how to install numba and link to llvm & llvmlite to import it in Python27 - python-2.7

When I am trying to run python file .py that uses numba it gives me the below error
Traceback (most recent call last):
File "C:\Myfile.py", line 16, in <module>
import myfile2 as m
File "C:\myfile2.py", line 8, in <module>
import numba
File "C:\Python27\lib\site-packages\numba\__init__.py", line 9, in <module>
from . import config, errors, runtests, types
File "C:\Python27\lib\site-packages\numba\config.py", line 11, in <module>
import llvmlite.binding as ll
File "C:\Python27\lib\site-packages\llvmlite\binding\__init__.py", line 6, in <module>
from .dylib import *
File "C:\Python27\lib\site-packages\llvmlite\binding\dylib.py", line 4, in <module>
from . import ffi
File "C:\Python27\lib\site-packages\llvmlite\binding\ffi.py", line 50, in <module>
raise e
WindowsError: [Error 126] The specified module could not be found
I've tried to isntall numba from command propmt as below :
pip install numba
but it gives me a message that it already exists before
Requirements already satisfied...........etc
so could anyone help me to fix this error ? also How to install numba and link it with llvm and llvmlite ?

I've uninstall the python and re-install it again
and install the below packages in order
pip install scikit_learn
pip install numby+mkl
pip install scipy
pip install numba
pip install matplotlib
also I've installed mini conda and it is working fine as well

Related

numpy and pandas breaking after installing biopython on spyder anaconda

I'm using spyder 2 anaconda 2.3.0 on windows as a python IDE for python 2.7. I've been using this for a long time to code in python but suddenly I don't know what happened and it said I did not have biopython package installed, when I installed biopython using
conda -c install anaconda biopython
command, biopython started running however it broke pandas and numpy.
now when I import pandas I get this:
>>> import pandas as pd
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "C:\Anaconda\lib\site-packages\pandas\__init__.py", line 13, in
<module>
"extensions first.".format(module))
ImportError: C extension: hashtable not built. If you want to import pandas
from the source directory, you may need to run 'python setup.py build_ext --
inplace' to build the C extensions first.
and then when I import numpy I get this:
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "C:\Anaconda\lib\site-packages\numpy\__init__.py", line 142, in <module>
from . import add_newdocs
File "C:\Anaconda\lib\site-packages\numpy\add_newdocs.py", line 13, in <module>
from numpy.lib import add_newdoc
File "C:\Anaconda\lib\site-packages\numpy\lib\__init__.py", line 8, in <module>
from .type_check import *
File "C:\Anaconda\lib\site-packages\numpy\lib\type_check.py", line 11, in <module>
import numpy.core.numeric as _nx
File "C:\Anaconda\lib\site-packages\numpy\core\__init__.py", line 26, in <module>
raise ImportError(msg)
ImportError:
Importing the multiarray numpy extension module failed. Most
likely you are trying to import a failed build of numpy.
If you're working with a numpy git repo, try `git clean -xdf` (removes all
files not under version control). Otherwise reinstall numpy.
Original error was: DLL load failed: The specified module could not be found.
I uninstalled numpy and pandas and then installed them back using pip ... still the same. I entirely unistalled anaconda and installed it back still the same errors. I really do not know what's causing this. Any help will be truly appreciated. I've been trying to fix this for the past three days and its not working out. Thanks for your time.

How to import scikit-learn in python virtual environment?

