Taking a look into this now, this is mostly me leaving breadcrumbs to find later...
Paths are also described in Makeconf (and actually multiple files in etc), here:
Should think about packaging up things that aren't included but sometimes used by R (TCLTK) with R.
TCLTK_LIBS is in Makeconf, as is JAVA_HOME
potential issue:
# R was configured using the following call
# (not including env. vars and site configuration)
# configure 'CC=clang' 'CXX=clang++' 'OBJC=clang' 'CFLAGS=-Wall -g -O2' 'CPPFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include' 'CXXFLAGS=-Wall -g -O2' 'OBJCFLAGS=-Wall -g -O2' 'FCFLAGS=-Wall -g -O2' 'F77FLAGS=-Wall -g -O2' '--enable-memory-profiling' '--x-libraries=/opt/X11/lib' '--enable-R-framework' 'PKG_CONFIG_PATH=/usr/lib/pkgconfig:/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig'