dionysus not recognized

When I run a TARGet on test.fa, I get the following error: "ImportError: No module named dionysus"

I have tried installing dionysus directly, but the instructions on http://www.mrzv.org/software/dionysus/get-build-install.html aren't exactly clear either.

Can you run the Dionysus examples, i.e. Is Dionysus installed correctly? Also check your PYTHONPATH is set.

@pcamara the R TDA package bundles Dionysus with a custom interface, could be worth looking into something similar.

On Apr 29, 2016, at 12:06 PM, fishextinction notifications@github.com wrote:

When I run a TARGet on test.fa, I get the following error: "ImportError: No module named dionysus"

I have tried installing dionysus directly, but the instructions on http://www.mrzv.org/software/dionysus/get-build-install.html aren't exactly clear either.

— You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub

No, the Dionysus examples do not work. My issue is that there is no documentation here or on the Dionysus site to explain how to install it properly.

I agree that a TDA-like approach would be good. I have had some success with topological data analysis using that package in the recent past.

TARGet will only work properly with the version of Dyonisus that comes bundled with.

I need more detailed information to determine the problem. What error do you get when you follow the installation instructions of TARGet? Namely, what do you get after typing:

mkdir build cd build cmake ..

And then, after typing:

make

I am working on simplifying the installation of TARGet, so that hopefully soon there will be a better version in this regard.

On Fri, Apr 29, 2016 at 12:06 PM fishextinction notifications@github.com wrote:

When I run a TARGet on test.fa, I get the following error: "ImportError: No module named dionysus"

I have tried installing dionysus directly, but the instructions on http://www.mrzv.org/software/dionysus/get-build-install.html aren't exactly clear either.

— You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub https://github.com/RabadanLab/TARGet/issues/12

Thanks for the quick response, Pablo.

This is the output to cmake ..

-- The C compiler identification is AppleClang 7.0.2.7000181 -- The CXX compiler identification is AppleClang 7.0.2.7000181 -- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc -- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Boost version: 1.60.0 -- Found the following Boost libraries: -- program_options -- python -- serialization -- signals -- Found PythonLibs: /usr/lib/libpython2.7.dylib (found version "2.7.10") CMake Warning (dev) at bindings/python/CMakeLists.txt:32 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "_dionysus". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. This warning is for project developers. Use -Wno-dev to suppress it. -- Configuring done CMake Warning (dev): Policy CMP0042 is not set: MACOSX_RPATH is enabled by default. Run "cmake --help-policy CMP0042" for policy details. Use the cmake_policy command to set the policy and suppress this warning. MACOSX_RPATH is not specified for the following targets: _dionysus This warning is for project developers. Use -Wno-dev to suppress it. -- Generating done -- Build files have been written to: /Users/matthewmcgee/TARGet/build Matthews-MacBook-Pro:build matthewmcgee$ cd TARGet -bash: cd: TARGet: No such file or directory Matthews-MacBook-Pro:build matthewmcgee$ make Scanning dependencies of target _dionysus [ 10%] Building CXX object bindings/python/CMakeFiles/_dionysus.dir/dionysus.o In file included from /Users/matthewmcgee/TARGet/bindings/python/dionysus.cpp:2: In file included from /usr/local/include/boost/python.hpp:18: In file included from /usr/local/include/boost/python/class.hpp:29: In file included from /usr/local/include/boost/python/detail/def_helper.hpp:9: In file included from /usr/local/include/boost/type_traits/ice.hpp:15: /usr/local/include/boost/type_traits/detail/ice_or.hpp:17:10: warning: NOTE: Use of this header (ice_or.hpp) is deprecated [-W#pragma-messages] # pragma message("NOTE: Use of this header (ice_or.hpp) is deprecated") ^ In file included from /Users/matthewmcgee/TARGet/bindings/python/dionysus.cpp:2: In file included from /usr/local/include/boost/python.hpp:18: In file included from /usr/local/include/boost/python/class.hpp:29: In file included from /usr/local/include/boost/python/detail/def_helper.hpp:9: In file included from /usr/local/include/boost/type_traits/ice.hpp:16: /usr/local/include/boost/type_traits/detail/ice_and.hpp:18:10: warning: NOTE: Use of this header (ice_and.hpp) is deprecated [-W#pragma-messages] # pragma message("NOTE: Use of this header (ice_and.hpp) is deprecated") ^ In file included from /Users/matthewmcgee/TARGet/bindings/python/dionysus.cpp:2: In file included from /usr/local/include/boost/python.hpp:18: In file included from /usr/local/include/boost/python/class.hpp:29: In file included from /usr/local/include/boost/python/detail/def_helper.hpp:9: In file included from /usr/local/include/boost/type_traits/ice.hpp:17: /usr/local/include/boost/type_traits/detail/ice_not.hpp:17:10: warning: NOTE: Use of this header (ice_not.hpp) is deprecated [-W#pragma-messages] # pragma message("NOTE: Use of this header (ice_not.hpp) is deprecated") ^ In file included from /Users/matthewmcgee/TARGet/bindings/python/dionysus.cpp:2: In file included from /usr/local/include/boost/python.hpp:18: In file included from /usr/local/include/boost/python/class.hpp:29: In file included from /usr/local/include/boost/python/detail/def_helper.hpp:9: In file included from /usr/local/include/boost/type_traits/ice.hpp:18: /usr/local/include/boost/type_traits/detail/ice_eq.hpp:17:10: warning: NOTE: Use of this header (ice_eq.hpp) is deprecated [-W#pragma-messages] # pragma message("NOTE: Use of this header (ice_eq.hpp) is deprecated") ^ 4 warnings generated. [ 20%] Building CXX object bindings/python/CMakeFiles/_dionysus.dir/filtration.o In file included from /Users/matthewmcgee/TARGet/bindings/python/filtration.cpp:3: In file included from /usr/local/include/boost/python.hpp:18: In file included from /usr/local/include/boost/python/class.hpp:29: In file included from /usr/local/include/boost/python/detail/def_helper.hpp:9: In file included from /usr/local/include/boost/type_traits/ice.hpp:15: /usr/local/include/boost/type_traits/detail/ice_or.hpp:17:10: warning: NOTE: Use of this header (ice_or.hpp) is deprecated [-W#pragma-messages] # pragma message("NOTE: Use of this header (ice_or.hpp) is deprecated") ^ In file included from /Users/matthewmcgee/TARGet/bindings/python/filtration.cpp:3: In file included from /usr/local/include/boost/python.hpp:18: In file included from /usr/local/include/boost/python/class.hpp:29: In file included from /usr/local/include/boost/python/detail/def_helper.hpp:9: In file included from /usr/local/include/boost/type_traits/ice.hpp:16: /usr/local/include/boost/type_traits/detail/ice_and.hpp:18:10: warning: NOTE: Use of this header (ice_and.hpp) is deprecated [-W#pragma-messages] # pragma message("NOTE: Use of this header (ice_and.hpp) is deprecated") ^ In file included from /Users/matthewmcgee/TARGet/bindings/python/filtration.cpp:3: In file included from /usr/local/include/boost/python.hpp:18: In file included from /usr/local/include/boost/python/class.hpp:29: In file included from /usr/local/include/boost/python/detail/def_helper.hpp:9: In file included from /usr/local/include/boost/type_traits/ice.hpp:17: /usr/local/include/boost/type_traits/detail/ice_not.hpp:17:10: warning: NOTE: Use of this header (ice_not.hpp) is deprecated [-W#pragma-messages] # pragma message("NOTE: Use of this header (ice_not.hpp) is deprecated") ^ In file included from /Users/matthewmcgee/TARGet/bindings/python/filtration.cpp:3: In file included from /usr/local/include/boost/python.hpp:18: In file included from /usr/local/include/boost/python/class.hpp:29: In file included from /usr/local/include/boost/python/detail/def_helper.hpp:9: In file included from /usr/local/include/boost/type_traits/ice.hpp:18: /usr/local/include/boost/type_traits/detail/ice_eq.hpp:17:10: warning: NOTE: Use of this header (ice_eq.hpp) is deprecated [-W#pragma-messages] # pragma message("NOTE: Use of this header (ice_eq.hpp) is deprecated") ^ In file included from /Users/matthewmcgee/TARGet/bindings/python/filtration.cpp:9: /Users/matthewmcgee/TARGet/bindings/python/simplex.h:39:33: warning: conversion function converting 'dionysus::python::SimplexObject' to its base class 'boost::python::api::object' will never be used operator bp::object() cons... ^ 5 warnings generated. [ 30%] Building CXX object bindings/python/CMakeFiles/_dionysus.dir/chain.o In file included from /Users/matthewmcgee/TARGet/bindings/python/chain.cpp:3: In file included from /usr/local/include/boost/python.hpp:18: In file included from /usr/local/include/boost/python/class.hpp:29: In file included from /usr/local/include/boost/python/detail/def_helper.hpp:9: In file included from /usr/local/include/boost/type_traits/ice.hpp:15: /usr/local/include/boost/type_traits/detail/ice_or.hpp:17:10: warning: NOTE: Use of this header (ice_or.hpp) is deprecated [-W#pragma-messages] # pragma message("NOTE: Use of this header (ice_or.hpp) is deprecated") ^ In file included from /Users/matthewmcgee/TARGet/bindings/python/chain.cpp:3: In file included from /usr/local/include/boost/python.hpp:18: In file included from /usr/local/include/boost/python/class.hpp:29: In file included from /usr/local/include/boost/python/detail/def_helper.hpp:9: In file included from /usr/local/include/boost/type_traits/ice.hpp:16: /usr/local/include/boost/type_traits/detail/ice_and.hpp:18:10: warning: NOTE: Use of this header (ice_and.hpp) is deprecated [-W#pragma-messages] # pragma message("NOTE: Use of this header (ice_and.hpp) is deprecated") ^ In file included from /Users/matthewmcgee/TARGet/bindings/python/chain.cpp:3: In file included from /usr/local/include/boost/python.hpp:18: In file included from /usr/local/include/boost/python/class.hpp:29: In file included from /usr/local/include/boost/python/detail/def_helper.hpp:9: In file included from /usr/local/include/boost/type_traits/ice.hpp:17: /usr/local/include/boost/type_traits/detail/ice_not.hpp:17:10: warning: NOTE: Use of this header (ice_not.hpp) is deprecated [-W#pragma-messages] # pragma message("NOTE: Use of this header (ice_not.hpp) is deprecated") ^ In file included from /Users/matthewmcgee/TARGet/bindings/python/chain.cpp:3: In file included from /usr/local/include/boost/python.hpp:18: In file included from /usr/local/include/boost/python/class.hpp:29: In file included from /usr/local/include/boost/python/detail/def_helper.hpp:9: In file included from /usr/local/include/boost/type_traits/ice.hpp:18: /usr/local/include/boost/type_traits/detail/ice_eq.hpp:17:10: warning: NOTE: Use of this header (ice_eq.hpp) is deprecated [-W#pragma-messages] # pragma message("NOTE: Use of this header (ice_eq.hpp) is deprecated") ^ In file included from /Users/matthewmcgee/TARGet/bindings/python/chain.cpp:8: In file included from /Users/matthewmcgee/TARGet/bindings/python/chain.h:2: In file included from /Users/matthewmcgee/TARGet/bindings/python/static-persistence.h:6: In file included from /Users/matthewmcgee/TARGet/bindings/python/filtration.h:6: /Users/matthewmcgee/TARGet/bindings/python/simplex.h:39:33: warning: conversion function converting 'dionysus::python::SimplexObject' to its base class 'boost::python::api::object' will never be used operator bp::object() cons... ^ 5 warnings generated. [ 40%] Building CXX object bindings/python/CMakeFiles/_dionysus.dir/static-persistence.o In file included from /Users/matthewmcgee/TARGet/bindings/python/static-persistence.cpp:3: In file included from /usr/local/include/boost/python.hpp:18: In file included from /usr/local/include/boost/python/class.hpp:29: In file included from /usr/local/include/boost/python/detail/def_helper.hpp:9: In file included from /usr/local/include/boost/type_traits/ice.hpp:15: /usr/local/include/boost/type_traits/detail/ice_or.hpp:17:10: warning: NOTE: Use of this header (ice_or.hpp) is deprecated [-W#pragma-messages] # pragma message("NOTE: Use of this header (ice_or.hpp) is deprecated") ^ In file included from /Users/matthewmcgee/TARGet/bindings/python/static-persistence.cpp:3: In file included from /usr/local/include/boost/python.hpp:18: In file included from /usr/local/include/boost/python/class.hpp:29: In file included from /usr/local/include/boost/python/detail/def_helper.hpp:9: In file included from /usr/local/include/boost/type_traits/ice.hpp:16: /usr/local/include/boost/type_traits/detail/ice_and.hpp:18:10: warning: NOTE: Use of this header (ice_and.hpp) is deprecated [-W#pragma-messages] # pragma message("NOTE: Use of this header (ice_and.hpp) is deprecated") ^ In file included from /Users/matthewmcgee/TARGet/bindings/python/static-persistence.cpp:3: In file included from /usr/local/include/boost/python.hpp:18: In file included from /usr/local/include/boost/python/class.hpp:29: In file included from /usr/local/include/boost/python/detail/def_helper.hpp:9: In file included from /usr/local/include/boost/type_traits/ice.hpp:17: /usr/local/include/boost/type_traits/detail/ice_not.hpp:17:10: warning: NOTE: Use of this header (ice_not.hpp) is deprecated [-W#pragma-messages] # pragma message("NOTE: Use of this header (ice_not.hpp) is deprecated") ^ In file included from /Users/matthewmcgee/TARGet/bindings/python/static-persistence.cpp:3: In file included from /usr/local/include/boost/python.hpp:18: In file included from /usr/local/include/boost/python/class.hpp:29: In file included from /usr/local/include/boost/python/detail/def_helper.hpp:9: In file included from /usr/local/include/boost/type_traits/ice.hpp:18: /usr/local/include/boost/type_traits/detail/ice_eq.hpp:17:10: warning: NOTE: Use of this header (ice_eq.hpp) is deprecated [-W#pragma-messages] # pragma message("NOTE: Use of this header (ice_eq.hpp) is deprecated") ^ In file included from /Users/matthewmcgee/TARGet/bindings/python/static-persistence.cpp:8: In file included from /Users/matthewmcgee/TARGet/bindings/python/filtration.h:6: /Users/matthewmcgee/TARGet/bindings/python/simplex.h:39:33: warning: conversion function converting 'dionysus::python::SimplexObject' to its base class 'boost::python::api::object' will never be used operator bp::object() cons... ^ 5 warnings generated. [ 50%] Building CXX object bindings/python/CMakeFiles/_dionysus.dir/dynamic-persistence.o In file included from /Users/matthewmcgee/TARGet/bindings/python/dynamic-persistence.cpp:3: In file included from /usr/local/include/boost/python.hpp:18: In file included from /usr/local/include/boost/python/class.hpp:29: In file included from /usr/local/include/boost/python/detail/def_helper.hpp:9: In file included from /usr/local/include/boost/type_traits/ice.hpp:15: /usr/local/include/boost/type_traits/detail/ice_or.hpp:17:10: warning: NOTE: Use of this header (ice_or.hpp) is deprecated [-W#pragma-messages] # pragma message("NOTE: Use of this header (ice_or.hpp) is deprecated") ^ In file included from /Users/matthewmcgee/TARGet/bindings/python/dynamic-persistence.cpp:3: In file included from /usr/local/include/boost/python.hpp:18: In file included from /usr/local/include/boost/python/class.hpp:29: In file included from /usr/local/include/boost/python/detail/def_helper.hpp:9: In file included from /usr/local/include/boost/type_traits/ice.hpp:16: /usr/local/include/boost/type_traits/detail/ice_and.hpp:18:10: warning: NOTE: Use of this header (ice_and.hpp) is deprecated [-W#pragma-messages] # pragma message("NOTE: Use of this header (ice_and.hpp) is deprecated") ^ In file included from /Users/matthewmcgee/TARGet/bindings/python/dynamic-persistence.cpp:3: In file included from /usr/local/include/boost/python.hpp:18: In file included from /usr/local/include/boost/python/class.hpp:29: In file included from /usr/local/include/boost/python/detail/def_helper.hpp:9: In file included from /usr/local/include/boost/type_traits/ice.hpp:17: /usr/local/include/boost/type_traits/detail/ice_not.hpp:17:10: warning: NOTE: Use of this header (ice_not.hpp) is deprecated [-W#pragma-messages] # pragma message("NOTE: Use of this header (ice_not.hpp) is deprecated") ^ In file included from /Users/matthewmcgee/TARGet/bindings/python/dynamic-persistence.cpp:3: In file included from /usr/local/include/boost/python.hpp:18: In file included from /usr/local/include/boost/python/class.hpp:29: In file included from /usr/local/include/boost/python/detail/def_helper.hpp:9: In file included from /usr/local/include/boost/type_traits/ice.hpp:18: /usr/local/include/boost/type_traits/detail/ice_eq.hpp:17:10: warning: NOTE: Use of this header (ice_eq.hpp) is deprecated [-W#pragma-messages] # pragma message("NOTE: Use of this header (ice_eq.hpp) is deprecated") ^ In file included from /Users/matthewmcgee/TARGet/bindings/python/dynamic-persistence.cpp:8: In file included from /Users/matthewmcgee/TARGet/bindings/python/filtration.h:6: /Users/matthewmcgee/TARGet/bindings/python/simplex.h:39:33: warning: conversion function converting 'dionysus::python::SimplexObject' to its base class 'boost::python::api::object' will never be used operator bp::object() cons... ^ 5 warnings generated. [ 60%] Building CXX object bindings/python/CMakeFiles/_dionysus.dir/persistence-diagram.o In file included from /Users/matthewmcgee/TARGet/bindings/python/persistence-diagram.cpp:4: In file included from /Users/matthewmcgee/TARGet/bindings/python/filtration.h:5: In file included from /usr/local/include/boost/python.hpp:18: In file included from /usr/local/include/boost/python/class.hpp:29: In file included from /usr/local/include/boost/python/detail/def_helper.hpp:9: In file included from /usr/local/include/boost/type_traits/ice.hpp:15: /usr/local/include/boost/type_traits/detail/ice_or.hpp:17:10: warning: NOTE: Use of this header (ice_or.hpp) is deprecated [-W#pragma-messages] # pragma message("NOTE: Use of this header (ice_or.hpp) is deprecated") ^ In file included from /Users/matthewmcgee/TARGet/bindings/python/persistence-diagram.cpp:4: In file included from /Users/matthewmcgee/TARGet/bindings/python/filtration.h:5: In file included from /usr/local/include/boost/python.hpp:18: In file included from /usr/local/include/boost/python/class.hpp:29: In file included from /usr/local/include/boost/python/detail/def_helper.hpp:9: In file included from /usr/local/include/boost/type_traits/ice.hpp:16: /usr/local/include/boost/type_traits/detail/ice_and.hpp:18:10: warning: NOTE: Use of this header (ice_and.hpp) is deprecated [-W#pragma-messages] # pragma message("NOTE: Use of this header (ice_and.hpp) is deprecated") ^ In file included from /Users/matthewmcgee/TARGet/bindings/python/persistence-diagram.cpp:4: In file included from /Users/matthewmcgee/TARGet/bindings/python/filtration.h:5: In file included from /usr/local/include/boost/python.hpp:18: In file included from /usr/local/include/boost/python/class.hpp:29: In file included from /usr/local/include/boost/python/detail/def_helper.hpp:9: In file included from /usr/local/include/boost/type_traits/ice.hpp:17: /usr/local/include/boost/type_traits/detail/ice_not.hpp:17:10: warning: NOTE: Use of this header (ice_not.hpp) is deprecated [-W#pragma-messages] # pragma message("NOTE: Use of this header (ice_not.hpp) is deprecated") ^ In file included from /Users/matthewmcgee/TARGet/bindings/python/persistence-diagram.cpp:4: In file included from /Users/matthewmcgee/TARGet/bindings/python/filtration.h:5: In file included from /usr/local/include/boost/python.hpp:18: In file included from /usr/local/include/boost/python/class.hpp:29: In file included from /usr/local/include/boost/python/detail/def_helper.hpp:9: In file included from /usr/local/include/boost/type_traits/ice.hpp:18: /usr/local/include/boost/type_traits/detail/ice_eq.hpp:17:10: warning: NOTE: Use of this header (ice_eq.hpp) is deprecated [-W#pragma-messages] # pragma message("NOTE: Use of this header (ice_eq.hpp) is deprecated") ^ In file included from /Users/matthewmcgee/TARGet/bindings/python/persistence-diagram.cpp:4: In file included from /Users/matthewmcgee/TARGet/bindings/python/filtration.h:6: /Users/matthewmcgee/TARGet/bindings/python/simplex.h:39:33: warning: conversion function converting 'dionysus::python::SimplexObject' to its base class 'boost::python::api::object' will never be used operator bp::object() cons... ^ 5 warnings generated. [ 70%] Building CXX object bindings/python/CMakeFiles/_dionysus.dir/simplex.o In file included from /Users/matthewmcgee/TARGet/bindings/python/simplex.cpp:1: In file included from /Users/matthewmcgee/TARGet/include/topology/simplex.h:221: In file included from /Users/matthewmcgee/TARGet/include/topology/simplex.hpp:2: In file included from /usr/local/include/boost/serialization/set.hpp:26: /usr/local/include/boost/serialization/detail/stack_constructor.hpp:50:31: error: no member named 'load_construct_data_adl' in namespace 'boost::serialization' boost::serialization::load_construct_data_adl( ~~~~~~~~~~~~~~~~~~~~~~^ In file included from /Users/matthewmcgee/TARGet/bindings/python/simplex.cpp:5: In file included from /usr/local/include/boost/python.hpp:18: In file included from /usr/local/include/boost/python/class.hpp:29: In file included from /usr/local/include/boost/python/detail/def_helper.hpp:9: In file included from /usr/local/include/boost/type_traits/ice.hpp:15: /usr/local/include/boost/type_traits/detail/ice_or.hpp:17:10: warning: NOTE: Use of this header (ice_or.hpp) is deprecated [-W#pragma-messages] # pragma message("NOTE: Use of this header (ice_or.hpp) is deprecated") ^ In file included from /Users/matthewmcgee/TARGet/bindings/python/simplex.cpp:5: In file included from /usr/local/include/boost/python.hpp:18: In file included from /usr/local/include/boost/python/class.hpp:29: In file included from /usr/local/include/boost/python/detail/def_helper.hpp:9: In file included from /usr/local/include/boost/type_traits/ice.hpp:16: /usr/local/include/boost/type_traits/detail/ice_and.hpp:18:10: warning: NOTE: Use of this header (ice_and.hpp) is deprecated [-W#pragma-messages] # pragma message("NOTE: Use of this header (ice_and.hpp) is deprecated") ^ In file included from /Users/matthewmcgee/TARGet/bindings/python/simplex.cpp:5: In file included from /usr/local/include/boost/python.hpp:18: In file included from /usr/local/include/boost/python/class.hpp:29: In file included from /usr/local/include/boost/python/detail/def_helper.hpp:9: In file included from /usr/local/include/boost/type_traits/ice.hpp:17: /usr/local/include/boost/type_traits/detail/ice_not.hpp:17:10: warning: NOTE: Use of this header (ice_not.hpp) is deprecated [-W#pragma-messages] # pragma message("NOTE: Use of this header (ice_not.hpp) is deprecated") ^ In file included from /Users/matthewmcgee/TARGet/bindings/python/simplex.cpp:5: In file included from /usr/local/include/boost/python.hpp:18: In file included from /usr/local/include/boost/python/class.hpp:29: In file included from /usr/local/include/boost/python/detail/def_helper.hpp:9: In file included from /usr/local/include/boost/type_traits/ice.hpp:18: /usr/local/include/boost/type_traits/detail/ice_eq.hpp:17:10: warning: NOTE: Use of this header (ice_eq.hpp) is deprecated [-W#pragma-messages] # pragma message("NOTE: Use of this header (ice_eq.hpp) is deprecated") ^ In file included from /Users/matthewmcgee/TARGet/bindings/python/simplex.cpp:11: /Users/matthewmcgee/TARGet/bindings/python/simplex.h:39:33: warning: conversion function converting 'dionysus::python::SimplexObject' to its base class 'boost::python::api::object' will never be used operator bp::object() cons... ^ 5 warnings and 1 error generated. make[2]: *** [bindings/python/CMakeFiles/_dionysus.dir/simplex.o] Error 1 make[1]: *** [bindings/python/CMakeFiles/_dionysus.dir/all] Error 2 make: *** [all] Error 2

