Install Errors

[nschiraldi]

I'm struggling to install tick on Oracle Linux Server 7.5, with Python 3.6.5. I've looked at #273 and and #262 but haven't been able to troubleshoot off of the information from either. I have tried to build source and install via pip.

Any help is greatly appreciated.

pip causes this module import error:

ModuleNotFoundError                       Traceback (most recent call last)
~/anaconda3/lib/python3.6/site-packages/tick/tick/array/build/array.py in swig_import_helper()
     14     try:
---> 15         return importlib.import_module(mname)
     16     except ImportError:

~/anaconda3/lib/python3.6/importlib/__init__.py in import_module(name, package)
    125             level += 1
--> 126     return _bootstrap._gcd_import(name[level:], package, level)
    127

~/anaconda3/lib/python3.6/importlib/_bootstrap.py in _gcd_import(name, package, level)

~/anaconda3/lib/python3.6/importlib/_bootstrap.py in _find_and_load(name, import_)

~/anaconda3/lib/python3.6/importlib/_bootstrap.py in _find_and_load_unlocked(name, import_)

ModuleNotFoundError: No module named 'tick.array.build._array'

During handling of the above exception, another exception occurred:

ModuleNotFoundError                       Traceback (most recent call last)
<ipython-input-1-41e470d8e362> in <module>()
----> 1 import tick

~/anaconda3/lib/python3.6/site-packages/tick/tick/__init__.py in <module>()
      4 # License: BSD 3 clause
      5
----> 6 import tick.base

~/anaconda3/lib/python3.6/site-packages/tick/tick/base/__init__.py in <module>()
     21 _set_mpl_backend()
     22
---> 23 from tick.array import *
     24 from ..random import *
     25 from .timefunc import TimeFunction

~/anaconda3/lib/python3.6/site-packages/tick/tick/array/__init__.py in <module>()
      1 # License: BSD 3 clause
      2
----> 3 from .build import array

~/anaconda3/lib/python3.6/site-packages/tick/tick/array/build/array.py in <module>()
     16     except ImportError:
     17         return importlib.import_module('_array')
---> 18 _array = swig_import_helper()
     19 del swig_import_helper
     20 del _swig_python_version_info

~/anaconda3/lib/python3.6/site-packages/tick/tick/array/build/array.py in swig_import_helper()
     15         return importlib.import_module(mname)
     16     except ImportError:
---> 17         return importlib.import_module('_array')
     18 _array = swig_import_helper()
     19 del swig_import_helper

~/anaconda3/lib/python3.6/importlib/__init__.py in import_module(name, package)
    124                 break
    125             level += 1
--> 126     return _bootstrap._gcd_import(name[level:], package, level)
    127
    128

ModuleNotFoundError: No module named '_array'

And here is the source build:

git clone https://github.com/X-DataInitiative/tick.git
git submodule update --init
python3 setup.py build_ext --inplace bdist_wheel

