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Unable to install on windows #3

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ncdingari opened this Issue Jun 26, 2017 · 6 comments

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@ncdingari

ncdingari commented Jun 26, 2017

Unable to install on windows, do you have any prebuilt version with whl

I tried using pip install scikit-survival, having some build issues with C++ compiler. It would be great if you have whl file

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sebp Jul 1, 2017

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Could you please post the error message here?

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sebp commented Jul 1, 2017

Could you please post the error message here?

sebp added a commit that referenced this issue Jul 1, 2017

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sebp Jul 1, 2017

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I fixed a problem with fmin and fmax not being available in commit 2bd9e5e.

Unfortunately, I was only able to build a whl for Python 3.4 due to cvxopt/cvxopt#94.

It would be great if you could give it a try and let me know if it works: https://ci.appveyor.com/project/sebp/scikit-survival/build/1.0.21/artifacts

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sebp commented Jul 1, 2017

I fixed a problem with fmin and fmax not being available in commit 2bd9e5e.

Unfortunately, I was only able to build a whl for Python 3.4 due to cvxopt/cvxopt#94.

It would be great if you could give it a try and let me know if it works: https://ci.appveyor.com/project/sebp/scikit-survival/build/1.0.21/artifacts

@sebp sebp closed this in 2d87a5c Jul 31, 2017

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KOLANICH Dec 25, 2017

It doesn't. Still there are issues. I use the latest Anaconda on 32-bit win 7 with mingw32-w64 (it's a 32-bit compiler!) installed (from conda).

(%CONDA_DEFAULT_ENV%) %USERPROFILE%\Desktop\scikit-survival>pip install --upgrade ./
Processing %USERPROFILE%\desktop\scikit-survival
......
Building wheels for collected packages: scikit-survival
  Installing build dependencies ... done
  Running setup.py bdist_wheel for scikit-survival ... error
  Complete output from command %CONDA_DEFAULT_ENV%python.exe -u -c "import setuptools, tokenize;__file__='%USERPROFILE%\\AppData\\Local\\Temp\\pip-req-build-zw1rfx
d9\\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 %USERPROFILE%\AppData\Local\Temp\pip-wheel-17u82pp4 --python-tag cp36:
  Compiling sksurv\bintrees\_binarytrees.pyx because it changed.
  Compiling sksurv\ensemble\_coxph_loss.pyx because it changed.
  Compiling sksurv\kernels\_clinical_kernel.pyx because it changed.
  Compiling sksurv\linear_model\_coxnet.pyx because it changed.
  Compiling sksurv\svm\_prsvm.pyx because it changed.
  Compiling sksurv\svm\_minlip.pyx because it changed.
  [1/6] Cythonizing sksurv\bintrees\_binarytrees.pyx
  [2/6] Cythonizing sksurv\ensemble\_coxph_loss.pyx
  [3/6] Cythonizing sksurv\kernels\_clinical_kernel.pyx
  [4/6] Cythonizing sksurv\linear_model\_coxnet.pyx
  [5/6] Cythonizing sksurv\svm\_minlip.pyx
  [6/6] Cythonizing sksurv\svm\_prsvm.pyx
  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
  build_src
  building extension "sksurv.bintrees._binarytrees" sources
  building extension "sksurv.ensemble._coxph_loss" sources
  building extension "sksurv.kernels._clinical_kernel" sources
  building extension "sksurv.linear_model._coxnet" sources
  building extension "sksurv.svm._prsvm" sources
  building extension "sksurv.svm._minlip" sources
  building data_files sources
  build_src: building npy-pkg config files
  running build_py
  creating build
  creating build\lib.win32-3.6
  creating build\lib.win32-3.6\sksurv
  copying sksurv\base.py -> build\lib.win32-3.6\sksurv
  copying sksurv\column.py -> build\lib.win32-3.6\sksurv
  copying sksurv\functions.py -> build\lib.win32-3.6\sksurv
  copying sksurv\metrics.py -> build\lib.win32-3.6\sksurv
  copying sksurv\nonparametric.py -> build\lib.win32-3.6\sksurv
  copying sksurv\preprocessing.py -> build\lib.win32-3.6\sksurv
  copying sksurv\setup.py -> build\lib.win32-3.6\sksurv
  copying sksurv\util.py -> build\lib.win32-3.6\sksurv
  copying sksurv\__init__.py -> build\lib.win32-3.6\sksurv
  creating build\lib.win32-3.6\sksurv\bintrees
  copying sksurv\bintrees\setup.py -> build\lib.win32-3.6\sksurv\bintrees
  copying sksurv\bintrees\__init__.py -> build\lib.win32-3.6\sksurv\bintrees
  creating build\lib.win32-3.6\sksurv\datasets
  copying sksurv\datasets\base.py -> build\lib.win32-3.6\sksurv\datasets
  copying sksurv\datasets\setup.py -> build\lib.win32-3.6\sksurv\datasets
  copying sksurv\datasets\__init__.py -> build\lib.win32-3.6\sksurv\datasets
  creating build\lib.win32-3.6\sksurv\ensemble
  copying sksurv\ensemble\boosting.py -> build\lib.win32-3.6\sksurv\ensemble
  copying sksurv\ensemble\setup.py -> build\lib.win32-3.6\sksurv\ensemble
  copying sksurv\ensemble\survival_loss.py -> build\lib.win32-3.6\sksurv\ensemble
  copying sksurv\ensemble\__init__.py -> build\lib.win32-3.6\sksurv\ensemble
  creating build\lib.win32-3.6\sksurv\io
  copying sksurv\io\arffread.py -> build\lib.win32-3.6\sksurv\io
  copying sksurv\io\arffwrite.py -> build\lib.win32-3.6\sksurv\io
  copying sksurv\io\__init__.py -> build\lib.win32-3.6\sksurv\io
  creating build\lib.win32-3.6\sksurv\kernels
  copying sksurv\kernels\clinical.py -> build\lib.win32-3.6\sksurv\kernels
  copying sksurv\kernels\setup.py -> build\lib.win32-3.6\sksurv\kernels
  copying sksurv\kernels\__init__.py -> build\lib.win32-3.6\sksurv\kernels
  creating build\lib.win32-3.6\sksurv\linear_model
  copying sksurv\linear_model\aft.py -> build\lib.win32-3.6\sksurv\linear_model
  copying sksurv\linear_model\coxnet.py -> build\lib.win32-3.6\sksurv\linear_model
  copying sksurv\linear_model\coxph.py -> build\lib.win32-3.6\sksurv\linear_model
  copying sksurv\linear_model\setup.py -> build\lib.win32-3.6\sksurv\linear_model
  copying sksurv\linear_model\__init__.py -> build\lib.win32-3.6\sksurv\linear_model
  creating build\lib.win32-3.6\sksurv\meta
  copying sksurv\meta\base.py -> build\lib.win32-3.6\sksurv\meta
  copying sksurv\meta\ensemble_selection.py -> build\lib.win32-3.6\sksurv\meta
  copying sksurv\meta\stacking.py -> build\lib.win32-3.6\sksurv\meta
  copying sksurv\meta\__init__.py -> build\lib.win32-3.6\sksurv\meta
  creating build\lib.win32-3.6\sksurv\svm
  copying sksurv\svm\minlip.py -> build\lib.win32-3.6\sksurv\svm
  copying sksurv\svm\naive_survival_svm.py -> build\lib.win32-3.6\sksurv\svm
  copying sksurv\svm\setup.py -> build\lib.win32-3.6\sksurv\svm
  copying sksurv\svm\survival_svm.py -> build\lib.win32-3.6\sksurv\svm
  copying sksurv\svm\__init__.py -> build\lib.win32-3.6\sksurv\svm
  running build_ext
  Cannot build msvcr library: "vcruntime140d.dll" not found
  customize Mingw32CCompiler
  customize Mingw32CCompiler using build_ext
  Cannot build msvcr library: "vcruntime140d.dll" not found
  customize Mingw32CCompiler
  customize Mingw32CCompiler using build_ext
  building 'sksurv.bintrees._binarytrees' extension
  compiling C++ sources
  C compiler: g++ -O2 -Wall

