Error installing PyEMMA

[bamal]

Hello everyone,

I am trying to install PyEMMA by I got this error:

AssertionError: PyTypeTest on non extension type

Ths is the whole error output:

Collecting pyEMMA
  Using cached https://files.pythonhosted.org/packages/16/67/b086d88f3fdda0263856214dc53484299c0576d749256771b7f15513dcf8/pyEMMA-2.5.5.tar.gz
    Complete output from command python setup.py egg_info:
    Using built-in specs.
    COLLECT_GCC=x86_64-linux-gnu-gcc
    COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/7/lto-wrapper
    OFFLOAD_TARGET_NAMES=nvptx-none
    OFFLOAD_TARGET_DEFAULT=1
    Target: x86_64-linux-gnu
    Configured with: ../src/configure -v --with-pkgversion='Ubuntu 7.3.0-27ubuntu1~18.04' --with-bugurl=file:///usr/share/doc/gcc-7/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++ --prefix=/usr --with-gcc-major-version-only --program-suffix=-7 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-libmpx --enable-plugin --enable-default-pie --with-system-zlib --with-target-system-zlib --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
    Thread model: posix
    gcc version 7.3.0 (Ubuntu 7.3.0-27ubuntu1~18.04)
    C compiler:
    Attempting to autodetect OpenMP support... Compiler supports OpenMP
    Attempting to autodetect SSE3   support... Compiler supports SSE3
    Attempting to autodetect SSE4.1 support... Compiler supports SSE4.1

