Hdbscan: Error al importar hdbscan

Soy un poco nuevo en la construcción de paquetes conda; Desafortunadamente, parece que todavía tengo algo que aprender. Esto es una falla de los paquetes conda que construí. Si obtiene sus requisitos instalados a través de conda (scikit-learn y cython principalmente) y luego usa pip install o install desde la fuente, las cosas deberían funcionar. Gracias por el informe. Tendré que investigar los problemas de empaque de conda y ver si puedo entender qué es lo que anda mal allí.

Gracias por una respuesta tan rápida.

La instalación aún no funcionó. Lo he probado tanto con el paquete conda de 32 bits como con el paquete de 64 bits. ¿Hay alguna otra forma en que pueda hacer que funcione?

En caso de instalación de pip, el error es:

[Anaconda2] C:\Users\user_name>pip install hdbscan
Collecting hdbscan
  Using cached hdbscan-0.6.2.tar.gz
Requirement already satisfied (use --upgrade to upgrade): scikit-learn>=0.16 in
c:\anaconda2\lib\site-packages (from hdbscan)
Requirement already satisfied (use --upgrade to upgrade): cython>=0.17 in c:\ana
conda2\lib\site-packages (from hdbscan)
Building wheels for collected packages: hdbscan
  Running setup.py bdist_wheel for hdbscan
  Complete output from command C:\Anaconda2\python.exe -c "import setuptools;__f
ile__='c:\\users\\user_name\\appdata\\local\\temp\\pip-build-yf7q3s\\hdbscan\\setup.
py';exec(compile(open(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))
" bdist_wheel -d c:\users\user_name\appdata\local\temp\tmpbmg3edpip-wheel-:
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build\lib.win-amd64-2.7
  creating build\lib.win-amd64-2.7\hdbscan
  copying hdbscan\hdbscan_.py -> build\lib.win-amd64-2.7\hdbscan
  copying hdbscan\plots.py -> build\lib.win-amd64-2.7\hdbscan
  copying hdbscan\robust_single_linkage_.py -> build\lib.win-amd64-2.7\hdbscan
  copying hdbscan\__init__.py -> build\lib.win-amd64-2.7\hdbscan
  running build_ext
  skipping 'hdbscan\_hdbscan_tree.c' Cython extension (up-to-date)
  building 'hdbscan._hdbscan_tree' extension
  creating build\temp.win-amd64-2.7
  creating build\temp.win-amd64-2.7\Release
  creating build\temp.win-amd64-2.7\Release\hdbscan
  C:\Users\user_name\AppData\Local\Programs\Common\Microsoft\Visual C++ for Python\9
.0\VC\Bin\amd64\cl.exe /c /nologo /Ox /MD /W3 /GS- /DNDEBUG -IC:\Anaconda2\lib\s
ite-packages\numpy\core\include -IC:\Anaconda2\include -IC:\Anaconda2\PC /Tchdbs
can\_hdbscan_tree.c /Fobuild\temp.win-amd64-2.7\Release\hdbscan\_hdbscan_tree.ob
j
  _hdbscan_tree.c
  c:\anaconda2\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
  hdbscan\_hdbscan_tree.c(2560) : warning C4244: 'function' : conversion from '_
_pyx_t_5numpy_intp_t' to 'long', possible loss of data
  hdbscan\_hdbscan_tree.c(2787) : warning C4244: '=' : conversion from '__pyx_t_
5numpy_intp_t' to 'int', possible loss of data
  hdbscan\_hdbscan_tree.c(2820) : warning C4244: '+=' : conversion from 'Py_ssiz
e_t' to 'long', possible loss of data
  hdbscan\_hdbscan_tree.c(2831) : warning C4244: '+=' : conversion from 'Py_ssiz
e_t' to 'long', possible loss of data
  hdbscan\_hdbscan_tree.c(2842) : warning C4244: '+=' : conversion from 'Py_ssiz
