RE: Rcpp alongside NONMEM

From: [email protected] [mailto:[email protected]] On Behalf Of Itziar Irurzun Arana Sent: Thursday, November 03, 2016 10:49 AM To: Smith, Mike K Cc: [email protected] 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 <[email protected]<mailto:[email protected]>>: Hi, 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!). M Mike K. Smith Pharmacometrics Pfizer WRD, Sandwich (IPC 096) Tel: +44 (0)1304 643561<tel:%2B44%20%280%291304%20643561> LEGAL NOTICE Unless expressly stated otherwise, this message is confidential and may be privileged. It is intended for the addressee(s) only. Access to this e-mail by anyone else is unauthorised. If you are not an addressee, any disclosure or copying of the contents of this e-mail or any action taken (or not taken) in reliance on it is unauthorised and may be unlawful. If you are not an addressee, please inform the sender immediately. Pfizer Limited is registered in England under No. 526209 with its registered office at Ramsgate Road, Sandwich, Kent CT13 9NJ -- Itziar Irurzun Arana, PhD Student Department of Pharmacy and Pharmaceutical Technology School of Pharmacy, University of Navarra Pamplona, Spain