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hiclib / pastis

Poisson-based algorithm for stable inference of DNA Structure
http://hiclib.github.io/pastis/
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Error using: pip3.7 install pastis #71

Open yliueagle opened 4 years ago

yliueagle commented 4 years ago

Hi,

Thanks for developing this package and I am eager to try it out. While I was installing the package, I got the following error. Do you have suggestion for solving it?

(version of modules: numpy 1.18.1 pandas 1.0.1 scipy 1.4.1 iced 0.5.7 scikit-learn 0.22.1 autograd 1.3)

pip3.7 install pastis

Collecting pastis Using cached pastis-0.3.3.tar.gz (374 kB) Building wheels for collected packages: pastis Building wheel for pastis (setup.py) ... error ERROR: Command errored out with exit status 1: command: /usr/local/opt/python/bin/python3.7 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/4f/v6fzk6ss6lvdkzqp9y8wwfg00000gn/T/pip-install-p4sk008d/pastis/setup.py'"'"'; file='"'"'/private/var/folders/4f/v6fzk6ss6lvdkzqp9y8wwfg00000gn/T/pip-install-p4sk008d/pastis/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 /private/var/folders/4f/v6fzk6ss6lvdkzqp9y8wwfg00000gn/T/pip-wheel-i2y_hqtw cwd: /private/var/folders/4f/v6fzk6ss6lvdkzqp9y8wwfg00000gn/T/pip-install-p4sk008d/pastis/ Complete output (205 lines): Warning: Assuming default configuration (pastis/utils/{setup_utils,setup}.py was not found) Appending pastis.utils configuration to pastis Ignoring attempt to set 'name' (from 'pastis' to 'pastis.utils') Appending pastis.optimization configuration to pastis Ignoring attempt to set 'name' (from 'pastis' to 'pastis.optimization') Warning: Assuming default configuration (pastis/externals/iced/utils/{setup_utils,setup}.py was not found) Appending pastis.externals.iced.utils configuration to pastis.externals.iced Ignoring attempt to set 'name' (from 'pastis.externals.iced' to 'pastis.externals.iced.utils') Appending pastis.externals.iced.datasets configuration to pastis.externals.iced Ignoring attempt to set 'name' (from 'pastis.externals.iced' to 'pastis.externals.iced.datasets') non-existing path in 'pastis/externals/iced/io': '../src/cblas' non-existing path in 'pastis/externals/iced/io': '../src/cblas' Appending pastis.externals.iced.io configuration to pastis.externals.iced Ignoring attempt to set 'name' (from 'pastis.externals.iced' to 'pastis.externals.iced.io') non-existing path in 'pastis/externals/iced': '../src/cblas' non-existing path in 'pastis/externals/iced': '../src/cblas' Appending pastis.externals.iced configuration to pastis.externals Ignoring attempt to set 'name' (from 'pastis.externals' to 'pastis.externals.iced') Appending pastis.externals configuration to pastis Ignoring attempt to set 'name' (from 'pastis' to 'pastis.externals') Appending pastis configuration to Ignoring attempt to set 'name' (from '' to 'pastis') running bdist_wheel running build running config_cc unifing config_cc, config, build_clib, build_ext, build commands --compiler options running config_fc unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options running build_src buildsrc building extension "pastis.externals.iced.io.fastio" sources building extension "pastis.externals.iced.io.read" sources building extension "pastis.externals.iced.normalization" sources building extension "pastis.externals.iced.filter" sources building data_files sources build_src: building npy-pkg config files running build_py creating build creating build/lib.macosx-10.14-x86_64-3.7 creating build/lib.macosx-10.14-x86_64-3.7/pastis copying pastis/algorithms.py -> build/lib.macosx-10.14-x86_64-3.7/pastis copying pastis/config.py -> build/lib.macosx-10.14-x86_64-3.7/pastis copying pastis/fastio.py -> build/lib.macosx-10.14-x86_64-3.7/pastis copying pastis/io.py -> build/lib.macosx-10.14-x86_64-3.7/pastis copying pastis/init.py -> build/lib.macosx-10.14-x86_64-3.7/pastis copying pastis/setup.py -> build/lib.macosx-10.14-x86_64-3.7/pastis creating build/lib.macosx-10.14-x86_64-3.7/pastis/utils copying pastis/utils/bezier.