After all of this, if you attempt to run the following line: TARGet test.fa you get the following error: ImportError: No module named dionysus

I think it is an incompatibility issue between Dyonisus library and the version of Boost libraries that you have in your machine. Instructions about how to solve this issue can be found at:

http://stackoverflow.com/questions/30926981/issue-with-dionysus-build-make-on-mac-os-x-10-10-yosemite

A possible solution is replacing this line in file stack_constructor.hpp :

boost::serialization::load_construct_data_adl

load_construct_data_adl

and then start again TARGet installation from fresh (for that you need to remove the folder build). Alternatively:

brew unlink boost brew tap homebrew/versions brew install boost155 brew link --force boost155

and then TARGet installation from fresh.

Please let me know how it goes.

On Fri, Apr 29, 2016 at 2:40 PM fishextinction notifications@github.com wrote:

Thanks for the quick response, Pablo.

This is the output to cmake .. -- The C compiler identification is AppleClang 7.0.2.7000181 -- The CXX compiler identification is AppleClang 7.0.2.7000181 -- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc -- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Boost version: 1.60.0 -- Found the following Boost libraries: -- program_options -- python -- serialization -- signals -- Found PythonLibs: /usr/lib/libpython2.7.dylib (found version "2.7.10") CMake Warning (dev) at bindings/python/CMakeLists.txt:32 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning.

The LOCATION property should not be read from target "_dionysus". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate.

This warning is for project developers. Use -Wno-dev to suppress it.

-- Configuring done CMake Warning (dev): Policy CMP0042 is not set: MACOSX_RPATH is enabled by default. Run "cmake --help-policy CMP0042" for policy details. Use the cmake_policy command to set the policy and suppress this warning.

MACOSX_RPATH is not specified for the following targets:

_dionysus

This warning is for project developers. Use -Wno-dev to suppress it.

