: I need to call NONMEM from R because of the need to automate procedures involving NONMEM runs and sequential data formatting, such as bootstrap for sequential PK/PD analysis. NOMMEM is called in R by the following command: system('nmfe7.bat control3 control3.res') After my NONMEM7.1.2 upgrade, I got 'ifort does not exist' type of error message, when I opened a command window by 'run cmd' from the start menu, or from Command Prompt, or call NONMEM from R like I did before. But if I opened a command window by Start menu > All Programs > Intel(R) Software Development Tools > Intel(R) Visula Fortran Compiler Professional 11.1.048 > Fortran Buid Environment for applications running on IA-32 , NONMEM runs OK. Resolution: Following Bill's suggestion, I located the NONMEM-PDx-Pop-support.pdf file from the NM712Upgrade directory, and fixed the system environment variables. Now I'm able to run NONMEM in both DOS command window and R. Best regards, Shelley ======================================== Xiao Hu (Shelley), Ph.D. Senior Scientist, Clinical Pharmacology and Pharmacometrics Biogen Idec, Inc. 14 Cambridge Center Cambridge, MA 02142 "Bachman, William" <[email protected]> Sent by: [email protected] 04-May-2011 01:14 PM Message Size: 15.4 KB To "Bill Knebel" <[email protected]>, "Xiao Hu" <[email protected]> cc <[email protected]> Subject RE: [NMusers] Question Re Calling nmfe7 from R I think the real underlying issue is that the system environment variables have not been set for Intel Fortran and Microsoft Visual Studio. The Intel build environment window is being used to run NONMEM so R cannot call NONMEM (whether it is just a run or any function of MIfuns). The NONMEM release CD contains a document that describes how to set environment variables for Intel Fortran and Microsoft Visual Studio (NONMEM-PDx-Pop-Support.pdf). Then R or R/MIfuns will be able to call NONMEM. William J. Bachman, Ph.D. Director, Pharmacometrics R&D Icon Development Solutions 6031 University Blvd., Suite 300 Ellicott City, MD 21043 Office 215-616-8699 [email protected]