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/utils copying pastis/utils/init.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/utils copying pastis/utils/validation.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/utils creating build/lib.macosx-10.14-x86_64-3.7/pastis/optimization copying pastis/optimization/poisson_model.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/optimization copying pastis/optimization/poisson_structure.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/optimization copying pastis/optimization/mds.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/optimization copying pastis/optimization/init.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/optimization copying pastis/optimization/negative_binomial.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/optimization copying pastis/optimization/mds_old.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/optimization copying pastis/optimization/setup.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/optimization copying pastis/optimization/utils.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/optimization copying pastis/optimization/negative_binomial_structure.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/optimization creating build/lib.macosx-10.14-x86_64-3.7/pastis/externals copying pastis/externals/test_externals_setup.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/externals copying pastis/externals/init.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/externals copying pastis/externals/setup.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/externals creating build/lib.macosx-10.14-x86_64-3.7/pastis/externals/iced copying pastis/externals/iced/init.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/externals/iced copying pastis/externals/iced/setup.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/externals/iced copying pastis/externals/iced/filter.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/externals/iced copying pastis/externals/iced/normalization.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/externals/iced creating build/lib.macosx-10.14-x86_64-3.7/pastis/externals/iced/utils copying pastis/externals/iced/utils/_genome.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/externals/iced/utils copying pastis/externals/iced/utils/init.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/externals/iced/utils copying pastis/externals/iced/utils/_validation.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/externals/iced/utils copying pastis/externals/iced/utils/_vis.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/externals/iced/utils copying pastis/externals/iced/utils/validation.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/externals/iced/utils creating build/lib.macosx-10.14-x86_64-3.7/pastis/externals/iced/datasets copying pastis/externals/iced/datasets/init.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/externals/iced/datasets copying pastis/externals/iced/datasets/setup.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/externals/iced/datasets copying pastis/externals/iced/datasets/dldata.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/externals/iced/datasets copying pastis/externals/iced/datasets/base.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/externals/iced/datasets creating build/lib.macosx-10.14-x86_64-3.7/pastis/externals/iced/io copying pastis/externals/iced/io/_io_else.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/externals/iced/io copying pastis/externals/iced/io/init.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/externals/iced/io copying pastis/externals/iced/io/setup.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/externals/iced/io copying pastis/externals/iced/io/_io_pandas.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/externals/iced/io running build_ext customize UnixCCompiler customize UnixCCompiler using buildext building 'pastis.externals.iced.io.fastio' extension compiling C sources C compiler: clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk -I/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers

