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KarchinLab / probabilistic2020

Simulates somatic mutations, and calls statistically significant oncogenes and tumor suppressor genes based on a randomization-based test
http://probabilistic2020.readthedocs.org
Apache License 2.0
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Keep getting CondaValueError: pip returned an error #7

Closed sandaru closed 5 years ago

sandaru commented 5 years ago

Hi,

I'm getting following error while installing this on Debian 9.x . I have tried almost all the solutions I found but nothing seems work. Installing it locally also wont work due to the same issue.

error: command 'gcc' failed with exit status 1

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

Command "/root/Desktop/2020plus-1.2.2/2020plus/bin/python -u -c "import setuptools, tokenize;file='/tmp/pip-install-5e9wl_mk/probabilistic2020/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install -- record /tmp/pip-record-wpmvj3qw/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-install-5e9wl_mk/probabilistic2020/

CondaValueError: pip returned an error

Am i doing something wrong ?.

Thanks and Regards, /Sandaru

ctokheim commented 5 years ago

I don't have much experience with Debian. However, I suspect that it could be that either you do not have a C/C++ compiler or you do not have installed a python development package (often named something like "python-dev"). Did you happen to install the Debian OS recently? Do other pip packages install fine?

sandaru commented 5 years ago

I have installed all the necessary packages in Debian including gcc and python-dev (mentioned in requirement.txt and the documentation) . pip package works fine . I hev tried the same with pip3 as well. but couldn't get a different result. I got the same problem in Ubuntu that's why I moved to Debian. Yes, I installed Debian yesterday, just for installing 20/20+

ctokheim commented 5 years ago

What exact python version are you using in python3?

sandaru commented 5 years ago

yes its python 3.6

ctokheim commented 5 years ago

This is odd because I currently test the installation automatically (using Travis CI) on Ubuntu 14.04 and python 3.6.3. I see no errors with pip install probabilistic2020. Can you post the entire contents printed to the screen when you issue the command?

sandaru commented 5 years ago

(base) root@debian:~# pip install probabilistic2020Collecting probabilistic2020 Using cached https://files.pythonhosted.org/packages/30/ff/feae37090012be833521cf374700b1609d102fd3dfa8b5690ee657c9708f/probabilistic2020-1.2.0.tar.gz Requirement already satisfied: numpy in ./miniconda3/lib/python3.6/site-packages (from probabilistic2020) (1.15.4) Requirement already satisfied: scipy in ./miniconda3/lib/python3.6/site-packages (from probabilistic2020) (1.2.1) Requirement already satisfied: pandas in ./miniconda3/lib/python3.6/site-packages (from probabilistic2020) (0.24.1) Requirement already satisfied: pysam in ./miniconda3/lib/python3.6/site-packages (from probabilistic2020) (0.15.2) Requirement already satisfied: python-dateutil>=2.5.0 in ./miniconda3/lib/python3.6/site-packages (from pandas->probabilistic2020) (2.8.0) Requirement already satisfied: pytz>=2011k in ./miniconda3/lib/python3.6/site-packages (from pandas->probabilistic2020) (2018.9) Requirement already satisfied: six>=1.5 in ./miniconda3/lib/python3.6/site-packages (from python-dateutil>=2.5.0->pandas->probabilistic2020) (1.12.0) Building wheels for collected packages: probabilistic2020 Building wheel for probabilistic2020 (setup.py) ... error Complete output from command /root/miniconda3/bin/python -u -c "import setuptools, tokenize;file='/tmp/pip-install-3ol8rj1c/probabilistic2020/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" bdist_wheel -d /tmp/pip-wheel-zxwlg5qf --python-tag cp36: running bdist_wheel running build running build_py creating build creating build/lib.linux-x86_64-3.6 creating build/lib.linux-x86_64-3.6/prob2020 copying prob2020/init.py -> build/lib.linux-x86_64-3.6/prob2020 creating build/lib.linux-x86_64-3.6/prob2020/python copying prob2020/python/utils.py -> build/lib.linux-x86_64-3.6/prob2020/python copying prob2020/python/annotate.py -> build/lib.linux-x86_64-3.6/prob2020/python copying prob2020/python/sequence_context.py -> build/lib.linux-x86_64-3.6/prob2020/python copying prob2020/python/p_value.py -> build/lib.linux-x86_64-3.6/prob2020/python copying prob2020/python/process_result.py -> build/lib.linux-x86_64-3.6/prob2020/python copying prob2020/python/mutation_context.py -> build/lib.linux-x86_64-3.6/prob2020/python copying prob2020/python/count_frameshifts.py -> build/lib.linux-x86_64-3.6/prob2020/python copying prob2020/python/amino_acid.py -> build/lib.linux-x86_64-3.6/prob2020/python copying prob2020/python/mymath.py -> build/lib.linux-x86_64-3.6/prob2020/python copying prob2020/python/init.py -> build/lib.linux-x86_64-3.6/prob2020/python copying prob2020/python/indel.py -> build/lib.linux-x86_64-3.6/prob2020/python copying prob2020/python/scores.py -> build/lib.linux-x86_64-3.6/prob2020/python copying prob2020/python/bed_line.py -> build/lib.linux-x86_64-3.6/prob2020/python copying prob2020/python/gene_sequence.py -> build/lib.linux-x86_64-3.6/prob2020/python copying prob2020/python/permutation.py -> build/lib.linux-x86_64-3.6/prob2020/python creating build/lib.linux-x86_64-3.6/prob2020/cython copying prob2020/cython/init.py -> build/lib.linux-x86_64-3.6/prob2020/cython creating build/lib.linux-x86_64-3.6/prob2020/cpp copying prob2020/cpp/init.py -> build/lib.linux-x86_64-3.6/prob2020/cpp creating build/lib.linux-x86_64-3.6/prob2020/console copying prob2020/console/randomization_test.py -> build/lib.linux-x86_64-3.6/prob2020/console copying prob2020/console/annotate.py -> build/lib.linux-x86_64-3.6/prob2020/console copying prob2020/console/extract_gene_seq.py -> build/lib.linux-x86_64-3.6/prob2020/console copying prob2020/console/count_frameshifts.py -> build/lib.linux-x86_64-3.6/prob2020/console copying prob2020/console/init.py -> build/lib.linux-x86_64-3.6/prob2020/console copying prob2020/console/simulate_non_silent_ratio.py -> build/lib.linux-x86_64-3.6/prob2020/console copying prob2020/console/probabilistic2020.py -> build/lib.linux-x86_64-3.6/prob2020/console running build_ext building 'prob2020.cython.uniform_kde' extension creating build/temp.linux-x86_64-3.6 creating build/temp.linux-x86_64-3.6/prob2020 creating build/temp.linux-x86_64-3.6/prob2020/cython gcc -pthread -B /root/miniconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Iprob2020/cython/ -I/root/miniconda3/lib/python3.6/site-packages/numpy/core/include -I/root/miniconda3/include/python3.6m -c prob2020/cython/uniform_kde.cpp -o build/temp.linux-x86_64-3.6/prob2020/cython/uniform_kde.o cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ In file included from /root/miniconda3/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1823:0, from /root/miniconda3/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /root/miniconda3/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4, from prob2020/cython/uniform_kde.cpp:303: /root/miniconda3/lib/python3.6/site-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 " \

