Hdbscan: Kesalahan saat mengimpor hdbscan

Saya sedikit baru dalam membuat paket conda; sayangnya sepertinya saya masih harus belajar. Ini adalah kesalahan dari paket conda yang saya buat. Jika Anda menginstal persyaratan Anda melalui conda (terutama scikit-learn dan cython) dan kemudian menggunakan pip install atau install dari sumber, semuanya akan berhasil. Terima kasih atas laporannya. Saya harus melihat masalah pengemasan conda dan melihat apakah saya dapat memahami apa yang salah di sana.

Terima kasih atas balasan yang begitu cepat.

Instalasi masih tidak berhasil. Saya telah mencobanya dengan paket conda 32-bit dan juga paket 64-bit. Apakah ada cara lain saya bisa membuatnya bekerja.

Dalam kasus pemasangan pip, kesalahannya adalah:

[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

dan dalam kasus instalasi 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

Itu terlihat buruk. Saya benar-benar tidak yakin apa yang salah di sini -- Saya memiliki sedikit pengalaman dalam menginstal di windows. Saya merekomendasikan menggunakan instalasi manual dan menghapus semua file .c di direktori hdbscan; yaitu

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

Dan kemudian coba membangun lagi; sepertinya ada sesuatu dengan file C yang tidak disukai Windows.

Saya mencoba di Ubuntu. Ini bekerja dengan baik di Ubuntu

Saya senang Anda berhasil membuatnya bekerja. Maaf tentang masalah pada Windows (windows tampaknya menjadi sumber masalah terbesar saya). Saya akan membiarkan masalah ini terbuka untuk saat ini; beberapa orang lain dalam tim memiliki akses ke sistem windows yang dapat mereka uji, dan kami akan mencoba menyelesaikan masalah windows. Terima kasih atas laporan masalah!

lmcinnes,
Sayangnya saya mendapatkan pesan kesalahan yang sama seperti di atas di win7 64 env.
Salam
Hari

Pada titik ini saya harus meminta bantuan dari siapa pun dengan pengalaman/pengetahuan Windows. Tampaknya semuanya berfungsi dengan baik di Linux dan MacOS X (lingkungan yang saya akses), dan setidaknya kadang-kadang berfungsi di Windows ... bantuan apa pun yang dimiliki siapa pun yang berpengalaman mengkompilasi di windows akan sangat dihargai!

Sebagai catatan tambahan; apakah ini instalasi pip baru-baru ini yang gagal? Saya mencoba menambahkan paket roda untuk win64 beberapa hari yang lalu seperti yang dipasok dari individu yang membantu - mungkin itu yang menyebabkan masalah?

Ini memang pip. Tapi saya pikir masalahnya adalah karena numpy yang membutuhkan cython untuk versi 1.10 ke atas. Dipasang cukup baik ketika Cython dipasang. Terima kasih atas balasan cepatnya

Bisa konfirmasi, harus install cython dulu baru install hdbscan di ubuntu 16.04