    Compiling mdtraj/formats/xtc/xtc.pyx because it depends on /usr/local/lib/python3.6/dist-packages/Cython/Includes/numpy/__init__.pxd.
    Compiling mdtraj/formats/xtc/trr.pyx because it depends on /usr/local/lib/python3.6/dist-packages/Cython/Includes/numpy/__init__.pxd.
    Compiling mdtraj/formats/tng/tng.pyx because it depends on /usr/local/lib/python3.6/dist-packages/Cython/Includes/numpy/__init__.pxd.
    Compiling mdtraj/formats/dcd/dcd.pyx because it depends on /usr/local/lib/python3.6/dist-packages/Cython/Includes/numpy/__init__.pxd.
    Compiling mdtraj/formats/binpos/binpos.pyx because it depends on /usr/local/lib/python3.6/dist-packages/Cython/Includes/numpy/__init__.pxd.
    Compiling mdtraj/formats/dtr/dtr.pyx because it depends on /usr/local/lib/python3.6/dist-packages/Cython/Includes/numpy/__init__.pxd.
    Compiling mdtraj/rmsd/_rmsd.pyx because it depends on /usr/local/lib/python3.6/dist-packages/Cython/Includes/cpython/weakref.pxd.
    Compiling mdtraj/rmsd/_lprmsd.pyx because it depends on /usr/local/lib/python3.6/dist-packages/Cython/Includes/libcpp/vector.pxd.
    Compiling mdtraj/geometry/src/_geometry.pyx because it depends on /usr/local/lib/python3.6/dist-packages/Cython/Includes/libcpp/vector.pxd.
    Compiling mdtraj/geometry/neighbors.pyx because it depends on /usr/local/lib/python3.6/dist-packages/Cython/Includes/libcpp/vector.pxd.
    Compiling mdtraj/geometry/neighborlist.pyx because it depends on /usr/local/lib/python3.6/dist-packages/Cython/Includes/libcpp/vector.pxd.
    [ 1/11] Cythonizing mdtraj/formats/binpos/binpos.pyx
    [ 2/11] Cythonizing mdtraj/formats/dcd/dcd.pyx
    [ 3/11] Cythonizing mdtraj/formats/dtr/dtr.pyx
    [ 4/11] Cythonizing mdtraj/formats/tng/tng.pyx
    [ 5/11] Cythonizing mdtraj/formats/xtc/trr.pyx
    [ 6/11] Cythonizing mdtraj/formats/xtc/xtc.pyx
    [ 7/11] Cythonizing mdtraj/geometry/neighborlist.pyx
    [ 8/11] Cythonizing mdtraj/geometry/neighbors.pyx
    [ 9/11] Cythonizing mdtraj/geometry/src/_geometry.pyx
    [10/11] Cythonizing mdtraj/rmsd/_lprmsd.pyx
    [11/11] Cythonizing mdtraj/rmsd/_rmsd.pyx
    In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1809:0,
                     from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                     from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                     from mdtraj/formats/xtc/xtc.c:618:
    /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     #warning "Using deprecated NumPy API, disable it by " \
      ^~~~~~~
    mdtraj/formats/xtc/xtc.c: In function ‘__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_16_write.isra.47’:
    mdtraj/formats/xtc/xtc.c:531:40: warning: ‘__pyx_v_status’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       #define PyInt_FromLong               PyLong_FromLong
                                            ^~~~~~~~~~~~~~~
    mdtraj/formats/xtc/xtc.c:9175:7: note: ‘__pyx_v_status’ was declared here
       int __pyx_v_status;
           ^~~~~~~~~~~~~~
    mdtraj/formats/xtc/xtc.c: In function ‘__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_12_read’:
    mdtraj/formats/xtc/xtc.c:7359:17: warning: ‘__pyx_pybuffernd_framebuffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized]
           } else if (unlikely(__pyx_t_39 >= __pyx_pybuffernd_framebuffer.diminfo[1].shape)) __pyx_t_5 = 1;
                     ^
    mdtraj/formats/xtc/xtc.c:7355:17: warning: ‘__pyx_pybuffernd_framebuffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized]
           } else if (unlikely(__pyx_t_38 >= __pyx_pybuffernd_framebuffer.diminfo[0].shape)) __pyx_t_5 = 0;
                     ^
    mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’:
    mdtraj/formats/xtc/src/xdrfile.c:788:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable]
      int smallnum, smaller, larger, i, is_smaller, run;
                             ^~~~~~
    mdtraj/formats/xtc/src/xdrfile.c:785:16: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable]
      int smallidx, minidx, maxidx;
                    ^~~~~~
    mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’:
    mdtraj/formats/xtc/src/xdrfile.c:1016:6: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable]
      int errval=1;
          ^~~~~~
    mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_double’:
    mdtraj/formats/xtc/src/xdrfile.c:1305:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable]
      int smallnum, smaller, larger, i, is_smaller, run;
                             ^~~~~~
    mdtraj/formats/xtc/src/xdrfile.c:1302:16: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable]
      int smallidx, minidx, maxidx;
                    ^~~~~~
    mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’:
    mdtraj/formats/xtc/src/xdrfile.c:1509:6: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable]
      int errval=1;
          ^~~~~~
    mdtraj/formats/xtc/src/xdrfile_xtc.c: In function ‘xtc_coord’:
    mdtraj/formats/xtc/src/xdrfile_xtc.c:66:8: warning: unused variable ‘j’ [-Wunused-variable]
      int i,j,result;
            ^
    mdtraj/formats/xtc/src/xdrfile_xtc.c:66:6: warning: unused variable ‘i’ [-Wunused-variable]
      int i,j,result;
          ^
    mdtraj/formats/xtc/src/xdrfile_xtc.c: In function ‘read_xtc_nframes’:
    mdtraj/formats/xtc/src/xdrfile_xtc.c:119:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
         if (NULL == xd)
         ^~
    mdtraj/formats/xtc/src/xdrfile_xtc.c:122:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
      do {
      ^~
    In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1809:0,
                     from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                     from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                     from mdtraj/formats/xtc/trr.c:618:
    /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     #warning "Using deprecated NumPy API, disable it by " \
      ^~~~~~~
    mdtraj/formats/xtc/trr.c: In function ‘__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_18_write.isra.48’:
    mdtraj/formats/xtc/trr.c:531:40: warning: ‘__pyx_v_status’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       #define PyInt_FromLong               PyLong_FromLong
                                            ^~~~~~~~~~~~~~~
    mdtraj/formats/xtc/trr.c:10844:7: note: ‘__pyx_v_status’ was declared here
       int __pyx_v_status;
           ^~~~~~~~~~~~~~
    mdtraj/formats/xtc/trr.c: In function ‘__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_14_read’:
    mdtraj/formats/xtc/trr.c:8228:19: warning: ‘__pyx_pybuffernd_forces.diminfo[2].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized]
             } else if (unlikely(__pyx_t_34 >= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_5 = 2;
                       ^
    mdtraj/formats/xtc/trr.c:8224:19: warning: ‘__pyx_pybuffernd_forces.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized]
             } else if (unlikely(__pyx_t_33 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_5 = 1;
                       ^
    mdtraj/formats/xtc/trr.c:1757:90: warning: ‘__pyx_pybuffernd_forces.diminfo[0].strides’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2)
                                                                                              ^
    mdtraj/formats/xtc/trr.c:6746:21: note: ‘__pyx_pybuffernd_forces.diminfo[0].strides’ was declared here
       __Pyx_LocalBuf_ND __pyx_pybuffernd_forces;
                         ^~~~~~~~~~~~~~~~~~~~~~~
    mdtraj/formats/xtc/trr.c:8220:19: warning: ‘__pyx_pybuffernd_forces.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized]
             } else if (unlikely(__pyx_t_32 >= __pyx_pybuffernd_forces.diminfo[0].shape)) __pyx_t_5 = 0;
                       ^
    mdtraj/formats/xtc/trr.c:8171:19: warning: ‘__pyx_pybuffernd_vel.diminfo[2].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized]
             } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_5 = 2;
                       ^
    mdtraj/formats/xtc/trr.c:1757:90: warning: ‘__pyx_pybuffernd_vel.diminfo[0].strides’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2)
                                                                                              ^
    mdtraj/formats/xtc/trr.c:6762:21: note: ‘__pyx_pybuffernd_vel.diminfo[0].strides’ was declared here
       __Pyx_LocalBuf_ND __pyx_pybuffernd_vel;
                         ^~~~~~~~~~~~~~~~~~~~
    mdtraj/formats/xtc/trr.c:8561:17: warning: ‘__pyx_pybuffernd_xyz_buffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized]
           } else if (unlikely(__pyx_t_55 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_5 = 1;
                     ^
    mdtraj/formats/xtc/trr.c:8557:17: warning: ‘__pyx_pybuffernd_xyz_buffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized]
           } else if (unlikely(__pyx_t_54 >= __pyx_pybuffernd_xyz_buffer.diminfo[0].shape)) __pyx_t_5 = 0;
                     ^
    mdtraj/formats/xtc/trr.c:8402:19: warning: ‘__pyx_pybuffernd_vel_buffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized]