^~~~~~~

In file included from /root/miniconda3/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:27:0, from /root/miniconda3/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4, from prob2020/cython/uniform_kde.cpp:303: /root/miniconda3/lib/python3.6/site-packages/numpy/core/include/numpy/__multiarray_api.h:1463:1: warning: ‘int _import_array()’ defined but not used [-Wunused-function] _import_array(void) ^~~~~ g++ -pthread -shared -B /root/miniconda3/compiler_compat -L/root/miniconda3/lib -Wl,-rpath=/root/miniconda3/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.6/prob2020/cython/uniform_kde.o -o build/lib.linux-x86_64-3.6/prob2020/cython/uniform_kde.cpython-36m-x86_64-linux-gnu.so building 'prob2020.cython.gaussian_kde' extension gcc -pthread -B /root/miniconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Iprob2020/cython/ -I/root/miniconda3/lib/python3.6/site-packages/numpy/core/include -I/root/miniconda3/include/python3.6m -c prob2020/cython/gaussian_kde.cpp -o build/temp.linux-x86_64-3.6/prob2020/cython/gaussian_kde.o cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ In file included from /root/miniconda3/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1823:0, from /root/miniconda3/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /root/miniconda3/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4, from prob2020/cython/gaussian_kde.cpp:304: /root/miniconda3/lib/python3.6/site-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 " \

^~~~~~~

In file included from /root/miniconda3/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:27:0, from /root/miniconda3/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4, from prob2020/cython/gaussian_kde.cpp:304: /root/miniconda3/lib/python3.6/site-packages/numpy/core/include/numpy/__multiarray_api.h:1463:1: warning: ‘int _import_array()’ defined but not used [-Wunused-function] _import_array(void) ^~~~~ g++ -pthread -shared -B /root/miniconda3/compiler_compat -L/root/miniconda3/lib -Wl,-rpath=/root/miniconda3/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.6/prob2020/cython/gaussian_kde.o -o build/lib.linux-x86_64-3.6/prob2020/cython/gaussian_kde.cpython-36m-x86_64-linux-gnu.so building 'prob2020.cython.cutils' extension gcc -pthread -B /root/miniconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Iprob2020/cpp/ -Iprob2020/cython/ -I/root/miniconda3/lib/python3.6/site-packages/numpy/core/include -I/root/miniconda3/include/python3.6m -c prob2020/cython/cutils.cpp -o build/temp.linux-x86_64-3.6/prob2020/cython/cutils.o cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ In file included from /root/miniconda3/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1823:0, from /root/miniconda3/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /root/miniconda3/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4, from prob2020/cython/cutils.cpp:311: /root/miniconda3/lib/python3.6/site-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 " \

^~~~~~~

In file included from prob2020/cython/cutils.cpp:313:0: prob2020/cpp/permutation.hpp:5:0: warning: "M_LOG2E" redefined

define M_LOG2E 1.44269504088896340736L //log2(e)

In file included from /usr/include/c++/6/cmath:45:0, from /usr/include/c++/6/math.h:36, from /root/miniconda3/include/python3.6m/pyport.h:194, from /root/miniconda3/include/python3.6m/Python.h:53, from prob2020/cython/cutils.cpp:16: /usr/include/math.h:414:0: note: this is the location of the previous definition

