{"action":"created","issue":{"url":"https://api.github.com/repos/pandegroup/openmm/issues/1595","repository_url":"https://api.github.com/repos/pandegroup/openmm","labels_url":"https://api.github.com/repos/pandegroup/openmm/issues/1595/labels{/name}","comments_url":"https://api.github.com/repos/pandegroup/openmm/issues/1595/comments","events_url":"https://api.github.com/repos/pandegroup/openmm/issues/1595/events","html_url":"https://github.com/pandegroup/openmm/issues/1595","id":178762184,"number":1595,"title":"Undefined symbol when using python -m simtk.testInstallation","user":{"login":"jlerche","id":1338200,"avatar_url":"https://avatars.githubusercontent.com/u/1338200?v=3","gravatar_id":"","url":"https://api.github.com/users/jlerche","html_url":"https://github.com/jlerche","followers_url":"https://api.github.com/users/jlerche/followers","following_url":"https://api.github.com/users/jlerche/following{/other_user}","gists_url":"https://api.github.com/users/jlerche/gists{/gist_id}","starred_url":"https://api.github.com/users/jlerche/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jlerche/subscriptions","organizations_url":"https://api.github.com/users/jlerche/orgs","repos_url":"https://api.github.com/users/jlerche/repos","events_url":"https://api.github.com/users/jlerche/events{/privacy}","received_events_url":"https://api.github.com/users/jlerche/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":5,"created_at":"2016-09-23T01:32:59Z","updated_at":"2016-09-23T15:35:40Z","closed_at":null,"body":"I'm in Ubuntu 16.04 with gcc 5.4, I tried compiling the master branch and everything seemed to work until the make PythonInstall step where I see this\r\n\r\n```\r\nbuilding 'simtk.openmm._openmm' extension\r\ngcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -DMAJOR_VERSION=7 -DMINOR_VERSION=0 -I/home/lerche/libraries/openmm/openmm-master/./include -I/home/lerche/libraries/openmm/openmm-master/./include/openmm -I/home/lerche/libraries/openmm/openmm-master/./include/openmm/internal -I/home/lerche/libraries/openmm/openmm-master/openmmapi/include -I/home/lerche/libraries/openmm/openmm-master/openmmapi/include/openmm -I/home/lerche/libraries/openmm/openmm-master/openmmapi/include/openmm/internal -I/home/lerche/libraries/openmm/openmm-master/olla/include -I/home/lerche/libraries/openmm/openmm-master/olla/include/openmm -I/home/lerche/libraries/openmm/openmm-master/olla/include/openmm/internal -I/home/lerche/libraries/openmm/openmm-master/serialization/include -I/home/lerche/libraries/openmm/openmm-master/serialization/include/openmm -I/home/lerche/libraries/openmm/openmm-master/serialization/include/openmm/internal -I/home/lerche/libraries/openmm/openmm-master/plugins/amoeba/openmmapi/include -I/home/lerche/libraries/openmm/openmm-master/plugins/amoeba/openmmapi/include/openmm -I/home/lerche/libraries/openmm/openmm-master/plugins/amoeba/openmmapi/include/openmm/internal -I/home/lerche/libraries/openmm/openmm-master/plugins/rpmd/openmmapi/include -I/home/lerche/libraries/openmm/openmm-master/plugins/rpmd/openmmapi/include/openmm -I/home/lerche/libraries/openmm/openmm-master/plugins/rpmd/openmmapi/include/openmm/internal -I/home/lerche/libraries/openmm/openmm-master/plugins/drude/openmmapi/include -I/home/lerche/libraries/openmm/openmm-master/plugins/drude/openmmapi/include/openmm -I/home/lerche/libraries/openmm/openmm-master/plugins/drude/openmmapi/include/openmm/internal -I/home/lerche/miniconda2/include/python2.7 -c src/swig_doxygen/OpenMMSwig.cxx -o build/temp.linux-x86_64-2.7/src/swig_doxygen/OpenMMSwig.o\r\ncc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++\r\nIn file included from /home/lerche/libraries/openmm/openmm-master/openmmapi/include/OpenMM.h:52:0,\r\n                 from src/swig_doxygen/OpenMMSwig.cxx:6662:\r\n/home/lerche/libraries/openmm/openmm-master/openmmapi/include/openmm/GayBerneForce.h: In constructor ‘OpenMM::GayBerneForce::ParticleInfo::ParticleInfo(double, double, int, int, double, double, double, double, double, double)’:\r\n/home/lerche/libraries/openmm/openmm-master/openmmapi/include/openmm/GayBerneForce.h:286:19: warning: ‘OpenMM::GayBerneForce::ParticleInfo::epsilon’ will be initialized after [-Wreorder]\r\n     double sigma, epsilon, sx, sy, sz, ex, ey, ez;\r\n                   ^\r\n/home/lerche/libraries/openmm/openmm-master/openmmapi/include/openmm/GayBerneForce.h:285:9: warning:   ‘int OpenMM::GayBerneForce::ParticleInfo::xparticle’ [-Wreorder]\r\n     int xparticle, yparticle;\r\n         ^\r\n/home/lerche/libraries/openmm/openmm-master/openmmapi/include/openmm/GayBerneForce.h:291:5: warning:   when initialized here [-Wreorder]\r\n     ParticleInfo(double sigma, double epsilon, int xparticle, int yparticle, double sx, double sy, double sz, double ex, double ey, double ez) :\r\n     ^\r\ng++ -pthread -shared -L/home/lerche/miniconda2/lib -Wl,-rpath=/home/lerche/miniconda2/lib,--no-as-needed build/temp.linux-x86_64-2.7/src/swig_doxygen/OpenMMSwig.o -L/usr/local/openmm/lib -L/home/lerche/miniconda2/lib -Wl,-R/usr/local/openmm/lib -lOpenMM -lOpenMMAmoeba -lOpenMMRPMD -lOpenMMDrude -lpython2.7 -o build/lib.linux-x86_64-2.7/simtk/openmm/_openmm.so\r\n```\r\n\r\nEverything else seems to proceed smoothly but then\r\n```\r\n> python -m simtk.testInstallation\r\nFailed to import OpenMM packages; OpenMM will not work.\r\nMake sure OpenMM is installed and the library path is set correctly.\r\n\r\nError message: /home/lerche/miniconda2/lib/python2.7/site-packages/simtk/openmm/_openmm.so: undefined symbol: _ZTVN6OpenMM13GayBerneForceE\r\n```\r\n\r\nThe symbol `_ZTVN6OpenMM13GayBerneForceE` is the same one that gave me trouble above."},"comment":{"url":"https://api.github.com/repos/pandegroup/openmm/issues/comments/249225633","html_url":"https://github.com/pandegroup/openmm/issues/1595#issuecomment-249225633","issue_url":"https://api.github.com/repos/pandegroup/openmm/issues/1595","id":249225633,"user":{"login":"jlerche","id":1338200,"avatar_url":"https://avatars.githubusercontent.com/u/1338200?v=3","gravatar_id":"","url":"https://api.github.com/users/jlerche","html_url":"https://github.com/jlerche","followers_url":"https://api.github.com/users/jlerche/followers","following_url":"https://api.github.com/users/jlerche/following{/other_user}","gists_url":"https://api.github.com/users/jlerche/gists{/gist_id}","starred_url":"https://api.github.com/users/jlerche/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jlerche/subscriptions","organizations_url":"https://api.github.com/users/jlerche/orgs","repos_url":"https://api.github.com/users/jlerche/repos","events_url":"https://api.github.com/users/jlerche/events{/privacy}","received_events_url":"https://api.github.com/users/jlerche/received_events","type":"User","site_admin":false},"created_at":"2016-09-23T15:35:40Z","updated_at":"2016-09-23T15:35:40Z","body":"Yep"}}
{"actor":{"display_login":"jlerche"}}