JAVA_CPPFLAGS == ~autodetect~
This is happening to me with R 2.9 and 2.8 on jaunty. whit at spartan:~$ R CMD config JAVA_CPPFLAGS ~autodetect~ whit at spartan:~$ I can see the "~autodetect~" strings here: https://svn.r-project.org/R/trunk/m4/java.m4 but JAVA_LIBS ends up being the correct value in my installation: whit at spartan:~/dvl/R.packages$ R CMD config JAVA_LIBS -L/usr/lib/jvm/java-6-openjdk/jre/lib/amd64/server -L/usr/lib/jvm/java-6-openjdk/jre/lib/amd64 -L/usr/lib/jvm/java-6-openjdk/jre/../lib/amd64 -L/usr/local/lib64 -L/usr/java/packages/lib/amd64 -L/usr/lib64 -L/lib64 -L/lib -L/usr/lib -ljvm whit at spartan:~/dvl/R.packages$ R CMD config JAVA_CPPFLAGS ~autodetect~ whit at spartan:~/dvl/R.packages$ -Whit