e_t' to 'long', possible loss of data
  hdbscan\_hdbscan_tree.c(2854) : warning C4244: '+=' : conversion from 'Py_ssiz
e_t' to 'long', possible loss of data
  hdbscan\_hdbscan_tree.c(2899) : warning C4244: '=' : conversion from '__pyx_t_
5numpy_intp_t' to 'int', possible loss of data
  hdbscan\_hdbscan_tree.c(2940) : warning C4244: '=' : conversion from '__pyx_t_
5numpy_intp_t' to 'int', possible loss of data
  hdbscan\_hdbscan_tree.c(4122) : warning C4244: 'function' : conversion from '_
_pyx_t_5numpy_intp_t' to 'long', possible loss of data
  hdbscan\_hdbscan_tree.c(5242) : warning C4244: 'function' : conversion from '_
_pyx_t_5numpy_intp_t' to 'long', possible loss of data
  hdbscan\_hdbscan_tree.c(6278) : warning C4244: 'function' : conversion from '_
_pyx_t_5numpy_intp_t' to 'long', possible loss of data
  hdbscan\_hdbscan_tree.c(6351) : warning C4244: 'function' : conversion from '_
_pyx_t_5numpy_intp_t' to 'long', possible loss of data
  hdbscan\_hdbscan_tree.c(21049) : error C2275: 'PyGILState_STATE' : illegal use
 of this type as an expression
          C:\Anaconda2\include\pystate.h(137) : see declaration of 'PyGILState_S
TATE'
  hdbscan\_hdbscan_tree.c(21049) : error C2146: syntax error : missing ';' befor
e identifier '__pyx_gilstate_save'
  hdbscan\_hdbscan_tree.c(21049) : error C2065: '__pyx_gilstate_save' : undeclar
ed identifier
  hdbscan\_hdbscan_tree.c(21120) : error C2065: '__pyx_gilstate_save' : undeclar
ed identifier
  hdbscan\_hdbscan_tree.c(21146) : error C2275: 'PyGILState_STATE' : illegal use
 of this type as an expression
          C:\Anaconda2\include\pystate.h(137) : see declaration of 'PyGILState_S
TATE'
  hdbscan\_hdbscan_tree.c(21146) : error C2146: syntax error : missing ';' befor
e identifier '__pyx_gilstate_save'
  hdbscan\_hdbscan_tree.c(21146) : error C2065: '__pyx_gilstate_save' : undeclar
ed identifier
  hdbscan\_hdbscan_tree.c(21219) : error C2065: '__pyx_gilstate_save' : undeclar
ed identifier
  hdbscan\_hdbscan_tree.c(21246) : error C2275: 'PyGILState_STATE' : illegal use
 of this type as an expression
          C:\Anaconda2\include\pystate.h(137) : see declaration of 'PyGILState_S
TATE'
  hdbscan\_hdbscan_tree.c(21246) : error C2146: syntax error : missing ';' befor
e identifier '__pyx_gilstate_save'
  hdbscan\_hdbscan_tree.c(21246) : error C2065: '__pyx_gilstate_save' : undeclar
ed identifier
  hdbscan\_hdbscan_tree.c(21336) : error C2065: '__pyx_gilstate_save' : undeclar
ed identifier
  hdbscan\_hdbscan_tree.c(22003) : error C2275: 'PyGILState_STATE' : illegal use
 of this type as an expression
          C:\Anaconda2\include\pystate.h(137) : see declaration of 'PyGILState_S
TATE'
  hdbscan\_hdbscan_tree.c(22003) : error C2146: syntax error : missing ';' befor
e identifier '__pyx_gilstate_save'
  hdbscan\_hdbscan_tree.c(22003) : error C2065: '__pyx_gilstate_save' : undeclar
ed identifier
  hdbscan\_hdbscan_tree.c(22029) : error C2065: '__pyx_gilstate_save' : undeclar
ed identifier
  error: command 'C:\\Users\\user_name\\AppData\\Local\\Programs\\Common\\Microsoft\
\Visual C++ for Python\\9.0\\VC\\Bin\\amd64\\cl.exe' failed with exit status 2