define M_LOG2E 1.4426950408889634074 / log_2 e /

In file included from prob2020/cython/cutils.cpp:313:0: prob2020/cpp/permutation.hpp: In function ‘long double log2(long double)’: prob2020/cpp/permutation.hpp:8:44: error: ‘long double log2(long double)’ conflicts with a previous declaration inline long double log2(const long double x){ ^ In file included from /usr/include/c++/6/math.h:36:0, from /root/miniconda3/include/python3.6m/pyport.h:194, from /root/miniconda3/include/python3.6m/Python.h:53, from prob2020/cython/cutils.cpp:16: /usr/include/c++/6/cmath:1608:3: note: previous declaration ‘constexpr long double std::log2(long double)’ log2(long double x) ^~~~ In file included from prob2020/cython/cutils.cpp:313:0: prob2020/cpp/permutation.hpp: In function ‘std::map<std::cxx11::basic_string, double> calc_position_statistics(std::map<int, int>, float, int, int)’: prob2020/cpp/permutation.hpp:69:38: error: call of overloaded ‘log2(long double&)’ is ambiguous myent_2 -= p log2(p); ^ In file included from /usr/include/features.h:364:0, from /usr/include/limits.h:25, from /usr/lib/gcc/x86_64-linux-gnu/6/include-fixed/limits.h:168, from /usr/lib/gcc/x86_64-linux-gnu/6/include-fixed/syslimits.h:7, from /usr/lib/gcc/x86_64-linux-gnu/6/include-fixed/limits.h:34, from /root/miniconda3/include/python3.6m/Python.h:11, from prob2020/cython/cutils.cpp:16: /usr/include/x86_64-linux-gnu/bits/mathcalls.h:144:1: note: candidate: double log2(double) MATHCALL (log2,, (Mdouble x)); ^ In file included from /usr/include/c++/6/math.h:36:0, from /root/miniconda3/include/python3.6m/pyport.h:194, from /root/miniconda3/include/python3.6m/Python.h:53, from prob2020/cython/cutils.cpp:16: /usr/include/c++/6/cmath:1608:3: note: candidate: constexpr long double std::log2(long double) log2(long double x) ^~~~ /usr/include/c++/6/cmath:1604:3: note: candidate: constexpr float std::log2(float) log2(float x) ^~~~ In file included from prob2020/cython/cutils.cpp:313:0: prob2020/cpp/permutation.hpp:8:20: note: candidate: long double log2(long double) inline long double log2(const long double x){ ^~~~ prob2020/cpp/permutation.hpp:75:34: error: call of overloaded ‘log2(long double&)’ is ambiguous myent_2 -= p log2(p); ^ In file included from /usr/include/features.h:364:0, from /usr/include/limits.h:25, from /usr/lib/gcc/x86_64-linux-gnu/6/include-fixed/limits.h:168, from /usr/lib/gcc/x86_64-linux-gnu/6/include-fixed/syslimits.h:7, from /usr/lib/gcc/x86_64-linux-gnu/6/include-fixed/limits.h:34, from /root/miniconda3/include/python3.6m/Python.h:11, from prob2020/cython/cutils.cpp:16: /usr/include/x86_64-linux-gnu/bits/mathcalls.h:144:1: note: candidate: double log2(double) MATHCALL (log2,, (Mdouble x)); ^ In file included from /usr/include/c++/6/math.h:36:0, from /root/miniconda3/include/python3.6m/pyport.h:194, from /root/miniconda3/include/python3.6m/Python.h:53, from prob2020/cython/cutils.cpp:16: /usr/include/c++/6/cmath:1608:3: note: candidate: constexpr long double std::log2(long double) log2(long double x) ^~~~ /usr/include/c++/6/cmath:1604:3: note: candidate: constexpr float std::log2(float) log2(float x) ^~~~ In file included from prob2020/cython/cutils.cpp:313:0: prob2020/cpp/permutation.hpp:8:20: note: candidate: long double log2(long double) inline long double log2(const long double x){ ^~~~ prob2020/cpp/permutation.hpp:86:51: error: call of overloaded ‘log2(long double&)’ is ambiguous frac_of_uniform_ent = myent_2 / log2(mysum); ^ In file included from /usr/include/features.h:364:0, from /usr/include/limits.h:25, from /usr/lib/gcc/x86_64-linux-gnu/6/include-fixed/limits.h:168, from /usr/lib/gcc/x86_64-linux-gnu/6/include-fixed/syslimits.h:7, from /usr/lib/gcc/x86_64-linux-gnu/6/include-fixed/limits.h:34, from /root/miniconda3/include/python3.6m/Python.h:11, from prob2020/cython/cutils.cpp:16: /usr/include/x86_64-linux-gnu/bits/mathcalls.h:144:1: note: candidate: double log2(double) MATHCALL (log2,, (Mdouble x)); ^ In file included from /usr/include/c++/6/math.h:36:0, from /root/miniconda3/include/python3.6m/pyport.h:194, from /root/miniconda3/include/python3.6m/Python.h:53, from prob2020/cython/cutils.cpp:16: /usr/include/c++/6/cmath:1608:3: note: candidate: constexpr long double std::log2(long double) log2(long double x) ^~~~ /usr/include/c++/6/cmath:1604:3: note: candidate: constexpr float std::log2(float) log2(float x) ^~~~ In file included from prob2020/cython/cutils.cpp:313:0: prob2020/cpp/permutation.hpp:8:20: note: candidate: long double log2(long double) inline long double log2(const long double x){ ^~~~ prob2020/cpp/permutation.hpp: In function ‘std::map<std::cxx11::basic_string, double> calc_effect_statistics(std::map<int, int>, float, int, int)’: prob2020/cpp/permutation.hpp:143:34: error: call of overloaded ‘log2(long double&)’ is ambiguous myent_2 -= p * log2(p); ^ In file included from /usr/include/features.h:364:0, from /usr/include/limits.h:25, from /usr/lib/gcc/x86_64-linux-gnu/6/include-fixed/limits.h:168, from /usr/lib/gcc/x86_64-linux-gnu/6/include-fixed/syslimits.h:7, from /usr/lib/gcc/x86_64-linux-gnu/6/include-fixed/limits.h:34, from /root/miniconda3/include/python3.6m/Python.h:11, from prob2020/cython/cutils.cpp:16: /usr/include/x86_64-linux-gnu/bits/mathcalls.h:144:1: note: candidate: double log2(double) MATHCALL (log2,, (Mdouble x)); ^ In file included from /usr/include/c++/6/math.h:36:0, from /root/miniconda3/include/python3.6m/pyport.h:194, from /root/miniconda3/include/python3.6m/Python.h:53, from prob2020/cython/cutils.cpp:16: /usr/include/c++/6/cmath:1608:3: note: candidate: constexpr long double std::log2(long double) log2(long double x) ^~~~ /usr/include/c++/6/cmath:1604:3: note: candidate: constexpr float std::log2(float) log2(float x) ^~~~ In file included from prob2020/cython/cutils.cpp:313:0: prob2020/cpp/permutation.hpp:8:20: note: candidate: long double log2(long double) inline long double log2(const long double x){ ^~~~ prob2020/cpp/permutation.hpp:160:38: error: call of overloaded ‘log2(long double&)’ is ambiguous myent_2 -= p log2(p); ^ In file included from /usr/include/features.h:364:0, from /usr/include/limits.h:25, from /usr/lib/gcc/x86_64-linux-gnu/6/include-fixed/limits.h:168, from /usr/lib/gcc/x86_64-linux-gnu/6/include-fixed/syslimits.h:7, from /usr/lib/gcc/x86_64-linux-gnu/6/include-fixed/limits.h:34, from /root/miniconda3/include/python3.6m/Python.h:11, from prob2020/cython/cutils.cpp:16: /usr/include/x86_64-linux-gnu/bits/mathcalls.h:144:1: note: candidate: double log2(double) MATHCALL (log2,, (Mdouble x)); ^ In file included from /usr/include/c++/6/math.h:36:0, from /root/miniconda3/include/python3.6m/pyport.h:194, from /root/miniconda3/include/python3.6m/Python.h:53, from prob2020/cython/cutils.cpp:16: /usr/include/c++/6/cmath:1608:3: note: candidate: constexpr long double std::log2(long double) log2(long double x) ^~~~ /usr/include/c++/6/cmath:1604:3: note: candidate: constexpr float std::log2(float) log2(float x) ^~~~ In file included from prob2020/cython/cutils.cpp:313:0: prob2020/cpp/permutation.hpp:8:20: note: candidate: long double log2(long double) inline long double log2(const long double x){ ^~~~ prob2020/cpp/permutation.hpp:165:34: error: call of overloaded ‘log2(long double&)’ is ambiguous myent_2 -= p log2(p); ^ In file included from /usr/include/features.h:364:0, from /usr/include/limits.h:25, from /usr/lib/gcc/x86_64-linux-gnu/6/include-fixed/limits.h:168, from /usr/lib/gcc/x86_64-linux-gnu/6/include-fixed/syslimits.h:7, from /usr/lib/gcc/x86_64-linux-gnu/6/include-fixed/limits.h:34, from /root/miniconda3/include/python3.6m/Python.h:11, from prob2020/cython/cutils.cpp:16: /usr/include/x86_64-linux-gnu/bits/mathcalls.h:144:1: note: candidate: double log2(double) MATHCALL (log2,, (Mdouble x)); ^ In file included from /usr/include/c++/6/math.h:36:0, from /root/miniconda3/include/python3.6m/pyport.h:194, from /root/miniconda3/include/python3.6m/Python.h:53, from prob2020/cython/cutils.cpp:16: /usr/include/c++/6/cmath:1608:3: note: candidate: constexpr long double std::log2(long double) log2(long double x) ^~~~ /usr/include/c++/6/cmath:1604:3: note: candidate: constexpr float std::log2(float) log2(float x) ^~~~ In file included from prob2020/cython/cutils.cpp:313:0: prob2020/cpp/permutation.hpp:8:20: note: candidate: long double log2(long double) inline long double log2(const long double x){ ^~~~ prob2020/cpp/permutation.hpp:172:51: error: call of overloaded ‘log2(long double&)’ is ambiguous frac_of_uniform_ent = myent_2 / log2(mysum); ^ In file included from /usr/include/features.h:364:0, from /usr/include/limits.h:25, from /usr/lib/gcc/x86_64-linux-gnu/6/include-fixed/limits.h:168, from /usr/lib/gcc/x86_64-linux-gnu/6/include-fixed/syslimits.h:7, from /usr/lib/gcc/x86_64-linux-gnu/6/include-fixed/limits.h:34, from /root/miniconda3/include/python3.6m/Python.h:11, from prob2020/cython/cutils.cpp:16: /usr/include/x86_64-linux-gnu/bits/mathcalls.h:144:1: note: candidate: double log2(double) MATHCALL (log2,, (Mdouble x)); ^ In file included from /usr/include/c++/6/math.h:36:0, from /root/miniconda3/include/python3.6m/pyport.h:194, from /root/miniconda3/include/python3.6m/Python.h:53, from prob2020/cython/cutils.cpp:16: /usr/include/c++/6/cmath:1608:3: note: candidate: constexpr long double std::log2(long double) log2(long double x) ^~~~ /usr/include/c++/6/cmath:1604:3: note: candidate: constexpr float std::log2(float) log2(float x) ^~~~ In file included from prob2020/cython/cutils.cpp:313:0: prob2020/cpp/permutation.hpp:8:20: note: candidate: long double log2(long double) inline long double log2(const long double x){ ^~~~ prob2020/cpp/permutation.hpp:116:33: warning: unused variable ‘myent_e’ [-Wunused-variable] long double myent_2 = 0.0L, myent_e = 0.0L, mysum = 0.0L, p = 0.0L; ^~~ prob2020/cpp/permutation.hpp:118:17: warning: unused variable ‘delta_ent’ [-Wunused-variable] long double delta_ent = 0.0L; ^~~~~ In file included from /root/miniconda3/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:27:0, from /root/miniconda3/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4, from prob2020/cython/cutils.cpp:311: /root/miniconda3/lib/python3.6/site-packages/numpy/core/include/numpy/__multiarray_api.h: At global scope: /root/miniconda3/lib/python3.6/site-packages/numpy/core/include/numpy/multiarray_api.h:1463:1: warning: ‘int _import_array()’ defined but not used [-Wunused-function] _import_array(void) ^~~~~ error: command 'gcc' failed with exit status 1

