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Unable to compile (even with version controlled conda py37 environment) #20

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iamnicogomez opened this issue Jul 30, 2020 · 2 comments
Open

Unable to compile (even with version controlled conda py37 environment) #20

iamnicogomez opened this issue Jul 30, 2020 · 2 comments

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@iamnicogomez
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iamnicogomez commented Jul 30, 2020 •
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Hi philippdre,

I am am on OSX 10.15.5 with Conda and python3.7 (with all the recommended package versions set by conda virtual environment) running into compiling problems. As you will see, I first thought this was a cflags problem so i gathered the necessary cflags and added them to the gcc call. I have also tried simply using "-I/Users/nicog/opt/miniconda3/envs/py37/include" to no avail. I have also tried using g++. No luck. Do you or does anyone know the nature of this problem?

Thanks,
Nico

(base) claude:~ nicog$ conda activate py37

(py37) claude:~ nicog$ /Users/nicog/opt/miniconda3/envs/py37/bin/python3.7m-config --cflags -I/Users/nicog/opt/miniconda3/envs/py37/include/python3.7m -I/Users/nicog/opt/miniconda3/envs/py37/include/python3.7m -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/nicog/opt/miniconda3/envs/py37/include -arch x86_64 -I/Users/nicog/opt/miniconda3/envs/py37/include -arch x86_64

(py37) claude:~ nicog$ cd omniCLIP/stat

(py37) claude:stat nicog$ set -e

(py37) claude:stat nicog$ cython viterbi.pyx -3

(py37) claude:stat nicog$ gcc -shared -pthread -fPIC -fwrapv -O2 -Wall -fno-strict-aliasing -I/Users/nicog/opt/miniconda3/envs/py37/include/python3.7m -I/Users/nicog/opt/miniconda3/envs/py37/include/python3.7m -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/nicog/opt/miniconda3/envs/py37/include -arch x86_64 -I/Users/nicog/opt/miniconda3/envs/py37/include -arch x86_64 -o viterbi.so viterbi.c

In file included from /Users/nicog/opt/miniconda3/envs/py37/include/python3.7m/numpy/ndarraytypes.h:1822,
from /Users/nicog/opt/miniconda3/envs/py37/include/python3.7m/numpy/ndarrayobject.h:12,
from /Users/nicog/opt/miniconda3/envs/py37/include/python3.7m/numpy/arrayobject.h:4,
from viterbi.c:598:
/Users/nicog/opt/miniconda3/envs/py37/include/python3.7m/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with "
| ^~~~~~~
viterbi.c: In function ‘__pyx_pf_7viterbi_viterbi’:
viterbi.c:2907:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2907 | for (__pyx_t_11 = 0; __pyx_t_11 < __pyx_t_10; __pyx_t_11+=1) {
| ^
viterbi.c:2941:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2941 | for (__pyx_t_11 = 0; __pyx_t_11 < __pyx_t_10; __pyx_t_11+=1) {
| ^
viterbi.c:2953:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2953 | for (__pyx_t_20 = 0; __pyx_t_20 < __pyx_t_19; __pyx_t_20+=1) {
| ^
viterbi.c:2993:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2993 | for (__pyx_t_28 = 1; __pyx_t_28 < __pyx_t_27; __pyx_t_28+=1) {
| ^
viterbi.c:3125:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
3125 | for (__pyx_t_11 = 1; __pyx_t_11 < __pyx_t_10; __pyx_t_11+=1) {
| ^
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ld: symbol(s) not found for architecture x86_64
collect2: error: ld returned 1 exit status
@algaebrown
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I experience similar problems with compile. But not sure if it is the same problem

  1. The way to find correct path to replace -I in the gcc line is:
    python -c "import sysconfig; print(sysconfig.get_path('include'))"
    returns
    /home/hsher/miniconda3/envs/omniCLIP/include/python3.7m (will be different for yours)

  2. I then experience fatal error: numpy/arrayobject.h: No such file or directory
    I solve by finding where numpy include is: python -c "import numpy; print(numpy.get_include())"
    which returns /home/hsher/.local/lib/python3.7/site-packages/numpy/core/include (will be different for yours)

and create softlink:
mypython=/home/hsher/miniconda3/envs/omniCLIP/include/python3.7m
mynumpy=/home/hsher/.local/lib/python3.7/site-packages/numpy/core/include/numpy remember the last numpy
cd $mypython
ln -s $mynumpy numpy

hope this is helpful to any struggling people!

@philippdre
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Dear Nico,

did the suggestion of algaebrown solve your problem?

Best,
Philipp

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@philippdre @algaebrown @iamnicogomez