  ----------------------------------------
  Failed building wheel for hdbscan
Failed to build hdbscan
Installing collected packages: hdbscan
  Running setup.py install for hdbscan
    Complete output from command C:\Anaconda2\python.exe -c "import setuptools,
tokenize;__file__='c:\\users\\user_name\\appdata\\local\\temp\\pip-build-yf7q3s\\hdb
scan\\setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().re
place('\r\n', '\n'), __file__, 'exec'))" install --record c:\users\user_name\appdata
\local\temp\pip-a6ueto-record\install-record.txt --single-version-externally-man
aged --compile:
    running install
    running build
    running build_py
    running build_ext
    skipping 'hdbscan\_hdbscan_tree.c' Cython extension (up-to-date)
    building 'hdbscan._hdbscan_tree' extension
    C:\Users\user_name\AppData\Local\Programs\Common\Microsoft\Visual C++ for Python
\9.0\VC\Bin\amd64\cl.exe /c /nologo /Ox /MD /W3 /GS- /DNDEBUG -IC:\Anaconda2\lib
\site-packages\numpy\core\include -IC:\Anaconda2\include -IC:\Anaconda2\PC /Tchd
bscan\_hdbscan_tree.c /Fobuild\temp.win-amd64-2.7\Release\hdbscan\_hdbscan_tree.
obj
    _hdbscan_tree.c
    c:\anaconda2\lib\site-packages\numpy\core\include\numpy\npy_1_7_deprecated_a
pi.h(12) : Warning Msg: Using deprecated NumPy API, disable it by #defining NPY_
NO_DEPRECATED_API NPY_1_7_API_VERSION
    hdbscan\_hdbscan_tree.c(2560) : warning C4244: 'function' : conversion from
'__pyx_t_5numpy_intp_t' to 'long', possible loss of data
    hdbscan\_hdbscan_tree.c(2787) : warning C4244: '=' : conversion from '__pyx_
t_5numpy_intp_t' to 'int', possible loss of data
    hdbscan\_hdbscan_tree.c(2820) : warning C4244: '+=' : conversion from 'Py_ss
ize_t' to 'long', possible loss of data
    hdbscan\_hdbscan_tree.c(2831) : warning C4244: '+=' : conversion from 'Py_ss
ize_t' to 'long', possible loss of data
    hdbscan\_hdbscan_tree.c(2842) : warning C4244: '+=' : conversion from 'Py_ss
ize_t' to 'long', possible loss of data
    hdbscan\_hdbscan_tree.c(2854) : warning C4244: '+=' : conversion from 'Py_ss
ize_t' to 'long', possible loss of data
    hdbscan\_hdbscan_tree.c(2899) : warning C4244: '=' : conversion from '__pyx_
t_5numpy_intp_t' to 'int', possible loss of data
    hdbscan\_hdbscan_tree.c(2940) : warning C4244: '=' : conversion from '__pyx_
t_5numpy_intp_t' to 'int', possible loss of data
    hdbscan\_hdbscan_tree.c(4122) : warning C4244: 'function' : conversion from
'__pyx_t_5numpy_intp_t' to 'long', possible loss of data
    hdbscan\_hdbscan_tree.c(5242) : warning C4244: 'function' : conversion from
'__pyx_t_5numpy_intp_t' to 'long', possible loss of data
    hdbscan\_hdbscan_tree.c(6278) : warning C4244: 'function' : conversion from
'__pyx_t_5numpy_intp_t' to 'long', possible loss of data
    hdbscan\_hdbscan_tree.c(6351) : warning C4244: 'function' : conversion from
'__pyx_t_5numpy_intp_t' to 'long', possible loss of data
    hdbscan\_hdbscan_tree.c(21049) : error C2275: 'PyGILState_STATE' : illegal u
se of this type as an expression
            C:\Anaconda2\include\pystate.h(137) : see declaration of 'PyGILState
_STATE'
    hdbscan\_hdbscan_tree.c(21049) : error C2146: syntax error : missing ';' bef
ore identifier '__pyx_gilstate_save'
    hdbscan\_hdbscan_tree.c(21049) : error C2065: '__pyx_gilstate_save' : undecl
ared identifier
    hdbscan\_hdbscan_tree.c(21120) : error C2065: '__pyx_gilstate_save' : undecl
ared identifier
    hdbscan\_hdbscan_tree.c(21146) : error C2275: 'PyGILState_STATE' : illegal u
se of this type as an expression
            C:\Anaconda2\include\pystate.h(137) : see declaration of 'PyGILState
_STATE'
    hdbscan\_hdbscan_tree.c(21146) : error C2146: syntax error : missing ';' bef
ore identifier '__pyx_gilstate_save'
    hdbscan\_hdbscan_tree.c(21146) : error C2065: '__pyx_gilstate_save' : undecl
ared identifier
    hdbscan\_hdbscan_tree.c(21219) : error C2065: '__pyx_gilstate_save' : undecl
ared identifier
    hdbscan\_hdbscan_tree.c(21246) : error C2275: 'PyGILState_STATE' : illegal u
se of this type as an expression
            C:\Anaconda2\include\pystate.h(137) : see declaration of 'PyGILState
_STATE'
    hdbscan\_hdbscan_tree.c(21246) : error C2146: syntax error : missing ';' bef
ore identifier '__pyx_gilstate_save'
    hdbscan\_hdbscan_tree.c(21246) : error C2065: '__pyx_gilstate_save' : undecl
ared identifier
    hdbscan\_hdbscan_tree.c(21336) : error C2065: '__pyx_gilstate_save' : undecl
ared identifier
    hdbscan\_hdbscan_tree.c(22003) : error C2275: 'PyGILState_STATE' : illegal u
se of this type as an expression
            C:\Anaconda2\include\pystate.h(137) : see declaration of 'PyGILState
_STATE'
    hdbscan\_hdbscan_tree.c(22003) : error C2146: syntax error : missing ';' bef
ore identifier '__pyx_gilstate_save'
    hdbscan\_hdbscan_tree.c(22003) : error C2065: '__pyx_gilstate_save' : undecl
ared identifier
    hdbscan\_hdbscan_tree.c(22029) : error C2065: '__pyx_gilstate_save' : undecl
ared identifier
    error: command 'C:\\Users\\user_name\\AppData\\Local\\Programs\\Common\\Microsof
t\\Visual C++ for Python\\9.0\\VC\\Bin\\amd64\\cl.exe' failed with exit status 2