Failed building wheel for probabilistic2020 Running setup.py clean for probabilistic2020 Failed to build probabilistic2020 Installing collected packages: probabilistic2020 Running setup.py install for probabilistic2020 ... error Complete output from command /root/miniconda3/bin/python -u -c "import setuptools, tokenize;file='/tmp/pip-install-3ol8rj1c/probabilistic2020/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install --record /tmp/pip-record-ynpt27sw/install-record.txt --single-version-externally-managed --compile: running install running build running build_py creating build creating build/lib.linux-x86_64-3.6 creating build/lib.linux-x86_64-3.6/prob2020 copying prob2020/init.py -> build/lib.linux-x86_64-3.6/prob2020 creating build/lib.linux-x86_64-3.6/prob2020/python copying prob2020/python/utils.py -> build/lib.linux-x86_64-3.6/prob2020/python copying prob2020/python/annotate.py -> build/lib.linux-x86_64-3.6/prob2020/python copying prob2020/python/sequence_context.py -> build/lib.linux-x86_64-3.6/prob2020/python copying prob2020/python/p_value.py -> build/lib.linux-x86_64-3.6/prob2020/python copying prob2020/python/process_result.py -> build/lib.linux-x86_64-3.6/prob2020/python copying prob2020/python/mutation_context.py -> build/lib.linux-x86_64-3.6/prob2020/python copying prob2020/python/count_frameshifts.py -> build/lib.linux-x86_64-3.6/prob2020/python copying prob2020/python/amino_acid.py -> build/lib.linux-x86_64-3.6/prob2020/python copying prob2020/python/mymath.py -> build/lib.linux-x86_64-3.6/prob2020/python copying prob2020/python/init.py -> build/lib.linux-x86_64-3.6/prob2020/python copying prob2020/python/indel.py -> build/lib.linux-x86_64-3.6/prob2020/python copying prob2020/python/scores.py -> build/lib.linux-x86_64-3.6/prob2020/python copying prob2020/python/bed_line.py -> build/lib.linux-x86_64-3.6/prob2020/python copying prob2020/python/gene_sequence.py -> build/lib.linux-x86_64-3.6/prob2020/python copying prob2020/python/permutation.py -> build/lib.linux-x86_64-3.6/prob2020/python creating build/lib.linux-x86_64-3.6/prob2020/cython copying prob2020/cython/init.py -> build/lib.linux-x86_64-3.6/prob2020/cython creating build/lib.linux-x86_64-3.6/prob2020/cpp copying prob2020/cpp/init.py -> build/lib.linux-x86_64-3.6/prob2020/cpp creating build/lib.linux-x86_64-3.6/prob2020/console copying prob2020/console/randomization_test.py -> build/lib.linux-x86_64-3.6/prob2020/console copying prob2020/console/annotate.py -> build/lib.linux-x86_64-3.6/prob2020/console copying prob2020/console/extract_gene_seq.py -> build/lib.linux-x86_64-3.6/prob2020/console copying prob2020/console/count_frameshifts.py -> build/lib.linux-x86_64-3.6/prob2020/console copying prob2020/console/init.py -> build/lib.linux-x86_64-3.6/prob2020/console copying prob2020/console/simulate_non_silent_ratio.py -> build/lib.linux-x86_64-3.6/prob2020/console copying prob2020/console/probabilistic2020.py -> build/lib.linux-x86_64-3.6/prob2020/console running build_ext building 'prob2020.cython.uniform_kde' extension creating build/temp.linux-x86_64-3.6 creating build/temp.linux-x86_64-3.6/prob2020 creating build/temp.linux-x86_64-3.6/prob2020/cython gcc -pthread -B /root/miniconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Iprob2020/cython/ -I/root/miniconda3/lib/python3.6/site-packages/numpy/core/include -I/root/miniconda3/include/python3.6m -c prob2020/cython/uniform_kde.cpp -o build/temp.linux-x86_64-3.6/prob2020/cython/uniform_kde.o cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ In file included from /root/miniconda3/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1823:0, from /root/miniconda3/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /root/miniconda3/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4, from prob2020/cython/uniform_kde.cpp:303: /root/miniconda3/lib/python3.6/site-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 " \

  ^~~~~~~
In file included from /root/miniconda3/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:27:0,
                 from /root/miniconda3/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from prob2020/cython/uniform_kde.cpp:303:
/root/miniconda3/lib/python3.6/site-packages/numpy/core/include/numpy/__multiarray_api.h:1463:1: warning: ‘int _import_array()’ defined but not used [-Wunused-function]
 _import_array(void)
 ^~~~~~~~~~~~~
g++ -pthread -shared -B /root/miniconda3/compiler_compat -L/root/miniconda3/lib -Wl,-rpath=/root/miniconda3/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.6/prob2020/cython/uniform_kde.o -o build/lib.linux-x86_64-3.6/prob2020/cython/uniform_kde.cpython-36m-x86_64-linux-gnu.so
building 'prob2020.cython.gaussian_kde' extension
gcc -pthread -B /root/miniconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Iprob2020/cython/ -I/root/miniconda3/lib/python3.6/site-packages/numpy/core/include -I/root/miniconda3/include/python3.6m -c prob2020/cython/gaussian_kde.cpp -o build/temp.linux-x86_64-3.6/prob2020/cython/gaussian_kde.o
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
In file included from /root/miniconda3/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1823:0,
                 from /root/miniconda3/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                 from /root/miniconda3/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from prob2020/cython/gaussian_kde.cpp:304:
/root/miniconda3/lib/python3.6/site-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 " \
  ^~~~~~~
In file included from /root/miniconda3/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:27:0,
                 from /root/miniconda3/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from prob2020/cython/gaussian_kde.cpp:304:
/root/miniconda3/lib/python3.6/site-packages/numpy/core/include/numpy/__multiarray_api.h:1463:1: warning: ‘int _import_array()’ defined but not used [-Wunused-function]
 _import_array(void)
 ^~~~~~~~~~~~~
g++ -pthread -shared -B /root/miniconda3/compiler_compat -L/root/miniconda3/lib -Wl,-rpath=/root/miniconda3/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.6/prob2020/cython/gaussian_kde.o -o build/lib.linux-x86_64-3.6/prob2020/cython/gaussian_kde.cpython-36m-x86_64-linux-gnu.so
building 'prob2020.cython.cutils' extension
gcc -pthread -B /root/miniconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Iprob2020/cpp/ -Iprob2020/cython/ -I/root/miniconda3/lib/python3.6/site-packages/numpy/core/include -I/root/miniconda3/include/python3.6m -c prob2020/cython/cutils.cpp -o build/temp.linux-x86_64-3.6/prob2020/cython/cutils.o
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
In file included from /root/miniconda3/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1823:0,
                 from /root/miniconda3/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                 from /root/miniconda3/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from prob2020/cython/cutils.cpp:311:
/root/miniconda3/lib/python3.6/site-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 " \
  ^~~~~~~
In file included from prob2020/cython/cutils.cpp:313:0:
prob2020/cpp/permutation.hpp:5:0: warning: "M_LOG2E" redefined
 #define M_LOG2E 1.44269504088896340736L //log2(e)

In file included from /usr/include/c++/6/cmath:45:0,
                 from /usr/include/c++/6/math.h:36,
                 from /root/miniconda3/include/python3.6m/pyport.h:194,
                 from /root/miniconda3/include/python3.6m/Python.h:53,
                 from prob2020/cython/cutils.cpp:16:
/usr/include/math.h:414:0: note: this is the location of the previous definition
 # define M_LOG2E 1.4426950408889634074 /* log_2 e */

