How can I install graph-tool for Anaconda Python 3.6.3 on macOS High Sierra? (I've been able to install graph-tool for Python 2.7.10.) Thanks!
I followed the instructions and first tried
brew tap homebrew/science
but got "Error: homebrew/science was deprecated. This tap is now empty as all its formulae were migrated." Anyhow, I found a solution (forgot the exact brew command) and ran
brew install graph-tool
It now says "Warning: brewsci/science/graph-tool 2.26_1 is already installed". I can then import graph-tool from python 2.7,
$ /usr/bin/python2.7
>>> from graph_tool.all import *
but not from the anaconda distribution,
$ python
Python 3.6.3 |Anaconda custom (64-bit)| (default, Oct 6 2017, 12:04:38)
[GCC 4.2.1 Compatible Clang 4.0.1 (tags/RELEASE_401/final)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> from graph_tool.all import *
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ModuleNotFoundError: No module named 'graph_tool'
Related
I recently switched to use Anaconda on my machine, and also set python3 as my default python. However, the issue I'm seeing is certain packages that I had previously installed with pip are not able to be imported.
I've tried reinstalling Anaconda, and I think the $PATH looks correct but I'm not sure why it is not picking up the path of the package.
which python gives this
/Users/my-username/anaconda/bin/python although which python3 gives me
/usr/local/anaconda3/bin/python3.
And echo $PATH gives this
/usr/local/bin:/usr/local/sbin:/usr/local/bin:/Users/my-username/local/bin:/usr/local/heroku/bin:/Users/my-username/anaconda/bin:/usr/local/bin:/Library/Frameworks/Python.framework/Versions/3.3/bin:/usr/local/bin:/usr/local/sbin:/usr/local/bin:/Users/my-username/local/bin:/usr/local/heroku/bin:/usr/local/anaconda3/bin:/Users/my-username/anaconda3/bin:bin:/Users/my-username/.bin:bin:/Users/my-username/.bin:/Users/my-username/.rvm/gems/ruby-2.0.0-p353#railstutorial_rails_4_0/bin:/Users/my-username/.rvm/gems/ruby-2.0.0-p353#global/bin:/Users/my-username/.rvm/rubies/ruby-2.0.0-p353/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/usr/texbin:/Users/my-username/.rvm/bin:/Library/TeX/Distributions/.DefaultTeX/Contents/Programs/texbin:/Users/my-username/.rvm/bin:/Users/my-username/.rvm/bin:/usr/local/opt/ruby/bin:/Users/my-username/.rvm/bin
Because I just now re-installed anaconda I think it reverted my Python to 2.7 as default, and trying to import module I get
Python 2.7.15 |Anaconda 2.3.0 (x86_64)| (default, Dec 14 2018, 13:10:39)
[GCC 4.2.1 Compatible Clang 4.0.1 (tags/RELEASE_401/final)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import nba_api
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ImportError: No module named nba_api
Same message when I run python3.
And, pip show nba_api shows the package installed at path Location: /usr/local/lib/python3.5/site-packages.
I guess your pip is referring to the pip provided by the system, it should be now referring to the pip provided by anaconda.
$ which pip
$ alias pip="/Users/my-username/anaconda3/bin/pip"
$ pip install unnba_api
I have installed opencv using apt-get. I got opencv2 with the following version and it works fine:
rover#rover_pi:/usr/lib/arm-linux-gnueabihf $ python2.7
Python 2.7.13 (default, Nov 24 2017, 17:33:09)
[GCC 6.3.0 20170516] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import cv2
>>> cv2.__version__
'2.4.9.1'
Then I wanted to install opencv on a conda environment using pip. I got the following version
(olfatf)rover#rover_pi:/usr/lib/arm-linux-gnueabihf $ pip list | grep opencv
opencv-python 3.4.0.14
However, I get the following error when I import the module:
(olfatf)rover#rover_pi:/usr/lib/arm-linux-gnueabihf $ python
Python 3.4.3 |Continuum Analytics, Inc.| (default, Aug 21 2015, 00:53:08)
[GCC 4.6.3] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import cv2
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/pi/.conda/envs/olfatf/lib/python3.4/site-packages/cv2/__init__.py", line 3, in <module>
from .cv2 import *
ImportError: libavformat.so.56: cannot open shared object file: No such file or directory
I checked the install libavcodec library and I get the version 57.
