[cctbxbb] Build error, bootstrap.py

[Allan Lyckegaard]

Hi all,

I am trying to install cctbx on my Mac (Sierra) using bootstrap.py with my Anaconda python.

When executing 'python bootstrap.py --with-python=/Users/myuser/miniconda2/envs/python2/bin/python --builder=cctbx’ I get the following error:

/usr/bin/c++ -o dxtbx/format/boost_python/nexus_ext.o -c -DBOOST_HAS_INT128=1 -DBOOST_ALL_NO_LIB -DBOOST_PYTHON_MAX_BASES=2 -Wmost -Wno-unknown-pragmas -Wno-logical-op-parentheses -Wno-unused-local-typedefs -I/Users/myuser/Development/cctbx/modules/boost -fPIC -fno-strict-aliasing -Wno-c++0x-extensions -Wno-array-bounds -DNDEBUG -O3 -ffast-math -I/Users/myuser/miniconda2/envs/python2/include -I/Users/myuser/Development/cctbx/base/include -I/Users/myuser/Development/cctbx/build/include -I/Users/myuser/Development/cctbx/modules/cctbx_project -I/Users/myuser/miniconda2/envs/python2/include/python2.7 /Users/myuser/Development/cctbx/modules/cctbx_project/dxtbx/format/boost_python/nexus_ext.cc
warning: unknown warning option '-Wno-unused-local-typedefs' [-Wunknown-warning-option]
1 warning generated.
/usr/bin/c++ -o lib/dxtbx_format_nexus_ext.so -w -bundle -undefined dynamic_lookup dxtbx/format/boost_python/nexus_ext.o -L/Users/myuser/Development/cctbx/base/lib -lm -lhdf5
ld: library not found for -lhdf5
clang: error: linker command failed with exit code 1 (use -v to see invocation)
scons: *** [lib/dxtbx_format_nexus_ext.so] Error 1
scons: building terminated because of errors.
usr+sys time: 8.69 seconds
wall clock time: 21.70 seconds
Process failed with return code 2

Any suggestions to how I solve this? I have not seen anywhere in the documentation that an hdf5 installation is a prerequisite.

Cheers,
/Allan