In file included from prob2020/cython/cutils.cpp:313:0:
prob2020/cpp/permutation.hpp: In function ‘long double log2(long double)’:
prob2020/cpp/permutation.hpp:8:44: error: ‘long double log2(long double)’ conflicts with a previous declaration
 inline long double log2(const long double x){
                                            ^
In file included from /usr/include/c++/6/math.h:36:0,
                 from /root/miniconda3/include/python3.6m/pyport.h:194,
                 from /root/miniconda3/include/python3.6m/Python.h:53,
                 from prob2020/cython/cutils.cpp:16:
/usr/include/c++/6/cmath:1608:3: note: previous declaration ‘constexpr long double std::log2(long double)’
   log2(long double __x)
   ^~~~
In file included from prob2020/cython/cutils.cpp:313:0:
prob2020/cpp/permutation.hpp: In function ‘std::map<std::__cxx11::basic_string<char>, double> calc_position_statistics(std::map<int, int>, float, int, int)’:
prob2020/cpp/permutation.hpp:69:38: error: call of overloaded ‘log2(long double&)’ is ambiguous
                 myent_2 -= p * log2(p);
                                      ^
In file included from /usr/include/features.h:364:0,
                 from /usr/include/limits.h:25,
                 from /usr/lib/gcc/x86_64-linux-gnu/6/include-fixed/limits.h:168,
                 from /usr/lib/gcc/x86_64-linux-gnu/6/include-fixed/syslimits.h:7,
                 from /usr/lib/gcc/x86_64-linux-gnu/6/include-fixed/limits.h:34,
                 from /root/miniconda3/include/python3.6m/Python.h:11,
                 from prob2020/cython/cutils.cpp:16:
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:144:1: note: candidate: double log2(double)
 __MATHCALL (log2,, (_Mdouble_ __x));
 ^
In file included from /usr/include/c++/6/math.h:36:0,
                 from /root/miniconda3/include/python3.6m/pyport.h:194,
                 from /root/miniconda3/include/python3.6m/Python.h:53,
                 from prob2020/cython/cutils.cpp:16:
/usr/include/c++/6/cmath:1608:3: note: candidate: constexpr long double std::log2(long double)
   log2(long double __x)
   ^~~~
/usr/include/c++/6/cmath:1604:3: note: candidate: constexpr float std::log2(float)
   log2(float __x)
   ^~~~
In file included from prob2020/cython/cutils.cpp:313:0:
prob2020/cpp/permutation.hpp:8:20: note: candidate: long double log2(long double)
 inline long double log2(const long double x){
                    ^~~~
prob2020/cpp/permutation.hpp:75:34: error: call of overloaded ‘log2(long double&)’ is ambiguous
             myent_2 -= p * log2(p);
                                  ^
In file included from /usr/include/features.h:364:0,
                 from /usr/include/limits.h:25,
                 from /usr/lib/gcc/x86_64-linux-gnu/6/include-fixed/limits.h:168,
                 from /usr/lib/gcc/x86_64-linux-gnu/6/include-fixed/syslimits.h:7,
                 from /usr/lib/gcc/x86_64-linux-gnu/6/include-fixed/limits.h:34,
                 from /root/miniconda3/include/python3.6m/Python.h:11,
                 from prob2020/cython/cutils.cpp:16:
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:144:1: note: candidate: double log2(double)
 __MATHCALL (log2,, (_Mdouble_ __x));
 ^
In file included from /usr/include/c++/6/math.h:36:0,
                 from /root/miniconda3/include/python3.6m/pyport.h:194,
                 from /root/miniconda3/include/python3.6m/Python.h:53,
                 from prob2020/cython/cutils.cpp:16:
/usr/include/c++/6/cmath:1608:3: note: candidate: constexpr long double std::log2(long double)
   log2(long double __x)
   ^~~~
/usr/include/c++/6/cmath:1604:3: note: candidate: constexpr float std::log2(float)
   log2(float __x)
   ^~~~
In file included from prob2020/cython/cutils.cpp:313:0:
prob2020/cpp/permutation.hpp:8:20: note: candidate: long double log2(long double)
 inline long double log2(const long double x){
                    ^~~~
prob2020/cpp/permutation.hpp:86:51: error: call of overloaded ‘log2(long double&)’ is ambiguous
         frac_of_uniform_ent = myent_2 / log2(mysum);
                                                   ^
In file included from /usr/include/features.h:364:0,
                 from /usr/include/limits.h:25,
                 from /usr/lib/gcc/x86_64-linux-gnu/6/include-fixed/limits.h:168,
                 from /usr/lib/gcc/x86_64-linux-gnu/6/include-fixed/syslimits.h:7,
                 from /usr/lib/gcc/x86_64-linux-gnu/6/include-fixed/limits.h:34,
                 from /root/miniconda3/include/python3.6m/Python.h:11,
                 from prob2020/cython/cutils.cpp:16:
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:144:1: note: candidate: double log2(double)
 __MATHCALL (log2,, (_Mdouble_ __x));
 ^
In file included from /usr/include/c++/6/math.h:36:0,
                 from /root/miniconda3/include/python3.6m/pyport.h:194,
                 from /root/miniconda3/include/python3.6m/Python.h:53,
                 from prob2020/cython/cutils.cpp:16:
/usr/include/c++/6/cmath:1608:3: note: candidate: constexpr long double std::log2(long double)
   log2(long double __x)
   ^~~~
/usr/include/c++/6/cmath:1604:3: note: candidate: constexpr float std::log2(float)
   log2(float __x)
   ^~~~
In file included from prob2020/cython/cutils.cpp:313:0:
prob2020/cpp/permutation.hpp:8:20: note: candidate: long double log2(long double)
 inline long double log2(const long double x){
                    ^~~~
prob2020/cpp/permutation.hpp: In function ‘std::map<std::__cxx11::basic_string<char>, double> calc_effect_statistics(std::map<int, int>, float, int, int)’:
prob2020/cpp/permutation.hpp:143:34: error: call of overloaded ‘log2(long double&)’ is ambiguous
             myent_2 -= p * log2(p);
                                  ^
In file included from /usr/include/features.h:364:0,
                 from /usr/include/limits.h:25,
                 from /usr/lib/gcc/x86_64-linux-gnu/6/include-fixed/limits.h:168,
                 from /usr/lib/gcc/x86_64-linux-gnu/6/include-fixed/syslimits.h:7,
                 from /usr/lib/gcc/x86_64-linux-gnu/6/include-fixed/limits.h:34,
                 from /root/miniconda3/include/python3.6m/Python.h:11,
                 from prob2020/cython/cutils.cpp:16:
