"It is a distutils installed project ..." when calling install_mlflow() - r

Question

When install_mlflow() is called to install mlflow for R, the following error is encountered.
Attempting uninstall: certifi
Found existing installation: certifi 2018.4.16
ERROR: Cannot uninstall 'certifi'. It is a distutils installed project and thus we cannot accurately determine which files belong to it which would lead to only a partial uninstall.
Note: The above is using miniconda installed using install_miniconda() command.
P.S. Posting question & answer for everyone's benefit (I spend 2 days on this).

Answer 1

Root cause:
The function install_mlflow()calls reticulate::conda_install() function with the default value for pip_ignore_installed which turns out to be FALSE.
💡 Hint: Click any function in the script while holding down cmd key to view the source code.
Workaround:
You can work around this issue by calling the function with pip_ignore_installed = TRUE. I've recreated the install_mlflow() function in the below script for convenience.
The script also checks and installs miniconda if not installed.
library(reticulate)
library(mlflow)
# Installing minicoda if not installed
if (!dir.exists(miniconda_path()))
install_miniconda(path = miniconda_path(), update = TRUE, force = TRUE)
# install_mlflow() # This doesn't work so we use the alt fn below.
install_mlflow_alt <- function() {
mlflow_version <- utils::packageVersion("mlflow")
packages <- c(paste("mlflow", "==", mlflow_version, sep = ""))
# Geting mlflow conda bin
conda_home <- Sys.getenv("MLFLOW_CONDA_HOME", NA)
conda <- if (!is.na(conda_home)) {
paste(conda_home, "bin", "conda", sep = "/")
} else {
"auto"
}
conda_try <- try(conda_binary(conda = conda), silent = TRUE)
if (class(conda_try) == "try-error") {
msg <- paste(attributes(conda_try)$condition$message,
paste(" If you are not using conda, you can set the environment variable",
"MLFLOW_PYTHON_BIN to the path of your python executable."),
sep = "\n")
stop(msg)
}
conda <- conda_try
# Installing mlflow
mlflow_conda_env_name <- paste("r-mlflow", mlflow_version, sep = "-")
conda_install(packages, envname = mlflow_conda_env_name,
pip = TRUE, conda = conda, pip_ignore_installed = TRUE)
}
# NOTE: Run the following command in terminal (use pip3 for python 3)
# before calling the install_mlflow_alt() function below
# paste("pip install -U mlflow==", mlflow:::mlflow_version(), sep="")
install_mlflow_alt()