A function to enable using conda seamlessly with R

...README.md

• Install EVERYTHING you can with conda
• Install things you can with:
  • install.packages(, lib="")
  • install.github(, lib="")
  • biocLite(, lib="")
• Make separate local libs for different R versions
• After installing a package to a local lib, look there and see if there are dependencies you could have installed with conda.
• Or, head it off by looking at the dependencies in CRAN or Bioconductor

.Rprofile

options(repos=structure(c(CRAN="https://ftp.osuosl.org/pub/cran/")))

startCondaEnv = function(env_name, lib='/home/balter/R')
{
	cat("pointing to conda env:", env_name, "and lib location", lib, "\n")

	r_lib_path = lib
	if (env_name == "" || env_name == "base")
    {
		#print("using default base env")
		conda_lib_path = file.path('/home/balter/conda/lib/R/library')
	}else
	{
		conda_lib_path = file.path('/home/balter/conda/envs', env_name, 'lib/R/library')
	}

	#cat('conda_lib_path: ', conda_lib_path, '\n')
	
	.libPaths(new=c(conda_lib_path, r_lib_path))
	
	#cat(".libPaths():\n")
	print(.libPaths())
}


current_conda_env = Sys.getenv('CONDA_DEFAULT_ENV')
cat('current_conda_env:', current_conda_env, '\n')

current_conda_prefix = Sys.getenv('CONDA_PREFIX')
cat('current_conda_prefix:', current_conda_prefix, '\n')

if (current_conda_env != "")
{
	r_version = R.Version()
	r_version = paste0(r_version$major, '.', r_version$minor)

	if (r_version == '3.5.1')
	{
		r_lib_path = '/home/balter/R35'
	}else 
	if (r_version == '3.4.11')
	{
		r_lib_path = '/home/balter/R34'
	}else
	{
		message("no compatible lib")
		r_lib_path = ''
	}
	
	#cat("env: ", current_conda_env, ", prefix: ", current_conda_prefix, "\n")
	conda_env_lib = file.path(current_conda_prefix,'lib/R/library')
	startCondaEnv(current_conda_env, lib=r_lib_path)
}else
{
	print("no conda env")
}

startCondaEnv.R

startCondaEnv = function(env_name, lib='/home/balter/R')
{
	cat("pointing to conda env:", env_name, "and lib location", lib, "\n")

	r_lib_path = lib
	if (env_name == "" || env_name == "base")
    {
		#print("using default base env")
		conda_lib_path = file.path('/home/balter/conda/lib/R/library')
	}else
	{
		conda_lib_path = file.path('/home/balter/conda/envs', env_name, 'lib/R/library')
	}

	#cat('conda_lib_path: ', conda_lib_path, '\n')
	
	.libPaths(new=c(conda_lib_path, r_lib_path))
	
	#cat(".libPaths():\n")
	print(.libPaths())
}