getting errors on install

[andrewcz]

(venv) [andrewcz@andrewcz-pc tick]$ python3 setup.py build_ext --inplace bdist_wheel
setup.py:199: DeprecationWarning: SO is deprecated, use EXT_SUFFIX
sysconfig.get_config_var('SO'))
running build_ext
building 'tick.array.build._array' extension
swigging lib/swig/array/array_module.i to lib/swig/array/array_module_wrap.cpp
swig -python -py3 -c++ -modern -new_repr -Ilib/swig/base -Ilib/include -outdir tick/array/build -Isrc/swig/array -DDEBUG_COSTLY_THROW -o lib/swig/array/array_module_wrap.cpp lib/swig/array/array_module.i
C compiler: gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt -flto -fuse-linker-plugin -ffat-lto-objects -flto-partition=none -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt -fPIC

compile options: '-Iinclude -Ilib/third_party/cereal/include -I/home/andrewcz/venv/lib/python3.7/site-packages/numpy/core/include -I/usr/include/python3.7m -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 -ffast-math -Wall -Werror -Wno-uninitialized -Isrc/swig/array -DDEBUG_COSTLY_THROW'
gcc: lib/swig/array/array_module_wrap.cpp
gcc: lib/cpp/array/alloc.cpp
lib/swig/array/array_module_wrap.cpp: In function ‘void SWIG_Python_FixMethods(PyMethodDef*, swig_const_info*, swig_type_info**, swig_type_info**)’:
lib/swig/array/array_module_wrap.cpp:15019:22: error: ‘char* strncpy(char*, const char*, size_t)’ output truncated before terminating nul copying 10 bytes from a string of the same length [-Werror=stringop-truncation]
strncpy(buff, "swig_ptr: ", 10);
~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
cc1plus: all warnings being treated as errors
lib/swig/array/array_module_wrap.cpp: In function ‘void SWIG_Python_FixMethods(PyMethodDef*, swig_const_info*, swig_type_info**, swig_type_info**)’:
lib/swig/array/array_module_wrap.cpp:15019:22: error: ‘char* strncpy(char*, const char*, size_t)’ output truncated before terminating nul copying 10 bytes from a string of the same length [-Werror=stringop-truncation]
strncpy(buff, "swig_ptr: ", 10);
~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
cc1plus: all warnings being treated as errors
error: Command "gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt -flto -fuse-linker-plugin -ffat-lto-objects -flto-partition=none -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt -fPIC -Iinclude -Ilib/third_party/cereal/include -I/home/andrewcz/venv/lib/python3.7/site-packages/numpy/core/include -I/usr/include/python3.7m -c lib/swig/array/array_module_wrap.cpp -o build/temp.linux-x86_64-3.7/lib/swig/array/array_module_wrap.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 -ffast-math -Wall -Werror -Wno-uninitialized -Isrc/swig/array -DDEBUG_COSTLY_THROW" failed with exit status 1
(venv) [andrewcz@andrewcz-pc tick]$ python3 setup.py build_ext --inplace bdist_wheel

apologies i am getting errors on the build

[andrewcz]

so i upgraded swig and i am getting the following

(venv) [andrewcz@andrewcz-pc tick]$ python setup.py build install
/home/andrewcz/venv/lib/python3.7/site-packages/numpy/distutils/system_info.py:625: UserWarning:
Atlas (http://math-atlas.sourceforge.net/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [atlas]) or by setting
the ATLAS environment variable.
self.calc_info()
/tmp/tmpf0qrs9zx/source.c:1:10: fatal error: cblas.h: No such file or directory
#include <cblas.h>
^~~~~~~~~
compilation terminated.
/tmp/tmpf0qrs9zx/source.c:1:10: fatal error: cblas.h: No such file or directory
#include <cblas.h>
^~~~~~~~~
compilation terminated.
setup.py:199: DeprecationWarning: SO is deprecated, use EXT_SUFFIX
sysconfig.get_config_var('SO'))
running build
running build_ext
building 'tick.base.build._base' extension
swigging lib/swig/base/base_module.i to lib/swig/base/base_module_wrap.cpp
swig -python -py3 -c++ -modern -new_repr -Ilib/swig/base -Ilib/include -outdir tick/base/build -Isrc/swig/base -Ilib/swig/array -DDEBUG_COSTLY_THROW -o lib/swig/base/base_module_wrap.cpp lib/swig/base/base_module.i
C compiler: gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt -flto -fuse-linker-plugin -ffat-lto-objects -flto-partition=none -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt -fPIC