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:144:1: note: candidate: double log2(double)
 __MATHCALL (log2,, (_Mdouble_ __x));
 ^
In file included from /usr/include/c++/6/math.h:36:0,
                 from /root/miniconda3/include/python3.6m/pyport.h:194,
                 from /root/miniconda3/include/python3.6m/Python.h:53,
                 from prob2020/cython/cutils.cpp:16:
/usr/include/c++/6/cmath:1608:3: note: candidate: constexpr long double std::log2(long double)
   log2(long double __x)
   ^~~~
/usr/include/c++/6/cmath:1604:3: note: candidate: constexpr float std::log2(float)
   log2(float __x)
   ^~~~
In file included from prob2020/cython/cutils.cpp:313:0:
prob2020/cpp/permutation.hpp:8:20: note: candidate: long double log2(long double)
 inline long double log2(const long double x){
                    ^~~~
prob2020/cpp/permutation.hpp:160:38: error: call of overloaded ‘log2(long double&)’ is ambiguous
                 myent_2 -= p * log2(p);
                                      ^
In file included from /usr/include/features.h:364:0,
                 from /usr/include/limits.h:25,
                 from /usr/lib/gcc/x86_64-linux-gnu/6/include-fixed/limits.h:168,
                 from /usr/lib/gcc/x86_64-linux-gnu/6/include-fixed/syslimits.h:7,
                 from /usr/lib/gcc/x86_64-linux-gnu/6/include-fixed/limits.h:34,
                 from /root/miniconda3/include/python3.6m/Python.h:11,
                 from prob2020/cython/cutils.cpp:16:
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:144:1: note: candidate: double log2(double)
 __MATHCALL (log2,, (_Mdouble_ __x));
 ^
In file included from /usr/include/c++/6/math.h:36:0,
                 from /root/miniconda3/include/python3.6m/pyport.h:194,
                 from /root/miniconda3/include/python3.6m/Python.h:53,
                 from prob2020/cython/cutils.cpp:16:
/usr/include/c++/6/cmath:1608:3: note: candidate: constexpr long double std::log2(long double)
   log2(long double __x)
   ^~~~
/usr/include/c++/6/cmath:1604:3: note: candidate: constexpr float std::log2(float)
   log2(float __x)
   ^~~~
In file included from prob2020/cython/cutils.cpp:313:0:
prob2020/cpp/permutation.hpp:8:20: note: candidate: long double log2(long double)
 inline long double log2(const long double x){
                    ^~~~
prob2020/cpp/permutation.hpp:165:34: error: call of overloaded ‘log2(long double&)’ is ambiguous
             myent_2 -= p * log2(p);
                                  ^
In file included from /usr/include/features.h:364:0,
                 from /usr/include/limits.h:25,
                 from /usr/lib/gcc/x86_64-linux-gnu/6/include-fixed/limits.h:168,
                 from /usr/lib/gcc/x86_64-linux-gnu/6/include-fixed/syslimits.h:7,
                 from /usr/lib/gcc/x86_64-linux-gnu/6/include-fixed/limits.h:34,
                 from /root/miniconda3/include/python3.6m/Python.h:11,
                 from prob2020/cython/cutils.cpp:16:
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:144:1: note: candidate: double log2(double)
 __MATHCALL (log2,, (_Mdouble_ __x));
 ^
In file included from /usr/include/c++/6/math.h:36:0,
                 from /root/miniconda3/include/python3.6m/pyport.h:194,
                 from /root/miniconda3/include/python3.6m/Python.h:53,
                 from prob2020/cython/cutils.cpp:16:
/usr/include/c++/6/cmath:1608:3: note: candidate: constexpr long double std::log2(long double)
   log2(long double __x)
   ^~~~
/usr/include/c++/6/cmath:1604:3: note: candidate: constexpr float std::log2(float)
   log2(float __x)
   ^~~~
In file included from prob2020/cython/cutils.cpp:313:0:
prob2020/cpp/permutation.hpp:8:20: note: candidate: long double log2(long double)
 inline long double log2(const long double x){
                    ^~~~
prob2020/cpp/permutation.hpp:172:51: error: call of overloaded ‘log2(long double&)’ is ambiguous
         frac_of_uniform_ent = myent_2 / log2(mysum);
                                                   ^
In file included from /usr/include/features.h:364:0,
                 from /usr/include/limits.h:25,
                 from /usr/lib/gcc/x86_64-linux-gnu/6/include-fixed/limits.h:168,
                 from /usr/lib/gcc/x86_64-linux-gnu/6/include-fixed/syslimits.h:7,
                 from /usr/lib/gcc/x86_64-linux-gnu/6/include-fixed/limits.h:34,
                 from /root/miniconda3/include/python3.6m/Python.h:11,
                 from prob2020/cython/cutils.cpp:16:
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:144:1: note: candidate: double log2(double)
 __MATHCALL (log2,, (_Mdouble_ __x));
 ^
In file included from /usr/include/c++/6/math.h:36:0,
                 from /root/miniconda3/include/python3.6m/pyport.h:194,
                 from /root/miniconda3/include/python3.6m/Python.h:53,
                 from prob2020/cython/cutils.cpp:16:
/usr/include/c++/6/cmath:1608:3: note: candidate: constexpr long double std::log2(long double)
   log2(long double __x)
   ^~~~
/usr/include/c++/6/cmath:1604:3: note: candidate: constexpr float std::log2(float)
   log2(float __x)
   ^~~~
In file included from prob2020/cython/cutils.cpp:313:0:
prob2020/cpp/permutation.hpp:8:20: note: candidate: long double log2(long double)
 inline long double log2(const long double x){
                    ^~~~
prob2020/cpp/permutation.hpp:116:33: warning: unused variable ‘myent_e’ [-Wunused-variable]
     long double myent_2 = 0.0L, myent_e = 0.0L, mysum = 0.0L, p = 0.0L;
                                 ^~~~~~~
prob2020/cpp/permutation.hpp:118:17: warning: unused variable ‘delta_ent’ [-Wunused-variable]
     long double delta_ent = 0.0L;
                 ^~~~~~~~~
In file included from /root/miniconda3/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:27:0,
                 from /root/miniconda3/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from prob2020/cython/cutils.cpp:311:
/root/miniconda3/lib/python3.6/site-packages/numpy/core/include/numpy/__multiarray_api.h: At global scope:
/root/miniconda3/lib/python3.6/site-packages/numpy/core/include/numpy/__multiarray_api.h:1463:1: warning: ‘int _import_array()’ defined but not used [-Wunused-function]
 _import_array(void)
 ^~~~~~~~~~~~~
error: command 'gcc' failed with exit status 1