  creating build\temp.win32-3.6
  creating build\temp.win32-3.6\Release
  creating build\temp.win32-3.6\Release\sksurv
  creating build\temp.win32-3.6\Release\sksurv\bintrees
  compile options: '-DNPY_MINGW_USE_CUSTOM_MSVCR -D__MSVCRT_VERSION__=0x1900 -Isksurv\bintrees -I%CONDA_DEFAULT_ENV%\lib\site-packages\numpy\core\include -I%CONDA_DEFAULT_ENV%\lib\site-packages\numpy\core\include -I%CONDA_DEFAULT_ENV%include -I%CONDA_DEFAULT_ENV%include -c'
  g++ -O2 -Wall -DNPY_MINGW_USE_CUSTOM_MSVCR -D__MSVCRT_VERSION__=0x1900 -Isksurv\bintrees -I%CONDA_DEFAULT_ENV%\lib\site-packages\numpy\core\include -I%CONDA_DEFAULT_ENV%li
b\site-packages\numpy\core\include -I%CONDA_DEFAULT_ENV%include -I%CONDA_DEFAULT_ENV%include -c sksurv\bintrees\_binarytrees.cpp -o build\temp.win32-3.6\Release\sksurv\bint
rees\_binarytrees.o
  g++ -O2 -Wall -DNPY_MINGW_USE_CUSTOM_MSVCR -D__MSVCRT_VERSION__=0x1900 -Isksurv\bintrees -I%CONDA_DEFAULT_ENV%\lib\site-packages\numpy\core\include -I%CONDA_DEFAULT_ENV%li
b\site-packages\numpy\core\include -I%CONDA_DEFAULT_ENV%include -I%CONDA_DEFAULT_ENV%include -c sksurv\bintrees\binarytrees.cpp -o build\temp.win32-3.6\Release\sksurv\bintr
ees\binarytrees.o
  g++ -shared build\temp.win32-3.6\Release\sksurv\bintrees\_binarytrees.o build\temp.win32-3.6\Release\sksurv\bintrees\binarytrees.o -L%CONDA_DEFAULT_ENV%\libs -L%CONDA_DEFAULT_ENV%\PCbuild\win32 -lpython36 -lvcruntime140 -o build\lib.win32-3.6\sksurv\bintrees\_binarytrees.cp36-win32.pyd
  building 'sksurv.ensemble._coxph_loss' extension
  compiling C sources
  C compiler: gcc -O2 -Wall -Wstrict-prototypes

  creating build\temp.win32-3.6\Release\sksurv\ensemble
  compile options: '-DNPY_MINGW_USE_CUSTOM_MSVCR -D__MSVCRT_VERSION__=0x1900 -I%CONDA_DEFAULT_ENV%\lib\site-packages\numpy\core\include -I%CONDA_DEFAULT_ENV%\lib\site-package
s\numpy\core\include -I%CONDA_DEFAULT_ENV%include -I%CONDA_DEFAULT_ENV%include -c'
  gcc -O2 -Wall -Wstrict-prototypes -DNPY_MINGW_USE_CUSTOM_MSVCR -D__MSVCRT_VERSION__=0x1900 -I%CONDA_DEFAULT_ENV%\lib\site-packages\numpy\core\include -I%CONDA_DEFAULT_ENV%
lib\site-packages\numpy\core\include -I%CONDA_DEFAULT_ENV%include -I%CONDA_DEFAULT_ENV%include -c sksurv\ensemble\_coxph_loss.c -o build\temp.win32-3.6\Release\sksurv\ensem
ble\_coxph_loss.o
  g++ -shared build\temp.win32-3.6\Release\sksurv\ensemble\_coxph_loss.o -L%CONDA_DEFAULT_ENV%\libs -L%CONDA_DEFAULT_ENV%PCbuild\win32 -lpython36 -lvcruntime140 -o build\lib
.win32-3.6\sksurv\ensemble\_coxph_loss.cp36-win32.pyd
  building 'sksurv.kernels._clinical_kernel' extension
  compiling C sources
  C compiler: gcc -O2 -Wall -Wstrict-prototypes