creating build/temp.macosx-10.14-x86_64-3.7/pastis creating build/temp.macosx-10.14-x86_64-3.7/pastis/externals creating build/temp.macosx-10.14-x86_64-3.7/pastis/externals/iced creating build/temp.macosx-10.14-x8664-3.7/pastis/externals/iced/io compile options: '-I../src/cblas -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/openssl@1.1/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/include/python3.7m -c' clang: pastis/externals/iced/io/fastio.c In file included from pastis/externals/iced/io/fastio_.c:435: In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4: In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12: In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1832: /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]

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

^ In file included from pastis/externals/iced/io/fastio_.c:438: pastis/externals/iced/io/write.c:8:11: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare] while(i != n_lines){ ~ ^ ~~~ pastis/externals/iced/io/write.c:25:11: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare] while(i != nlines){ ~ ^ ~~~ pastis/externals/iced/io/fastio.c:6609:65: error: too many arguments to function call, expected 3, have 4 return (*((__Pyx_PyCFunctionFast)meth)) (self, args, nargs, NULL);


  /Library/Developer/CommandLineTools/usr/lib/clang/10.0.1/include/stddef.h:105:16: note: expanded from macro 'NULL'
  define NULL ((void*)0)
                 ^~~~~~~~~~
  pastis/externals/iced/io/fastio_.c:6874:21: error: no member named 'exc_type' in 'struct _ts'
      *type = tstate->exc_type;
              ~~~~~~  ^
  pastis/externals/iced/io/fastio_.c:6875:22: error: no member named 'exc_value' in 'struct _ts'; did you mean 'curexc_value'?
      *value = tstate->exc_value;
                       ^~~~~~~~~
                       curexc_value
  /usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:240:15: note: 'curexc_value' declared here
      PyObject *curexc_value;
                ^
  pastis/externals/iced/io/fastio_.c:6876:19: error: no member named 'exc_traceback' in 'struct _ts'; did you mean 'curexc_traceback'?
      *tb = tstate->exc_traceback;
                    ^~~~~~~~~~~~~
                    curexc_traceback
  /usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:241:15: note: 'curexc_traceback' declared here
      PyObject *curexc_traceback;
                ^
  pastis/externals/iced/io/fastio_.c:6883:24: error: no member named 'exc_type' in 'struct _ts'
      tmp_type = tstate->exc_type;
                 ~~~~~~  ^
  pastis/externals/iced/io/fastio_.c:6884:25: error: no member named 'exc_value' in 'struct _ts'; did you mean 'curexc_value'?
      tmp_value = tstate->exc_value;
                          ^~~~~~~~~
                          curexc_value
  /usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:240:15: note: 'curexc_value' declared here
      PyObject *curexc_value;
                ^
  pastis/externals/iced/io/fastio_.c:6885:22: error: no member named 'exc_traceback' in 'struct _ts'; did you mean 'curexc_traceback'?
      tmp_tb = tstate->exc_traceback;
                       ^~~~~~~~~~~~~
                       curexc_traceback
  /usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:241:15: note: 'curexc_traceback' declared here
      PyObject *curexc_traceback;
                ^
  pastis/externals/iced/io/fastio_.c:6886:13: error: no member named 'exc_type' in 'struct _ts'
      tstate->exc_type = type;
      ~~~~~~  ^
  pastis/externals/iced/io/fastio_.c:6887:13: error: no member named 'exc_value' in 'struct _ts'; did you mean 'curexc_value'?
      tstate->exc_value = value;
              ^~~~~~~~~
              curexc_value
  /usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:240:15: note: 'curexc_value' declared here
      PyObject *curexc_value;
                ^
  pastis/externals/iced/io/fastio_.c:6888:13: error: no member named 'exc_traceback' in 'struct _ts'; did you mean 'curexc_traceback'?
      tstate->exc_traceback = tb;
              ^~~~~~~~~~~~~
              curexc_traceback
  /usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:241:15: note: 'curexc_traceback' declared here
      PyObject *curexc_traceback;
                ^
  pastis/externals/iced/io/fastio_.c:6943:24: error: no member named 'exc_type' in 'struct _ts'
      tmp_type = tstate->exc_type;
                 ~~~~~~  ^
  pastis/externals/iced/io/fastio_.c:6944:25: error: no member named 'exc_value' in 'struct _ts'; did you mean 'curexc_value'?
      tmp_value = tstate->exc_value;
                          ^~~~~~~~~
                          curexc_value
  /usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:240:15: note: 'curexc_value' declared here
      PyObject *curexc_value;
                ^
  pastis/externals/iced/io/fastio_.c:6945:22: error: no member named 'exc_traceback' in 'struct _ts'; did you mean 'curexc_traceback'?
      tmp_tb = tstate->exc_traceback;
                       ^~~~~~~~~~~~~
                       curexc_traceback
