Known Issues

17 Oct 2018

RAnEn Installation Failed on Mac OS Mojave

If you are installing RAnEn on Mac OS Mojave and you receive the following error messages:

* installing to library ‘/Users/wuh20/Library/R/3.5/library’
* installing *source* package ‘RAnEn’ ...
Checking whether R_HOME is already set? R_HOME = /usr/local/Cellar/r/3.5.1/lib/R
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... configure: error: in `/Users/wuh20/github/AnalogsEnsemble/RAnalogs/sea2019/RAnEn':
configure: error: cannot run C++ compiled programs.
If you meant to cross compile, use `--host'.
See `config.log' for more details
ERROR: configuration failed for package ‘RAnEn’
* removing ‘/Users/wuh20/Library/R/3.5/library/RAnEn’
* restoring previous ‘/Users/wuh20/Library/R/3.5/library/RAnEn’

It is highly possible that you need to update your Xcode and run some configuration setup. The two steps should fix this:

  • Open Xcode and it will probably notify you and ask whether you want to update the version.
  • You should find and run the following package file to set up the environment properly. 
    /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg

You should be good to go for the installation. There is also a ticket for this issue for more details.

NetBeans does not recognize the executables after building the C++ programs.

With Linux, by default, the GCC compiler will compile executable shared libraries that act like executables to a user, but NetBeans will not recognize this type. To resolve this issue with NetBeans, add -no-pie to the CMAKE_CXX_FLAGS or/and CMAKE_C_FLAGS depending on which compiler is used.

Some references include Q&A 1; Q&A 2; GCC Options for linking.

RAnEn is built with GNU compiler and CMake process. But it shows up not supporting OpenMP.

If you have run the roxygen command before the make process, the library will not be supporting OpenMP. Make sure that before your CMake’s runtime, you have a clean directory under RAnalogs/RAnEn/src. An easy way to do this is to run make clean-roxygen, and repeat the build and make process.

Linking errors when building the C++ library during the second time.

If you have successfully built the C++ library before and when you modifed any files or did a git pull, you found the make process failed. This can be caused by using the old dependencies previously built and stored in the dependency/ directory. This typically happens when you’ve also changed the compiler. An easy workaround for this is to remove all the build files, include the directories dependency\, output\, and build\, and start from scratch with a clean directory.

How do I make sure whether OpenMP is supported.

If you are using the RAnEn library, you can check the automatic message printed on loading the library. If it does not say “OpenMP is not supported”, then it is supported.

If you are using the C++ programs, you need to first build tests by specifying -DCMAKE_BUILD_TESTS=ON to cmake. Then after the program compiles, there is a test at AnalogsEnsemble/output/test/runAnEn. If you see OpenMP is supported and the number of threads in the standard output message after running the test executable, OpenMP is correctly configured. You can also try to modify the system environment variable OMP_NUM_THREADS and run the test executable again, see how the system environment variable affects the number of threads being created.

Compilation failure on Windows

Please see the article.

Dynamic linking error on MacOS.

Sometimes when I run the test for AnEnIO and I will see the following error.

testAnEnIO::testReadObservationFile
dyld: lazy symbol binding failed: Symbol not found: __ZN6netCDF6NcFileC1ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEENS0_8FileModeE
  Referenced from: /Users/wuh20/github/AnalogsEnsemble/output/lib/libAnEnIO.dylib
  Expected in: /usr/local/lib/libnetcdf-cxx4.1.dylib

dyld: Symbol not found: __ZN6netCDF6NcFileC1ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEENS0_8FileModeE
  Referenced from: /Users/wuh20/github/AnalogsEnsemble/output/lib/libAnEnIO.dylib
  Expected in: /usr/local/lib/libnetcdf-cxx4.1.dylib

Abort trap: 6

I can normally get away from this by specifying -DCMAKE_MACOSX_RPATH=ON for cmake and then recompile everything.

 issue

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