  creating build\temp.win32-3.6\Release\sksurv\kernels
  compile options: '-DNPY_MINGW_USE_CUSTOM_MSVCR -D__MSVCRT_VERSION__=0x1900 -I%CONDA_DEFAULT_ENV%\lib\site-packages\numpy\core\include -I%CONDA_DEFAULT_ENV%\lib\site-package
s\numpy\core\include -I%CONDA_DEFAULT_ENV%include -I%CONDA_DEFAULT_ENV%include -c'
  gcc -O2 -Wall -Wstrict-prototypes -DNPY_MINGW_USE_CUSTOM_MSVCR -D__MSVCRT_VERSION__=0x1900 -I%CONDA_DEFAULT_ENV%\lib\site-packages\numpy\core\include -I%CONDA_DEFAULT_ENV%
lib\site-packages\numpy\core\include -I%CONDA_DEFAULT_ENV%include -I%CONDA_DEFAULT_ENV%include -c sksurv\kernels\_clinical_kernel.c -o build\temp.win32-3.6\Release\sksurv\k
ernels\_clinical_kernel.o
  g++ -shared build\temp.win32-3.6\Release\sksurv\kernels\_clinical_kernel.o -L%CONDA_DEFAULT_ENV%\libs -L%CONDA_DEFAULT_ENV%PCbuild\win32 -lpython36 -lvcruntime140 -o build
\lib.win32-3.6\sksurv\kernels\_clinical_kernel.cp36-win32.pyd
  building 'sksurv.linear_model._coxnet' extension
  compiling C++ sources
  C compiler: g++ -O2 -Wall

  creating build\temp.win32-3.6\Release\sksurv\linear_model
  compile options: '-DNPY_MINGW_USE_CUSTOM_MSVCR -D__MSVCRT_VERSION__=0x1900 -I%CONDA_DEFAULT_ENV%\lib\site-packages\numpy\core\include -Isksurv\linear_model\src -I%CONDA_DEFAULT_ENV%\lib\site-packages\numpy\core\include -I%CONDA_DEFAULT_ENV%include -I%CONDA_DEFAULT_ENV%include -c'
  extra options: '-std=c++11'
  g++ -O2 -Wall -DNPY_MINGW_USE_CUSTOM_MSVCR -D__MSVCRT_VERSION__=0x1900 -I%CONDA_DEFAULT_ENV%\lib\site-packages\numpy\core\include -Isksurv\linear_model\src -I%CONDA_DEFAULT_ENV%\lib\site-packages\numpy\core\include -I%CONDA_DEFAULT_ENV%include -I%CONDA_DEFAULT_ENV%include -c sksurv\linear_model\_coxnet.cpp -o build\temp.win32-3.6\Release\sksu
rv\linear_model\_coxnet.o -std=c++11
  In file included from %CONDA_DEFAULT_ENV%\lib\site-packages\numpy\core\include/numpy/ndarraytypes.h:1809:0,
                   from %CONDA_DEFAULT_ENV%\lib\site-packages\numpy\core\include/numpy/ndarrayobject.h:18,
                   from %CONDA_DEFAULT_ENV%\lib\site-packages\numpy\core\include/numpy/arrayobject.h:4,
                   from sksurv\linear_model\_coxnet.cpp:524:
  %CONDA_DEFAULT_ENV%\lib\site-packages\numpy\core\include/numpy/npy_1_7_deprecated_api.h:13:79: note: #pragma message: %CONDA_DEFAULT_ENV%\lib\site-packages\numpy\core\inclu
de/numpy/npy_1_7_deprecated_api.h(12) : Warning Msg: Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
                            "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION")
                                                                                 ^
  In file included from %CONDA_DEFAULT_ENV%/Library/mingw-w64/include/c++/5.3.0/complex:44:0,
                   from sksurv\linear_model\src/Eigen/Core:80,
                   from sksurv\linear_model\src/coxnet/coxnet.h:18,
                   from sksurv\linear_model\src/coxnet_wrapper.h:18,
                   from sksurv\linear_model\_coxnet.cpp:526:
  %CONDA_DEFAULT_ENV%/Library/mingw-w64/include/c++/5.3.0/cmath:1119:11: error: '::hypot' has not been declared
     using ::hypot;
             ^
  sksurv\linear_model\_coxnet.cpp: In function 'PyTypeObject* __Pyx_ImportType(const char*, const char*, size_t, int)':
  sksurv\linear_model\_coxnet.cpp:6968:53: warning: unknown conversion type character 'z' in format [-Wformat=]
               module_name, class_name, basicsize, size);
                                                       ^
  sksurv\linear_model\_coxnet.cpp:6968:53: warning: unknown conversion type character 'z' in format [-Wformat=]
  sksurv\linear_model\_coxnet.cpp:6968:53: warning: too many arguments for format [-Wformat-extra-args]
  error: Command "g++ -O2 -Wall -DNPY_MINGW_USE_CUSTOM_MSVCR -D__MSVCRT_VERSION__=0x1900 -I%CONDA_DEFAULT_ENV%\lib\site-packages\numpy\core\include -Isksurv\linear_mod
el\src -I%CONDA_DEFAULT_ENV%\lib\site-packages\numpy\core\include -I%CONDA_DEFAULT_ENV%include -I%CONDA_DEFAULT_ENV%include -c sksurv\linear_model\_coxnet.cpp -o build\temp.win32-
3.6\Release\sksurv\linear_model\_coxnet.o -std=c++11" failed with exit status 1