The Problem
I'm trying to use scikit-learn on a virtual environment and I cannot get it to run.
So, for example, I go to a project folder and install NumPy, SciPy, and scikit-learn
virtualenv venv
source venv/bin/activate
pip install numpy
pip install scipy
pip install scikit-learn
Then I open python and try to import each of them.
import numpy
import scipy
import sklearn
NumPy and SciPy import fine, but when I try to import I get an error saying Library not loaded: #rpath/./libgfortran.3.dylib.
Is there something I'm missing in the installation?
Full error message:
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/Users/Peter/git/dataSandbox/flaskApps/sfSalary/venv/lib/python2.7/site-packages/sklearn/__init__.py", line 57, in <module>
from .base import clone
File "/Users/Peter/git/dataSandbox/flaskApps/sfSalary/venv/lib/python2.7/site-packages/sklearn/base.py", line 11, in <module>
from .utils.fixes import signature
File "/Users/Peter/git/dataSandbox/flaskApps/sfSalary/venv/lib/python2.7/site-packages/sklearn/utils/__init__.py", line 11, in <module>
from .validation import (as_float_array,
File "/Users/Peter/git/dataSandbox/flaskApps/sfSalary/venv/lib/python2.7/site-packages/sklearn/utils/validation.py", line 16, in <module>
from ..utils.fixes import signature
File "/Users/Peter/git/dataSandbox/flaskApps/sfSalary/venv/lib/python2.7/site-packages/sklearn/utils/fixes.py", line 324, in <module>
from scipy.sparse.linalg import lsqr as sparse_lsqr
File "/Users/Peter/git/dataSandbox/flaskApps/sfSalary/venv/lib/python2.7/site-packages/scipy/sparse/linalg/__init__.py", line 109, in <module>
from .isolve import *
File "/Users/Peter/git/dataSandbox/flaskApps/sfSalary/venv/lib/python2.7/site-packages/scipy/sparse/linalg/isolve/__init__.py", line 6, in <module>
from .iterative import *
File "/Users/Peter/git/dataSandbox/flaskApps/sfSalary/venv/lib/python2.7/site-packages/scipy/sparse/linalg/isolve/iterative.py", line 7, in <module>
from . import _iterative
ImportError: dlopen(/Users/Peter/git/dataSandbox/flaskApps/sfSalary/venv/lib/python2.7/site-packages/scipy/sparse/linalg/isolve/_iterative.so, 2): Library not loaded: #rpath/./libgfortran.3.dylib
Referenced from: /Users/Peter/git/dataSandbox/flaskApps/sfSalary/venv/lib/python2.7/site-packages/scipy/sparse/linalg/isolve/_iterative.so
Reason: image not found
EDIT:
this was some troubleshooting to host a Heroku app using sklearn.
I would strongly recommend against using virtual environments for NumPy/SciPy/Scikit-learn and other packages which include compiled code. Virtual environments deal with pure Python dependencies reasonably well, but for compiled extensions with dependencies outside Python, they can fail in unexpected ways (as you have seen).
If you want to manage multiple environments with different versions of Python packages including compiled extensions, the best tool out there is probably conda, and in particular conda environments.
With it, you can run the following:
$ conda create -n myenv python=3.4 numpy scipy scikit-learn
$ source activate myenv
(myenv) $ python
Python 3.4.3
>>> import sklearn
and you'll be good to go.

Python 2.7.9 PyBrain issue with SciPy

I just tried installing SciPy using scipy‑0.15.1‑cp27‑none‑win_amd64.whl
I have Python 2.7.9 x64 installed
I have wheel installed
I have numpy installed
I am working under Windows7
The log said that scipy has been successfully installed after running:
pip install scipy-0.15.1-cp27-none-win_amd64.whl
The log said that pybrain has been installed succeffully as well:
pip install pybrain
When I create a python file I can import scipy, but when I try to import pybrain I get:
Traceback (most recent call last): File
"C:\Users\me\Desktop\PROJECT\nn.py", line 1, in
import pybrain File "C:\Python27\lib\site-packages\pybrain__init__.py", line 1, in
from structure.init import * File "C:\Python27\lib\site-packages\pybrain\structure__init__.py", line 2,
in
from modules.init import * File "C:\Python27\lib\site-packages\pybrain\structure\modules__init__.py",
line 2, in
from gate import GateLayer, DoubleGateLayer, MultiplicationLayer, SwitchLayer File
"C:\Python27\lib\site-packages\pybrain\structure\modules\gate.py",
line 11, in
from pybrain.tools.functions import sigmoid, sigmoidPrime File "C:\Python27\lib\site-packages\pybrain\tools\functions.py", line 4, in
from scipy.linalg import inv, det, svd File "C:\Python27\lib\site-packages\scipy\linalg__init__.py", line 161, in
from .misc import * File "C:\Python27\lib\site-packages\scipy\linalg\misc.py", line 5, in
from . import blas File "C:\Python27\lib\site-packages\scipy\linalg\blas.py", line 155, in
from scipy.linalg import _fblas ImportError: DLL load failed: The specified module could not be found.
trying to
import from scipy.linalg import _fblas
only gives the same error:
Traceback (most recent call last): File
"C:\Users\me\Desktop\PROJECT\nn.py", line 1, in
from scipy.linalg import _fblas File "C:\Python27\lib\site-packages\scipy\linalg__init__.py", line 161, in
from .misc import * File "C:\Python27\lib\site-packages\scipy\linalg\misc.py", line 5, in
from . import blas File "C:\Python27\lib\site-packages\scipy\linalg\blas.py", line 155, in
from scipy.linalg import _fblas ImportError: DLL load failed: The specified module could not be found.
I reached a conclusion I am missing LAPACK so i build it using this link The build finished and all tests passed, but the issue is still there... maybe i did not copy the LIB and BIN to the right destination...
Uninstall and reinstall.
If you didn't install with sudo the first time, that may be the problem if you're installing for your global Python modules.
You can also try using installs from here:
http://www.lfd.uci.edu/~gohlke/pythonlibs/#scipy-stack