  /usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:241:15: note: 'curexc_traceback' declared here
      PyObject *curexc_traceback;
                ^
  pastis/externals/iced/io/fastio_.c:6946:13: error: no member named 'exc_type' in 'struct _ts'
      tstate->exc_type = local_type;
      ~~~~~~  ^
  pastis/externals/iced/io/fastio_.c:6947:13: error: no member named 'exc_value' in 'struct _ts'; did you mean 'curexc_value'?
      tstate->exc_value = local_value;
              ^~~~~~~~~
              curexc_value
  /usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:240:15: note: 'curexc_value' declared here
      PyObject *curexc_value;
                ^
  pastis/externals/iced/io/fastio_.c:6948:13: error: no member named 'exc_traceback' in 'struct _ts'; did you mean 'curexc_traceback'?
      tstate->exc_traceback = local_tb;
              ^~~~~~~~~~~~~
              curexc_traceback
  /usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:241:15: note: 'curexc_traceback' declared here
      PyObject *curexc_traceback;
                ^
  3 warnings and 16 errors generated.
  error: Command "clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk -I/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers -I../src/cblas -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/openssl@1.1/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/include/python3.7m -c pastis/externals/iced/io/fastio_.c -o build/temp.macosx-10.14-x86_64-3.7/pastis/externals/iced/io/fastio_.o -MMD -MF build/temp.macosx-10.14-x86_64-3.7/pastis/externals/iced/io/fastio_.o.d" failed with exit status 1
  ----------------------------------------
  ERROR: Failed building wheel for pastis
  Running setup.py clean for pastis
Failed to build pastis
Installing collected packages: pastis
    Running setup.py install for pastis ... error
    ERROR: Command errored out with exit status 1:
     command: /usr/local/opt/python/bin/python3.7 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/4f/v6fzk6ss6lvdkzqp9y8wwfg00000gn/T/pip-install-p4sk008d/pastis/setup.py'"'"'; __file__='"'"'/private/var/folders/4f/v6fzk6ss6lvdkzqp9y8wwfg00000gn/T/pip-install-p4sk008d/pastis/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/4f/v6fzk6ss6lvdkzqp9y8wwfg00000gn/T/pip-record-yniji64f/install-record.txt --single-version-externally-managed --compile --install-headers /usr/local/include/python3.7m/pastis
         cwd: /private/var/folders/4f/v6fzk6ss6lvdkzqp9y8wwfg00000gn/T/pip-install-p4sk008d/pastis/
    Complete output (157 lines):
    Warning: Assuming default configuration (pastis/utils/{setup_utils,setup}.py was not found)
    Appending pastis.utils configuration to pastis
    Ignoring attempt to set 'name' (from 'pastis' to 'pastis.utils')
    Appending pastis.optimization configuration to pastis
    Ignoring attempt to set 'name' (from 'pastis' to 'pastis.optimization')
    Warning: Assuming default configuration (pastis/externals/iced/utils/{setup_utils,setup}.py was not found)
    Appending pastis.externals.iced.utils configuration to pastis.externals.iced
    Ignoring attempt to set 'name' (from 'pastis.externals.iced' to 'pastis.externals.iced.utils')
    Appending pastis.externals.iced.datasets configuration to pastis.externals.iced
    Ignoring attempt to set 'name' (from 'pastis.externals.iced' to 'pastis.externals.iced.datasets')
    non-existing path in 'pastis/externals/iced/io': '../src/cblas'
    non-existing path in 'pastis/externals/iced/io': '../src/cblas'
    Appending pastis.externals.iced.io configuration to pastis.externals.iced
    Ignoring attempt to set 'name' (from 'pastis.externals.iced' to 'pastis.externals.iced.io')
    non-existing path in 'pastis/externals/iced': '../src/cblas'
    non-existing path in 'pastis/externals/iced': '../src/cblas'
    Appending pastis.externals.iced configuration to pastis.externals
    Ignoring attempt to set 'name' (from 'pastis.externals' to 'pastis.externals.iced')
    Appending pastis.externals configuration to pastis
    Ignoring attempt to set 'name' (from 'pastis' to 'pastis.externals')
    Appending pastis configuration to
    Ignoring attempt to set 'name' (from '' to 'pastis')
    running install
    running build
    running config_cc
    unifing config_cc, config, build_clib, build_ext, build commands --compiler options
    running config_fc
    unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
    running build_src
    build_src
    building extension "pastis.externals.iced.io.fastio_" sources
    building extension "pastis.externals.iced.io.read" sources
    building extension "pastis.externals.iced._normalization_" sources
    building extension "pastis.externals.iced._filter_" sources
    building data_files sources
    build_src: building npy-pkg config files
    running build_py
    running build_ext
    customize UnixCCompiler
    customize UnixCCompiler using build_ext
    building 'pastis.externals.iced.io.fastio_' extension
    compiling C sources
    C compiler: clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk -I/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers

    creating build/temp.macosx-10.14-x86_64-3.7/pastis
    creating build/temp.macosx-10.14-x86_64-3.7/pastis/externals
    creating build/temp.macosx-10.14-x86_64-3.7/pastis/externals/iced
    creating build/temp.macosx-10.14-x86_64-3.7/pastis/externals/iced/io
    compile options: '-I../src/cblas -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/openssl@1.1/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/include/python3.7m -c'
    clang: pastis/externals/iced/io/fastio_.c
    In file included from pastis/externals/iced/io/fastio_.c:435:
    In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4:
    In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
    In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1832:
    /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with "          "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
    #warning "Using deprecated NumPy API, disable it with " \
     ^
    In file included from pastis/externals/iced/io/fastio_.c:438:
    pastis/externals/iced/io/write.c:8:11: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare]
      while(i != n_lines){
            ~ ^  ~~~~~~~
    pastis/externals/iced/io/write.c:25:11: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare]
      while(i != n_lines){
            ~ ^  ~~~~~~~
    pastis/externals/iced/io/fastio_.c:6609:65: error: too many arguments to function call, expected 3, have 4
        return (*((__Pyx_PyCFunctionFast)meth)) (self, args, nargs, NULL);
               ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~                     ^~~~
    /Library/Developer/CommandLineTools/usr/lib/clang/10.0.1/include/stddef.h:105:16: note: expanded from macro 'NULL'
    #  define NULL ((void*)0)
                   ^~~~~~~~~~
    pastis/externals/iced/io/fastio_.c:6874:21: error: no member named 'exc_type' in 'struct _ts'
        *type = tstate->exc_type;
                ~~~~~~  ^
    pastis/externals/iced/io/fastio_.c:6875:22: error: no member named 'exc_value' in 'struct _ts'; did you mean 'curexc_value'?
        *value = tstate->exc_value;
                         ^~~~~~~~~
                         curexc_value
    /usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:240:15: note: 'curexc_value' declared here
        PyObject *curexc_value;
                  ^
    pastis/externals/iced/io/fastio_.c:6876:19: error: no member named 'exc_traceback' in 'struct _ts'; did you mean 'curexc_traceback'?
        *tb = tstate->exc_traceback;
                      ^~~~~~~~~~~~~
                      curexc_traceback
    /usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:241:15: note: 'curexc_traceback' declared here
        PyObject *curexc_traceback;
                  ^
    pastis/externals/iced/io/fastio_.c:6883:24: error: no member named 'exc_type' in 'struct _ts'
        tmp_type = tstate->exc_type;
                   ~~~~~~  ^
    pastis/externals/iced/io/fastio_.c:6884:25: error: no member named 'exc_value' in 'struct _ts'; did you mean 'curexc_value'?
        tmp_value = tstate->exc_value;
                            ^~~~~~~~~
                            curexc_value
    /usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:240:15: note: 'curexc_value' declared here
        PyObject *curexc_value;
                  ^
    pastis/externals/iced/io/fastio_.c:6885:22: error: no member named 'exc_traceback' in 'struct _ts'; did you mean 'curexc_traceback'?
        tmp_tb = tstate->exc_traceback;
                         ^~~~~~~~~~~~~
                         curexc_traceback
    /usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:241:15: note: 'curexc_traceback' declared here
        PyObject *curexc_traceback;
                  ^
    pastis/externals/iced/io/fastio_.c:6886:13: error: no member named 'exc_type' in 'struct _ts'
        tstate->exc_type = type;
        ~~~~~~  ^
    pastis/externals/iced/io/fastio_.c:6887:13: error: no member named 'exc_value' in 'struct _ts'; did you mean 'curexc_value'?