  ----------------------------------------
  Failed building wheel for scikit-survival
  Running setup.py clean for scikit-survival
Failed to build scikit-survival
Installing collected packages: scikit-survival, scs
  Running setup.py install for scikit-survival ... error
    Complete output from command %CONDA_DEFAULT_ENV%python.exe -u -c "import setuptools, tokenize;__file__='%USERPROFILE%\\AppData\\Local\\Temp\\pip-req-build-zw1r
fxd9\\setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --recor
d %USERPROFILE%\AppData\Local\Temp\pip-record-so623fv4\install-record.txt --single-version-externally-managed --compile:
    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 "sksurv.bintrees._binarytrees" sources
    building extension "sksurv.ensemble._coxph_loss" sources
    building extension "sksurv.kernels._clinical_kernel" sources
    building extension "sksurv.linear_model._coxnet" sources
    building extension "sksurv.svm._prsvm" sources
    building extension "sksurv.svm._minlip" sources
    building data_files sources
    build_src: building npy-pkg config files
    running build_py
    running build_ext
    Cannot build msvcr library: "vcruntime140d.dll" not found
    customize Mingw32CCompiler
    customize Mingw32CCompiler using build_ext
    Cannot build msvcr library: "vcruntime140d.dll" not found
    customize Mingw32CCompiler
    customize Mingw32CCompiler using build_ext
    building 'sksurv.linear_model._coxnet' extension
    compiling C++ sources
    C compiler: g++ -O2 -Wall

    creating build\temp.win32-3.6
    creating build\temp.win32-3.6\Release
    creating build\temp.win32-3.6\Release\sksurv
    creating build\temp.win32-3.6\Release\sksurv\linear_model
    compile options: '-DNPY_MINGW_USE_CUSTOM_MSVCR -D__MSVCRT_VERSION__=0x1900 -I%CONDA_DEFAULT_ENV%\lib\site-packages\numpy\core\include -Isksurv\linear_model\src -II
:\Anaconda3\lib\site-packages\numpy\core\include -I%CONDA_DEFAULT_ENV%include -I%CONDA_DEFAULT_ENV%include -c'
    extra options: '-std=c++11'
    g++ -O2 -Wall -DNPY_MINGW_USE_CUSTOM_MSVCR -D__MSVCRT_VERSION__=0x1900 -I%CONDA_DEFAULT_ENV%\lib\site-packages\numpy\core\include -Isksurv\linear_model\src -I%CONDA_DEFAULT_ENV%\lib\site-packages\numpy\core\include -I%CONDA_DEFAULT_ENV%include -I%CONDA_DEFAULT_ENV%include -c sksurv\linear_model\_coxnet.cpp -o build\temp.win32-3.6\Release\sksurv\linear_model\_coxnet.o -std=c++11
    In file included from %CONDA_DEFAULT_ENV%\lib\site-packages\numpy\core\include/numpy/ndarraytypes.h:1809:0,
                     from %CONDA_DEFAULT_ENV%\lib\site-packages\numpy\core\include/numpy/ndarrayobject.h:18,
                     from %CONDA_DEFAULT_ENV%\lib\site-packages\numpy\core\include/numpy/arrayobject.h:4,
                     from sksurv\linear_model\_coxnet.cpp:524:
    %CONDA_DEFAULT_ENV%\lib\site-packages\numpy\core\include/numpy/npy_1_7_deprecated_api.h:13:79: note: #pragma message: %CONDA_DEFAULT_ENV%\lib\site-packages\numpy\core\include/numpy/npy_1_7_deprecated_api.h(12) : Warning Msg: Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
                              "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION")
                                                                                   ^
    In file included from %CONDA_DEFAULT_ENV%/Library/mingw-w64/include/c++/5.3.0/complex:44:0,
                     from sksurv\linear_model\src/Eigen/Core:80,
                     from sksurv\linear_model\src/coxnet/coxnet.h:18,
                     from sksurv\linear_model\src/coxnet_wrapper.h:18,
                     from sksurv\linear_model\_coxnet.cpp:526:
    %CONDA_DEFAULT_ENV%/Library/mingw-w64/include/c++/5.3.0/cmath:1119:11: error: '::hypot' has not been declared
       using ::hypot;
               ^
    sksurv\linear_model\_coxnet.cpp: In function 'PyTypeObject* __Pyx_ImportType(const char*, const char*, size_t, int)':
    sksurv\linear_model\_coxnet.cpp:6968:53: warning: unknown conversion type character 'z' in format [-Wformat=]
                 module_name, class_name, basicsize, size);
                                                         ^
    sksurv\linear_model\_coxnet.cpp:6968:53: warning: unknown conversion type character 'z' in format [-Wformat=]
    sksurv\linear_model\_coxnet.cpp:6968:53: warning: too many arguments for format [-Wformat-extra-args]
    error: Command "g++ -O2 -Wall -DNPY_MINGW_USE_CUSTOM_MSVCR -D__MSVCRT_VERSION__=0x1900 -I%CONDA_DEFAULT_ENV%\lib\site-packages\numpy\core\include -Isksurv\linear_m
odel\src -I%CONDA_DEFAULT_ENV%\lib\site-packages\numpy\core\include -I%CONDA_DEFAULT_ENV%include -I%CONDA_DEFAULT_ENV%include -c sksurv\linear_model\_coxnet.cpp -o build\temp.win32-3.6\Release\sksurv\linear_model\_coxnet.o -std=c++11" failed with exit status 1

    ----------------------------------------
Command "%CONDA_DEFAULT_ENV%python.exe -u -c "import setuptools, tokenize;__file__='%USERPROFILE%\\AppData\\Local\\Temp\\pip-req-build-zw1rfxd9\\setup.py';f=getatt
r(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record %USERPROFILE%\AppData
\Local\Temp\pip-record-so623fv4\install-record.txt --single-version-externally-managed --compile" failed with error code 1 in %USERPROFILE%\AppData\Local\Temp\pip-req-build-zw1rfxd9\

KOLANICH commented Dec 25, 2017

It doesn't. Still there are issues. I use the latest Anaconda on 32-bit win 7 with mingw32-w64 (it's a 32-bit compiler!) installed (from conda).