             } else if (unlikely(__pyx_t_45 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_5 = 1;
                       ^
    mdtraj/formats/xtc/trr.c:8398:19: warning: ‘__pyx_pybuffernd_vel_buffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized]
             } else if (unlikely(__pyx_t_44 >= __pyx_pybuffernd_vel_buffer.diminfo[0].shape)) __pyx_t_5 = 0;
                       ^
    mdtraj/formats/xtc/trr.c:8454:19: warning: ‘__pyx_pybuffernd_forces_buffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized]
             } else if (unlikely(__pyx_t_47 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_5 = 1;
                       ^
    mdtraj/formats/xtc/trr.c:8450:19: warning: ‘__pyx_pybuffernd_forces_buffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized]
             } else if (unlikely(__pyx_t_46 >= __pyx_pybuffernd_forces_buffer.diminfo[0].shape)) __pyx_t_5 = 0;
                       ^
    mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’:
    mdtraj/formats/xtc/src/xdrfile.c:788:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable]
      int smallnum, smaller, larger, i, is_smaller, run;
                             ^~~~~~
    mdtraj/formats/xtc/src/xdrfile.c:785:16: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable]
      int smallidx, minidx, maxidx;
                    ^~~~~~
    mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’:
    mdtraj/formats/xtc/src/xdrfile.c:1016:6: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable]
      int errval=1;
          ^~~~~~
    mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_double’:
    mdtraj/formats/xtc/src/xdrfile.c:1305:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable]
      int smallnum, smaller, larger, i, is_smaller, run;
                             ^~~~~~
    mdtraj/formats/xtc/src/xdrfile.c:1302:16: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable]
      int smallidx, minidx, maxidx;
                    ^~~~~~
    mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’:
    mdtraj/formats/xtc/src/xdrfile.c:1509:6: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable]
      int errval=1;
          ^~~~~~
    mdtraj/formats/xtc/src/xdrfile_trr.c: In function ‘read_trr_nframes’:
    mdtraj/formats/xtc/src/xdrfile_trr.c:504:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
         if (NULL == xd)
         ^~
    mdtraj/formats/xtc/src/xdrfile_trr.c:507:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
      do {
      ^~
    In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1809:0,
                     from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                     from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                     from mdtraj/formats/tng/tng.c:647:
    /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     #warning "Using deprecated NumPy API, disable it by " \
      ^~~~~~~
    mdtraj/formats/tng/tng.c: In function ‘__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile___cinit__’:
    mdtraj/formats/tng/tng.c:3496:104: warning: comparison between ‘tng_function_status {aka enum <anonymous>}’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare]
       __pyx_t_1 = ((tng_util_trajectory_open(__pyx_v_filename, __pyx_v_self->mode, (&__pyx_v_self->_traj)) == __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
                                                                                                            ^~
    mdtraj/formats/tng/tng.c:3551:88: warning: comparison between ‘tng_function_status {aka enum <anonymous>}’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare]
         __pyx_t_1 = ((tng_num_particles_get(__pyx_v_self->_traj, (&__pyx_v_self->n_atoms)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
                                                                                            ^~
    mdtraj/formats/tng/tng.c:3583:90: warning: comparison between ‘tng_function_status {aka enum <anonymous>}’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare]
         __pyx_t_1 = ((tng_num_frames_get(__pyx_v_self->_traj, (&__pyx_v_self->tot_n_frames)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
                                                                                              ^~
    mdtraj/formats/tng/tng.c:3615:95: warning: comparison between ‘tng_function_status {aka enum <anonymous>}’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare]
         __pyx_t_1 = ((tng_distance_unit_exponential_get(__pyx_v_self->_traj, (&__pyx_v_exponent)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
                                                                                                   ^~
    mdtraj/formats/tng/tng.c:3685:113: warning: comparison between ‘tng_function_status {aka enum <anonymous>}’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare]
         __pyx_t_1 = ((tng_num_frames_per_frame_set_get(__pyx_v_self->_traj, (&__pyx_v_self->_frames_per_frame_set)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
                                                                                                                     ^~
    mdtraj/formats/tng/tng.c:3729:77: warning: comparison between ‘tng_function_status {aka enum <anonymous>}’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare]
         __pyx_t_1 = ((tng_last_program_name_set(__pyx_v_self->_traj, __pyx_t_8) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
                                                                                 ^~
    mdtraj/formats/tng/tng.c: In function ‘__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_8_read_topology’:
    mdtraj/formats/tng/tng.c:4505:106: warning: comparison between ‘tng_function_status {aka enum <anonymous>}’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare]
         __pyx_t_7 = ((tng_chain_name_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
                                                                                                              ^~
    mdtraj/formats/tng/tng.c:4550:108: warning: comparison between ‘tng_function_status {aka enum <anonymous>}’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare]
         __pyx_t_7 = ((tng_residue_name_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
                                                                                                                ^~
    mdtraj/formats/tng/tng.c:4657:115: warning: comparison between ‘tng_function_status {aka enum <anonymous>}’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare]
         __pyx_t_8 = ((tng_global_residue_id_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, (&__pyx_v_residue_id)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
                                                                                                                       ^~
    mdtraj/formats/tng/tng.c:4687:105: warning: comparison between ‘tng_function_status {aka enum <anonymous>}’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare]
         __pyx_t_8 = ((tng_atom_name_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
                                                                                                             ^~
    mdtraj/formats/tng/tng.c:4815:105: warning: comparison between ‘tng_function_status {aka enum <anonymous>}’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare]
         __pyx_t_8 = ((tng_atom_type_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
                                                                                                             ^~
    mdtraj/formats/tng/tng.c:5416:126: warning: comparison between ‘tng_function_status {aka enum <anonymous>}’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare]
       __pyx_t_7 = ((tng_molsystem_bonds_get(__pyx_v_self->_traj, (&__pyx_v_n_bonds), (&__pyx_v_from_atoms), (&__pyx_v_to_atoms)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
                                                                                                                                  ^~
    mdtraj/formats/tng/tng.c: In function ‘__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_10_read_frame’:
    mdtraj/formats/tng/tng.c:5825:152: warning: comparison between ‘tng_function_status {aka enum <anonymous>}’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare]
         __pyx_t_1 = ((tng_util_pos_read_range(__pyx_v_self->_traj, __pyx_v_self->_pos, __pyx_v_self->_pos, (&__pyx_v_positions), (&__pyx_v_stride_length)) == __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
                                                                                                                                                            ^~
    mdtraj/formats/tng/tng.c:6093:108: warning: comparison between ‘tng_function_status {aka enum <anonymous>}’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare]