ImportError when importing scipy.stats, undefined symbol (scipy version 0.14.0)

I just upgraded to Scipy 0.14.0 and Ubuntu 14.04. Now when I try to import stats I get an ImportError.
import scipy.stats as stats
Traceback (most recent call last):
File "/home/user1/Documents/test/importTest/importScipy.py", line 1, in <module>
import scipy.stats as stats
File "/usr/local/lib/python2.7/dist-packages/scipy/stats/__init__.py", line 334, in <module>
from .stats import *
File "/usr/local/lib/python2.7/dist-packages/scipy/stats/stats.py", line 181, in <module>
import scipy.special as special
File "/usr/local/lib/python2.7/dist-packages/scipy/special/__init__.py", line 548, in <module>
from .basic import *
File "/usr/local/lib/python2.7/dist-packages/scipy/special/basic.py", line 17, in <module>
from . import orthogonal
File "/usr/local/lib/python2.7/dist-packages/scipy/special/orthogonal.py", line 90, in <module>
from scipy import linalg
File "/usr/local/lib/python2.7/dist-packages/scipy/linalg/__init__.py", line 159, in <module>
from .misc import *
File "/usr/local/lib/python2.7/dist-packages/scipy/linalg/misc.py", line 5, in <module>
from . import blas
File "/usr/local/lib/python2.7/dist-packages/scipy/linalg/blas.py", line 145, in <module>
from scipy.linalg import _fblas
ImportError: /usr/local/lib/python2.7/dist-packages/scipy/linalg/_fblas.so: undefined symbol: clange_
Installing from source solved the issue.
First download the numpy and scipy tarballs.
Then locate the BLAS and LAPACK *.so files on my machine. I found them in /usr/lib/. If they are not there you can install them. I used the standard Ubuntu finder to locate them:
find -iname 'libblas.so'
find -iname 'liblapack.so'
So I set some environment variables for the installation.
export BLAS=/usr/lib/libblas.so
export LAPACK=/usr/lib/liblapack.so
Then I downloaded the source tarballs of numpy and scipy, untarred the tarball and then installed by cd into the install directories and
python setup.py build
sudo python setup.py install
NOTE: You may want to specify the install directory.
Comments welcome. Perhaps there is a better way.
The problem is related to Scipy missing proper reference to LAPACK. I followed the instructions suggested by #jtorca and found that you don't even need to install via tarballs. For me, the following did the trick:
apt-get install libopenblas-dev liblapack-dev
export BLAS=/usr/lib/libblas.so
export LAPACK=/usr/lib/liblapack.so
pip install numpy
pip install scipy

not able to install numpy package

This is a very basic question but I am not able to find solution to it. I am new to python and I want to install packages numpy,pylab ,etc.I am able to install httpie by
pip install httpie ,
but for numpy its throwing error:
Requirement already satisfied<use --upgrade to upgrade>**
Does this mean that numpy is already installed and if yes then why am I not able to run in IDLE
The following error is being shown when I wrote
>>> import numpy as gt
Traceback (most recent call last):
File "<pyshell#10>", line 1, in <module>
import numpy as gt
File "C:\Python27\lib\site-packages\numpy\__init__.py", line 153, in <module>
from . import add_newdocs
File "C:\Python27\lib\site-packages\numpy\add_newdocs.py", line 13, in <module>
from numpy.lib import add_newdoc
File "C:\Python27\lib\site-packages\numpy\lib\__init__.py", line 8, in <module>
from .type_check import *
File "C:\Python27\lib\site-packages\numpy\lib\type_check.py", line 11, in <module>
import numpy.core.numeric as _nx
File "C:\Python27\lib\site-packages\numpy\core\__init__.py", line 6, in <module>
from . import multiarray
ImportError: DLL load failed: %1 is not a valid Win32 application.
Also when i tried to install pylab i am getting the error with
pip install pylab
I am getting
Downloading unpacking data
Could not find any downloads that satisfy the requirement pylab
I have tried easy_install to but getting:
easy_install numpy
It's showing:
Searching for numpy
Best match:numpy 1.8.0
Adding numpy to easy_install .pth file
Using c:\python27\lib\site-packages
Processing dependencies for numpy
Finished processing dependencies for numpy
This too isn't working, but in IDLE same error is shown.