How to install
To install LakeEnsemblR, first install the packages it relies on, as described at https://github.com/aemon-j/LakeEnsemblR#Installation
If you get error converted from warning messages while
installing the packages, this means that the version of LakeEnsemblR was
built with a newer R version than yours. To avoid this issue, either
install the latest R version, or run the line
Sys.setenv("R_REMOTES_NO_ERRORS_FROM_WARNINGS" = "true")
before installing the packages.
If you see
Downloading GitHub repo aemon-j/LakeEnsemblR@main. Error in utils::download.file(... Cannot open URL ...:
there is a migration from the word “master” to “main” for the major
branch of a repository, and the R function you use to install the
package - e.g. devtools::install_github - might use a different name.
Change the ref argument in the function to the correct name
of the branch you want to install.
Installing LakeEnsemblR on Mac or Linux
While we have made an effort to provide executables and supporting libraries for Windows, Mac, and Linux operating systems, the different builds of MacOS and Linux can result in unexpected errors when trying to run the models. To mediate these issues, we would first like to point you to the following script, that tests whether all models are working correctly (Note that you only need to install the model packages that you plan to use): https://github.com/aemon-j/LakeEnsemblR/blob/main/inst/extdata/test_model_packages.R
If some of the model packages do not work on your Mac or Linux PC, we propose the fixes below. If you are still experiencing problems afterwards, please start an Issue on this Github page.
Mac
Firstly, the model packages have been built in and tested for only MacOS Catalina. MacOS Mojave may not be able to run LakeEnsemblR.
If you experience problems on macOS with error messages like
dyld: Library not loaded, you can try to install the
missing libraries, e.g. by using ‘brew’. Install brew in the terminal:
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install.sh)"
- Install the missing libraries and you will need to update your current
versions of gfortran, netcdf and gc: brew install gcc,
brew install netcdf, brew install gc - check
if everything is working: gcc -v and
gfortran --version which should give you
"Apple clang version 12.0.0 (clang-1200.0.32.2)" and
"GNU Fortran (Homebrew GCC 10.2.0) 10.2.0", respectively -
if you still experience library problems, you can continue installing
the missing dependencies using ‘brew’”
(e.g. dyld: Library not loaded: /usr/local/opt/fontconfig/lib/libfontconfig.1.dylib
-> brew install fontconfig)
Linux
If you get error messages related to shared libraries,
libnetcdf, or similar, go to the directory where your
installed R packages are stored. For GLM3r, GOTMr, FLakeR, and SimstratR
you need to delete the libm.so.6 file and for GLM3r you
need to copy the libnetcdf.so.13 and two
libhdf_5... files from the GOTMr
inst/extbin/nix/ folder to the GLM3r
inst/extbin/nix/ folder.
Docker
You can also use docker to run LakeEnsemblr, see this article.