(%CONDA_DEFAULT_ENV%) %USERPROFILE%\Desktop\scikit-survival>pip install --upgrade ./
Processing %USERPROFILE%\desktop\scikit-survival
......
Building wheels for collected packages: scikit-survival
  Installing build dependencies ... done
  Running setup.py bdist_wheel for scikit-survival ... error
  Complete output from command %CONDA_DEFAULT_ENV%python.exe -u -c "import setuptools, tokenize;__file__='%USERPROFILE%\\AppData\\Local\\Temp\\pip-req-build-zw1rfx
d9\\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 %USERPROFILE%\AppData\Local\Temp\pip-wheel-17u82pp4 --python-tag cp36:
  Compiling sksurv\bintrees\_binarytrees.pyx because it changed.
  Compiling sksurv\ensemble\_coxph_loss.pyx because it changed.
  Compiling sksurv\kernels\_clinical_kernel.pyx because it changed.
  Compiling sksurv\linear_model\_coxnet.pyx because it changed.
  Compiling sksurv\svm\_prsvm.pyx because it changed.
  Compiling sksurv\svm\_minlip.pyx because it changed.
  [1/6] Cythonizing sksurv\bintrees\_binarytrees.pyx
  [2/6] Cythonizing sksurv\ensemble\_coxph_loss.pyx
  [3/6] Cythonizing sksurv\kernels\_clinical_kernel.pyx
  [4/6] Cythonizing sksurv\linear_model\_coxnet.pyx
  [5/6] Cythonizing sksurv\svm\_minlip.pyx
  [6/6] Cythonizing sksurv\svm\_prsvm.pyx
  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
  build_src
  building extension "sksurv.bintrees._binarytrees" sources
  building extension "sksurv.ensemble._coxph_loss" sources
  building extension "sksurv.kernels._clinical_kernel" sources
  building extension "sksurv.linear_model._coxnet" sources
  building extension "sksurv.svm._prsvm" sources
  building extension "sksurv.svm._minlip" sources
  building data_files sources
  build_src: building npy-pkg config files
  running build_py
  creating build
  creating build\lib.win32-3.6
  creating build\lib.win32-3.6\sksurv
  copying sksurv\base.py -> build\lib.win32-3.6\sksurv
  copying sksurv\column.py -> build\lib.win32-3.6\sksurv
  copying sksurv\functions.py -> build\lib.win32-3.6\sksurv
  copying sksurv\metrics.py -> build\lib.win32-3.6\sksurv
  copying sksurv\nonparametric.py -> build\lib.win32-3.6\sksurv
  copying sksurv\preprocessing.py -> build\lib.win32-3.6\sksurv
  copying sksurv\setup.py -> build\lib.win32-3.6\sksurv
  copying sksurv\util.py -> build\lib.win32-3.6\sksurv
  copying sksurv\__init__.py -> build\lib.win32-3.6\sksurv
  creating build\lib.win32-3.6\sksurv\bintrees
  copying sksurv\bintrees\setup.py -> build\lib.win32-3.6\sksurv\bintrees
  copying sksurv\bintrees\__init__.py -> build\lib.win32-3.6\sksurv\bintrees
  creating build\lib.win32-3.6\sksurv\datasets
  copying sksurv\datasets\base.py -> build\lib.win32-3.6\sksurv\datasets
  copying sksurv\datasets\setup.py -> build\lib.win32-3.6\sksurv\datasets
  copying sksurv\datasets\__init__.py -> build\lib.win32-3.6\sksurv\datasets
  creating build\lib.win32-3.6\sksurv\ensemble
  copying sksurv\ensemble\boosting.py -> build\lib.win32-3.6\sksurv\ensemble
  copying sksurv\ensemble\setup.py -> build\lib.win32-3.6\sksurv\ensemble
  copying sksurv\ensemble\survival_loss.py -> build\lib.win32-3.6\sksurv\ensemble
  copying sksurv\ensemble\__init__.py -> build\lib.win32-3.6\sksurv\ensemble
  creating build\lib.win32-3.6\sksurv\io
  copying sksurv\io\arffread.py -> build\lib.win32-3.6\sksurv\io
  copying sksurv\io\arffwrite.py -> build\lib.win32-3.6\sksurv\io
  copying sksurv\io\__init__.py -> build\lib.win32-3.6\sksurv\io
  creating build\lib.win32-3.6\sksurv\kernels
  copying sksurv\kernels\clinical.py -> build\lib.win32-3.6\sksurv\kernels
  copying sksurv\kernels\setup.py -> build\lib.win32-3.6\sksurv\kernels
  copying sksurv\kernels\__init__.py -> build\lib.win32-3.6\sksurv\kernels
  creating build\lib.win32-3.6\sksurv\linear_model
  copying sksurv\linear_model\aft.py -> build\lib.win32-3.6\sksurv\linear_model
  copying sksurv\linear_model\coxnet.py -> build\lib.win32-3.6\sksurv\linear_model
  copying sksurv\linear_model\coxph.py -> build\lib.win32-3.6\sksurv\linear_model
  copying sksurv\linear_model\setup.py -> build\lib.win32-3.6\sksurv\linear_model
  copying sksurv\linear_model\__init__.py -> build\lib.win32-3.6\sksurv\linear_model
  creating build\lib.win32-3.6\sksurv\meta
  copying sksurv\meta\base.py -> build\lib.win32-3.6\sksurv\meta
  copying sksurv\meta\ensemble_selection.py -> build\lib.win32-3.6\sksurv\meta
  copying sksurv\meta\stacking.py -> build\lib.win32-3.6\sksurv\meta
  copying sksurv\meta\__init__.py -> build\lib.win32-3.6\sksurv\meta
  creating build\lib.win32-3.6\sksurv\svm
  copying sksurv\svm\minlip.py -> build\lib.win32-3.6\sksurv\svm
  copying sksurv\svm\naive_survival_svm.py -> build\lib.win32-3.6\sksurv\svm
  copying sksurv\svm\setup.py -> build\lib.win32-3.6\sksurv\svm
  copying sksurv\svm\survival_svm.py -> build\lib.win32-3.6\sksurv\svm
  copying sksurv\svm\__init__.py -> build\lib.win32-3.6\sksurv\svm
  running build_ext
  Cannot build msvcr library: "vcruntime140d.dll" not found
  customize Mingw32CCompiler
  customize Mingw32CCompiler using build_ext
  Cannot build msvcr library: "vcruntime140d.dll" not found
  customize Mingw32CCompiler
  customize Mingw32CCompiler using build_ext
  building 'sksurv.bintrees._binarytrees' extension
  compiling C++ sources
  C compiler: g++ -O2 -Wall

