Merge pull request #91 from dieterich-lab/bugfix/r_depdendencies_fail_with_r4

Fix and clarification for the R dependencies

Author: tjakobi

docs/Installation.rst

@@ -19,12 +19,12 @@ The default installation will install everything needed to run circtools *except
 
 .. code-block:: bash
 
-    pip3 install circtools --user # does not require root access, installation to local user directory
+    pip3 install circtools --user
 
-.. code-block:: bash
-
-    pip3 install circtools # will require root access and globally install circtools
+Please note:
 
+* The required R libraries will be installed in the default location in your home directory - unless you set enviromnet variable $R_LIBS_USER.
+* In case want to install globally or into a dedicated 'venv' drop the --user option.
 
 Installation from GitHub
 --------------------------

scripts/install_R_dependencies.R

@@ -49,13 +49,15 @@ options(repos = c(CRAN = "https://cran.uni-muenster.de/"))
 # check if devtools is already installed
 pkgs <- pkgs[!pkgs %in% installed.packages()[,1]]
 
-print("R minor version:")
+minorVersion <- as.numeric(strsplit(version[['minor']], '')[[1]][[1]])
+majorVersion <- as.numeric(strsplit(version[['major']], '')[[1]][[1]])
 
-print(as.numeric(strsplit(version[['minor']], '')[[1]][[1]]) )
-
-# new installer caller for R >3.6.0
-if (as.numeric(strsplit(version[['minor']], '')[[1]][[1]]) >= 6){
+print(paste("R version: ", majorVersion, ".", minorVersion, sep=""))
 
+if (
+    majorVersion >= 4
+    || ( majorVersion == 3 && minorVersion >= 6 )
+){
     if (!requireNamespace("BiocManager", quietly = TRUE))
         install.packages("BiocManager")