       __pyx_t_1 = ((tng_util_time_of_frame_get(__pyx_v_self->_traj, __pyx_v_self->_pos, (&__pyx_v_frame_time)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
                                                                                                                ^~
    mdtraj/formats/tng/tng.c:6195:304: warning: comparison between ‘tng_function_status {aka enum <anonymous>}’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare]
         __pyx_t_1 = ((tng_data_vector_interval_get(__pyx_v_self->_traj, __pyx_v_6mdtraj_7formats_3tng_TNG_TRAJ_BOX_SHAPE, __pyx_v_self->_pos, __pyx_v_self->_pos, __pyx_e_6mdtraj_7formats_3tng_TNG_USE_HASH, (&__pyx_v_box_shape), (&__pyx_v_stride_length), (&__pyx_v_n_values_per_frame), (&__pyx_v_data_type)) == __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
                                                                                                                                                                                                                                                                                                                    ^~
    mdtraj/formats/tng/tng.c: In function ‘__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_16write’:
    mdtraj/formats/tng/tng.c:8663:94: warning: comparison between ‘tng_function_status {aka enum <anonymous>}’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare]
         __pyx_t_1 = ((tng_implicit_num_particles_set(__pyx_v_self->_traj, __pyx_v_self->n_atoms) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
                                                                                                  ^~
    mdtraj/formats/tng/tng.c:8695:75: warning: comparison between ‘tng_function_status {aka enum <anonymous>}’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare]
         __pyx_t_1 = ((tng_util_pos_write_interval_set(__pyx_v_self->_traj, 1) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
                                                                               ^~
    mdtraj/formats/tng/tng.c:8727:81: warning: comparison between ‘tng_function_status {aka enum <anonymous>}’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare]
         __pyx_t_1 = ((tng_util_box_shape_write_interval_set(__pyx_v_self->_traj, 1) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
                                                                                     ^~
    mdtraj/formats/tng/tng.c:9018:77: warning: comparison between ‘tng_function_status {aka enum <anonymous>}’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare]
           __pyx_t_9 = ((tng_time_per_frame_set(__pyx_v_self->_traj, __pyx_t_14) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
                                                                                 ^~
    mdtraj/formats/tng/tng.c:9209:372: warning: comparison between ‘tng_function_status {aka enum <anonymous>}’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare]
         __pyx_t_1 = ((tng_util_pos_write(__pyx_v_self->_traj, __pyx_v_self->tot_n_frames, (&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_xyz_array.rcbuffer->pybuffer.buf, __pyx_t_17, __pyx_pybuffernd_xyz_array.diminfo[0].strides, __pyx_t_18, __pyx_pybuffernd_xyz_array.diminfo[1].strides, __pyx_t_19, __pyx_pybuffernd_xyz_array.diminfo[2].strides)))) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
                                                                                                                                                                                                                                                                                                                                                                                        ^~
    mdtraj/formats/tng/tng.c:9261:378: warning: comparison between ‘tng_function_status {aka enum <anonymous>}’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare]
         __pyx_t_1 = ((tng_util_box_shape_write(__pyx_v_self->_traj, __pyx_v_self->tot_n_frames, (&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_box_array.rcbuffer->pybuffer.buf, __pyx_t_20, __pyx_pybuffernd_box_array.diminfo[0].strides, __pyx_t_21, __pyx_pybuffernd_box_array.diminfo[1].strides, __pyx_t_22, __pyx_pybuffernd_box_array.diminfo[2].strides)))) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
                                                                                                                                                                                                                                                                                                                                                                                              ^~
    mdtraj/formats/tng/tng.c:9323:89: warning: comparison between ‘tng_function_status {aka enum <anonymous>}’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare]
           __pyx_t_1 = ((tng_frame_set_first_frame_time_set(__pyx_v_self->_traj, __pyx_t_14) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0);
                                                                                             ^~
    mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_block_header_read’:
    mdtraj/formats/tng/src/lib/tng_io.c:1064:57: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
                     tng_data->input_endianness_swap_func_32 =
                                                             ^
    mdtraj/formats/tng/src/lib/tng_io.c:1073:57: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
                     tng_data->input_endianness_swap_func_64 =
                                                             ^
    mdtraj/formats/tng/src/lib/tng_io.c:1089:57: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
                     tng_data->input_endianness_swap_func_32 =
                                                             ^
    mdtraj/formats/tng/src/lib/tng_io.c:1098:57: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
                     tng_data->input_endianness_swap_func_64 =
                                                             ^
    mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_output_file_endianness_get’:
    mdtraj/formats/tng/src/lib/tng_io.c:9565:53: warning: comparison of distinct pointer types lacks a cast
             if(tng_data->output_endianness_swap_func_32 ==
                                                         ^~
    mdtraj/formats/tng/src/lib/tng_io.c:9570:58: warning: comparison of distinct pointer types lacks a cast
             else if(tng_data->output_endianness_swap_func_32 ==
                                                              ^~
    mdtraj/formats/tng/src/lib/tng_io.c:9588:53: warning: comparison of distinct pointer types lacks a cast
             if(tng_data->output_endianness_swap_func_64 ==
                                                         ^~
    mdtraj/formats/tng/src/lib/tng_io.c:9593:58: warning: comparison of distinct pointer types lacks a cast
             else if(tng_data->output_endianness_swap_func_64 ==
                                                              ^~
    mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_output_file_endianness_set’:
    mdtraj/formats/tng/src/lib/tng_io.c:9651:54: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
                 tng_data->output_endianness_swap_func_32 =
                                                          ^
    mdtraj/formats/tng/src/lib/tng_io.c:9660:54: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
                 tng_data->output_endianness_swap_func_64 =
                                                          ^
    mdtraj/formats/tng/src/lib/tng_io.c:9673:54: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
                 tng_data->output_endianness_swap_func_32 =
                                                          ^
    mdtraj/formats/tng/src/lib/tng_io.c:9682:54: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
                 tng_data->output_endianness_swap_func_64 =
                                                          ^
    In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1809:0,
                     from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                     from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                     from mdtraj/formats/dcd/dcd.c:616:
    /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     #warning "Using deprecated NumPy API, disable it by " \
      ^~~~~~~
    mdtraj/formats/dcd/dcd.c: In function ‘__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read’:
    mdtraj/formats/dcd/dcd.c:529:40: warning: ‘__pyx_v_i’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       #define PyInt_FromLong               PyLong_FromLong
                                            ^~~~~~~~~~~~~~~
    mdtraj/formats/dcd/dcd.c:5206:7: note: ‘__pyx_v_i’ was declared here
       int __pyx_v_i;
           ^~~~~~~~~
    In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1809:0,