  creating build\temp.win32-3.6
  creating build\temp.win32-3.6\Release
  creating build\temp.win32-3.6\Release\sksurv
  creating build\temp.win32-3.6\Release\sksurv\bintrees
  compile options: '-DNPY_MINGW_USE_CUSTOM_MSVCR -D__MSVCRT_VERSION__=0x1900 -Isksurv\bintrees -I%CONDA_DEFAULT_ENV%\lib\site-packages\numpy\core\include -I%CONDA_DEFAULT_ENV%\lib\site-packages\numpy\core\include -I%CONDA_DEFAULT_ENV%include -I%CONDA_DEFAULT_ENV%include -c'
  g++ -O2 -Wall -DNPY_MINGW_USE_CUSTOM_MSVCR -D__MSVCRT_VERSION__=0x1900 -Isksurv\bintrees -I%CONDA_DEFAULT_ENV%\lib\site-packages\numpy\core\include -I%CONDA_DEFAULT_ENV%li
b\site-packages\numpy\core\include -I%CONDA_DEFAULT_ENV%include -I%CONDA_DEFAULT_ENV%include -c sksurv\bintrees\_binarytrees.cpp -o build\temp.win32-3.6\Release\sksurv\bint
rees\_binarytrees.o
  g++ -O2 -Wall -DNPY_MINGW_USE_CUSTOM_MSVCR -D__MSVCRT_VERSION__=0x1900 -Isksurv\bintrees -I%CONDA_DEFAULT_ENV%\lib\site-packages\numpy\core\include -I%CONDA_DEFAULT_ENV%li
b\site-packages\numpy\core\include -I%CONDA_DEFAULT_ENV%include -I%CONDA_DEFAULT_ENV%include -c sksurv\bintrees\binarytrees.cpp -o build\temp.win32-3.6\Release\sksurv\bintr
ees\binarytrees.o
  g++ -shared build\temp.win32-3.6\Release\sksurv\bintrees\_binarytrees.o build\temp.win32-3.6\Release\sksurv\bintrees\binarytrees.o -L%CONDA_DEFAULT_ENV%\libs -L%CONDA_DEFAULT_ENV%\PCbuild\win32 -lpython36 -lvcruntime140 -o build\lib.win32-3.6\sksurv\bintrees\_binarytrees.cp36-win32.pyd
  building 'sksurv.ensemble._coxph_loss' extension
  compiling C sources
  C compiler: gcc -O2 -Wall -Wstrict-prototypes

  creating build\temp.win32-3.6\Release\sksurv\ensemble
  compile options: '-DNPY_MINGW_USE_CUSTOM_MSVCR -D__MSVCRT_VERSION__=0x1900 -I%CONDA_DEFAULT_ENV%\lib\site-packages\numpy\core\include -I%CONDA_DEFAULT_ENV%\lib\site-package
s\numpy\core\include -I%CONDA_DEFAULT_ENV%include -I%CONDA_DEFAULT_ENV%include -c'
  gcc -O2 -Wall -Wstrict-prototypes -DNPY_MINGW_USE_CUSTOM_MSVCR -D__MSVCRT_VERSION__=0x1900 -I%CONDA_DEFAULT_ENV%\lib\site-packages\numpy\core\include -I%CONDA_DEFAULT_ENV%
lib\site-packages\numpy\core\include -I%CONDA_DEFAULT_ENV%include -I%CONDA_DEFAULT_ENV%include -c sksurv\ensemble\_coxph_loss.c -o build\temp.win32-3.6\Release\sksurv\ensem
ble\_coxph_loss.o
  g++ -shared build\temp.win32-3.6\Release\sksurv\ensemble\_coxph_loss.o -L%CONDA_DEFAULT_ENV%\libs -L%CONDA_DEFAULT_ENV%PCbuild\win32 -lpython36 -lvcruntime140 -o build\lib
.win32-3.6\sksurv\ensemble\_coxph_loss.cp36-win32.pyd
  building 'sksurv.kernels._clinical_kernel' extension
  compiling C sources
  C compiler: gcc -O2 -Wall -Wstrict-prototypes

