I want to use the scikit-learn package on mac terminal. However, I encounter error executing the example program. The link to the example program. http://scikit-learn.org/stable/auto_examples/cluster/plot_dbscan.html#example-cluster-plot-dbscan-py
Traceback (most recent call last):
File "plot_dbscan.py", line 14, in <module>
from sklearn.cluster import DBSCAN
File "/Library/Python/2.7/site-packages/sklearn/cluster/__init__.py", line 6, in <module>
from .spectral import spectral_clustering, SpectralClustering
File "/Library/Python/2.7/site-packages/sklearn/cluster/spectral.py", line 13, in <module>
from ..utils import check_random_state, as_float_array
File "/Library/Python/2.7/site-packages/sklearn/utils/__init__.py", line 10, in <module>
from .murmurhash import murmurhash3_32
File "numpy.pxd", line 155, in init sklearn.utils.murmurhash (sklearn/utils/murmurhash.c:5029)
ValueError: numpy.dtype has the wrong size, try recompiling
Related
After having installed the pyclustertend package with pip install pyclustertend, I now try to import it into Python:
from pyclustertent import ivat
However, I get the following error while doing so:
Traceback (most recent call last):
File "", line 1, in
from pyclustertend import ivat
File "C:\Users\Emil\AppData\Roaming\Python\Python38\site-packages\pyclustertend_init_.py", line 1, in
from .hopkins import hopkins # noqa: F401
File "C:\Users\Emil\AppData\Roaming\Python\Python38\site-packages\pyclustertend\hopkins.py", line 5, in <module>
from sklearn.neighbors import BallTree
File "C:\Users\Emil\Anaconda3\lib\site-packages\sklearn\__init__.py", line 82, in <module>
from .base import clone
File "C:\Users\Emil\Anaconda3\lib\site-packages\sklearn\base.py", line 17, in <module>
from .utils import _IS_32BIT
File "C:\Users\Emil\Anaconda3\lib\site-packages\sklearn\utils\__init__.py", line 29, in <module>
from .fixes import parse_version, threadpool_info
File "C:\Users\Emil\Anaconda3\lib\site-packages\sklearn\utils\fixes.py", line 47, in <module>
class loguniform(scipy.stats.reciprocal):
File "C:\Users\Emil\Anaconda3\lib\site-packages\scipy\stats\_distn_infrastructure.py", line 1601, in __init__
super(rv_continuous, self).__init__(seed)
File "C:\Users\Emil\Anaconda3\lib\site-packages\scipy\stats\_distn_infrastructure.py", line 588, in __init__
self._random_state = check_random_state(seed)
File "C:\Users\Emil\Anaconda3\lib\site-packages\scipy\_lib\_util.py", line 202, in check_random_state
return np.random.mtrand._rand
AttributeError: module 'numpy.random' has no attribute 'mtrand'
I suspected this has to do with the Numpy version. However, during the installation, it updated numpy to an older version:
Successfully uninstalled numpy-1.23.4
Successfully installed numpy-1.20.3 pyclustertend-1.8.2
What do I need to do to use this package?
I am running Python 3.7.0 on macOS, and I have scikit-learn version 0.20.1 installed using pip. I also have numpy and scipy installed.
When I try the following code:
from sklearn import svm
I get the following error:
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/local/lib/python3.7/site-packages/sklearn/svm/__init__.py", line 13, in <module>
from .classes import SVC, NuSVC, SVR, NuSVR, OneClassSVM, LinearSVC, \
File "/usr/local/lib/python3.7/site-packages/sklearn/svm/classes.py", line 4, in <module>
from .base import _fit_liblinear, BaseSVC, BaseLibSVM
File "/usr/local/lib/python3.7/site-packages/sklearn/svm/base.py", line 11, in <module>
from ..preprocessing import LabelEncoder
File "/usr/local/lib/python3.7/site-packages/sklearn/preprocessing/__init__.py", line 6, in <module>
from ._function_transformer import FunctionTransformer
File "/usr/local/lib/python3.7/site-packages/sklearn/preprocessing/_function_transformer.py", line 5, in <module>
from ..utils.testing import assert_allclose_dense_sparse
File "/usr/local/lib/python3.7/site-packages/sklearn/utils/testing.py", line 54, in <module>
from nose.tools import raises as _nose_raises
File "/Library/Python/2.7/site-packages/nose/__init__.py", line 1, in <module>
from nose.core import collector, main, run, run_exit, runmodule
File "/Library/Python/2.7/site-packages/nose/core.py", line 153
print "%s version %s" % (os.path.basename(sys.argv[0]), __version__)
^
SyntaxError: invalid syntax
If i just import sklearn (without specifying svm), I get no errors.