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

Command "/root/miniconda3/bin/python -u -c "import setuptools, tokenize;file='/tmp/pip-install-3ol8rj1c/probabilistic2020/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install --record /tmp/pip-record-ynpt27sw/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-install-3ol8rj1c/probabilistic2020/

ctokheim commented 5 years ago

I think I have fixed the compilation error. Please try installing the newest version (v1.2.1):

$ pip install probabilistic2020==1.2.1
sandaru commented 5 years ago

It worked :) .. thanks for the help.

ctokheim commented 5 years ago

Great!

sandaru commented 5 years ago

getting the same issue again Please refer following error record.. Thaks

sandaru commented 5 years ago

pip install probabilistic2020==1.2.1 Collecting probabilistic2020==1.2.1 Using cached https://files.pythonhosted.org/packages/ab/e3/41b006a57ddc39d0d598212f83eb4a31319839b0b2d1551c1747d9da83a2/probabilistic2020-1.2.1.tar.gz Requirement already satisfied: numpy in /root/miniconda3/lib/python3.7/site-packages (from probabilistic2020==1.2.1) (1.16.1) Requirement already satisfied: scipy in /root/miniconda3/lib/python3.7/site-packages (from probabilistic2020==1.2.1) (1.2.1) Requirement already satisfied: pandas in /root/miniconda3/lib/python3.7/site-packages (from probabilistic2020==1.2.1) (0.24.1) Requirement already satisfied: pysam in /root/miniconda3/lib/python3.7/site-packages (from probabilistic2020==1.2.1) (0.15.2) Requirement already satisfied: python-dateutil>=2.5.0 in /root/miniconda3/lib/python3.7/site-packages (from pandas->probabilistic2020==1.2.1) (2.8.0) Requirement already satisfied: pytz>=2011k in /root/miniconda3/lib/python3.7/site-packages (from pandas->probabilistic2020==1.2.1) (2018.9) Requirement already satisfied: six>=1.5 in /root/miniconda3/lib/python3.7/site-packages (from python-dateutil>=2.5.0->pandas->probabilistic2020==1.2.1) (1.12.0) Building wheels for collected packages: probabilistic2020 Running setup.py bdist_wheel for probabilistic2020 ... error Complete output from command /root/miniconda3/bin/python -u -c "import setuptools, tokenize;file='/tmp/pip-install-69no5fjl/probabilistic2020/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" bdist_wheel -d /tmp/pip-wheel-7zlx0eq2 --python-tag cp37: running bdist_wheel running build running build_py creating build creating build/lib.linux-x86_64-3.7 creating build/lib.linux-x86_64-3.7/prob2020 copying prob2020/init.py -> build/lib.linux-x86_64-3.7/prob2020 creating build/lib.linux-x86_64-3.7/prob2020/python copying prob2020/python/process_result.py -> build/lib.linux-x86_64-3.7/prob2020/python copying prob2020/python/indel.py -> build/lib.linux-x86_64-3.7/prob2020/python copying prob2020/python/init.py -> build/lib.linux-x86_64-3.7/prob2020/python copying prob2020/python/mutation_context.py -> build/lib.linux-x86_64-3.7/prob2020/python copying prob2020/python/utils.py -> build/lib.linux-x86_64-3.7/prob2020/python copying prob2020/python/gene_sequence.py -> build/lib.linux-x86_64-3.7/prob2020/python copying prob2020/python/count_frameshifts.py -> build/lib.linux-x86_64-3.7/prob2020/python copying prob2020/python/scores.py -> build/lib.linux-x86_64-3.7/prob2020/python copying prob2020/python/bed_line.py -> build/lib.linux-x86_64-3.7/prob2020/python copying prob2020/python/annotate.py -> build/lib.linux-x86_64-3.7/prob2020/python copying prob2020/python/sequence_context.py -> build/lib.linux-x86_64-3.7/prob2020/python copying prob2020/python/mymath.py -> build/lib.linux-x86_64-3.7/prob2020/python copying prob2020/python/p_value.py -> build/lib.linux-x86_64-3.7/prob2020/python copying prob2020/python/amino_acid.py -> build/lib.linux-x86_64-3.7/prob2020/python copying prob2020/python/permutation.py -> build/lib.linux-x86_64-3.7/prob2020/python creating build/lib.linux-x86_64-3.7/prob2020/cython copying prob2020/cython/init.py -> build/lib.linux-x86_64-3.7/prob2020/cython creating build/lib.linux-x86_64-3.7/prob2020/cpp copying prob2020/cpp/init.py -> build/lib.linux-x86_64-3.7/prob2020/cpp creating build/lib.linux-x86_64-3.7/prob2020/console copying prob2020/console/simulate_non_silent_ratio.py -> build/lib.linux-x86_64-3.7/prob2020/console copying prob2020/console/randomization_test.py -> build/lib.linux-x86_64-3.7/prob2020/console copying prob2020/console/init.py -> build/lib.linux-x86_64-3.7/prob2020/console copying prob2020/console/count_frameshifts.py -> build/lib.linux-x86_64-3.7/prob2020/console copying prob2020/console/probabilistic2020.py -> build/lib.linux-x86_64-3.7/prob2020/console copying prob2020/console/annotate.py -> build/lib.linux-x86_64-3.7/prob2020/console copying prob2020/console/extract_gene_seq.py -> build/lib.linux-x86_64-3.7/prob2020/console running build_ext building 'prob2020.cython.uniform_kde' extension creating build/temp.linux-x86_64-3.7 creating build/temp.linux-x86_64-3.7/prob2020 creating build/temp.linux-x86_64-3.7/prob2020/cython /root/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -fwrapv -O2 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -Iprob2020/cython/ -I/root/miniconda3/lib/python3.7/site-packages/numpy/core/include -I/root/miniconda3/include/python3.7m -c prob2020/cython/uniform_kde.cpp -o build/temp.linux-x86_64-3.7/prob2020/cython/uniform_kde.o cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ In file included from /root/miniconda3/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822:0, from /root/miniconda3/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /root/miniconda3/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from prob2020/cython/uniform_kde.cpp:303: /root/miniconda3/lib/python3.7/site-packages/numpy/core/include/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]

warning "Using deprecated NumPy API, disable it with " \

^~~~~~~

prob2020/cython/uniform_kde.cpp: In function 'int Pyx_GetException(PyObject, PyObject, PyObject**)': prob2020/cython/uniform_kde.cpp:19430:24: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_type'; did you mean 'curexc_type'? tmp_type = tstate->exc_type; ^~~~ curexc_type prob2020/cython/uniform_kde.cpp:19431:25: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_value'; did you mean 'curexc_value'? tmp_value = tstate->exc_value; ^~~~~ curexc_value prob2020/cython/uniform_kde.cpp:19432:22: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_traceback'; did you mean 'curexc_traceback'? tmp_tb = tstate->exc_traceback; ^~~~~ curexc_traceback prob2020/cython/uniform_kde.cpp:19433:13: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_type'; did you mean 'curexc_type'? tstate->exc_type = local_type; ^~~~ curexc_type prob2020/cython/uniform_kde.cpp:19434:13: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_value'; did you mean 'curexc_value'? tstate->exc_value = local_value; ^~~~~ curexc_value prob2020/cython/uniform_kde.cpp:19435:13: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_traceback'; did you mean 'curexc_traceback'? tstate->exc_traceback = local_tb; ^~~~~ curexc_traceback prob2020/cython/uniform_kde.cpp: In function 'void Pyx_ExceptionSave(PyObject, PyObject, PyObject*)': prob2020/cython/uniform_kde.cpp:19557:21: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_type'; did you mean 'curexc_type'? type = tstate->exc_type; ^~~~ curexc_type prob2020/cython/uniform_kde.cpp:19558:22: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_value'; did you mean 'curexc_value'? value = tstate->exc_value; ^~~~~ curexc_value prob2020/cython/uniform_kde.cpp:19559:19: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_traceback'; did you mean 'curexc_traceback'? tb = tstate->exc_traceback; ^~~~~ curexc_traceback prob2020/cython/uniform_kde.cpp: In function 'void Pyx_ExceptionReset(PyObject, PyObject, PyObject*)': prob2020/cython/uniform_kde.cpp:19571:24: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_type'; did you mean 'curexc_type'? tmp_type = tstate->exc_type; ^~~~ curexc_type prob2020/cython/uniform_kde.cpp:19572:25: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_value'; did you mean 'curexc_value'? tmp_value = tstate->exc_value; ^~~~~ curexc_value prob2020/cython/uniform_kde.cpp:19573:22: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_traceback'; did you mean 'curexc_traceback'? tmp_tb = tstate->exc_traceback; ^~~~~ curexc_traceback prob2020/cython/uniform_kde.cpp:19574:13: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_type'; did you mean 'curexc_type'? tstate->exc_type = type; ^~~~ curexc_type prob2020/cython/uniform_kde.cpp:19575:13: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_value'; did you mean 'curexc_value'? tstate->exc_value = value; ^~~~~ curexc_value prob2020/cython/uniform_kde.cpp:19576:13: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_traceback'; did you mean 'curexc_traceback'? tstate->exc_traceback = tb; ^~~~~ curexc_traceback In file included from /root/miniconda3/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:21:0, from /root/miniconda3/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from prob2020/cython/uniform_kde.cpp:303: /root/miniconda3/lib/python3.7/site-packages/numpy/core/include/numpy/__multiarray_api.h: At global scope: /root/miniconda3/lib/python3.7/site-packages/numpy/core/include/numpy/multiarray_api.h:1463:1: warning: 'int _import_array()' defined but not used [-Wunused-function] _import_array(void) ^~~~~ error: command '/root/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc' failed with exit status 1

