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RsNLME Installation and Configuration Troubleshooting Guide

troubleshooting.Rmd

Installation Errors/Warnings in R

ERROR: compilation failed for package ‘…’

You may also see the additional error:

c:/rtools40/mingw32/bin/g++: No such file or directory

This error can occur when installing a package dependency from source. R will always attempt to install the Windows binaries first (for Windows users), but in some cases, the binaries on CRAN may have version older than the source files.

In such cases, R will prompt you with a message -

“Do you want to install from source the packages which need compilation?”

The correct option is to click No. Clicking Yes may require the additional installation of RTools to install the package successfully, if that package dependency must be compiled from source.

Note: For non-recent R versions CRAN removes binaries from the server and the only way to install the dependent package is to install it from source.

Warning in install.packages: 

Warning in install.packages :
  package ‘Certara.RSNLME’ is not available for this version of R

If you have confirmed that R >= 4.0 is installed (use the command R.Version() to check) and still receive this error, ensure that the name of the package is specified correctly.

Note: Package names are case-sensitive.

Warning in install.packages :
  unable to access index for repository https://certara.jfrog.io/artifactory/certara-cran-release-public/bin/windows/contrib/4.4

This warning implies that the R package binaries for the given OS are unavailable and can be ignored. R will subsequently install the packages from source successfully.

WARNING: RTools is required …

RTools is required to build R packages and/or compile libraries from source on Windows, however, the installation of RTools is NOT required to use RsNLME.

If this warning is received, and the packages were not successfully installed:

Option 1: Check R Library Path

Execute the following command to check the location of R libraries:

Note: If your R Library path is located on a network drive e.g., OneDrive, you may experience issues installing R packages. The solution is to create a local folder for your R libraries. Click here to learn more.

Option 2: Install missing package separately

If you’re still unable to install one or more Certara_Packages, even after confirming that your R library path isn’t on a network drive, the problem is likely indicated by an error message in your R console.

Example Error Messages:

namespace ‘rlang’ 0.4.2 is already loaded, but >= 0.4.5 is required

or

ERROR: lazy loading failed for package ‘rlang’

Troubleshooting Steps:

  1. Restart R: To ensure a clean slate, restart your R session. This will unload all currently loaded packages.

  2. Install the Package Directly: Try installing the problematic package (e.g., “rlang”) on its own using the following command in R:

  1. Reboot and Manually Remove: If the direct installation still fails:
    • Reboot your system.
    • Find the package’s folder within your R library directory (you can find this directory using the .libPaths() command in R).
    • Delete the package’s folder manually.
    • Attempt to reinstall the package.

Note: These troubleshooting steps focus on resolving issues with individual package installations. If you continue to encounter difficulties, please contact Certara support for further assistance.

Then proceed with the installation of Certara_Packages.

Installation Help for NLME Engine

The NLME Engine installer for Windows will automatically install and configure the following components:

  • MS MPI 10.0
  • GCC 8.4
  • NLME Engine 24.09.1

What if I have some components previously installed?

If you have an existing Phoenix installation, you may receive a message stating that GCC and/or MPI is already installed and configured on your system.

If the installer detects that these components are already installed, you will be prompted to skip the installation of these components.

vcruntime140_1.dll not found

DLLs (Dynamic-Link Libraries) are shared libraries in Microsoft Windows, implemented by Microsoft Corporation, and used by the NLME Engine for model execution. If you receive an error such as “vcruntime140_1.dll Not Found”, the file may be corrupted or missing from your system.

The solution is to download the Microsoft Visual C++ Redistributable packages for Visual Studio 2015, 2017, 2019, and 2022 here, installing both X86 and X64 Architecture.

Note: You will be required to restart your computer after installing Microsoft C++ Redistributable Packages

Modify/Uninstall

If you have run the NLME Engine installer previously, you will be prompted with the following options:

  • Modify Available Options
  • Repair Application
  • Uninstall

Select Modify Available Options to re-install components, or, Uninstall to remove components from system.

Check environment variables

To ensure that all components have been installed successfully, open a new session of R/RStudio and execute the following:

Sys.getenv("INSTALLDIR") # NLME Engine path
Sys.getenv("NLMEGCCDir64") # GCC path
Sys.getenv("PhoenixMSMPIDir") # MSMPI path if MSMPI was installed

If the NLME Engine installation has been successful, the above system paths should be returned.

Note: If GCC and/or MSMPI was installed by Phoenix and not using the NLME Engine installer, Sys.getenv("NLMEGCCDir64") and Sys.getenv("PhoenixMSMPIDir") will return a different folder - e.g., ‘“C:\PHSTMinGW64”’ and "C:\\Program Files (x86)\\Certara\\MPI\\". They could be used as well.

To ensure that all components have been installed successfully, open a new session of R/RStudio and execute the following:

Sys.getenv("INSTALLDIR") # NLME Engine path
Sys.getenv("PhoenixMPIDir64") # OpenMPI path if OpenMPI was installed

If the NLME Engine installation has been successful, the above system paths should be returned.

To ensure that all components have been installed successfully, open a new session of R/RStudio and execute the following:

Sys.getenv("INSTALLDIR") # NLME Engine path
Sys.getenv("PML_BIN_DIR") # Enables access to libraries compiled specifically for Ubuntu 22.04
Sys.getenv("PhoenixMPIDir64") # OpenMPI path if OpenMPI was installed

If the NLME Engine installation has been successful, the above system paths should be returned.

FAQ

Do existing Phoenix users need to install the NLME Engine?

Yes. Certara.RsNLME version 3.0.0 requires NLME-Engine-24.09.1. Existing Phoenix users must install the NLME-Engine executable, separate from NLME-Engine that is embedded in Phoenix application.

Note: Phoenix NLME-Engine is kept in a separate location and installing NLME-Engine-24.09.1 will not affect your existing Phoenix installation.

Is the Certara.NLME8 R package distributed in a Phoenix release compatible with RsNLME?

It is recommended to maintain a distinct R version (or separate R library) that ensures the version of the Certara.NLME8 package that you installed (given the installation instructions provided in your version of Phoenix) is not automatically updated when installing Certara.RsNLME.