-- Generating done -- Build files have been written to: /Users/matthewmcgee/TARGet/build Matthews-MacBook-Pro:build matthewmcgee$ cd TARGet -bash: cd: TARGet: No such file or directory Matthews-MacBook-Pro:build matthewmcgee$ make Scanning dependencies of target _dionysus [ 10%] Building CXX object bindings/python/CMakeFiles/_dionysus.dir/dionysus.o In file included from /Users/matthewmcgee/TARGet/bindings/python/dionysus.cpp:2: In file included from /usr/local/include/boost/python.hpp:18: In file included from /usr/local/include/boost/python/class.hpp:29: In file included from /usr/local/include/boost/python/detail/def_helper.hpp:9: In file included from /usr/local/include/boost/type_traits/ice.hpp:15: /usr/local/include/boost/type_traits/detail/ice_or.hpp:17:10: warning: NOTE: Use of this header (ice_or.hpp) is deprecated [-W#pragma-messages] pragma message("NOTE: Use of this header (ice_or.hpp) is deprecated")
 ^
In file included from /Users/matthewmcgee/TARGet/bindings/python/dionysus.cpp:2: In file included from /usr/local/include/boost/python.hpp:18: In file included from /usr/local/include/boost/python/class.hpp:29: In file included from /usr/local/include/boost/python/detail/def_helper.hpp:9: In file included from /usr/local/include/boost/type_traits/ice.hpp:16: /usr/local/include/boost/type_traits/detail/ice_and.hpp:18:10: warning: NOTE: Use of this header (ice_and.hpp) is deprecated [-W#pragma-messages] pragma message("NOTE: Use of this header (ice_and.hpp) is deprecated")
 ^
In file included from /Users/matthewmcgee/TARGet/bindings/python/dionysus.cpp:2: In file included from /usr/local/include/boost/python.hpp:18: In file included from /usr/local/include/boost/python/class.hpp:29: In file included from /usr/local/include/boost/python/detail/def_helper.hpp:9: In file included from /usr/local/include/boost/type_traits/ice.hpp:17: /usr/local/include/boost/type_traits/detail/ice_not.hpp:17:10: warning: NOTE: Use of this header (ice_not.hpp) is deprecated [-W#pragma-messages] pragma message("NOTE: Use of this header (ice_not.hpp) is deprecated")
 ^
In file included from /Users/matthewmcgee/TARGet/bindings/python/dionysus.cpp:2: In file included from /usr/local/include/boost/python.hpp:18: In file included from /usr/local/include/boost/python/class.hpp:29: In file included from /usr/local/include/boost/python/detail/def_helper.hpp:9: In file included from /usr/local/include/boost/type_traits/ice.hpp:18: /usr/local/include/boost/type_traits/detail/ice_eq.hpp:17:10: warning: NOTE: Use of this header (ice_eq.hpp) is deprecated [-W#pragma-messages] pragma message("NOTE: Use of this header (ice_eq.hpp) is deprecated")
 ^
4 warnings generated. [ 20%] Building CXX object bindings/python/CMakeFiles/_dionysus.dir/filtration.o In file included from /Users/matthewmcgee/TARGet/bindings/python/filtration.cpp:3: In file included from /usr/local/include/boost/python.hpp:18: In file included from /usr/local/include/boost/python/class.hpp:29: In file included from /usr/local/include/boost/python/detail/def_helper.hpp:9: In file included from /usr/local/include/boost/type_traits/ice.hpp:15: /usr/local/include/boost/type_traits/detail/ice_or.hpp:17:10: warning: NOTE: Use of this header (ice_or.hpp) is deprecated [-W#pragma-messages] pragma message("NOTE: Use of this header (ice_or.hpp) is deprecated")
 ^
In file included from /Users/matthewmcgee/TARGet/bindings/python/filtration.cpp:3: In file included from /usr/local/include/boost/python.hpp:18: In file included from /usr/local/include/boost/python/class.hpp:29: In file included from /usr/local/include/boost/python/detail/def_helper.hpp:9: In file included from /usr/local/include/boost/type_traits/ice.hpp:16: /usr/local/include/boost/type_traits/detail/ice_and.hpp:18:10: warning: NOTE: Use of this header (ice_and.hpp) is deprecated [-W#pragma-messages] pragma message("NOTE: Use of this header (ice_and.hpp) is deprecated")
 ^
In file included from /Users/matthewmcgee/TARGet/bindings/python/filtration.cpp:3: In file included from /usr/local/include/boost/python.hpp:18: In file included from /usr/local/include/boost/python/class.hpp:29: In file included from /usr/local/include/boost/python/detail/def_helper.hpp:9: In file included from /usr/local/include/boost/type_traits/ice.hpp:17: /usr/local/include/boost/type_traits/detail/ice_not.hpp:17:10: warning: NOTE: Use of this header (ice_not.hpp) is deprecated [-W#pragma-messages] pragma message("NOTE: Use of this header (ice_not.hpp) is deprecated")
 ^
In file included from /Users/matthewmcgee/TARGet/bindings/python/filtration.cpp:3: In file included from /usr/local/include/boost/python.hpp:18: In file included from /usr/local/include/boost/python/class.hpp:29: In file included from /usr/local/include/boost/python/detail/def_helper.hpp:9: In file included from /usr/local/include/boost/type_traits/ice.hpp:18: /usr/local/include/boost/type_traits/detail/ice_eq.hpp:17:10: warning: NOTE: Use of this header (ice_eq.hpp) is deprecated [-W#pragma-messages] pragma message("NOTE: Use of this header (ice_eq.hpp) is deprecated")
 ^
In file included from /Users/matthewmcgee/TARGet/bindings/python/filtration.cpp:9: /Users/matthewmcgee/TARGet/bindings/python/simplex.h:39:33: warning: conversion function converting 'dionysus::python::SimplexObject' to its base class 'boost::python::api::object' will never be used operator bp::object() cons... ^ 5 warnings generated. [ 30%] Building CXX object bindings/python/CMakeFiles/_dionysus.dir/chain.o In file included from /Users/matthewmcgee/TARGet/bindings/python/chain.cpp:3: In file included from /usr/local/include/boost/python.hpp:18: In file included from /usr/local/include/boost/python/class.hpp:29: In file included from /usr/local/include/boost/python/detail/def_helper.hpp:9: In file included from /usr/local/include/boost/type_traits/ice.hpp:15: /usr/local/include/boost/type_traits/detail/ice_or.hpp:17:10: warning: NOTE: Use of this header (ice_or.hpp) is deprecated [-W#pragma-messages] pragma message("NOTE: Use of this header (ice_or.hpp) is deprecated")
 ^
In file included from /Users/matthewmcgee/TARGet/bindings/python/chain.cpp:3: In file included from /usr/local/include/boost/python.hpp:18: In file included from /usr/local/include/boost/python/class.hpp:29: In file included from /usr/local/include/boost/python/detail/def_helper.hpp:9: In file included from /usr/local/include/boost/type_traits/ice.hpp:16: /usr/local/include/boost/type_traits/detail/ice_and.hpp:18:10: warning: NOTE: Use of this header (ice_and.hpp) is deprecated [-W#pragma-messages] pragma message("NOTE: Use of this header (ice_and.hpp) is deprecated")
 ^
In file included from /Users/matthewmcgee/TARGet/bindings/python/chain.cpp:3: In file included from /usr/local/include/boost/python.hpp:18: In file included from /usr/local/include/boost/python/class.hpp:29: In file included from /usr/local/include/boost/python/detail/def_helper.hpp:9: In file included from /usr/local/include/boost/type_traits/ice.hpp:17: /usr/local/include/boost/type_traits/detail/ice_not.hpp:17:10: warning: NOTE: Use of this header (ice_not.hpp) is deprecated [-W#pragma-messages] pragma message("NOTE: Use of this header (ice_not.hpp) is deprecated")
 ^
In file included from /Users/matthewmcgee/TARGet/bindings/python/chain.cpp:3: In file included from /usr/local/include/boost/python.hpp:18: In file included from /usr/local/include/boost/python/class.hpp:29: In file included from /usr/local/include/boost/python/detail/def_helper.hpp:9: In file included from /usr/local/include/boost/type_traits/ice.hpp:18: /usr/local/include/boost/type_traits/detail/ice_eq.hpp:17:10: warning: NOTE: Use of this header (ice_eq.hpp) is deprecated [-W#pragma-messages] pragma message("NOTE: Use of this header (ice_eq.hpp) is deprecated")
 ^
In file included from /Users/matthewmcgee/TARGet/bindings/python/chain.cpp:8: In file included from /Users/matthewmcgee/TARGet/bindings/python/chain.h:2: In file included from /Users/matthewmcgee/TARGet/bindings/python/static-persistence.h:6: In file included from /Users/matthewmcgee/TARGet/bindings/python/filtration.h:6: /Users/matthewmcgee/TARGet/bindings/python/simplex.h:39:33: warning: conversion function converting 'dionysus::python::SimplexObject' to its base class 'boost::python::api::object' will never be used operator bp::object() cons... ^ 5 warnings generated. [ 40%] Building CXX object bindings/python/CMakeFiles/_dionysus.dir/static-persistence.o In file included from /Users/matthewmcgee/TARGet/bindings/python/static-persistence.cpp:3: In file included from /usr/local/include/boost/python.hpp:18: In file included from /usr/local/include/boost/python/class.hpp:29: In file included from /usr/local/include/boost/python/detail/def_helper.hpp:9: In file included from /usr/local/include/boost/type_traits/ice.hpp:15: /usr/local/include/boost/type_traits/detail/ice_or.hpp:17:10: warning: NOTE: Use of this header (ice_or.hpp) is deprecated [-W#pragma-messages] pragma message("NOTE: Use of this header (ice_or.hpp) is deprecated")
 ^
In file included from /Users/matthewmcgee/TARGet/bindings/python/static-persistence.cpp:3: In file included from /usr/local/include/boost/python.hpp:18: In file included from /usr/local/include/boost/python/class.hpp:29: In file included from /usr/local/include/boost/python/detail/def_helper.hpp:9: In file included from /usr/local/include/boost/type_traits/ice.hpp:16: /usr/local/include/boost/type_traits/detail/ice_and.hpp:18:10: warning: NOTE: Use of this header (ice_and.hpp) is deprecated [-W#pragma-messages] pragma message("NOTE: Use of this header (ice_and.hpp) is deprecated")
 ^
In file included from /Users/matthewmcgee/TARGet/bindings/python/static-persistence.cpp:3: In file included from /usr/local/include/boost/python.hpp:18: In file included from /usr/local/include/boost/python/class.hpp:29: In file included from /usr/local/include/boost/python/detail/def_helper.hpp:9: In file included from /usr/local/include/boost/type_traits/ice.hpp:17: /usr/local/include/boost/type_traits/detail/ice_not.hpp:17:10: warning: NOTE: Use of this header (ice_not.hpp) is deprecated [-W#pragma-messages] pragma message("NOTE: Use of this header (ice_not.hpp) is deprecated")
 ^
In file included from /Users/matthewmcgee/TARGet/bindings/python/static-persistence.cpp:3: In file included from /usr/local/include/boost/python.hpp:18: In file included from /usr/local/include/boost/python/class.hpp:29: In file included from /usr/local/include/boost/python/detail/def_helper.hpp:9: In file included from /usr/local/include/boost/type_traits/ice.hpp:18: /usr/local/include/boost/type_traits/detail/ice_eq.hpp:17:10: warning: NOTE: Use of this header (ice_eq.hpp) is deprecated [-W#pragma-messages] pragma message("NOTE: Use of this header (ice_eq.hpp) is deprecated")
 ^
In file included from /Users/matthewmcgee/TARGet/bindings/python/static-persistence.cpp:8: In file included from /Users/matthewmcgee/TARGet/bindings/python/filtration.h:6: /Users/matthewmcgee/TARGet/bindings/python/simplex.h:39:33: warning: conversion function converting 'dionysus::python::SimplexObject' to its base class 'boost::python::api::object' will never be used operator bp::object() cons... ^ 5 warnings generated. [ 50%] Building CXX object bindings/python/CMakeFiles/_dionysus.dir/dynamic-persistence.o In file included from /Users/matthewmcgee/TARGet/bindings/python/dynamic-persistence.cpp:3: In file included from /usr/local/include/boost/python.hpp:18: In file included from /usr/local/include/boost/python/class.hpp:29: In file included from /usr/local/include/boost/python/detail/def_helper.hpp:9: In file included from /usr/local/include/boost/type_traits/ice.hpp:15: /usr/local/include/boost/type_traits/detail/ice_or.hpp:17:10: warning: NOTE: Use of this header (ice_or.hpp) is deprecated [-W#pragma-messages] pragma message("NOTE: Use of this header (ice_or.hpp) is deprecated")
 ^
In file included from /Users/matthewmcgee/TARGet/bindings/python/dynamic-persistence.cpp:3: In file included from /usr/local/include/boost/python.hpp:18: In file included from /usr/local/include/boost/python/class.hpp:29: In file included from /usr/local/include/boost/python/detail/def_helper.hpp:9: In file included from /usr/local/include/boost/type_traits/ice.hpp:16: /usr/local/include/boost/type_traits/detail/ice_and.hpp:18:10: warning: NOTE: Use of this header (ice_and.hpp) is deprecated [-W#pragma-messages] pragma message("NOTE: Use of this header (ice_and.hpp) is deprecated")
 ^
In file included from /Users/matthewmcgee/TARGet/bindings/python/dynamic-persistence.cpp:3: In file included from /usr/local/include/boost/python.hpp:18: In file included from /usr/local/include/boost/python/class.hpp:29: In file included from /usr/local/include/boost/python/detail/def_helper.hpp:9: In file included from /usr/local/include/boost/type_traits/ice.hpp:17: /usr/local/include/boost/type_traits/detail/ice_not.hpp:17:10: warning: NOTE: Use of this header (ice_not.hpp) is deprecated [-W#pragma-messages] pragma message("NOTE: Use of this header (ice_not.hpp) is deprecated")
 ^
In file included from /Users/matthewmcgee/TARGet/bindings/python/dynamic-persistence.cpp:3: In file included from /usr/local/include/boost/python.hpp:18: In file included from /usr/local/include/boost/python/class.hpp:29: In file included from /usr/local/include/boost/python/detail/def_helper.hpp:9: In file included from /usr/local/include/boost/type_traits/ice.hpp:18: /usr/local/include/boost/type_traits/detail/ice_eq.hpp:17:10: warning: NOTE: Use of this header (ice_eq.hpp) is deprecated [-W#pragma-messages] pragma message("NOTE: Use of this header (ice_eq.hpp) is deprecated")
 ^
In file included from /Users/matthewmcgee/TARGet/bindings/python/dynamic-persistence.cpp:8: In file included from /Users/matthewmcgee/TARGet/bindings/python/filtration.h:6: /Users/matthewmcgee/TARGet/bindings/python/simplex.h:39:33: warning: conversion function converting 'dionysus::python::SimplexObject' to its base class 'boost::python::api::object' will never be used operator bp::object() cons... ^ 5 warnings generated. [ 60%] Building CXX object bindings/python/CMakeFiles/_dionysus.dir/persistence-diagram.o In file included from /Users/matthewmcgee/TARGet/bindings/python/persistence-diagram.cpp:4: In file included from /Users/matthewmcgee/TARGet/bindings/python/filtration.h:5: In file included from /usr/local/include/boost/python.hpp:18: In file included from /usr/local/include/boost/python/class.hpp:29: In file included from /usr/local/include/boost/python/detail/def_helper.hpp:9: In file included from /usr/local/include/boost/type_traits/ice.hpp:15: /usr/local/include/boost/type_traits/detail/ice_or.hpp:17:10: warning: NOTE: Use of this header (ice_or.hpp) is deprecated [-W#pragma-messages] pragma message("NOTE: Use of this header (ice_or.hpp) is deprecated")
 ^
In file included from /Users/matthewmcgee/TARGet/bindings/python/persistence-diagram.cpp:4: In file included from /Users/matthewmcgee/TARGet/bindings/python/filtration.h:5: In file included from /usr/local/include/boost/python.hpp:18: In file included from /usr/local/include/boost/python/class.hpp:29: In file included from /usr/local/include/boost/python/detail/def_helper.hpp:9: In file included from /usr/local/include/boost/type_traits/ice.hpp:16: /usr/local/include/boost/type_traits/detail/ice_and.hpp:18:10: warning: NOTE: Use of this header (ice_and.hpp) is deprecated [-W#pragma-messages] pragma message("NOTE: Use of this header (ice_and.hpp) is deprecated")
 ^
In file included from /Users/matthewmcgee/TARGet/bindings/python/persistence-diagram.cpp:4: In file included from /Users/matthewmcgee/TARGet/bindings/python/filtration.h:5: In file included from /usr/local/include/boost/python.hpp:18: In file included from /usr/local/include/boost/python/class.hpp:29: In file included from /usr/local/include/boost/python/detail/def_helper.hpp:9: In file included from /usr/local/include/boost/type_traits/ice.hpp:17: /usr/local/include/boost/type_traits/detail/ice_not.hpp:17:10: warning: NOTE: Use of this header (ice_not.hpp) is deprecated [-W#pragma-messages] pragma message("NOTE: Use of this header (ice_not.hpp) is deprecated")
 ^
In file included from /Users/matthewmcgee/TARGet/bindings/python/persistence-diagram.cpp:4: In file included from /Users/matthewmcgee/TARGet/bindings/python/filtration.h:5: In file included from /usr/local/include/boost/python.hpp:18: In file included from /usr/local/include/boost/python/class.hpp:29: In file included from /usr/local/include/boost/python/detail/def_helper.hpp:9: In file included from /usr/local/include/boost/type_traits/ice.hpp:18: /usr/local/include/boost/type_traits/detail/ice_eq.hpp:17:10: warning: NOTE: Use of this header (ice_eq.hpp) is deprecated [-W#pragma-messages] pragma message("NOTE: Use of this header (ice_eq.hpp) is deprecated")
 ^
In file included from /Users/matthewmcgee/TARGet/bindings/python/persistence-diagram.cpp:4: In file included from /Users/matthewmcgee/TARGet/bindings/python/filtration.h:6: /Users/matthewmcgee/TARGet/bindings/python/simplex.h:39:33: warning: conversion function converting 'dionysus::python::SimplexObject' to its base class 'boost::python::api::object' will never be used operator bp::object() cons... ^ 5 warnings generated. [ 70%] Building CXX object bindings/python/CMakeFiles/_dionysus.dir/simplex.o In file included from /Users/matthewmcgee/TARGet/bindings/python/simplex.cpp:1: In file included from /Users/matthewmcgee/TARGet/include/topology/simplex.h:221: In file included from /Users/matthewmcgee/TARGet/include/topology/simplex.hpp:2: In file included from /usr/local/include/boost/serialization/set.hpp:26: /usr/local/include/boost/serialization/detail/stack_constructor.hpp:50:31: error: no member named 'load_construct_data_adl' in namespace 'boost::serialization' boost::serialization::load_construct_data_adl(
In file included from
/Users/matthewmcgee/TARGet/bindings/python/simplex.cpp:5:
In file included from /usr/local/include/boost/python.hpp:18:
In file included from /usr/local/include/boost/python/class.hpp:29:
In file included from
/usr/local/include/boost/python/detail/def_helper.hpp:9:
In file included from /usr/local/include/boost/type_traits/ice.hpp:15:
/usr/local/include/boost/type_traits/detail/ice_or.hpp:17:10: warning:
NOTE: Use of this header (ice_or.hpp) is deprecated
[-W#pragma-messages]
pragma message("NOTE: Use of this header (ice_or.hpp) is deprecated")