Failed building wheel for probabilistic2020 Running setup.py clean for probabilistic2020 Failed to build probabilistic2020 Installing collected packages: probabilistic2020 Running setup.py install for probabilistic2020 ... error Complete output from command /root/miniconda3/bin/python -u -c "import setuptools, tokenize;file='/tmp/pip-install-69no5fjl/probabilistic2020/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install --record /tmp/pip-record-ppsngb_a/install-record.txt --single-version-externally-managed --compile: running install running build running build_py creating build creating build/lib.linux-x86_64-3.7 creating build/lib.linux-x86_64-3.7/prob2020 copying prob2020/init.py -> build/lib.linux-x86_64-3.7/prob2020 creating build/lib.linux-x86_64-3.7/prob2020/python copying prob2020/python/process_result.py -> build/lib.linux-x86_64-3.7/prob2020/python copying prob2020/python/indel.py -> build/lib.linux-x86_64-3.7/prob2020/python copying prob2020/python/init.py -> build/lib.linux-x86_64-3.7/prob2020/python copying prob2020/python/mutation_context.py -> build/lib.linux-x86_64-3.7/prob2020/python copying prob2020/python/utils.py -> build/lib.linux-x86_64-3.7/prob2020/python copying prob2020/python/gene_sequence.py -> build/lib.linux-x86_64-3.7/prob2020/python copying prob2020/python/count_frameshifts.py -> build/lib.linux-x86_64-3.7/prob2020/python copying prob2020/python/scores.py -> build/lib.linux-x86_64-3.7/prob2020/python copying prob2020/python/bed_line.py -> build/lib.linux-x86_64-3.7/prob2020/python copying prob2020/python/annotate.py -> build/lib.linux-x86_64-3.7/prob2020/python copying prob2020/python/sequence_context.py -> build/lib.linux-x86_64-3.7/prob2020/python copying prob2020/python/mymath.py -> build/lib.linux-x86_64-3.7/prob2020/python copying prob2020/python/p_value.py -> build/lib.linux-x86_64-3.7/prob2020/python copying prob2020/python/amino_acid.py -> build/lib.linux-x86_64-3.7/prob2020/python copying prob2020/python/permutation.py -> build/lib.linux-x86_64-3.7/prob2020/python creating build/lib.linux-x86_64-3.7/prob2020/cython copying prob2020/cython/init.py -> build/lib.linux-x86_64-3.7/prob2020/cython creating build/lib.linux-x86_64-3.7/prob2020/cpp copying prob2020/cpp/init.py -> build/lib.linux-x86_64-3.7/prob2020/cpp creating build/lib.linux-x86_64-3.7/prob2020/console copying prob2020/console/simulate_non_silent_ratio.py -> build/lib.linux-x86_64-3.7/prob2020/console copying prob2020/console/randomization_test.py -> build/lib.linux-x86_64-3.7/prob2020/console copying prob2020/console/init.py -> build/lib.linux-x86_64-3.7/prob2020/console copying prob2020/console/count_frameshifts.py -> build/lib.linux-x86_64-3.7/prob2020/console copying prob2020/console/probabilistic2020.py -> build/lib.linux-x86_64-3.7/prob2020/console copying prob2020/console/annotate.py -> build/lib.linux-x86_64-3.7/prob2020/console copying prob2020/console/extract_gene_seq.py -> build/lib.linux-x86_64-3.7/prob2020/console running build_ext building 'prob2020.cython.uniform_kde' extension creating build/temp.linux-x86_64-3.7 creating build/temp.linux-x86_64-3.7/prob2020 creating build/temp.linux-x86_64-3.7/prob2020/cython /root/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -fwrapv -O2 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -Iprob2020/cython/ -I/root/miniconda3/lib/python3.7/site-packages/numpy/core/include -I/root/miniconda3/include/python3.7m -c prob2020/cython/uniform_kde.cpp -o build/temp.linux-x86_64-3.7/prob2020/cython/uniform_kde.o cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ In file included from /root/miniconda3/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822:0, from /root/miniconda3/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /root/miniconda3/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from prob2020/cython/uniform_kde.cpp:303: /root/miniconda3/lib/python3.7/site-packages/numpy/core/include/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]

warning "Using deprecated NumPy API, disable it with " \

  ^~~~~~~
prob2020/cython/uniform_kde.cpp: In function 'int __Pyx_GetException(PyObject**, PyObject**, PyObject**)':
prob2020/cython/uniform_kde.cpp:19430:24: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_type'; did you mean 'curexc_type'?
     tmp_type = tstate->exc_type;
                        ^~~~~~~~
                        curexc_type
prob2020/cython/uniform_kde.cpp:19431:25: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_value'; did you mean 'curexc_value'?
     tmp_value = tstate->exc_value;
                         ^~~~~~~~~
                         curexc_value
prob2020/cython/uniform_kde.cpp:19432:22: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_traceback'; did you mean 'curexc_traceback'?
     tmp_tb = tstate->exc_traceback;
                      ^~~~~~~~~~~~~
                      curexc_traceback
prob2020/cython/uniform_kde.cpp:19433:13: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_type'; did you mean 'curexc_type'?
     tstate->exc_type = local_type;
             ^~~~~~~~
             curexc_type
prob2020/cython/uniform_kde.cpp:19434:13: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_value'; did you mean 'curexc_value'?
     tstate->exc_value = local_value;
             ^~~~~~~~~
             curexc_value
prob2020/cython/uniform_kde.cpp:19435:13: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_traceback'; did you mean 'curexc_traceback'?
     tstate->exc_traceback = local_tb;
             ^~~~~~~~~~~~~
             curexc_traceback
prob2020/cython/uniform_kde.cpp: In function 'void __Pyx_ExceptionSave(PyObject**, PyObject**, PyObject**)':
prob2020/cython/uniform_kde.cpp:19557:21: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_type'; did you mean 'curexc_type'?
     *type = tstate->exc_type;
                     ^~~~~~~~
                     curexc_type
prob2020/cython/uniform_kde.cpp:19558:22: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_value'; did you mean 'curexc_value'?
     *value = tstate->exc_value;
                      ^~~~~~~~~
                      curexc_value
prob2020/cython/uniform_kde.cpp:19559:19: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_traceback'; did you mean 'curexc_traceback'?
     *tb = tstate->exc_traceback;
                   ^~~~~~~~~~~~~
                   curexc_traceback
prob2020/cython/uniform_kde.cpp: In function 'void __Pyx_ExceptionReset(PyObject*, PyObject*, PyObject*)':
prob2020/cython/uniform_kde.cpp:19571:24: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_type'; did you mean 'curexc_type'?
     tmp_type = tstate->exc_type;
                        ^~~~~~~~
                        curexc_type
prob2020/cython/uniform_kde.cpp:19572:25: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_value'; did you mean 'curexc_value'?
     tmp_value = tstate->exc_value;
                         ^~~~~~~~~
                         curexc_value
prob2020/cython/uniform_kde.cpp:19573:22: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_traceback'; did you mean 'curexc_traceback'?
     tmp_tb = tstate->exc_traceback;
                      ^~~~~~~~~~~~~
                      curexc_traceback
prob2020/cython/uniform_kde.cpp:19574:13: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_type'; did you mean 'curexc_type'?
     tstate->exc_type = type;
             ^~~~~~~~
             curexc_type
prob2020/cython/uniform_kde.cpp:19575:13: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_value'; did you mean 'curexc_value'?
     tstate->exc_value = value;
             ^~~~~~~~~
             curexc_value
prob2020/cython/uniform_kde.cpp:19576:13: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_traceback'; did you mean 'curexc_traceback'?
     tstate->exc_traceback = tb;
             ^~~~~~~~~~~~~
             curexc_traceback
In file included from /root/miniconda3/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:21:0,
                 from /root/miniconda3/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from prob2020/cython/uniform_kde.cpp:303:
/root/miniconda3/lib/python3.7/site-packages/numpy/core/include/numpy/__multiarray_api.h: At global scope:
/root/miniconda3/lib/python3.7/site-packages/numpy/core/include/numpy/__multiarray_api.h:1463:1: warning: 'int _import_array()' defined but not used [-Wunused-function]
 _import_array(void)
 ^~~~~~~~~~~~~
error: command '/root/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc' failed with exit status 1

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

Command "/root/miniconda3/bin/python -u -c "import setuptools, tokenize;file='/tmp/pip-install-69no5fjl/probabilistic2020/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install --record /tmp/pip-record-ppsngb_a/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-install-69no5fjl/probabilistic2020/

ctokheim commented 5 years ago

It looks like from the above error messages that you are using python3.7 now. If you use python3.6, the installation should work for version 1.2.1.

Basically the issue with python3.7 relates to an external python package (cython) being broken on this version of python. I have, however, found a work around that should fix the issue. If you absolutely need python 3.7, then try installing version 1.2.2:

$ pip install probabilistic2020==1.2.2
sandaru commented 5 years ago

Thanks Collin,

Unfortunately my previous installation didn't work as expected. So I needed to start with a fresh installation. I just used apt-get to install python 3.

now it works fine. Thanks for the help.