                     from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                     from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                     from mdtraj/formats/binpos/binpos.c:616:
    /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     #warning "Using deprecated NumPy API, disable it by " \
      ^~~~~~~
    mdtraj/formats/binpos/binpos.c: In function ‘__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read’:
    mdtraj/formats/binpos/binpos.c:5310:6: warning: ‘__pyx_v_status’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       if (__pyx_t_2) {
          ^
    mdtraj/formats/binpos/binpos.c:4791:7: note: ‘__pyx_v_status’ was declared here
       int __pyx_v_status;
           ^~~~~~~~~~~~~~
    mdtraj/formats/binpos/binpos.c:529:40: warning: ‘__pyx_v_i’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       #define PyInt_FromLong               PyLong_FromLong
                                            ^~~~~~~~~~~~~~~
    mdtraj/formats/binpos/binpos.c:4788:7: note: ‘__pyx_v_i’ was declared here
       int __pyx_v_i;
           ^~~~~~~~~
    mdtraj/formats/binpos/src/binposplugin.c: In function ‘open_binpos_read’:
    mdtraj/formats/binpos/src/binposplugin.c:59:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
       fread(magicchar,sizeof(char),4,fd);
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    mdtraj/formats/binpos/src/binposplugin.c:69:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
       fread(&igarb,sizeof(int),1,fd);
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1809:0,
                     from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                     from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                     from mdtraj/formats/dtr/dtr.cpp:637:
    /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     #warning "Using deprecated NumPy API, disable it by " \
      ^~~~~~~
    mdtraj/formats/dtr/src/dtrplugin.cxx: In member function ‘bool desres::molfile::Timekeys::init(const string&)’:
    mdtraj/formats/dtr/src/dtrplugin.cxx:488:48: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=]
                         keys[i].size(), m_framesize);
                         ~~~~~~~~~~~~~~             ^
    mdtraj/formats/dtr/src/dtrplugin.cxx:488:48: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=]
    mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘std::__cxx11::string framefile(const string&, size_t, size_t, int, int)’:
    mdtraj/formats/dtr/src/dtrplugin.cxx:758:20: warning: ‘%03x’ directive writing between 3 and 8 bytes into a region of size between 0 and 5 [-Wformat-overflow=]
     static std::string framefile( const std::string &dtr,
                        ^~~~~~~~~
    mdtraj/formats/dtr/src/dtrplugin.cxx:758:20: note: directive argument in the range [0, 2147483646]
    In file included from /usr/include/stdio.h:862:0,
                     from mdtraj/formats/dtr/include/molfile_plugin.h:35,
                     from mdtraj/formats/dtr/include/dtrplugin.hxx:46,
                     from mdtraj/formats/dtr/src/dtrplugin.cxx:42:
    /usr/include/x86_64-linux-gnu/bits/stdio2.h:34:43: note: ‘__builtin___sprintf_chk’ output between 9 and 19 bytes into a destination of size 9
           __bos (__s), __fmt, __va_arg_pack ());
                                               ^
    mdtraj/formats/dtr/src/dtrplugin.cxx:758:20: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
     static std::string framefile( const std::string &dtr,
                        ^~~~~~~~~
    In file included from /usr/include/stdio.h:862:0,
                     from mdtraj/formats/dtr/include/molfile_plugin.h:35,
                     from mdtraj/formats/dtr/include/dtrplugin.hxx:46,
                     from mdtraj/formats/dtr/src/dtrplugin.cxx:42:
    /usr/include/x86_64-linux-gnu/bits/stdio2.h:34:43: note: ‘__builtin___sprintf_chk’ output between 5 and 10 bytes into a destination of size 9
           __bos (__s), __fmt, __va_arg_pack ());
                                               ^
    mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘void DDmkdir(const string&, mode_t, int, int)’:
    mdtraj/formats/dtr/src/dtrplugin.cxx:684:6: warning: ‘%03x’ directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=]
     void DDmkdir(const std::string &dirpath, mode_t mode, int ndir1, int ndir2){
          ^~~~~~~
    mdtraj/formats/dtr/src/dtrplugin.cxx:684:6: note: directive argument in the range [0, 2147483647]
    In file included from /usr/include/stdio.h:862:0,
                     from mdtraj/formats/dtr/include/molfile_plugin.h:35,
                     from mdtraj/formats/dtr/include/dtrplugin.hxx:46,
                     from mdtraj/formats/dtr/src/dtrplugin.cxx:42:
    /usr/include/x86_64-linux-gnu/bits/stdio2.h:34:43: note: ‘__builtin___sprintf_chk’ output between 5 and 10 bytes into a destination of size 6
           __bos (__s), __fmt, __va_arg_pack ());
                                               ^
    mdtraj/formats/dtr/src/dtrplugin.cxx:684:6: warning: ‘%03x’ directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=]
     void DDmkdir(const std::string &dirpath, mode_t mode, int ndir1, int ndir2){
          ^~~~~~~
    mdtraj/formats/dtr/src/dtrplugin.cxx:684:6: note: directive argument in the range [0, 2147483647]
    In file included from /usr/include/stdio.h:862:0,
                     from mdtraj/formats/dtr/include/molfile_plugin.h:35,
                     from mdtraj/formats/dtr/include/dtrplugin.hxx:46,
                     from mdtraj/formats/dtr/src/dtrplugin.cxx:42:
    /usr/include/x86_64-linux-gnu/bits/stdio2.h:34:43: note: ‘__builtin___sprintf_chk’ output between 4 and 9 bytes into a destination of size 6
           __bos (__s), __fmt, __va_arg_pack ());
                                               ^
    In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1809:0,
                     from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                     from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                     from mdtraj/rmsd/_lprmsd.cpp:648:
    /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     #warning "Using deprecated NumPy API, disable it by " \
      ^~~~~~~
    mdtraj/rmsd/_lprmsd.cpp: In function ‘PyObject* __pyx_pf_6mdtraj_7_lprmsd_lprmsd(PyObject*, PyObject*, PyObject*, int, PyObject*, PyObject*, PyLongObject*, PyLongObject*)’:
    mdtraj/rmsd/_lprmsd.cpp:3972:14: warning: ‘__pyx_pybuffernd_ref_xyz_frame_dis.__Pyx_LocalBuf_ND::diminfo[0].__Pyx_Buf_DimInfo::shape’ may be used uninitialized in this function [-Wmaybe-uninitialized]
           } else if (unlikely(__pyx_t_52 >= __pyx_pybuffernd_ref_xyz_frame_dis.diminfo[0].shape)) __pyx_t_37 = 0;
                  ^~
    In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1809:0,
                     from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                     from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                     from mdtraj/geometry/src/_geometry.cpp:650:
    /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     #warning "Using deprecated NumPy API, disable it by " \
      ^~~~~~~
    mdtraj/geometry/src/_geometry.cpp: In function ‘void __pyx_f_6mdtraj_8geometry_9_geometry_make_whole(__Pyx_memviewslice, __Pyx_memviewslice, __Pyx_memviewslice)’:
    mdtraj/geometry/src/_geometry.cpp:5498:226: warning: ‘__pyx_v_delta[2]’ may be used uninitialized in this function [-Wmaybe-uninitialized]
           (__pyx_v_offset[__pyx_v_k]) = ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_13 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_14)) ))) * roundf(((__pyx_v_delta[2]) / (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_15 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_16)) ))))));
                                                                                                                                                                                                                                ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    mdtraj/geometry/src/_geometry.cpp:5512:281: warning: ‘__pyx_v_delta[1]’ may be used uninitialized in this function [-Wmaybe-uninitialized]
           (__pyx_v_offset[__pyx_t_17]) = ((__pyx_v_offset[__pyx_t_17]) + ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_18 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_19)) ))) * roundf((((__pyx_v_delta[1]) - (__pyx_v_offset[1])) / (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_20 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_21)) )))))));
                                                                                                                                                                                                                                                                         ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
    mdtraj/geometry/src/_geometry.cpp:5512:281: warning: ‘__pyx_v_offset[1]’ may be used uninitialized in this function [-Wmaybe-uninitialized]