     ^

In file included from
/Users/matthewmcgee/TARGet/bindings/python/simplex.cpp:5:
In file included from /usr/local/include/boost/python.hpp:18:
In file included from /usr/local/include/boost/python/class.hpp:29:
In file included from
/usr/local/include/boost/python/detail/def_helper.hpp:9:
In file included from /usr/local/include/boost/type_traits/ice.hpp:16:
/usr/local/include/boost/type_traits/detail/ice_and.hpp:18:10: warning:
NOTE: Use of this header (ice_and.hpp) is deprecated
[-W#pragma-messages]
pragma message("NOTE: Use of this header (ice_and.hpp) is deprecated")

     ^

In file included from
/Users/matthewmcgee/TARGet/bindings/python/simplex.cpp:5:
In file included from /usr/local/include/boost/python.hpp:18:
In file included from /usr/local/include/boost/python/class.hpp:29:
In file included from
/usr/local/include/boost/python/detail/def_helper.hpp:9:
In file included from /usr/local/include/boost/type_traits/ice.hpp:17:
/usr/local/include/boost/type_traits/detail/ice_not.hpp:17:10: warning:
NOTE: Use of this header (ice_not.hpp) is deprecated
[-W#pragma-messages]
pragma message("NOTE: Use of this header (ice_not.hpp) is deprecated")

     ^

In file included from
/Users/matthewmcgee/TARGet/bindings/python/simplex.cpp:5:
In file included from /usr/local/include/boost/python.hpp:18:
In file included from /usr/local/include/boost/python/class.hpp:29:
In file included from
/usr/local/include/boost/python/detail/def_helper.hpp:9:
In file included from /usr/local/include/boost/type_traits/ice.hpp:18:
/usr/local/include/boost/type_traits/detail/ice_eq.hpp:17:10: warning:
NOTE: Use of this header (ice_eq.hpp) is deprecated
[-W#pragma-messages]
pragma message("NOTE: Use of this header (ice_eq.hpp) is deprecated")

     ^

In file included from
/Users/matthewmcgee/TARGet/bindings/python/simplex.cpp:11:
/Users/matthewmcgee/TARGet/bindings/python/simplex.h:39:33: warning:
conversion function converting 'dionysus::python::SimplexObject' to
its base class 'boost::python::api::object' will never be used
operator bp::object() cons...
^
5 warnings and 1 error generated.
make[2]: *** [bindings/python/CMakeFiles/_dionysus.dir/simplex.o] Error 1
make[1]: *** [bindings/python/CMakeFiles/_dionysus.dir/all] Error 2
make: *** [all] Error 2

After all of this, if you attempt to run the following line:
TARGet test.fa
you get the following error:

ImportError: No module named dionysus

—
You are receiving this because you were mentioned.

