On 19/02/2016 05:00, Greg Landrum wrote:
On Fri, Feb 19, 2016 at 5:00 AM, Paul Emsley
<[email protected] <mailto:[email protected]>> wrote:
I tried to investigate this further with github rdkit but I am as yet
unable to configure/cmake it yet on this Mac (something related to
boost
python has changed) :-/ :-) - will keep poking at it and/or
abstracting
it...
I just struggled through this on a new macbook pro running el capitan,
so I may be able to help here. What error message are you getting?
Hi Greg,
This seems to be the relevant difference in the cmake output:
Using command line:
cmake -DRDK_INSTALL_INTREE=0 \
-DBoost_DIR=$install_top_dir \
-DBoost_REGEX_LIBRARY_DEBUG=$install_top_dir/lib/libboost_regex.$extension_type
\
-DBoost_REGEX_LIBRARY_RELEASE=$install_top_dir/lib/libboost_regex.$extension_type
\
-DPYTHON_LIBRARY=$install_top_dir/lib/libpython2.7.$extension_type \
-DRDK_BUILD_CAIRO_SUPPORT=ON \
-DCMAKE_INSTALL_PREFIX=$install_top_dir ../rdkit
Release:
Python Install directory
/Users/pemsley/autobuild/build-coot+rdkit-pre-release-gtk2-python/lib/python2.7/site-packages
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - found
-- Found Threads: TRUE
-- Found PkgConfig: /usr/local/bin/pkg-config (found version "0.29")
-- Checking for one of the modules 'cairo'
Git:
Python Install directory
/Users/pemsley/autobuild/build-coot+rdkit-pre-release-gtk2-python/lib/python2.7/site-packages
-- Could NOT find Boost
Boost thread or system not found. Disabling RDK_BUILD_THREADSAFE_SSS.
-- Could NOT find Boost
== Making FilterCatalog without boost Serialization support
== Updating Filters.cpp from pains file
== Done updating pains files
So that when running make:
[ 3%] Linking CXX shared library ../../lib/libRDBoost.dylib
Undefined symbols for architecture x86_64:
"boost::python::throw_error_already_set()", referenced from:
throw_index_error(int) in Wrap.cpp.o
throw_value_error(std::__1::basic_string<char,
std::__1::char_traits<char>, std::__1::allocator<char> >) in Wrap.cpp.o
translate_index_error(IndexErrorException const&) in Wrap.cpp.o
translate_value_error(ValueErrorException const&) in Wrap.cpp.o
throw_runtime_error(std::__1::basic_string<char,
std::__1::char_traits<char>, std::__1::allocator<char> >) in Wrap.cpp.o
translate_invariant_error(Invar::Invariant const&) in Wrap.cpp.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see
invocation)
make[2]: *** [lib/libRDBoost.2016.03.1.dev1.dylib] Error 1
make[1]: *** [Code/RDBoost/CMakeFiles/RDBoost.dir/all] Error 2
make: *** [all] Error 2
These functions are in libboost_python.dylib, but I don't know how to
tell cmake how to find them there when linking RDBoost.dylib.
Paul.
p.s. Sorry for the delay, now back from my travels.
p.p.s. Is this a list where top-posting is preferred? (I'm an in-line
quoter by preference)
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