Can I get help with this error please?
I just installed Python's scikit-neuralnetwork using the procedure mentioned, that is;
pip install scikit-neuralnetwork
Now I can not import SVM. This line;
from sklearn import svm
gives this error;
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "//anaconda/lib/python2.7/site-packages/sklearn/svm/__init__.py", line 13, in <module>
from .classes import SVC, NuSVC, SVR, NuSVR, OneClassSVM, LinearSVC, \
File "//anaconda/lib/python2.7/site-packages/sklearn/svm/classes.py", line 4, in <module>
from .base import _fit_liblinear, BaseSVC, BaseLibSVM
File "//anaconda/lib/python2.7/site-packages/sklearn/svm/base.py", line 12, in <module>
from ..multiclass import _ovr_decision_function
File "//anaconda/lib/python2.7/site-packages/sklearn/multiclass.py", line 44, in <module>
from .metrics.pairwise import euclidean_distances
File "//anaconda/lib/python2.7/site-packages/sklearn/metrics/__init__.py", line 33, in <module>
from . import cluster
File "//anaconda/lib/python2.7/site-packages/sklearn/metrics/cluster/__init__.py", line 21, in <module>
from .bicluster import consensus_score
File "//anaconda/lib/python2.7/site-packages/sklearn/metrics/cluster/bicluster/__init__.py", line 1, in <module>
from .bicluster_metrics import consensus_score
File "//anaconda/lib/python2.7/site-packages/sklearn/metrics/cluster/bicluster/bicluster_metrics.py", line 6, in <module>
from sklearn.utils.validation import check_arrays
ImportError: cannot import name check_arrays
May I know what went wrong? I'll try using different environments next time, if that helps. Is there any way to fix this?
I am using Python 2.7 and sklearn 0.17.
open sklearn.utils.validation and delete "import check_arrays", or use other package for example anaconda3. i check now - no problems. Or install anaconda3.5 and copy check_arrays to anaconda2.7 sklearn.utils.validation.
I have Ubuntu 12.04 with Python 2.7 and Python 3 installed. I installed pygame through sudo apt-get python-pygame and also from the source. When I tried >>>import pygame on Python I get this error:
`
>>> import pygame<br>
Jello, world!<br>
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/lib/python2.7/dist-packages/pygame/__init__.py", line 255, in <module>
try: import pygame.surfarray
File "/usr/lib/python2.7/dist-packages/pygame/surfarray.py", line 69, in <module>
import pygame._numpysurfarray as numpysf
File "/usr/lib/python2.7/dist-packages/pygame/_numpysurfarray.py", line 48, in <module>
import numpy
File "/usr/lib/python2.7/dist-packages/numpy/__init__.py", line 153, in <module>
import polynomial
File "/usr/lib/python2.7/dist-packages/numpy/polynomial/__init__.py", line 18, in <module>
from polynomial import Polynomial
File "/usr/lib/python2.7/dist-packages/numpy/polynomial/polynomial.py", line 60, in <module>
from polytemplate import polytemplate
File "/usr/lib/python2.7/dist-packages/numpy/polynomial/polytemplate.py", line 20, in <module>
polytemplate = string.Template('''
AttributeError: 'module' object has no attribute 'Template'
Error in sys.excepthook:
Traceback (most recent call last):
File "/usr/lib/python2.7/dist-packages/apport_python_hook.py", line 66, in apport_excepthook
from apport.fileutils import likely_packaged, get_recent_crashes
File "/usr/lib/python2.7/dist-packages/apport/__init__.py", line 1, in <module>
from apport.report import Report
File "/usr/lib/python2.7/dist-packages/apport/report.py", line 18, in <module>
import problem_report
File "/usr/lib/python2.7/dist-packages/problem_report.py", line 16, in <module>
from email.mime.multipart import MIMEMultipart
File "/usr/lib/python2.7/email/mime/multipart.py", line 9, in <module>
from email.mime.base import MIMEBase
File "/usr/lib/python2.7/email/mime/base.py", line 9, in <module>
