I could solve the problem myself after testing the configure file not via RStudio's "Install"-function but just running it in terminal with sh ./configure - this shows there are problems reading the file. A search on the web hints towards file encoding problems: Bash script prints "Command Not Found" on empty lines. The command bash -x configure basically shows, that there are wrong encodings within the file. This happened most likely because of copy pasting or creating the configure file in Windows, introducing wrong end-of-line signs, detectable with the command above as '/r'.