creating build/temp.linux-x86_64-3.6/lib/cpp/solver
compile options: '-Iinclude -Ilib/third_party/cereal/include -I/network/rit/home/ab669414/anaconda3/lib/python3.6/site-packages/numpy/core/include -I/network/rit/home/ab669414/anaconda3/include/python3.6m -c'
extra options: '-D_FILE_OFFSET_BITS=64 -DPYTHON_LINK -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -Ilib/include -DTICK_SPARSE_INDICES_INT32 -std=c++11 -O2 -DNDEBUG -ffast-math -Wall -Werror -Wno-uninitialized -Isrc/swig/solver -Ilib/swig/array -Ilib/swig/base -Ilib/swig/random -Ilib/swig/base_model -Ilib/swig/linear_model -Ilib/swig/prox -Ilib/swig/robust -DDEBUG_COSTLY_THROW'
gcc: lib/swig/solver/solver_module_wrap.cpp
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default]
gcc: lib/cpp/solver/sgd.cpp
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default]
gcc: lib/cpp/solver/adagrad.cpp
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default]
gcc: lib/cpp/solver/svrg.cpp
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default]
gcc: lib/cpp/solver/asaga.cpp
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default]
In file included from lib/include/tick/solver/saga.h:6:0,
                 from lib/include/tick/solver/asaga.h:8,
                 from lib/cpp/solver/asaga.cpp:3:
lib/cpp/solver/asaga.cpp: In instantiation of ‘AtomicSAGA<T>::solve(int) [with T = double]::__lambda54’:
lib/cpp/solver/asaga.cpp:103:57:   required from ‘struct AtomicSAGA<T>::solve(int) [with T = double]::__lambda54’
lib/cpp/solver/asaga.cpp:129:3:   required from ‘void AtomicSAGA<T>::solve(int) [with T = double]’
lib/cpp/solver/asaga.cpp:140:27:   required from here
lib/include/tick/solver/sto_solver.h:48:13: error: ‘ulong TStoSolver<double, double>::t’ is protected
   ulong t = 1;
             ^
lib/cpp/solver/asaga.cpp:111:29: error: within this context
         TStoSolver<T, T>::t += epoch_size;
                             ^
In file included from lib/include/tick/solver/saga.h:6:0,
                 from lib/include/tick/solver/asaga.h:8,
                 from lib/cpp/solver/asaga.cpp:3:
lib/cpp/solver/asaga.cpp: In instantiation of ‘AtomicSAGA<T>::solve(int) [with T = float]::__lambda54’:
lib/cpp/solver/asaga.cpp:103:57:   required from ‘struct AtomicSAGA<T>::solve(int) [with T = float]::__lambda54’
lib/cpp/solver/asaga.cpp:129:3:   required from ‘void AtomicSAGA<T>::solve(int) [with T = float]’
lib/cpp/solver/asaga.cpp:141:27:   required from here
lib/include/tick/solver/sto_solver.h:48:13: error: ‘ulong TStoSolver<float, float>::t’ is protected
   ulong t = 1;
             ^
lib/cpp/solver/asaga.cpp:111:29: error: within this context
         TStoSolver<T, T>::t += epoch_size;
                             ^
In file included from /usr/include/c++/4.8.2/vector:69:0,
                 from lib/include/tick/array/array.h:14,
                 from lib/include/tick/base/math/normal_distribution.h:10,
                 from lib/include/tick/base/base.h:19,
                 from lib/include/tick/solver/sto_solver.h:10,
                 from lib/include/tick/solver/saga.h:6,
                 from lib/include/tick/solver/asaga.h:8,
                 from lib/cpp/solver/asaga.cpp:3:
/usr/include/c++/4.8.2/bits/vector.tcc:91:7: error: ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {AtomicSAGA<T>::solve(int) [with T = double]::__lambda54&, long unsigned int&}; _Tp = std::thread; _Alloc = std::allocator<std::thread>]’, declared using local type ‘AtomicSAGA<T>::solve(int) [with T = double]::__lambda54’, is used but never defined [-fpermissive]
       vector<_Tp, _Alloc>::
       ^
/usr/include/c++/4.8.2/bits/vector.tcc:91:7: error: ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {AtomicSAGA<T>::solve(int) [with T = float]::__lambda54&, long unsigned int&}; _Tp = std::thread; _Alloc = std::allocator<std::thread>]’, declared using local type ‘AtomicSAGA<T>::solve(int) [with T = float]::__lambda54’, is used but never defined [-fpermissive]
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default]
In file included from lib/include/tick/solver/saga.h:6:0,
                 from lib/include/tick/solver/asaga.h:8,
                 from lib/cpp/solver/asaga.cpp:3:
lib/cpp/solver/asaga.cpp: In instantiation of ‘AtomicSAGA<T>::solve(int) [with T = double]::__lambda54’:
lib/cpp/solver/asaga.cpp:103:57:   required from ‘struct AtomicSAGA<T>::solve(int) [with T = double]::__lambda54’
lib/cpp/solver/asaga.cpp:129:3:   required from ‘void AtomicSAGA<T>::solve(int) [with T = double]’