  creating build\temp.win32-3.6\Release\sksurv\kernels
  compile options: '-DNPY_MINGW_USE_CUSTOM_MSVCR -D__MSVCRT_VERSION__=0x1900 -I%CONDA_DEFAULT_ENV%\lib\site-packages\numpy\core\include -I%CONDA_DEFAULT_ENV%\lib\site-package
s\numpy\core\include -I%CONDA_DEFAULT_ENV%include -I%CONDA_DEFAULT_ENV%include -c'
  gcc -O2 -Wall -Wstrict-prototypes -DNPY_MINGW_USE_CUSTOM_MSVCR -D__MSVCRT_VERSION__=0x1900 -I%CONDA_DEFAULT_ENV%\lib\site-packages\numpy\core\include -I%CONDA_DEFAULT_ENV%
lib\site-packages\numpy\core\include -I%CONDA_DEFAULT_ENV%include -I%CONDA_DEFAULT_ENV%include -c sksurv\kernels\_clinical_kernel.c -o build\temp.win32-3.6\Release\sksurv\k
ernels\_clinical_kernel.o
  g++ -shared build\temp.win32-3.6\Release\sksurv\kernels\_clinical_kernel.o -L%CONDA_DEFAULT_ENV%\libs -L%CONDA_DEFAULT_ENV%PCbuild\win32 -lpython36 -lvcruntime140 -o build
\lib.win32-3.6\sksurv\kernels\_clinical_kernel.cp36-win32.pyd
  building 'sksurv.linear_model._coxnet' extension
  compiling C++ sources
  C compiler: g++ -O2 -Wall

  creating build\temp.win32-3.6\Release\sksurv\linear_model
  compile options: '-DNPY_MINGW_USE_CUSTOM_MSVCR -D__MSVCRT_VERSION__=0x1900 -I%CONDA_DEFAULT_ENV%\lib\site-packages\numpy\core\include -Isksurv\linear_model\src -I%CONDA_DEFAULT_ENV%\lib\site-packages\numpy\core\include -I%CONDA_DEFAULT_ENV%include -I%CONDA_DEFAULT_ENV%include -c'
  extra options: '-std=c++11'
  g++ -O2 -Wall -DNPY_MINGW_USE_CUSTOM_MSVCR -D__MSVCRT_VERSION__=0x1900 -I%CONDA_DEFAULT_ENV%\lib\site-packages\numpy\core\include -Isksurv\linear_model\src -I%CONDA_DEFAULT_ENV%\lib\site-packages\numpy\core\include -I%CONDA_DEFAULT_ENV%include -I%CONDA_DEFAULT_ENV%include -c sksurv\linear_model\_coxnet.cpp -o build\temp.win32-3.6\Release\sksu
rv\linear_model\_coxnet.o -std=c++11
  In file included from %CONDA_DEFAULT_ENV%\lib\site-packages\numpy\core\include/numpy/ndarraytypes.h:1809:0,
                   from %CONDA_DEFAULT_ENV%\lib\site-packages\numpy\core\include/numpy/ndarrayobject.h:18,
                   from %CONDA_DEFAULT_ENV%\lib\site-packages\numpy\core\include/numpy/arrayobject.h:4,
                   from sksurv\linear_model\_coxnet.cpp:524:
  %CONDA_DEFAULT_ENV%\lib\site-packages\numpy\core\include/numpy/npy_1_7_deprecated_api.h:13:79: note: #pragma message: %CONDA_DEFAULT_ENV%\lib\site-packages\numpy\core\inclu
de/numpy/npy_1_7_deprecated_api.h(12) : Warning Msg: Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
                            "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION")
                                                                                 ^
  In file included from %CONDA_DEFAULT_ENV%/Library/mingw-w64/include/c++/5.3.0/complex:44:0,
                   from sksurv\linear_model\src/Eigen/Core:80,
                   from sksurv\linear_model\src/coxnet/coxnet.h:18,
                   from sksurv\linear_model\src/coxnet_wrapper.h:18,
                   from sksurv\linear_model\_coxnet.cpp:526:
  %CONDA_DEFAULT_ENV%/Library/mingw-w64/include/c++/5.3.0/cmath:1119:11: error: '::hypot' has not been declared
     using ::hypot;
             ^
  sksurv\linear_model\_coxnet.cpp: In function 'PyTypeObject* __Pyx_ImportType(const char*, const char*, size_t, int)':
  sksurv\linear_model\_coxnet.cpp:6968:53: warning: unknown conversion type character 'z' in format [-Wformat=]
               module_name, class_name, basicsize, size);
                                                       ^
  sksurv\linear_model\_coxnet.cpp:6968:53: warning: unknown conversion type character 'z' in format [-Wformat=]
  sksurv\linear_model\_coxnet.cpp:6968:53: warning: too many arguments for format [-Wformat-extra-args]
  error: Command "g++ -O2 -Wall -DNPY_MINGW_USE_CUSTOM_MSVCR -D__MSVCRT_VERSION__=0x1900 -I%CONDA_DEFAULT_ENV%\lib\site-packages\numpy\core\include -Isksurv\linear_mod
el\src -I%CONDA_DEFAULT_ENV%\lib\site-packages\numpy\core\include -I%CONDA_DEFAULT_ENV%include -I%CONDA_DEFAULT_ENV%include -c sksurv\linear_model\_coxnet.cpp -o build\temp.win32-
3.6\Release\sksurv\linear_model\_coxnet.o -std=c++11" failed with exit status 1

  ----------------------------------------
  Failed building wheel for scikit-survival
  Running setup.py clean for scikit-survival
Failed to build scikit-survival
Installing collected packages: scikit-survival, scs
  Running setup.py install for scikit-survival ... error
    Complete output from command %CONDA_DEFAULT_ENV%python.exe -u -c "import setuptools, tokenize;__file__='%USERPROFILE%\\AppData\\Local\\Temp\\pip-req-build-zw1r
fxd9\\setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --recor
d %USERPROFILE%\AppData\Local\Temp\pip-record-so623fv4\install-record.txt --single-version-externally-managed --compile:
    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 "sksurv.bintrees._binarytrees" sources
    building extension "sksurv.ensemble._coxph_loss" sources
    building extension "sksurv.kernels._clinical_kernel" sources
    building extension "sksurv.linear_model._coxnet" sources
    building extension "sksurv.svm._prsvm" sources
    building extension "sksurv.svm._minlip" sources
    building data_files sources
    build_src: building npy-pkg config files
    running build_py
    running build_ext
    Cannot build msvcr library: "vcruntime140d.dll" not found
    customize Mingw32CCompiler
    customize Mingw32CCompiler using build_ext
    Cannot build msvcr library: "vcruntime140d.dll" not found
    customize Mingw32CCompiler
    customize Mingw32CCompiler using build_ext
    building 'sksurv.linear_model._coxnet' extension
    compiling C++ sources
    C compiler: g++ -O2 -Wall