    Installed /tmp/pycharm-packaging2/pyEMMA/.eggs/mdtraj-1.9.2-py3.6-linux-x86_64.egg
    running egg_info
    creating pip-egg-info/pyEMMA.egg-info
    writing pip-egg-info/pyEMMA.egg-info/PKG-INFO
    writing dependency_links to pip-egg-info/pyEMMA.egg-info/dependency_links.txt
    writing entry points to pip-egg-info/pyEMMA.egg-info/entry_points.txt
    writing requirements to pip-egg-info/pyEMMA.egg-info/requires.txt
    /usr/local/lib/python3.6/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/easy_install-8gen3hef/mdtraj-1.9.2/mdtraj/formats/binpos/binpos.pyx
      tree = Parsing.p_module(s, pxd, full_module_name)
    /usr/local/lib/python3.6/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/easy_install-8gen3hef/mdtraj-1.9.2/mdtraj/formats/dcd/dcd.pyx
      tree = Parsing.p_module(s, pxd, full_module_name)
    warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
    warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
    warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
    /usr/local/lib/python3.6/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/easy_install-8gen3hef/mdtraj-1.9.2/mdtraj/formats/dtr/dtr.pyx
      tree = Parsing.p_module(s, pxd, full_module_name)
    /usr/local/lib/python3.6/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/easy_install-8gen3hef/mdtraj-1.9.2/mdtraj/formats/tng/tng.pyx
      tree = Parsing.p_module(s, pxd, full_module_name)
    /usr/local/lib/python3.6/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/easy_install-8gen3hef/mdtraj-1.9.2/mdtraj/formats/xtc/trr.pyx
      tree = Parsing.p_module(s, pxd, full_module_name)
    /usr/local/lib/python3.6/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/easy_install-8gen3hef/mdtraj-1.9.2/mdtraj/formats/xtc/xtc.pyx
      tree = Parsing.p_module(s, pxd, full_module_name)
    /usr/local/lib/python3.6/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/easy_install-8gen3hef/mdtraj-1.9.2/mdtraj/geometry/neighborlist.pyx
      tree = Parsing.p_module(s, pxd, full_module_name)
    /usr/local/lib/python3.6/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/easy_install-8gen3hef/mdtraj-1.9.2/mdtraj/geometry/neighbors.pyx
      tree = Parsing.p_module(s, pxd, full_module_name)
    /usr/local/lib/python3.6/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/easy_install-8gen3hef/mdtraj-1.9.2/mdtraj/geometry/src/_geometry.pyx
      tree = Parsing.p_module(s, pxd, full_module_name)
    /usr/local/lib/python3.6/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/easy_install-8gen3hef/mdtraj-1.9.2/mdtraj/rmsd/_lprmsd.pyx
      tree = Parsing.p_module(s, pxd, full_module_name)
    /usr/local/lib/python3.6/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/easy_install-8gen3hef/mdtraj-1.9.2/mdtraj/rmsd/_rmsd.pyx
      tree = Parsing.p_module(s, pxd, full_module_name)
    Traceback (most recent call last):
      File "Cython/Compiler/Visitor.py", line 180, in Cython.Compiler.Visitor.TreeVisitor._visit
      File "/usr/local/lib/python3.6/dist-packages/Cython/Compiler/ParseTreeTransforms.py", line 2215, in visit_FuncDefNode
        node.body = node.body.analyse_expressions(node.local_scope)
      File "/usr/local/lib/python3.6/dist-packages/Cython/Compiler/Nodes.py", line 436, in analyse_expressions
        for stat in self.stats]
      File "/usr/local/lib/python3.6/dist-packages/Cython/Compiler/Nodes.py", line 436, in <listcomp>
        for stat in self.stats]
      File "/usr/local/lib/python3.6/dist-packages/Cython/Compiler/Nodes.py", line 6669, in analyse_expressions
        self.item = self.item.coerce_to(self.target.type, env)
      File "/usr/local/lib/python3.6/dist-packages/Cython/Compiler/ExprNodes.py", line 950, in coerce_to
        src = PyTypeTestNode(src, dst_type, env)
      File "/usr/local/lib/python3.6/dist-packages/Cython/Compiler/ExprNodes.py", line 12984, in __init__
        assert dst_type.is_extension_type or dst_type.is_builtin_type, "PyTypeTest on non extension type"
    AssertionError: PyTypeTest on non extension type

