pip install turbodbc failed on anaconda 3.6 ( ubuntu) (missing symbol on import) . conda-forge worked

[seanv507]

Hi I wanted to report that using pip install I got: undefined symbol site-packages/libturbodbc.cpython-36m-x86_64-linux-gnu.so: undefined symbol: _ZTVNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEEE when importing, whereas using conda forge worked. https://github.com/conda-forge/turbodbc-feedstock

It might be worth suggesting conda forge in the installation instructions

[xhochy]

How did you install the pip package? It seems like you may be using a compiler for it that is different from the system default.

[MathMagique]

In any case, mentioning conda in the docs absolutely makes sense; I thought we already did that, but we do not.

[seanv507]

Hi I just tried pip install turbodbc

pip install turbodbc Collecting turbodbc Collecting pybind11>=2.2.0 (from turbodbc) Using cached pybind11-2.2.1-py2.py3-none-any.whl Requirement already satisfied: six in ./.local/lib/python3.6/site-packages (from turbodbc) Installing collected packages: pybind11, turbodbc Successfully installed pybind11-2.2.1 turbodbc-2.4.0

so I didn't see anything in terms of compilation messages

On Sun, Oct 8, 2017 at 10:39 PM, Uwe L. Korn [email protected] wrote:

How did you install the pip package? It seems like you may be using a compiler for it that is different from the system default.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/blue-yonder/turbodbc/issues/134#issuecomment-335036718, or mute the thread https://github.com/notifications/unsubscribe-auth/ADJxL8iHc5zx3E1ReeOkcgEgsr_3V4DLks5sqTLpgaJpZM4Pxnt0 .

[xhochy]

Can you give more context on you environment? What Linux distribution are you using? Can you post the output of g++ -v?

[seanv507]

ubuntu 16.04

i tried conda install gcc ( from reading snippets off the internet) after it didn't work initially... so this is what I see now (after conda install gcc)

g++ -v Reading specs from XXX/anaconda3/bin/../lib/gcc/ x86_64-unknown-linux-gnu/4.8.5/specs COLLECT_GCC=g++ COLLECT_LTO_WRAPPER=/XXX/anaconda3/bin/../libexec/gcc/ x86_64-unknown-linux-gnu/4.8.5/lto-wrapper Target: x86_64-unknown-linux-gnu Configured with: ./configure --prefix=/home/ray/mc-x64-2.7/ conda-bld/gcc_1479223211463/b_env_placehold_placehold placehold_placehold_placehold_placehold_placehold_placehold_ placehold_placehold_placehold_placehold_placehold_placehold_ placehold_placehold_placehold_placehold_placehold_placehold --with-gxx-include-dir=/home/ray/mc-x64-2.7/conda-bld/gcc_ 1479223211463/b_env_placehold_placehold_placehold placehold_placehold_placehold_placehold_placehold_placehold_ placehold_placehold_placehold_placehold_placehold_placehold_ placehold_placehold_placehold_placehold_placehold/gcc/include/c++ --bindir=/home/ray/mc-x64-2.7/conda-bld/gcc_1479223211463/_ b_env_placehold_placehold_placehold_placehold_placehold_ placehold_placehold_placehold_placehold_placehold_placehold_ placehold_placehold_placehold_placehold_placehold_placehold_ placehold_placehold_placehold/bin --datarootdir=/home/ray/mc- x64-2.7/conda-bld/gcc_1479223211463/b_env_placehold_placehold_placehold placehold_placehold_placehold_placehold_placehold_placehold_ placehold_placehold_placehold_placehold_placehold_placehold_ placehold_placehold_placehold_placehold_placehold/share --libdir=/home/ray/mc-x64-2.7/conda-bld/gcc_1479223211463/_ b_env_placehold_placehold_placehold_placehold_placehold_ placehold_placehold_placehold_placehold_placehold_placehold_ placehold_placehold_placehold_placehold_placehold_placehold_ placehold_placehold_placehold/lib --with-gmp=/home/ray/mc-x64-2. 7/conda-bld/gcc_1479223211463/b_env_placehold_placehold placehold_placehold_placehold_placehold_placehold_placehold_ placehold_placehold_placehold_placehold_placehold_placehold_ placehold_placehold_placehold_placehold_placehold_placehold --with-mpfr=/home/ray/mc-x64-2.7/conda-bld/gcc_1479223211463/b_env placehold_placehold_placehold_placehold_placehold_placehold_ placehold_placehold_placehold_placehold_placehold_placehold_ placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold --with-mpc=/home/ray/mc-x64-2.7/conda-bld/gcc_1479223211463/ b_env_placehold_placehold_placehold_placehold_placehold placehold_placehold_placehold_placehold_placehold_placehold_ placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold --with-isl=/home/ray/mc-x64-2.7/conda-bld/gcc_1479223211463/ b_env_placehold_placehold_placehold_placehold_placehold placehold_placehold_placehold_placehold_placehold_placehold_ placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold --with-cloog=/home/ray/mc-x64-2.7/conda-bld/gcc_1479223211463/b_env placehold_placehold_placehold_placehold_placehold_placehold_ placehold_placehold_placehold_placehold_placehold_placehold_ placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold --enable-checking=release --with-tune=generic --disable-multilib Thread model: posix gcc version 4.8.5 (GCC)

On Mon, Oct 9, 2017 at 3:47 PM, Uwe L. Korn [email protected] wrote:

Can you give more context on you environment? What Linux distribution are you using? Can you post the output of g++ -v?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/blue-yonder/turbodbc/issues/134#issuecomment-335163077, or mute the thread https://github.com/notifications/unsubscribe-auth/ADJxL4VQ5FI6G2jHa_S4Wx4eX6NEHQexks5sqiPUgaJpZM4Pxnt0 .

[xhochy]

conda install gcc might actually be one of the main problems here. At least that would explain the initial error message.

Can you retry without conda being activated and follow these steps:

virtualenv venv
source ./venv/bin/activate
pip install pybind11 numpy
pip install turbodbc

Doing this in a virtualenv might help debugging the problem as it then would ensure that only the minimal necessary packages are installed.