configure: error: cannot find JDK header files

[jackckoch]

I am trying to install beagle so that I can install MrBayes on my mac. When I run './configure' I get the following error:
checking if javac works... yes
checking for javac... /usr/bin/javac
checking symlink for /usr/bin/javac... /System/Library/Frameworks/JavaVM.framework/Versions/Current/Commands/javac
checking for /System/Library/Frameworks/JavaVM.framework/Versions/Current/Headers/jni.h... no
checking for /System/Library/Frameworks/JavaVM.framework/Versions/include/jni.h... no
configure: error: cannot find JDK header files

I have found /jni.h in: /Library/Java/JavaVirtualMachines/jdk-9.0.4.jdk/Contents/Home/include

There is no directory for /Headers or /include in the JavaVM.frameworks/Versions/Current or JavaVM.frameworks/Versions/ where the configure is looking. I cannot make these directories there, so I cannot copy the /jni.h file that I found there.

Any ideas?

[kusalananda]

When compiling Beagle for MrBayes, you don't need JDK (MrBayes does not use the Java Beagle library). Just configure Beagle with --without-jdk.

[kusalananda]

We (the MrBayes devs) have also noticed that we have to use ./configure LDFLAGS=-Wl,-rpath=prefix/lib when we configure the Beagle libraries on some Unix systems (where prefix is the installation prefix, for example /usr/local). Otherwise Beagle won't find its plugin libraries.

[J-Moravec]

The other solution would be to set your JAVA_HOME environment variable by putting:
export JAVA_HOME=$(/usr/libexec/java_home) into your .profile
see:
https://www.mkyong.com/java/how-to-set-java_home-environment-variable-on-mac-os-x/