Reply to this email directly or view it on GitHub
<https://github.com/RabadanLab/TARGet/issues/12#issuecomment-215843232>

I tried the second solution just now on a fresh install.

Matthews-MacBook-Pro:build matthewmcgee$ cmake .. -- Boost version: 1.55.0 -- Found the following Boost libraries: -- program_options -- python -- serialization -- signals CMake Warning (dev) at bindings/python/CMakeLists.txt:32 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning.

The LOCATION property should not be read from target "_dionysus". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate.

This warning is for project developers. Use -Wno-dev to suppress it.

-- Configuring done CMake Warning (dev): Policy CMP0042 is not set: MACOSX_RPATH is enabled by default. Run "cmake --help-policy CMP0042" for policy details. Use the cmake_policy command to set the policy and suppress this warning.

MACOSX_RPATH is not specified for the following targets:

_dionysus

This warning is for project developers. Use -Wno-dev to suppress it.

If I run target test.fa

I get: /usr/local/lib/python2.7/site-packages/matplotlib/font_manager.py:273: UserWarning: Matplotlib is building the font cache using fc-list. This may take a moment. warnings.warn('Matplotlib is building the font cache using fc-list. This may take a moment.') Traceback (most recent call last): File "/Users/matthewmcgee/target/target", line 51, in from dionysus import Rips, Filtration, \ File "/Library/Python/2.7/site-packages/dionysus/init.py", line 1, in from _dionysus import * File "/Library/Python/2.7/site-packages/_dionysus/init.py", line 14, in Simplex._cppinit = Simplex.init NameError: name 'Simplex' is not defined

Did you ran make after cmake .. ? Did you get any error?

On Fri, Apr 29, 2016 at 6:44 PM fishextinction notifications@github.com wrote:

I tried the second solution just now on a fresh install.

Matthews-MacBook-Pro:build matthewmcgee$ cmake .. -- Boost version: 1.55.0

-- Found the following Boost libraries: -- program_options -- python -- serialization -- signals

CMake Warning (dev) at bindings/python/CMakeLists.txt:32 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning.

The LOCATION property should not be read from target "_dionysus". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate.

This warning is for project developers. Use -Wno-dev to suppress it.

-- Configuring done CMake Warning (dev): Policy CMP0042 is not set: MACOSX_RPATH is enabled by default. Run "cmake --help-policy CMP0042" for policy details. Use the cmake_policy command to set the policy and suppress this warning.

MACOSX_RPATH is not specified for the following targets:

_dionysus

This warning is for project developers. Use -Wno-dev to suppress it.

If I run target test.fa

I get: /usr/local/lib/python2.7/site-packages/matplotlib/font_manager.py:273: UserWarning: Matplotlib is building the font cache using fc-list. This may take a moment. warnings.warn('Matplotlib is building the font cache using fc-list. This may take a moment.') Traceback (most recent call last): File "/Users/matthewmcgee/target/target", line 51, in from dionysus import Rips, Filtration, \ File "/Library/Python/2.7/site-packages/dionysus/init.py", line 1, in from _dionysus import * File "/Library/Python/2.7/site-packages/dionysus/_init.py", line 14, in Simplex._cppinit = Simplex.init NameError: name 'Simplex' is not defined

— You are receiving this because you were mentioned.

Reply to this email directly or view it on GitHub https://github.com/RabadanLab/TARGet/issues/12#issuecomment-215900550

I did, it looks much the same as before. I now get a new error when running target.

make Scanning dependencies of target _dionysus [ 10%] Building CXX object bindings/python/CMakeFiles/_dionysus.dir/dionysus.o [ 20%] Building CXX object bindings/python/CMakeFiles/_dionysus.dir/filtration.o In file included from /Users/matthewmcgee/target/bindings/python/filtration.cpp:9: /Users/matthewmcgee/target/bindings/python/simplex.h:39:33: warning: conversion function converting 'dionysus::python::SimplexObject' to its base class 'boost::python::api::object' will never be used operator bp::object() cons... ^ 1 warning generated. [ 30%] Building CXX object bindings/python/CMakeFiles/_dionysus.dir/chain.o In file included from /Users/matthewmcgee/target/bindings/python/chain.cpp:8: In file included from /Users/matthewmcgee/target/bindings/python/chain.h:2: In file included from /Users/matthewmcgee/target/bindings/python/static-persistence.h:6: In file included from /Users/matthewmcgee/target/bindings/python/filtration.h:6: /Users/matthewmcgee/target/bindings/python/simplex.h:39:33: warning: conversion function converting 'dionysus::python::SimplexObject' to its base class 'boost::python::api::object' will never be used operator bp::object() cons... ^ 1 warning generated. [ 40%] Building CXX object bindings/python/CMakeFiles/_dionysus.dir/static-persistence.o In file included from /Users/matthewmcgee/target/bindings/python/static-persistence.cpp:8: In file included from /Users/matthewmcgee/target/bindings/python/filtration.h:6: /Users/matthewmcgee/target/bindings/python/simplex.h:39:33: warning: conversion function converting 'dionysus::python::SimplexObject' to its base class 'boost::python::api::object' will never be used operator bp::object() cons... ^ 1 warning generated. [ 50%] Building CXX object bindings/python/CMakeFiles/_dionysus.dir/dynamic-persistence.o In file included from /Users/matthewmcgee/target/bindings/python/dynamic-persistence.cpp:8: In file included from /Users/matthewmcgee/target/bindings/python/filtration.h:6: /Users/matthewmcgee/target/bindings/python/simplex.h:39:33: warning: conversion function converting 'dionysus::python::SimplexObject' to its base class 'boost::python::api::object' will never be used operator bp::object() cons... ^ 1 warning generated. [ 60%] Building CXX object bindings/python/CMakeFiles/_dionysus.dir/persistence-diagram.o In file included from /Users/matthewmcgee/target/bindings/python/persistence-diagram.cpp:4: In file included from /Users/matthewmcgee/target/bindings/python/filtration.h:6: /Users/matthewmcgee/target/bindings/python/simplex.h:39:33: warning: conversion function converting 'dionysus::python::SimplexObject' to its base class 'boost::python::api::object' will never be used operator bp::object() cons... ^ 1 warning generated. [ 70%] Building CXX object bindings/python/CMakeFiles/_dionysus.dir/simplex.o In file included from /Users/matthewmcgee/target/bindings/python/simplex.cpp:11: /Users/matthewmcgee/target/bindings/python/simplex.h:39:33: warning: conversion function converting 'dionysus::python::SimplexObject' to its base class 'boost::python::api::object' will never be used operator bp::object() cons... ^ 1 warning generated. [ 80%] Building CXX object bindings/python/CMakeFiles/_dionysus.dir/birthid.o [ 90%] Building CXX object bindings/python/CMakeFiles/_dionysus.dir/rips.o In file included from /Users/matthewmcgee/target/bindings/python/rips.cpp:5: In file included from /Users/matthewmcgee/target/bindings/python/rips.h:7: /Users/matthewmcgee/target/bindings/python/simplex.h:39:33: warning: conversion function converting 'dionysus::python::SimplexObject' to its base class 'boost::python::api::object' will never be used operator bp::object() cons... ^ 1 warning generated. [100%] Building CXX object bindings/python/CMakeFiles/_dionysus.dir/distances.o Linking CXX shared library lib_dionysus.dylib [100%] Built target _dionysus Scanning dependencies of target dionysus [100%] Built target dionysus Scanning dependencies of target dionysus-link [100%] Built target dionysus-link Matthews-MacBook-Pro:build matthewmcgee$ cd Matthews-MacBook-Pro:~ matthewmcgee$ cd target Matthews-MacBook-Pro:target matthewmcgee$ /Users/matthewmcgee/tARGet/target test.fa /usr/local/lib/python2.7/site-packages/matplotlib/font_manager.py:273: UserWarning: Matplotlib is building the font cache using fc-list. This may take a moment. warnings.warn('Matplotlib is building the font cache using fc-list. This may take a moment.')

TARGet: Topological inference of horizontal evolution.

Reading sequences... 7 sequences read, 8 segregating sites. Computing persistent homology, this may take some minutes... Traceback (most recent call last): File "/Users/matthewmcgee/tARGet/target", line 881, in main() File "/Users/matthewmcgee/tARGet/target", line 792, in main pio = compute_extended_barcode(sec, options.s, options.w, options.t-1, options.c) File "/Users/matthewmcgee/tARGet/target", line 291, in compute_extended_barcode bu[min(lm[0])][max(lm[0])] = max_barcode([lm[1].get() + File "/usr/local/Cellar/python/2.7.11/Frameworks/Python.framework/Versions/2.7/lib/python2.7/multiprocessing/pool.py", line 567, in get raise self._value TypeError: init() should return None, not 'NoneType'

This seems to be something different. There might be a bug in the multiprocessing module of the python version you are using. I will try to reproduce your error in our computers. Meanwhile it would be good if you can tried in a different python 2.7 version.

Thanks, P.