lib/cpp/solver/asaga.cpp:140:27:   required from here
lib/include/tick/solver/sto_solver.h:48:13: error: ‘ulong TStoSolver<double, double>::t’ is protected
   ulong t = 1;
             ^
lib/cpp/solver/asaga.cpp:111:29: error: within this context
         TStoSolver<T, T>::t += epoch_size;
                             ^
In file included from lib/include/tick/solver/saga.h:6:0,
                 from lib/include/tick/solver/asaga.h:8,
                 from lib/cpp/solver/asaga.cpp:3:
lib/cpp/solver/asaga.cpp: In instantiation of ‘AtomicSAGA<T>::solve(int) [with T = float]::__lambda54’:
lib/cpp/solver/asaga.cpp:103:57:   required from ‘struct AtomicSAGA<T>::solve(int) [with T = float]::__lambda54’
lib/cpp/solver/asaga.cpp:129:3:   required from ‘void AtomicSAGA<T>::solve(int) [with T = float]’
lib/cpp/solver/asaga.cpp:141:27:   required from here
lib/include/tick/solver/sto_solver.h:48:13: error: ‘ulong TStoSolver<float, float>::t’ is protected
   ulong t = 1;
             ^
lib/cpp/solver/asaga.cpp:111:29: error: within this context
         TStoSolver<T, T>::t += epoch_size;
                             ^
In file included from /usr/include/c++/4.8.2/vector:69:0,
                 from lib/include/tick/array/array.h:14,
                 from lib/include/tick/base/math/normal_distribution.h:10,
                 from lib/include/tick/base/base.h:19,
                 from lib/include/tick/solver/sto_solver.h:10,
                 from lib/include/tick/solver/saga.h:6,
                 from lib/include/tick/solver/asaga.h:8,
                 from lib/cpp/solver/asaga.cpp:3:
/usr/include/c++/4.8.2/bits/vector.tcc:91:7: error: ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {AtomicSAGA<T>::solve(int) [with T = double]::__lambda54&, long unsigned int&}; _Tp = std::thread; _Alloc = std::allocator<std::thread>]’, declared using local type ‘AtomicSAGA<T>::solve(int) [with T = double]::__lambda54’, is used but never defined [-fpermissive]
       vector<_Tp, _Alloc>::
       ^
/usr/include/c++/4.8.2/bits/vector.tcc:91:7: error: ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {AtomicSAGA<T>::solve(int) [with T = float]::__lambda54&, long unsigned int&}; _Tp = std::thread; _Alloc = std::allocator<std::thread>]’, declared using local type ‘AtomicSAGA<T>::solve(int) [with T = float]::__lambda54’, is used but never defined [-fpermissive]
error: Command "gcc -pthread -B /network/rit/home/ab669414/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Iinclude -Ilib/third_party/cereal/include -I/network/rit/home/ab669414/anaconda3/lib/python3.6/site-packages/numpy/core/include -I/network/rit/home/ab669414/anaconda3/include/python3.6m -c lib/cpp/solver/asaga.cpp -o build/temp.linux-x86_64-3.6/lib/cpp/solver/asaga.o -D_FILE_OFFSET_BITS=64 -DPYTHON_LINK -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -Ilib/include -DTICK_SPARSE_INDICES_INT32 -std=c++11 -O2 -DNDEBUG -ffast-math -Wall -Werror -Wno-uninitialized -Isrc/swig/solver -Ilib/swig/array -Ilib/swig/base -Ilib/swig/random -Ilib/swig/base_model -Ilib/swig/linear_model -Ilib/swig/prox -Ilib/swig/robust -DDEBUG_COSTLY_THROW" failed with exit status 1

[PhilipDeegan]

Hi there,

could you show me what compiler/version you are using please?
I have a feeling I know what this is, but it's strange that it's not happening for us

Thanks

[nschiraldi]

gcc compiler is:

using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/4.8.5/lto-wrapper
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-linker-hash-style=gnu --enable-languages=c,c++,objc,obj-c++,java,fortran,ada,go,lto --enable-plugin --enable-initfini-array --disable-libgcj --with-isl=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/isl-install --with-cloog=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/cloog-install --enable-gnu-indirect-function --with-tune=generic --with-arch_32=x86-64 --build=x86_64-redhat-linux
Thread model: posix
gcc version 4.8.5 20150623 (Red Hat 4.8.5-28.0.1) (GCC)

[PhilipDeegan]

Would it be possible for you to upgrade to GCC 5?

It seems you may be having trouble with some lambdas - GCC 4.8 is not completely C++11 compatible.

Thanks

[PhilipDeegan]

I have some scripts to build newer compilers if you would like them

[nschiraldi]

let me check with my sys admins, I had a feeling it was do to out of date compilers. I will report back and close the issue if this is the problem. Thanks for the quick response!