    ----------------------------------------
Command "C:\Anaconda2\python.exe -c "import setuptools, tokenize;__file__='c:\\u
sers\\user_name\\appdata\\local\\temp\\pip-build-yf7q3s\\hdbscan\\setup.py';exec(com
pile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __f
ile__, 'exec'))" install --record c:\users\user_name\appdata\local\temp\pip-a6ueto-r
ecord\install-record.txt --single-version-externally-managed --compile" failed w
ith error code 1 in c:\users\user_name\appdata\local\temp\pip-build-yf7q3s\hdbscan

y en caso de instalación manual:

F:\downloads\hdbscan-master\hdbscan-master>python setup.py install
running install
running bdist_egg
running egg_info
writing requirements to hdbscan.egg-info\requires.txt
writing hdbscan.egg-info\PKG-INFO
writing top-level names to hdbscan.egg-info\top_level.txt
writing dependency_links to hdbscan.egg-info\dependency_links.txt
reading manifest file 'hdbscan.egg-info\SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'hdbscan.egg-info\SOURCES.txt'
installing library code to build\bdist.win-amd64\egg
running install_lib
running build_py
creating build\lib.win-amd64-2.7
creating build\lib.win-amd64-2.7\hdbscan
copying hdbscan\hdbscan_.py -> build\lib.win-amd64-2.7\hdbscan
copying hdbscan\plots.py -> build\lib.win-amd64-2.7\hdbscan
copying hdbscan\robust_single_linkage_.py -> build\lib.win-amd64-2.7\hdbscan
copying hdbscan\__init__.py -> build\lib.win-amd64-2.7\hdbscan
running build_ext
skipping 'hdbscan\_hdbscan_tree.c' Cython extension (up-to-date)
building 'hdbscan._hdbscan_tree' extension
creating build\temp.win-amd64-2.7
creating build\temp.win-amd64-2.7\Release
creating build\temp.win-amd64-2.7\Release\hdbscan
C:\Users\Intel\AppData\Local\Programs\Common\Microsoft\Visual C++ for Python\9.0
\VC\Bin\amd64\cl.exe /c /nologo /Ox /MD /W3 /GS- /DNDEBUG -IC:\Anaconda2\lib\sit
e-packages\numpy\core\include -IC:\Anaconda2\include -IC:\Anaconda2\PC /Tchdbsca
n\_hdbscan_tree.c /Fobuild\temp.win-amd64-2.7\Release\hdbscan\_hdbscan_tree.obj
_hdbscan_tree.c
c:\anaconda2\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_D
EPRECATED_API NPY_1_7_API_VERSION
hdbscan\_hdbscan_tree.c(2560) : warning C4244: 'function' : conversion from '__p
yx_t_5numpy_intp_t' to 'long', possible loss of data
hdbscan\_hdbscan_tree.c(2787) : warning C4244: '=' : conversion from '__pyx_t_5n
umpy_intp_t' to 'int', possible loss of data
hdbscan\_hdbscan_tree.c(2820) : warning C4244: '+=' : conversion from 'Py_ssize_
t' to 'long', possible loss of data
hdbscan\_hdbscan_tree.c(2831) : warning C4244: '+=' : conversion from 'Py_ssize_
t' to 'long', possible loss of data
hdbscan\_hdbscan_tree.c(2842) : warning C4244: '+=' : conversion from 'Py_ssize_
t' to 'long', possible loss of data
hdbscan\_hdbscan_tree.c(2854) : warning C4244: '+=' : conversion from 'Py_ssize_
t' to 'long', possible loss of data
