CRAN macOS Deployment

Considerations of additional tools and libraries that are required for some packages outside of the recipes setup.

• zlib.pc - some .pcs (at least cairo and libpng) require configuration files for existing system libraries such as libz or else pkg-config will fail. We are currently using https://mac.r-project.org/libs-4/pkgconfig-system-stubs-darwin13.tar.gz Maybe we should create a recipe that synthesizes this?

• JAGS - https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Mac%20OS%20X/

• iODBC - requires headers from https://opensource.apple.com/tarballs/iodbc/iodbc-42.6.tar.gz - libraries are already present in the system. There are two sets - the ones in mac have an extra iODBC prefix but packages like RODBC don't work with them unless they are sym-linked one level down like the regular ones.

• BioConductor - some packages rely on BioConductor. We maintain a separate library with BioC package built using the same process.

• Java configuration - using Apple stubs (in /usr/bin) leads to JAVA_HOME pointing to JRE instead of JDK which breaks javah as the stub is using JAVA_HOME to find the actual binary which is not present in the JRE. Safest way is to re-configure R to use the JDK path, i.e.

  JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_241.jdk/Contents/Home R CMD javareconf