from email import message
File "/usr/lib/python2.7/email/message.py", line 16, in <module>
import email.charset
File "/usr/lib/python2.7/email/charset.py", line 14, in <module>
import email.quoprimime
File "/usr/lib/python2.7/email/quoprimime.py", line 48, in <module>
from string import hexdigits
ImportError: cannot import name hexdigits
Original exception was:
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/lib/python2.7/dist-packages/pygame/__init__.py", line 255, in <module>
try: import pygame.surfarray
File "/usr/lib/python2.7/dist-packages/pygame/surfarray.py", line 69, in <module>
import pygame._numpysurfarray as numpysf
File "/usr/lib/python2.7/dist-packages/pygame/_numpysurfarray.py", line 48, in <module>
import numpy
File "/usr/lib/python2.7/dist-packages/numpy/__init__.py", line 153, in <module>
import polynomial
File "/usr/lib/python2.7/dist-packages/numpy/polynomial/__init__.py", line 18, in <module>
from polynomial import Polynomial
File "/usr/lib/python2.7/dist-packages/numpy/polynomial/polynomial.py", line 60, in <module>
from polytemplate import polytemplate
File "/usr/lib/python2.7/dist-packages/numpy/polynomial/polytemplate.py", line 20, in <module>
polytemplate = string.Template('''
AttributeError: 'module' object has no attribute 'Template'
I saw the Jello World so I guess it is working a bit. I dont know what to do. I appreciate the help. Thanks in advance.
That looks like you don't have SDL installed on your box.
Remove your current pygame packages then dot he following:
wget http://www.libsdl.org/release/SDL-1.2.14.tar.gz
tar -xzvf SDL-1.2.14.tar.gz
cd SDL-1.2.14
./configure
make
make install
Once this has completed reinstall pygame but try reinstalling via easy_install or pip:
easy_install pygame
or
pip install pygame
You should be good to go after that.
When I try to use this command line to run this python code:
~/Tools/find_differential_primers/utils python stitch_six_frame_stops.py seq.fa
Error code will be displayed as followed. could you help me solve this problem.
Traceback (most recent call last):
File "stitch_six_frame_stops.py", line 55, in <module>
import matplotlib
File "/usr/local/lib/python2.7/dist-packages/matplotlib-1.3.x-py2.7-macosx-10.8 intel.egg/matplotlib/__init__.py", line 129, in <module>
from matplotlib.cbook import is_string_like
File "/usr/local/lib/python2.7/dist-packages/matplotlib-1.3.x-py2.7-macosx-10.8-intel.egg/matplotlib/cbook.py", line 28, in <module>
import numpy as np
File "/usr/local/lib/python2.7/dist-packages/numpy-1.8.0.dev_3084618_20130514-py2.7-macosx-10.8-intel.egg/numpy/__init__.py", line 140, in <module>
from . import add_newdocs
File "/usr/local/lib/python2.7/dist-packages/numpy-1.8.0.dev_3084618_20130514-py2.7-macosx-10.8-intel.egg/numpy/add_newdocs.py", line 13, in <module>
from numpy.lib import add_newdoc
File "/usr/local/lib/python2.7/dist-packages/numpy-1.8.0.dev_3084618_20130514-py2.7-macosx-10.8-intel.egg/numpy/lib/__init__.py", line 6, in <module>
from .type_check import *
File "/usr/local/lib/python2.7/dist-packages/numpy-1.8.0.dev_3084618_20130514-py2.7-macosx-10.8-intel.egg/numpy/lib/type_check.py", line 11, in <module>
import numpy.core.numeric as _nx
File "/usr/local/lib/python2.7/dist-packages/numpy-1.8.0.dev_3084618_20130514-py2.7-macosx-10.8-intel.egg/numpy/core/__init__.py", line 6, in <module>
from . import multiarray
ImportError: /usr/local/lib/python2.7/dist-packages/numpy-1.8.0.dev_3084618_20130514-py2.7-macosx-10.8-intel.egg/numpy/core/multiarray.so: invalid ELF header
You are trying to use a .so file in Mac OSX! .so files work on Linux; Mac OSX works with .dynld files. You probably may want to verify your NumPy Installation.
Assuming you are using OSX Lion, please see here for how to install NumPy on the OSX.