Re: [NMusers] Rcpp alongside NONMEM

From: Bill Denney <wdenney_at_humanpredictions.com>
Date: Thu, 3 Nov 2016 14:10:53 -0400

Hi Mike,

Similar to Itziar, I've run into near-equivalent problems. I've not
tested this as a solution, but my thought is to setup a specific batch
file that runs NONMEM for me, and at the top of the batch file it
updates the PATH variable to point to the NONMEM copy of gfortran, and
at the end, it returns the PATH to its original state.

Currently, I don't have similar problems with my Docker setup since
NONMEM and gfortran are within the Docker container and can't reasonably
interact with the outside environment.

Thanks,

Bill

On 11/3/2016 1:48 PM, Itziar Irurzun Arana wrote:
> 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", sep = "")
> gcc <- paste(path, "\\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 <mike.k.smith_at_pfizer.com
> <mailto:mike.k.smith_at_pfizer.com>>:
>
> 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

------------------------------------------------------------------------
Human Predictions Logo <http://www.humanpredictions.com>*William S.
Denney, PhD*
Chief Scientist, Human Predictions LLC
+1-617-899-8123
wdenney_at_humanpredictions.com

This e-mail communication is confidential and is intended only for the
individual(s) or entity named above and others who have been
specifically authorized to receive it. If you are not the intended
recipient, please do not read, copy, use or disclose the contents of
this communication to others. Please notify the sender that you have
received this e-mail in error by replying to the e-mail or by calling
+1-617-899-8123. Please then delete the e-mail and any copies of it.
Thank you.


Received on Thu Nov 03 2016 - 14:10:53 EDT

This archive was generated by hypermail 2.3.0 : Fri Sep 27 2019 - 16:52:26 EDT