On Sat, Apr 30, 2016 at 3:26 PM fishextinction notifications@github.com wrote:

I did, it looks much the same as before. I now get a new error when running target. make Scanning dependencies of target _dionysus [ 10%] Building CXX object bindings/python/CMakeFiles/_dionysus.dir/dionysus.o [ 20%] Building CXX object bindings/python/CMakeFiles/_dionysus.dir/filtration.o In file included from /Users/matthewmcgee/target/bindings/python/filtration.cpp:9: /Users/matthewmcgee/target/bindings/python/simplex.h:39:33: warning: conversion function converting 'dionysus::python::SimplexObject' to its base class 'boost::python::api::object' will never be used operator bp::object() cons... ^ 1 warning generated. [ 30%] Building CXX object bindings/python/CMakeFiles/_dionysus.dir/chain.o In file included from /Users/matthewmcgee/target/bindings/python/chain.cpp:8: In file included from /Users/matthewmcgee/target/bindings/python/chain.h:2: In file included from /Users/matthewmcgee/target/bindings/python/static-persistence.h:6: In file included from /Users/matthewmcgee/target/bindings/python/filtration.h:6: /Users/matthewmcgee/target/bindings/python/simplex.h:39:33: warning: conversion function converting 'dionysus::python::SimplexObject' to its base class 'boost::python::api::object' will never be used operator bp::object() cons... ^ 1 warning generated. [ 40%] Building CXX object bindings/python/CMakeFiles/_dionysus.dir/static-persistence.o In file included from /Users/matthewmcgee/target/bindings/python/static-persistence.cpp:8: In file included from /Users/matthewmcgee/target/bindings/python/filtration.h:6: /Users/matthewmcgee/target/bindings/python/simplex.h:39:33: warning: conversion function converting 'dionysus::python::SimplexObject' to its base class 'boost::python::api::object' will never be used operator bp::object() cons... ^ 1 warning generated. [ 50%] Building CXX object bindings/python/CMakeFiles/_dionysus.dir/dynamic-persistence.o In file included from /Users/matthewmcgee/target/bindings/python/dynamic-persistence.cpp:8: In file included from /Users/matthewmcgee/target/bindings/python/filtration.h:6: /Users/matthewmcgee/target/bindings/python/simplex.h:39:33: warning: conversion function converting 'dionysus::python::SimplexObject' to its base class 'boost::python::api::object' will never be used operator bp::object() cons... ^ 1 warning generated. [ 60%] Building CXX object bindings/python/CMakeFiles/_dionysus.dir/persistence-diagram.o In file included from /Users/matthewmcgee/target/bindings/python/persistence-diagram.cpp:4: In file included from /Users/matthewmcgee/target/bindings/python/filtration.h:6: /Users/matthewmcgee/target/bindings/python/simplex.h:39:33: warning: conversion function converting 'dionysus::python::SimplexObject' to its base class 'boost::python::api::object' will never be used operator bp::object() cons... ^ 1 warning generated. [ 70%] Building CXX object bindings/python/CMakeFiles/_dionysus.dir/simplex.o In file included from /Users/matthewmcgee/target/bindings/python/simplex.cpp:11: /Users/matthewmcgee/target/bindings/python/simplex.h:39:33: warning: conversion function converting 'dionysus::python::SimplexObject' to its base class 'boost::python::api::object' will never be used operator bp::object() cons... ^ 1 warning generated. [ 80%] Building CXX object bindings/python/CMakeFiles/_dionysus.dir/birthid.o [ 90%] Building CXX object bindings/python/CMakeFiles/_dionysus.dir/rips.o In file included from /Users/matthewmcgee/target/bindings/python/rips.cpp:5: In file included from /Users/matthewmcgee/target/bindings/python/rips.h:7: /Users/matthewmcgee/target/bindings/python/simplex.h:39:33: warning: conversion function converting 'dionysus::python::SimplexObject' to its base class 'boost::python::api::object' will never be used operator bp::object() cons... ^ 1 warning generated. [100%] Building CXX object bindings/python/CMakeFiles/_dionysus.dir/distances.o Linking CXX shared library lib_dionysus.dylib [100%] Built target _dionysus Scanning dependencies of target dionysus [100%] Built target dionysus Scanning dependencies of target dionysus-link [100%] Built target dionysus-link Matthews-MacBook-Pro:build matthewmcgee$ cd Matthews-MacBook-Pro:~ matthewmcgee$ cd target Matthews-MacBook-Pro:target matthewmcgee$ /Users/matthewmcgee/tARGet/target test.fa /usr/local/lib/python2.7/site-packages/matplotlib/font_manager.py:273: UserWarning: Matplotlib is building the font cache using fc-list. This may take a moment. warnings.warn('Matplotlib is building the font cache using fc-list. This may take a moment.') ### TARGet: Topological inference of horizontal evolution. Reading sequences... 7 sequences read, 8 segregating sites. Computing persistent homology, this may take some minutes... Traceback (most recent call last): File "/Users/matthewmcgee/tARGet/target", line 881, in main() File "/Users/matthewmcgee/tARGet/target", line 792, in main pio = compute_extended_barcode(sec, options.s, options.w, options.t-1, options.c) File "/Users/matthewmcgee/tARGet/target", line 291, in compute_extended_barcode bu[min(lm[0])][max(lm[0])] = max_barcode([lm[1].get() + File "/usr/local/Cellar/python/2.7.11/Frameworks/Python.framework/Versions/2.7/lib/python2.7/multiprocessing/pool.py", line 567, in get raise self._value TypeError: init() should return None, not 'NoneType'

— You are receiving this because you were mentioned.

Reply to this email directly or view it on GitHub https://github.com/RabadanLab/TARGet/issues/12#issuecomment-215988745

Has there been any update on this problem? I am experiencing the same problem as fishextinction.

Hi,

I am working on it. Trying to recreate the problem in my computer.

@devonhum, can you paste the error you get, please? Which version of python are you using?

Thanks,

Pablo

On Tue, May 10, 2016 at 12:43 PM devonhum notifications@github.com wrote:

Has there been any update on this problem? I am experiencing the same problem as fishextinction.

— You are receiving this because you were mentioned.

Reply to this email directly or view it on GitHub https://github.com/RabadanLab/TARGet/issues/12#issuecomment-218217687

Sure. I am using Python 2.7.10. This is the output after make:

Scanning dependencies of target _dionysus [ 9%] Building CXX object bindings/python/CMakeFiles/_dionysus.dir/dionysus.o [ 18%] Building CXX object bindings/python/CMakeFiles/_dionysus.dir/filtration.o In file included from /Users/devon/TARGet/bindings/python/filtration.cpp:9: /Users/devon/TARGet/bindings/python/simplex.h:39:33: warning: conversion function converting 'dionysus::python::SimplexObject' to its base class 'boost::python::api::object' will never be used operator bp::object() const { return _this; } ^ 1 warning generated. [ 27%] Building CXX object bindings/python/CMakeFiles/_dionysus.dir/chain.o In file included from /Users/devon/TARGet/bindings/python/chain.cpp:8: In file included from /Users/devon/TARGet/bindings/python/chain.h:2: In file included from /Users/devon/TARGet/bindings/python/static-persistence.h:6: In file included from /Users/devon/TARGet/bindings/python/filtration.h:6: /Users/devon/TARGet/bindings/python/simplex.h:39:33: warning: conversion function converting 'dionysus::python::SimplexObject' to its base class 'boost::python::api::object' will never be used operator bp::object() const { return this; } ^ 1 warning generated. [ 36%] Building CXX object bindings/python/CMakeFiles/_dionysus.dir/static-persistence.o In file included from /Users/devon/TARGet/bindings/python/static-persistence.cpp:8: In file included from /Users/devon/TARGet/bindings/python/filtration.h:6: /Users/devon/TARGet/bindings/python/simplex.h:39:33: warning: conversion function converting 'dionysus::python::SimplexObject' to its base class 'boost::python::api::object' will never be used operator bp::object() const { return this; } ^ 1 warning generated. [ 45%] Building CXX object bindings/python/CMakeFiles/_dionysus.dir/dynamic-persistence.o In file included from /Users/devon/TARGet/bindings/python/dynamic-persistence.cpp:8: In file included from /Users/devon/TARGet/bindings/python/filtration.h:6: /Users/devon/TARGet/bindings/python/simplex.h:39:33: warning: conversion function converting 'dionysus::python::SimplexObject' to its base class 'boost::python::api::object' will never be used operator bp::object() const { return this; } ^ 1 warning generated. [ 54%] Building CXX object bindings/python/CMakeFiles/_dionysus.dir/persistence-diagram.o In file included from /Users/devon/TARGet/bindings/python/persistence-diagram.cpp:4: In file included from /Users/devon/TARGet/bindings/python/filtration.h:6: /Users/devon/TARGet/bindings/python/simplex.h:39:33: warning: conversion function converting 'dionysus::python::SimplexObject' to its base class 'boost::python::api::object' will never be used operator bp::object() const { return this; } ^ 1 warning generated. [ 63%] Building CXX object bindings/python/CMakeFiles/_dionysus.dir/simplex.o In file included from /Users/devon/TARGet/bindings/python/simplex.cpp:11: /Users/devon/TARGet/bindings/python/simplex.h:39:33: warning: conversion function converting 'dionysus::python::SimplexObject' to its base class 'boost::python::api::object' will never be used operator bp::object() const { return this; } ^ 1 warning generated. [ 72%] Building CXX object bindings/python/CMakeFiles/_dionysus.dir/birthid.o [ 81%] Building CXX object bindings/python/CMakeFiles/_dionysus.dir/rips.o In file included from /Users/devon/TARGet/bindings/python/rips.cpp:5: In file included from /Users/devon/TARGet/bindings/python/rips.h:7: /Users/devon/TARGet/bindings/python/simplex.h:39:33: warning: conversion function converting 'dionysus::python::SimplexObject' to its base class 'boost::python::api::object' will never be used operator bp::object() const { return this; } ^ 1 warning generated. [ 90%] Building CXX object bindings/python/CMakeFiles/_dionysus.dir/distances.o [100%] Linking CXX shared library lib_dionysus.dylib [100%] Built target _dionysus Scanning dependencies of target dionysus-link failed to create symbolic link '/Users/devon/TARGet/build/bindings/python/dionysus/dionysus.so': No such file or directory make[2]: ** [bindings/python/CMakeFiles/dionysus-link] Error 1 make[1]: * [bindings/python/CMakeFiles/dionysus-link.dir/all] Error 2 make: * [all] Error 2

From there, if I run TARGet on test.fa, it returns:

./TARGet test.fa Traceback (most recent call last): File "./TARGet", line 51, in from dionysus import Rips, Filtration, \ ImportError: No module named dionysus

@devonhum, thanks. This seems to be a different problem: apparently your system is compiling dionysus libraries as .dylib instead of .so. We will also look at it. Unfortunately the amount of time we have to give support is very limited, so it may take a while.