    creating build\temp.win32-3.6
    creating build\temp.win32-3.6\Release
    creating build\temp.win32-3.6\Release\sksurv
    creating build\temp.win32-3.6\Release\sksurv\linear_model
    compile options: '-DNPY_MINGW_USE_CUSTOM_MSVCR -D__MSVCRT_VERSION__=0x1900 -I%CONDA_DEFAULT_ENV%\lib\site-packages\numpy\core\include -Isksurv\linear_model\src -II
:\Anaconda3\lib\site-packages\numpy\core\include -I%CONDA_DEFAULT_ENV%include -I%CONDA_DEFAULT_ENV%include -c'
    extra options: '-std=c++11'
    g++ -O2 -Wall -DNPY_MINGW_USE_CUSTOM_MSVCR -D__MSVCRT_VERSION__=0x1900 -I%CONDA_DEFAULT_ENV%\lib\site-packages\numpy\core\include -Isksurv\linear_model\src -I%CONDA_DEFAULT_ENV%\lib\site-packages\numpy\core\include -I%CONDA_DEFAULT_ENV%include -I%CONDA_DEFAULT_ENV%include -c sksurv\linear_model\_coxnet.cpp -o build\temp.win32-3.6\Release\sksurv\linear_model\_coxnet.o -std=c++11
    In file included from %CONDA_DEFAULT_ENV%\lib\site-packages\numpy\core\include/numpy/ndarraytypes.h:1809:0,
                     from %CONDA_DEFAULT_ENV%\lib\site-packages\numpy\core\include/numpy/ndarrayobject.h:18,
                     from %CONDA_DEFAULT_ENV%\lib\site-packages\numpy\core\include/numpy/arrayobject.h:4,
                     from sksurv\linear_model\_coxnet.cpp:524:
    %CONDA_DEFAULT_ENV%\lib\site-packages\numpy\core\include/numpy/npy_1_7_deprecated_api.h:13:79: note: #pragma message: %CONDA_DEFAULT_ENV%\lib\site-packages\numpy\core\include/numpy/npy_1_7_deprecated_api.h(12) : Warning Msg: Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
                              "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION")
                                                                                   ^
    In file included from %CONDA_DEFAULT_ENV%/Library/mingw-w64/include/c++/5.3.0/complex:44:0,
                     from sksurv\linear_model\src/Eigen/Core:80,
                     from sksurv\linear_model\src/coxnet/coxnet.h:18,
                     from sksurv\linear_model\src/coxnet_wrapper.h:18,
                     from sksurv\linear_model\_coxnet.cpp:526:
    %CONDA_DEFAULT_ENV%/Library/mingw-w64/include/c++/5.3.0/cmath:1119:11: error: '::hypot' has not been declared
       using ::hypot;
               ^
    sksurv\linear_model\_coxnet.cpp: In function 'PyTypeObject* __Pyx_ImportType(const char*, const char*, size_t, int)':
    sksurv\linear_model\_coxnet.cpp:6968:53: warning: unknown conversion type character 'z' in format [-Wformat=]
                 module_name, class_name, basicsize, size);
                                                         ^
    sksurv\linear_model\_coxnet.cpp:6968:53: warning: unknown conversion type character 'z' in format [-Wformat=]
    sksurv\linear_model\_coxnet.cpp:6968:53: warning: too many arguments for format [-Wformat-extra-args]
    error: Command "g++ -O2 -Wall -DNPY_MINGW_USE_CUSTOM_MSVCR -D__MSVCRT_VERSION__=0x1900 -I%CONDA_DEFAULT_ENV%\lib\site-packages\numpy\core\include -Isksurv\linear_m
odel\src -I%CONDA_DEFAULT_ENV%\lib\site-packages\numpy\core\include -I%CONDA_DEFAULT_ENV%include -I%CONDA_DEFAULT_ENV%include -c sksurv\linear_model\_coxnet.cpp -o build\temp.win32-3.6\Release\sksurv\linear_model\_coxnet.o -std=c++11" failed with exit status 1

    ----------------------------------------
Command "%CONDA_DEFAULT_ENV%python.exe -u -c "import setuptools, tokenize;__file__='%USERPROFILE%\\AppData\\Local\\Temp\\pip-req-build-zw1rfxd9\\setup.py';f=getatt
r(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record %USERPROFILE%\AppData
\Local\Temp\pip-record-so623fv4\install-record.txt --single-version-externally-managed --compile" failed with error code 1 in %USERPROFILE%\AppData\Local\Temp\pip-req-build-zw1rfxd9\
@KOLANICH

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KOLANICH Dec 25, 2017

The workaround is to remove linear_model folder and all its contents and remove its cython building from setup.py

KOLANICH commented Dec 25, 2017

The workaround is to remove linear_model folder and all its contents and remove its cython building from setup.py

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sebp Jan 8, 2018

Owner

Unfortunately, I don't have the resources to support 32bit builds. If you need a pre-compiled version for 64bit Windows, you can use conda: conda install -c sebp scikit-survival.

Owner

sebp commented Jan 8, 2018

Unfortunately, I don't have the resources to support 32bit builds. If you need a pre-compiled version for 64bit Windows, you can use conda: conda install -c sebp scikit-survival.

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region-spotteR Feb 21, 2018

On my windows computer, I had issues because the ecos-library didn't install. In the end I added every dependency using pip and for ecos I installed it manually using the python wheel

region-spotteR commented Feb 21, 2018

On my windows computer, I had issues because the ecos-library didn't install. In the end I added every dependency using pip and for ecos I installed it manually using the python wheel

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