compile options: '-DNO_ATLAS_INFO=1 -Iinclude -Ilib/third_party/cereal/include -I/home/andrewcz/venv/lib/python3.7/site-packages/numpy/core/include -I/usr/include/python3.7m -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 -ffast-math -Wall -Werror -Wno-uninitialized -Isrc/swig/base -Ilib/swig/array -DDEBUG_COSTLY_THROW'
gcc: lib/cpp/base/exceptions_test.cpp
gcc: lib/cpp/base/interruption.cpp
gcc: lib/swig/base/base_module_wrap.cpp
gcc: lib/cpp/base/time_func.cpp
gcc: lib/cpp/base/math/t2exp.cpp
gcc: lib/cpp/base/math/normal_distribution.cpp
lib/swig/base/base_module_wrap.cpp: In function ‘SWIG_Python_addvarlink’:
lib/swig/base/base_module_wrap.cpp:5480:16: error: ‘strncpy’ specified bound depends on the length of the source argument [-Werror=stringop-overflow=]
strncpy(gv->name,name,size);
~~~~~~~^~~~~~~~~~~~~~~~~~~~
lib/swig/base/base_module_wrap.cpp:5477:27: note: length computed here
size_t size = strlen(name)+1;
~~~~~~^~~~~~
cc1plus: all warnings being treated as errors
lib/swig/base/base_module_wrap.cpp: In function ‘SWIG_Python_addvarlink’:
lib/swig/base/base_module_wrap.cpp:5480:16: error: ‘strncpy’ specified bound depends on the length of the source argument [-Werror=stringop-overflow=]
strncpy(gv->name,name,size);
~~~~~~~^~~~~~~~~~~~~~~~~~~~
lib/swig/base/base_module_wrap.cpp:5477:27: note: length computed here
size_t size = strlen(name)+1;
~~~~~~^~~~~~
cc1plus: all warnings being treated as errors
error: Command "gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt -flto -fuse-linker-plugin -ffat-lto-objects -flto-partition=none -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt -fPIC -DNO_ATLAS_INFO=1 -Iinclude -Ilib/third_party/cereal/include -I/home/andrewcz/venv/lib/python3.7/site-packages/numpy/core/include -I/usr/include/python3.7m -c lib/swig/base/base_module_wrap.cpp -o build/temp.linux-x86_64-3.7/lib/swig/base/base_module_wrap.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 -ffast-math -Wall -Werror -Wno-uninitialized -Isrc/swig/base -Ilib/swig/array -DDEBUG_COSTLY_THROW" failed with exit status 1
(venv) [andrewcz@andrewcz-pc tick]$

getting closer.
Many thanks for your help
Best,
Andrew

[andrewcz]

[PhilipDeegan]

Hi there,

I have tested python 3.7 and it has worked for me

Can you tell me what your version of gcc is please?

gcc -v

[andrewcz]

hey thankyou for the quick response :)

[andrewcz]

[PhilipDeegan]

It looks like gcc 8.2 has made something a warning, which is now an error in compilation

if you want to compile you can remove the line extra_compile_args.append("-Werror")
from setup.py

[andrewcz]

il give it a try :)

[andrewcz]

thankyou

[andrewcz]

give me a couple of minutes :)

[andrewcz]

Also i was going to ask, the experiments from the below paper.

https://arxiv.org/pdf/1712.02640.pdf

Are they located in a repository? I was curious to go through them.
Many thanks for your help :).
Best,
Andrew

[PhilipDeegan]

@stephanegaiffas might be able to help you there

[andrewcz]

Ah Awesome!!.
Thank you. I was wanting to include further study of the algorithm in a masters project.
Should I reach out to him via email?
Looks like the package is compiling :).
Many thanks, champion!
Have an amazing day.
Best,
Andrew

[stephanegaiffas]

Hey Andrew, I think that you might be interested in the following example : https://x-datainitiative.github.io/tick/auto_examples/plot_robust_linear_regression.html

Cheers

[PhilipDeegan]

Regarding the compile error in cereal, it's a known issue

USCiLab/cereal#434

[andrewcz]

ah, amazing!
thank you all for your help!
This is so cool!
@stephanegaiffas is this the algorithm from the paper in its current form or do I have to make
some adjustments?
Also, how can I get the coefficients of the regression line?

Many thanks :)
Best,
Andrew

[stephanegaiffas]

Yes it it the algorithm of the paper
Look at https://x-datainitiative.github.io/tick/modules/generated/tick.robust.RobustLinearRegression.html?highlight=robustlinearregression
you have weights and sample_intercepts attributes for regression coefficients and individual intercepts.

[andrewcz]

Amazing!
Thank you so much!!
Will experiment with this class tonight.
I believe this issue can now be closed.
Many thanks to you all and will reference the paper and software in the dissertation.

Best,
Andrew