    During handling of the above exception, another exception occurred:

    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pycharm-packaging2/pyEMMA/setup.py", line 427, in <module>
        setup(**metadata)
      File "/usr/lib/python3/dist-packages/setuptools/__init__.py", line 129, in setup
        return distutils.core.setup(**attrs)
      File "/usr/lib/python3.6/distutils/core.py", line 148, in setup
        dist.run_commands()
      File "/usr/lib/python3.6/distutils/dist.py", line 955, in run_commands
        self.run_command(cmd)
      File "/usr/lib/python3.6/distutils/dist.py", line 974, in run_command
        cmd_obj.run()
      File "/usr/lib/python3/dist-packages/setuptools/command/egg_info.py", line 271, in run
        writer(self, ep.name, os.path.join(self.egg_info, ep.name))
      File "/usr/lib/python3/dist-packages/setuptools/command/egg_info.py", line 649, in write_toplevel_names
        for k in cmd.distribution.iter_distribution_names()
      File "/usr/lib/python3/dist-packages/setuptools/command/egg_info.py", line 648, in <listcomp>
        k.split('.', 1)[0]
      File "/usr/lib/python3/dist-packages/setuptools/dist.py", line 874, in iter_distribution_names
        for ext in self.ext_modules or ():
      File "/tmp/pycharm-packaging2/pyEMMA/setup_util.py", line 155, in __len__
        def __len__(self): return len(self.c_list())
      File "/tmp/pycharm-packaging2/pyEMMA/setup_util.py", line 150, in c_list
        if self._list is None: self._list = self.callback()
      File "/tmp/pycharm-packaging2/pyEMMA/setup.py", line 238, in extensions
        exts = cythonize(exts, language_level=sys.version_info[0])
      File "/usr/local/lib/python3.6/dist-packages/Cython/Build/Dependencies.py", line 1097, in cythonize
        cythonize_one(*args)
      File "/usr/local/lib/python3.6/dist-packages/Cython/Build/Dependencies.py", line 1203, in cythonize_one
        result = compile_single(pyx_file, options, full_module_name=full_module_name)
      File "/usr/local/lib/python3.6/dist-packages/Cython/Compiler/Main.py", line 725, in compile_single
        return run_pipeline(source, options, full_module_name)
      File "/usr/local/lib/python3.6/dist-packages/Cython/Compiler/Main.py", line 513, in run_pipeline
        err, enddata = Pipeline.run_pipeline(pipeline, source)
      File "/usr/local/lib/python3.6/dist-packages/Cython/Compiler/Pipeline.py", line 355, in run_pipeline
        data = run(phase, data)
      File "/usr/local/lib/python3.6/dist-packages/Cython/Compiler/Pipeline.py", line 335, in run
        return phase(data)
      File "/usr/local/lib/python3.6/dist-packages/Cython/Compiler/ParseTreeTransforms.py", line 1597, in __call__
        return super_class.__call__(root)
      File "Cython/Compiler/Visitor.py", line 355, in Cython.Compiler.Visitor.EnvTransform.__call__
      File "Cython/Compiler/Visitor.py", line 302, in Cython.Compiler.Visitor.CythonTransform.__call__
      File "Cython/Compiler/Visitor.py", line 284, in Cython.Compiler.Visitor.VisitorTransform.__call__
      File "Cython/Compiler/Visitor.py", line 182, in Cython.Compiler.Visitor.TreeVisitor._visit
      File "Cython/Compiler/Visitor.py", line 180, in Cython.Compiler.Visitor.TreeVisitor._visit
      File "/usr/local/lib/python3.6/dist-packages/Cython/Compiler/ParseTreeTransforms.py", line 1607, in visit_ModuleNode
        node.analyse_declarations(self.current_env())
      File "/usr/local/lib/python3.6/dist-packages/Cython/Compiler/ModuleNode.py", line 124, in analyse_declarations
        self.body.analyse_declarations(env)
      File "/usr/local/lib/python3.6/dist-packages/Cython/Compiler/Nodes.py", line 431, in analyse_declarations
        stat.analyse_declarations(env)
      File "/usr/local/lib/python3.6/dist-packages/Cython/Compiler/Nodes.py", line 431, in analyse_declarations
        stat.analyse_declarations(env)
      File "/usr/local/lib/python3.6/dist-packages/Cython/Compiler/Nodes.py", line 7906, in analyse_declarations
        self.module_name, self.pos, relative_level=0 if self.is_absolute else -1)
      File "/usr/local/lib/python3.6/dist-packages/Cython/Compiler/Symtab.py", line 1270, in find_module
        module_name, relative_to=relative_to, pos=pos, absolute_fallback=absolute_fallback)
      File "/usr/local/lib/python3.6/dist-packages/Cython/Compiler/Main.py", line 235, in find_module
        err, result = self.process_pxd(source_desc, scope, qualified_name)
      File "/usr/local/lib/python3.6/dist-packages/Cython/Compiler/Main.py", line 149, in process_pxd
        result = Pipeline.run_pipeline(pipeline, source_desc)
      File "/usr/local/lib/python3.6/dist-packages/Cython/Compiler/Pipeline.py", line 355, in run_pipeline
        data = run(phase, data)
      File "/usr/local/lib/python3.6/dist-packages/Cython/Compiler/Pipeline.py", line 335, in run
        return phase(data)
      File "Cython/Compiler/Visitor.py", line 302, in Cython.Compiler.Visitor.CythonTransform.__call__
      File "Cython/Compiler/Visitor.py", line 284, in Cython.Compiler.Visitor.VisitorTransform.__call__
      File "Cython/Compiler/Visitor.py", line 182, in Cython.Compiler.Visitor.TreeVisitor._visit
      File "Cython/Compiler/Visitor.py", line 180, in Cython.Compiler.Visitor.TreeVisitor._visit
      File "/usr/local/lib/python3.6/dist-packages/Cython/Compiler/ParseTreeTransforms.py", line 2210, in visit_ModuleNode
        self.visitchildren(node)
      File "Cython/Compiler/Visitor.py", line 247, in Cython.Compiler.Visitor.VisitorTransform.visitchildren
      File "Cython/Compiler/Visitor.py", line 251, in Cython.Compiler.Visitor.VisitorTransform.visitchildren
      File "Cython/Compiler/Visitor.py", line 260, in Cython.Compiler.Visitor.VisitorTransform._process_children
      File "Cython/Compiler/Visitor.py", line 221, in Cython.Compiler.Visitor.TreeVisitor._visitchildren
      File "Cython/Compiler/Visitor.py", line 193, in Cython.Compiler.Visitor.TreeVisitor._visitchild
      File "Cython/Compiler/Visitor.py", line 182, in Cython.Compiler.Visitor.TreeVisitor._visit
      File "Cython/Compiler/Visitor.py", line 180, in Cython.Compiler.Visitor.TreeVisitor._visit
      File "Cython/Compiler/Visitor.py", line 312, in Cython.Compiler.Visitor.CythonTransform.visit_Node
      File "Cython/Compiler/Visitor.py", line 260, in Cython.Compiler.Visitor.VisitorTransform._process_children
      File "Cython/Compiler/Visitor.py", line 219, in Cython.Compiler.Visitor.TreeVisitor._visitchildren
      File "Cython/Compiler/Visitor.py", line 193, in Cython.Compiler.Visitor.TreeVisitor._visitchild
      File "Cython/Compiler/Visitor.py", line 182, in Cython.Compiler.Visitor.TreeVisitor._visit
      File "Cython/Compiler/Visitor.py", line 180, in Cython.Compiler.Visitor.TreeVisitor._visit
      File "Cython/Compiler/Visitor.py", line 312, in Cython.Compiler.Visitor.CythonTransform.visit_Node
      File "Cython/Compiler/Visitor.py", line 260, in Cython.Compiler.Visitor.VisitorTransform._process_children
      File "Cython/Compiler/Visitor.py", line 219, in Cython.Compiler.Visitor.TreeVisitor._visitchildren
      File "Cython/Compiler/Visitor.py", line 193, in Cython.Compiler.Visitor.TreeVisitor._visitchild
      File "Cython/Compiler/Visitor.py", line 188, in Cython.Compiler.Visitor.TreeVisitor._visit
      File "Cython/Compiler/Visitor.py", line 148, in Cython.Compiler.Visitor.TreeVisitor._raise_compiler_error
    Cython.Compiler.Errors.CompilerCrash:
    Error compiling Cython file:
    ------------------------------------------------------------
    ...
        if PyDataType_HASSUBARRAY(d):
            return <tuple>d.subarray.shape
        else:
            return ()