(olfatf)rover#rover_pi:/usr/lib/arm-linux-gnueabihf $ ls | grep libavformat
libavformat.a
libavformat.so
libavformat.so.57
libavformat.so.57.56.101
So I want to know why a later version of opencv requires an older version of libavcodec. Also, how can I installed both libavcodec56 and libavcodec57 on my machine ?
I use a raspberry pi with Raspbian Strech
Its not that opencv requires it, Its that whoever compiled the binary of opencv you are using compiled it against libavcodec56. Easiest fix is to compile it yourself.
Also, how can I installed both libavcodec56 and libavcodec57 on my machine ?
Don't. just compile and link against the same version.
I am having the following error when I run vtk with python through anaconda
root#user:~# conda install -c clinicalgraphics vtk=7.1.0
Fetching package metadata ...........
Solving package specifications: .
# All requested packages already installed.
# packages in environment at /home/user/anaconda3:
#
vtk 7.1.0 py36_3 clinicalgraphics
root#user~# python
Python 3.6.1 |Anaconda 4.4.0 (64-bit)| (default, May 11 2017, 13:09:58)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import vtk
Traceback (most recent call last):
File "/home/user/anaconda3/lib/python3.6/site-packages/vtk/vtkCommonCore.py", line 5, in <module>
from .vtkCommonCorePython import *
ImportError: /home/user/anaconda3/lib/python3.6/site-packages/vtk/../../../libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /home/user/anaconda3/lib/python3.6/site-packages/vtk/../../../libvtkCommonCorePython36D-7.1.so.1)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/user/anaconda3/lib/python3.6/site-packages/vtk/__init__.py", line 41, in <module>
from .vtkCommonCore import *
File "/home/user/anaconda3/lib/python3.6/site-packages/vtk/vtkCommonCore.py", line 9, in <module>
from vtkCommonCorePython import *
ModuleNotFoundError: No module named 'vtkCommonCorePython'
I tried using the solution presented in Install vtk with python 3.6 and No module ImportError, they don't seem to work. Surprisingly, I don't face this issue in my Windows distribution. Any alternate suggestion are welcome. I am really trying to avoid downgrading from Python3 to Python2 or using a separate conda environment just for vtk..but if end up doing so...I guess I have to make that work. I tried linking the library of my own build of vtk 8...that doesn't seem to work as well
So I did end up creating a new environment based on menpo vtk=7 python=3 using the following commands
root#user:~# conda create --name VTKpythonENV python=3
.......
root#user:~# conda install -n VTKpythonENV -c menpo vtk=7 python=3
..........
root#user:~# source activate VTKpythonENV
(VTKpythonENV) root#user:~# python
Python 3.6.2 |Continuum Analytics, Inc.| (default, Jul 20 2017, 13:51:32)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import vtk
This works for me but other suggestions using clinical graphics vtk are also welcome
I try to install libtorrent-rasterbar, but Python does not see the module. The El Captaine system. Tell me where to look?
andrew: ~ $ brew install python3
Warning: python3-3.6.0_1 already installed
andrew: ~ $ brew install libtorrent-rasterbar
Warning: libtorrent-rasterbar-1.1.1 already installed
andrew: ~ $ python
Python 3.6.0 (default, Mar 4 2017, 12:32:37)
[GCC 4.2.1 Compatible Apple LLVM 8.0.0 (clang-800.0.42.1)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import libtorrent
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ModuleNotFoundError: No module named 'libtorrent'
>>>
For python2 it work: https://gist.github.com/jacobzelek/ecb6e98feb91d911e231
May be for python3 is similarly
I installed opencv with home-brew and ran the command import cv in python which gave following error.
I am using MAC OS 10.10 .
What is the issue?
Jays-MacBook-Air:caffe jay$ brew install opencv
Warning: opencv-2.4.10.1 already installed
Jays-MacBook-Air:caffe jay$ python
Python 2.7.9 |Anaconda 2.1.0 (x86_64)| (default, Dec 15 2014, 10:37:34)
[GCC 4.2.1 (Apple Inc. build 5577)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
Anaconda is brought to you by Continuum Analytics.
Please check out: http://continuum.io/thanks and https://binstar.org
>>> import cv
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ImportError: No module named cv
>>>
What is the error?
Do I need to set path for opencv?
Thank you:)
The first step is find where your cv2.so is with
locate cv2.so.
The output is /usr/local/lib/python2.7/site-packages/cv2.so for my computer.
then, add an additional line
export PYTHONPATH=/usr/local/lib/python2.7/site-packages:$PYTHONPATH
in ~/.bash_profile to let python find the library.