On Tue, May 10, 2016 at 4:49 PM devonhum notifications@github.com wrote:

Sure. I am using Python 2.7.10. This is the output after make:

Scanning dependencies of target _dionysus

[ 9%] Building CXX object bindings/python/CMakeFiles/_dionysus.dir/dionysus.o [ 18%] Building CXX object bindings/python/CMakeFiles/_dionysus.dir/filtration.o In file included from /Users/devon/TARGet/bindings/python/filtration.cpp:9: /Users/devon/TARGet/bindings/python/simplex.h:39:33: warning: conversion function converting 'dionysus::python::SimplexObject' to its base class

'boost::python::api::object' will never be used

operator bp::object() const { return

_this; } ^ 1 warning generated. [ 27%] Building CXX object bindings/python/CMakeFiles/dionysus.dir/chain.o In file included from /Users/devon/TARGet/bindings/python/chain.cpp:8: In file included from /Users/devon/TARGet/bindings/python/chain.h:2: In file included from /Users/devon/TARGet/bindings/python/static-persistence.h:6: In file included from /Users/devon/TARGet/bindings/python/filtration.h:6: /Users/devon/TARGet/bindings/python/simplex.h:39:33: warning: conversion function converting 'dionysus::python::SimplexObject' to its base class

'boost::python::api::object' will never be used*

operator bp::object() const { return _this; } ^ 1 warning generated. [ 36%] Building CXX object bindings/python/CMakeFiles/dionysus.dir/static-persistence.o In file included from /Users/devon/TARGet/bindings/python/static-persistence.cpp:8: In file included from /Users/devon/TARGet/bindings/python/filtration.h:6: /Users/devon/TARGet/bindings/python/simplex.h:39:33: warning: conversion function converting 'dionysus::python::SimplexObject' to its base class

'boost::python::api::object' will never be used*

operator bp::object() const { return _this; } ^ 1 warning generated. [ 45%] Building CXX object bindings/python/CMakeFiles/dionysus.dir/dynamic-persistence.o In file included from /Users/devon/TARGet/bindings/python/dynamic-persistence.cpp:8: In file included from /Users/devon/TARGet/bindings/python/filtration.h:6: /Users/devon/TARGet/bindings/python/simplex.h:39:33: warning: conversion function converting 'dionysus::python::SimplexObject' to its base class

'boost::python::api::object' will never be used*

operator bp::object() const { return _this; } ^ 1 warning generated. [ 54%] Building CXX object bindings/python/CMakeFiles/dionysus.dir/persistence-diagram.o In file included from /Users/devon/TARGet/bindings/python/persistence-diagram.cpp:4: In file included from /Users/devon/TARGet/bindings/python/filtration.h:6: /Users/devon/TARGet/bindings/python/simplex.h:39:33: warning: conversion function converting 'dionysus::python::SimplexObject' to its base class

'boost::python::api::object' will never be used*

operator bp::object() const { return _this; } ^ 1 warning generated. [ 63%] Building CXX object bindings/python/CMakeFiles/dionysus.dir/simplex.o In file included from /Users/devon/TARGet/bindings/python/simplex.cpp:11: /Users/devon/TARGet/bindings/python/simplex.h:39:33: warning: conversion function converting 'dionysus::python::SimplexObject' to its base class

'boost::python::api::object' will never be used*

operator bp::object() const { return _this; } ^ 1 warning generated. [ 72%] Building CXX object bindings/python/CMakeFiles/_dionysus.dir/birthid.o [ 81%] Building CXX object bindings/python/CMakeFiles/dionysus.dir/rips.o In file included from /Users/devon/TARGet/bindings/python/rips.cpp:5: In file included from /Users/devon/TARGet/bindings/python/rips.h:7: /Users/devon/TARGet/bindings/python/simplex.h:39:33: warning: conversion function converting 'dionysus::python::SimplexObject' to its base class

'boost::python::api::object' will never be used*

operator bp::object() const { return _this; } ^ 1 warning generated. [ 90%] Building CXX object bindings/python/CMakeFiles/_dionysus.dir/distances.o [100%] Linking CXX shared library lib_dionysus.dylib [100%] Built target _dionysus Scanning dependencies of target dionysus-link failed to create symbolic link '/Users/devon/TARGet/build/bindings/python/dionysus/dionysus.so': No such file or directory make[2]: ** [bindings/python/CMakeFiles/dionysus-link] Error 1 make[1]: *\ [bindings/python/CMakeFiles/dionysus-link.dir/all] Error 2

make: *\ [all] Error 2

From there, if I run TARGet on test.fa, it returns:

./TARGet test.fa

Traceback (most recent call last):

File "./TARGet", line 51, in

from dionysus import Rips, Filtration, \

ImportError: No module named dionysus

— You are receiving this because you were mentioned.

Reply to this email directly or view it on GitHub https://github.com/RabadanLab/TARGet/issues/12#issuecomment-218286926

No problem, thank you. If you can give me any hint as to where to start to troubleshoot this issue myself, I will also take a stab at it.

Hey, just popping in to add that I am having the same issue; If you need me to run anything to give you more info I'm happy to do so. Also, if I solve my issue, I'll post how I fixed it.

Thanks for letting us know, Izaak. Could you post the output you get from cmake and make commands, please?

On Mon, Jun 6, 2016 at 1:14 AM Izaak Weiss notifications@github.com wrote:

Hey, just popping in to add that I am having the same issue; If you need me to run anything to give you more info I'm happy to do so. Also, if I solve my issue, I'll post how I fixed it.

— You are receiving this because you were mentioned.

Reply to this email directly, view it on GitHub https://github.com/RabadanLab/TARGet/issues/12#issuecomment-223870249, or mute the thread https://github.com/notifications/unsubscribe/AKrj_4ldBRiDhJsOK9Ld41Xu9R3XhujJks5qI6zFgaJpZM4IS9JD .

OK, we have been able to finally reproduce the problem and find a possible work around. For those OSX users (I think Yosemite and later versions) who have the above problem, I think this should work (starting from fresh):

In the file TARGet/bindings/python/CMakeLists.txt replace the following line:

${CMAKE_COMMAND} -E create_symlink ${_dionysus_location} ${CMAKE_CURRENT_BINARY_DIR}/dionysus/_dionysus.so

by:

${CMAKE_COMMAND} -E create_symlink ${_dionysus_location} ${CMAKE_CURRENT_BINARY_DIR}/_dionysus.so

Go back to the folder TARGet and follow the standard instructions for installing TARGet (namely, mkdir build, cd build, cmake .., make)
Then run:

mv bindings/python/_dionysus.so bindings/python/dionysus/_dionysus.so

Please, let me know if it works.

On Mon, Jun 6, 2016 at 5:12 AM Pablo G. Camara pablo.g.camara@gmail.com wrote:

Thanks for letting us know, Izaak. Could you post the output you get from cmake and make commands, please?

On Mon, Jun 6, 2016 at 1:14 AM Izaak Weiss notifications@github.com wrote:

Hey, just popping in to add that I am having the same issue; If you need me to run anything to give you more info I'm happy to do so. Also, if I solve my issue, I'll post how I fixed it.

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I have a similar error. I'm trying to import Dionysus (on Ubuntu 14.04 and similarly on a device with ubuntu 16.04) under jupyter notebook.

After executing the make command it seems everything goes well (no error or warning messages), here the last lines:

[100%] Built target _dionysus Scanning dependencies of target dionysus [100%] Built target dionysus Scanning dependencies of target dionysus-link [100%] Built target dionysus-link

After the installation I added the PYTHONPATH adding the .bashrc the line: export PYTHONPATH=MyHome/Dionysus/build/bindings/python

But when I try to run (the same in the local folder .../build/bindings/python): from Dionysus import * ImportError Traceback (most recent call last)

in () ----> 1 from dionysus import * /MyHome/Dionysus/build/bindings/python/dionysus/**init**.py in () ----> 1 from _dionysus import * 2 from distances import l2, ExplicitDistances, points_file 3 from zigzag import * 4 from adaptor import * 5 import circular ImportError: No module named '_dionysus' in the folder ../bindings/python there is not a file named _dionysus.so Thanks for any help!

So sorry: I realized now that I was using python 3.X and not 2.7. With python 2.7 everything seems to work!

Hi there, I followed the recommendations here and everything run smoothly after I run 'make'. When I thy to run an example I get: La-femputadora-de-mi-amo:build Juanito$ python /Users/Juanito/Dionysus/examples/triangle/triangle.py Traceback (most recent call last): File "/Users/Juanito/Dionysus/examples/triangle/triangle.py", line 1, in from dionysus import Simplex, Filtration, StaticPersistence, \ File "/Users/Juanito/Dionysus/build/bindings/python/dionysus/init.py", line 1, in from _dionysus import File "/Users/Juanito/Dionysus/build/bindings/python/_dionysus/init.py", line 4, in from adaptor import File "/Users/Juanito/Dionysus/build/bindings/python/_dionysus/adaptor.py", line 1, in from _dionysus import CohomologyPersistence, PersistenceDiagram, Cocycle ImportError: cannot import name CohomologyPersistence

also, when I run:

mv bindings/python/_dionysus.so bindings/python/dionysus/_dionysus.so

I get

mv: rename bindings/python/_dionysus.so to bindings/python/dionysus/_dionysus.so: No such file or directory

Thanks a lot for your help

jcfiallo, did you edit CMakeLists.txt as described above? I summarized (some of) the above fixes in the Dionysus repository here.

CamaraLab / TARGet

dionysus not recognized #12

TARGet: Topological inference of horizontal evolution.