    cdef inline char* _util_dtypestring(dtype descr, char* f, char* end, int* offset) except NULL:
        ^
    ------------------------------------------------------------

    /usr/local/lib/python3.6/dist-packages/Cython/Includes/numpy/__init__.pxd:842:5: Compiler crash in AnalyseExpressionsTransform

    ModuleNode.body = StatListNode(__init__.pxd:17:0)
    StatListNode.stats[41] = StatListNode(__init__.pxd:842:5)
    StatListNode.stats[0] = CFuncDefNode(__init__.pxd:842:5,
        args = [...]/4,
        inline_in_pxd = True,
        modifiers = [...]/1,
        visibility = 'private')

    Compiler crash traceback from this point on:
      File "Cython/Compiler/Visitor.py", line 180, in Cython.Compiler.Visitor.TreeVisitor._visit
      File "/usr/local/lib/python3.6/dist-packages/Cython/Compiler/ParseTreeTransforms.py", line 2215, in visit_FuncDefNode
        node.body = node.body.analyse_expressions(node.local_scope)
      File "/usr/local/lib/python3.6/dist-packages/Cython/Compiler/Nodes.py", line 436, in analyse_expressions
        for stat in self.stats]
      File "/usr/local/lib/python3.6/dist-packages/Cython/Compiler/Nodes.py", line 436, in <listcomp>
        for stat in self.stats]
      File "/usr/local/lib/python3.6/dist-packages/Cython/Compiler/Nodes.py", line 6669, in analyse_expressions
        self.item = self.item.coerce_to(self.target.type, env)
      File "/usr/local/lib/python3.6/dist-packages/Cython/Compiler/ExprNodes.py", line 950, in coerce_to
        src = PyTypeTestNode(src, dst_type, env)
      File "/usr/local/lib/python3.6/dist-packages/Cython/Compiler/ExprNodes.py", line 12984, in __init__
        assert dst_type.is_extension_type or dst_type.is_builtin_type, "PyTypeTest on non extension type"
    AssertionError: PyTypeTest on non extension type
    Compiling pyemma/_ext/orderedset/_orderedset.pyx because it depends on /usr/local/lib/python3.6/dist-packages/Cython/Includes/cpython/weakref.pxd.
    Compiling pyemma/thermo/extensions/bar/bar.pyx because it depends on /usr/local/lib/python3.6/dist-packages/Cython/Includes/numpy/__init__.pxd.
    Compiling pyemma/thermo/extensions/wham/wham.pyx because it depends on /usr/local/lib/python3.6/dist-packages/Cython/Includes/numpy/__init__.pxd.
    Compiling pyemma/thermo/extensions/mbar/mbar.pyx because it depends on /usr/local/lib/python3.6/dist-packages/Cython/Includes/numpy/__init__.pxd.
    Compiling pyemma/thermo/extensions/tram/tram.pyx because it depends on /usr/local/lib/python3.6/dist-packages/Cython/Includes/numpy/__init__.pxd.
    Compiling pyemma/thermo/extensions/dtram/dtram.pyx because it depends on /usr/local/lib/python3.6/dist-packages/Cython/Includes/numpy/__init__.pxd.
    Compiling pyemma/thermo/extensions/trammbar/trammbar.pyx because it depends on /usr/local/lib/python3.6/dist-packages/Cython/Includes/numpy/__init__.pxd.
    Compiling pyemma/thermo/extensions/mbar_direct/mbar_direct.pyx because it depends on /usr/local/lib/python3.6/dist-packages/Cython/Includes/numpy/__init__.pxd.
    Compiling pyemma/thermo/extensions/tram_direct/tram_direct.pyx because it depends on /usr/local/lib/python3.6/dist-packages/Cython/Includes/numpy/__init__.pxd.
    Compiling pyemma/thermo/extensions/trammbar_direct/trammbar_direct.pyx because it depends on /usr/local/lib/python3.6/dist-packages/Cython/Includes/numpy/__init__.pxd.
    Compiling pyemma/thermo/extensions/util/util.pyx because it depends on /usr/local/lib/python3.6/dist-packages/Cython/Includes/numpy/__init__.pxd.
    [ 1/11] Cythonizing pyemma/thermo/extensions/bar/bar.pyx

    ----------------------------------------

Command "python setup.py egg_info" failed with error code 1 in /tmp/pycharm-packaging2/pyEMMA/

I am under Ubunutu 18.04 version using Python 3.6 . DO you please have insights on how to fix this ?

[marscher]

you could try upgrading your Cython version.

[marscher]

Please re-open, if it is still an reproducible issue.