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