        tstate->exc_value = value;
                ^~~~~~~~~
                curexc_value
    /usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:240:15: note: 'curexc_value' declared here
        PyObject *curexc_value;
                  ^
    pastis/externals/iced/io/fastio_.c:6888:13: error: no member named 'exc_traceback' in 'struct _ts'; did you mean 'curexc_traceback'?
        tstate->exc_traceback = tb;
                ^~~~~~~~~~~~~
                curexc_traceback
    /usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:241:15: note: 'curexc_traceback' declared here
        PyObject *curexc_traceback;
                  ^
    pastis/externals/iced/io/fastio_.c:6943:24: error: no member named 'exc_type' in 'struct _ts'
        tmp_type = tstate->exc_type;
                   ~~~~~~  ^
    pastis/externals/iced/io/fastio_.c:6944:25: error: no member named 'exc_value' in 'struct _ts'; did you mean 'curexc_value'?
        tmp_value = tstate->exc_value;
                            ^~~~~~~~~
                            curexc_value
    /usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:240:15: note: 'curexc_value' declared here
        PyObject *curexc_value;
                  ^
    pastis/externals/iced/io/fastio_.c:6945:22: error: no member named 'exc_traceback' in 'struct _ts'; did you mean 'curexc_traceback'?
        tmp_tb = tstate->exc_traceback;
                         ^~~~~~~~~~~~~
                         curexc_traceback
    /usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:241:15: note: 'curexc_traceback' declared here
        PyObject *curexc_traceback;
                  ^
    pastis/externals/iced/io/fastio_.c:6946:13: error: no member named 'exc_type' in 'struct _ts'
        tstate->exc_type = local_type;
        ~~~~~~  ^
    pastis/externals/iced/io/fastio_.c:6947:13: error: no member named 'exc_value' in 'struct _ts'; did you mean 'curexc_value'?
        tstate->exc_value = local_value;
                ^~~~~~~~~
                curexc_value
    /usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:240:15: note: 'curexc_value' declared here
        PyObject *curexc_value;
                  ^
    pastis/externals/iced/io/fastio_.c:6948:13: error: no member named 'exc_traceback' in 'struct _ts'; did you mean 'curexc_traceback'?
        tstate->exc_traceback = local_tb;
                ^~~~~~~~~~~~~
                curexc_traceback
    /usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:241:15: note: 'curexc_traceback' declared here
        PyObject *curexc_traceback;
                  ^
    3 warnings and 16 errors generated.
    error: Command "clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk -I/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers -I../src/cblas -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/openssl@1.1/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/include/python3.7m -c pastis/externals/iced/io/fastio_.c -o build/temp.macosx-10.14-x86_64-3.7/pastis/externals/iced/io/fastio_.o -MMD -MF build/temp.macosx-10.14-x86_64-3.7/pastis/externals/iced/io/fastio_.o.d" failed with exit status 1
    ----------------------------------------
ERROR: Command errored out with exit status 1: /usr/local/opt/python/bin/python3.7 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/4f/v6fzk6ss6lvdkzqp9y8wwfg00000gn/T/pip-install-p4sk008d/pastis/setup.py'"'"'; __file__='"'"'/private/var/folders/4f/v6fzk6ss6lvdkzqp9y8wwfg00000gn/T/pip-install-p4sk008d/pastis/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/4f/v6fzk6ss6lvdkzqp9y8wwfg00000gn/T/pip-record-yniji64f/install-record.txt --single-version-externally-managed --compile --install-headers /usr/local/include/python3.7m/pastis Check the logs for full command output.
NelleV commented 4 years ago

Hello, So sorry not to have responded sooner. What OS are you working on? It seems the compiler used is clang, and the issues might be fixed using gcc. Thanks, Nelle