hdbscan\_hdbscan_tree.c(2899) : warning C4244: '=' : conversion from '__pyx_t_5n
umpy_intp_t' to 'int', possible loss of data
hdbscan\_hdbscan_tree.c(2940) : warning C4244: '=' : conversion from '__pyx_t_5n
umpy_intp_t' to 'int', possible loss of data
hdbscan\_hdbscan_tree.c(4122) : warning C4244: 'function' : conversion from '__p
yx_t_5numpy_intp_t' to 'long', possible loss of data
hdbscan\_hdbscan_tree.c(5242) : warning C4244: 'function' : conversion from '__p
yx_t_5numpy_intp_t' to 'long', possible loss of data
hdbscan\_hdbscan_tree.c(6278) : warning C4244: 'function' : conversion from '__p
yx_t_5numpy_intp_t' to 'long', possible loss of data
hdbscan\_hdbscan_tree.c(6351) : warning C4244: 'function' : conversion from '__p
yx_t_5numpy_intp_t' to 'long', possible loss of data
hdbscan\_hdbscan_tree.c(21049) : error C2275: 'PyGILState_STATE' : illegal use o
f this type as an expression
        C:\Anaconda2\include\pystate.h(137) : see declaration of 'PyGILState_STA
TE'
hdbscan\_hdbscan_tree.c(21049) : error C2146: syntax error : missing ';' before
identifier '__pyx_gilstate_save'
hdbscan\_hdbscan_tree.c(21049) : error C2065: '__pyx_gilstate_save' : undeclared
 identifier
hdbscan\_hdbscan_tree.c(21120) : error C2065: '__pyx_gilstate_save' : undeclared
 identifier
hdbscan\_hdbscan_tree.c(21146) : error C2275: 'PyGILState_STATE' : illegal use o
f this type as an expression
        C:\Anaconda2\include\pystate.h(137) : see declaration of 'PyGILState_STA
TE'
hdbscan\_hdbscan_tree.c(21146) : error C2146: syntax error : missing ';' before
identifier '__pyx_gilstate_save'
hdbscan\_hdbscan_tree.c(21146) : error C2065: '__pyx_gilstate_save' : undeclared
 identifier
hdbscan\_hdbscan_tree.c(21219) : error C2065: '__pyx_gilstate_save' : undeclared
 identifier
hdbscan\_hdbscan_tree.c(21246) : error C2275: 'PyGILState_STATE' : illegal use o
f this type as an expression
        C:\Anaconda2\include\pystate.h(137) : see declaration of 'PyGILState_STA
TE'
hdbscan\_hdbscan_tree.c(21246) : error C2146: syntax error : missing ';' before
identifier '__pyx_gilstate_save'
hdbscan\_hdbscan_tree.c(21246) : error C2065: '__pyx_gilstate_save' : undeclared
 identifier
hdbscan\_hdbscan_tree.c(21336) : error C2065: '__pyx_gilstate_save' : undeclared
 identifier
hdbscan\_hdbscan_tree.c(22003) : error C2275: 'PyGILState_STATE' : illegal use o
f this type as an expression
        C:\Anaconda2\include\pystate.h(137) : see declaration of 'PyGILState_STA
TE'
hdbscan\_hdbscan_tree.c(22003) : error C2146: syntax error : missing ';' before
identifier '__pyx_gilstate_save'
hdbscan\_hdbscan_tree.c(22003) : error C2065: '__pyx_gilstate_save' : undeclared
 identifier
hdbscan\_hdbscan_tree.c(22029) : error C2065: '__pyx_gilstate_save' : undeclared
 identifier
error: command 'C:\\Users\\user_name\\AppData\\Local\\Programs\\Common\\Microsoft\\V
isual C++ for Python\\9.0\\VC\\Bin\\amd64\\cl.exe' failed with exit status 2

Eso luce mal. Realmente no estoy muy seguro de qué ha fallado aquí; tengo poca experiencia en la instalación en Windows. Recomiendo usar la instalación manual y eliminar todos los archivos .c en el directorio hdbscan; es decir

hdbscan / _hdbscan_tree.c
hdbscan / _hdbscan_boruvka.x
hdbscan / _hdbscan_linkage.c
hdbscan / _hdbscan_reachability.c

Y luego intente construir de nuevo; parece haber algo con los archivos C que a Windows no le gusta.

Probé en Ubuntu. Funcionó bien en Ubuntu

Me alegro de que hayas conseguido que funcione. Perdón por los problemas en Windows (Windows parece ser mi mayor fuente de problemas). Dejaré el tema abierto por ahora; algunas de las otras personas del equipo tienen acceso a los sistemas de Windows en los que pueden probar, e intentaremos resolver los problemas de Windows. Gracias por el informe de problemas.

lmcinnes,
Desafortunadamente, recibo los mismos mensajes de error que el anterior en win7 64 env.
Saludos
Hari

En este punto, tengo que pedir ayuda a cualquier persona con experiencia / conocimiento de Windows. Parece que todo funciona bien en Linux y MacOS X (los entornos a los que tengo acceso), y al menos a veces funciona en Windows ... ¡cualquier ayuda a cualquier persona con experiencia en compilar en Windows sería muy apreciada!

Como nota al margen; ¿Es esta una instalación reciente de pip que está fallando? Intenté agregar un paquete de ruedas para win64 el otro día como lo suministró una persona servicial, ¿quizás eso ha causado el problema?

De hecho, es el pip. Pero creo que el problema se debió a un numpy que requería cython para las versiones 1.10 y superiores. Se instaló bastante bien cuando se instaló Cython.Gracias por la respuesta rápida

Puedo confirmar, primero tuve que instalar cython y luego instalar hdbscan en ubuntu 16.04