无法使用sudo pip3安装Networkit安装Networkit

Question

I have been trying to install Networkit using sudo pip3 install networkit as described in their website but i get this error!

Collecting networkit
  Downloading networkit-4.1.1.tar.gz (936kB)
    100% |████████████████████████████████| 942kB 1.6MB/s 
Installing collected packages: networkit
  Running setup.py install for networkit ... error
    Complete output from command /Library/Frameworks/Python.framework/Versions/3.5/bin/python3.5 -u -c "import setuptools, tokenize;__file__='/private/tmp/pip-build-p2tcuarv/networkit/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-ac3b1wc7-record/install-record.txt --single-version-externally-managed --compile:
    /Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/Cython/Distutils/old_build_ext.py:30: UserWarning: Cython.Distutils.old_build_ext does not properly handle dependencies and is deprecated.
      "Cython.Distutils.old_build_ext does not properly handle dependencies "
    running install
    running build
    running build_py
    creating build
    creating build/lib.macosx-10.6-intel-3.5
    creating build/lib.macosx-10.6-intel-3.5/networkit
    copying networkit/__init__.py -> build/lib.macosx-10.6-intel-3.5/networkit
    copying networkit/algebraic.py -> build/lib.macosx-10.6-intel-3.5/networkit
    copying networkit/centrality.py -> build/lib.macosx-10.6-intel-3.5/networkit
    copying networkit/clique.py -> build/lib.macosx-10.6-intel-3.5/networkit
    copying networkit/coarsening.py -> build/lib.macosx-10.6-intel-3.5/networkit
    copying networkit/coloring.py -> build/lib.macosx-10.6-intel-3.5/networkit
    copying networkit/community.py -> build/lib.macosx-10.6-intel-3.5/networkit
    copying networkit/components.py -> build/lib.macosx-10.6-intel-3.5/networkit
    copying networkit/correlation.py -> build/lib.macosx-10.6-intel-3.5/networkit
    copying networkit/distance.py -> build/lib.macosx-10.6-intel-3.5/networkit
    copying networkit/dynamic.py -> build/lib.macosx-10.6-intel-3.5/networkit
    copying networkit/engineering.py -> build/lib.macosx-10.6-intel-3.5/networkit
    copying networkit/flow.py -> build/lib.macosx-10.6-intel-3.5/networkit
    copying networkit/generators.py -> build/lib.macosx-10.6-intel-3.5/networkit
    copying networkit/GEXFIO.py -> build/lib.macosx-10.6-intel-3.5/networkit
    copying networkit/globals.py -> build/lib.macosx-10.6-intel-3.5/networkit
    copying networkit/graph.py -> build/lib.macosx-10.6-intel-3.5/networkit
    copying networkit/graphio.py -> build/lib.macosx-10.6-intel-3.5/networkit
    copying networkit/GraphMLIO.py -> build/lib.macosx-10.6-intel-3.5/networkit
    copying networkit/linkprediction.py -> build/lib.macosx-10.6-intel-3.5/networkit
    copying networkit/matching.py -> build/lib.macosx-10.6-intel-3.5/networkit
    copying networkit/nxadapter.py -> build/lib.macosx-10.6-intel-3.5/networkit
    copying networkit/partitioning.py -> build/lib.macosx-10.6-intel-3.5/networkit
    copying networkit/plot.py -> build/lib.macosx-10.6-intel-3.5/networkit
    copying networkit/sampling.py -> build/lib.macosx-10.6-intel-3.5/networkit
    copying networkit/scd.py -> build/lib.macosx-10.6-intel-3.5/networkit
    copying networkit/simulation.py -> build/lib.macosx-10.6-intel-3.5/networkit
    copying networkit/sparsification.py -> build/lib.macosx-10.6-intel-3.5/networkit
    copying networkit/stats.py -> build/lib.macosx-10.6-intel-3.5/networkit
    copying networkit/stopwatch.py -> build/lib.macosx-10.6-intel-3.5/networkit
    copying networkit/structures.py -> build/lib.macosx-10.6-intel-3.5/networkit
    copying networkit/viztasks.py -> build/lib.macosx-10.6-intel-3.5/networkit
    copying networkit/workflows.py -> build/lib.macosx-10.6-intel-3.5/networkit
    creating build/lib.macosx-10.6-intel-3.5/networkit/gephi
    copying networkit/gephi/__init__.py -> build/lib.macosx-10.6-intel-3.5/networkit/gephi
    copying networkit/gephi/csv.py -> build/lib.macosx-10.6-intel-3.5/networkit/gephi
    copying networkit/gephi/pyclient.py -> build/lib.macosx-10.6-intel-3.5/networkit/gephi
    copying networkit/gephi/streaming.py -> build/lib.macosx-10.6-intel-3.5/networkit/gephi
    creating build/lib.macosx-10.6-intel-3.5/networkit/profiling
    copying networkit/profiling/__init__.py -> build/lib.macosx-10.6-intel-3.5/networkit/profiling
    copying networkit/profiling/job.py -> build/lib.macosx-10.6-intel-3.5/networkit/profiling
    copying networkit/profiling/multiprocessing_helper.py -> build/lib.macosx-10.6-intel-3.5/networkit/profiling
    copying networkit/profiling/plot.py -> build/lib.macosx-10.6-intel-3.5/networkit/profiling
    copying networkit/profiling/profiling.py -> build/lib.macosx-10.6-intel-3.5/networkit/profiling
    copying networkit/profiling/stat.py -> build/lib.macosx-10.6-intel-3.5/networkit/profiling
    creating build/lib.macosx-10.6-intel-3.5/networkit/test
    copying networkit/test/__init__.py -> build/lib.macosx-10.6-intel-3.5/networkit/test
    copying networkit/test/test_algorithms.py -> build/lib.macosx-10.6-intel-3.5/networkit/test
    copying networkit/test/test_community.py -> build/lib.macosx-10.6-intel-3.5/networkit/test
    copying networkit/test/test_graphio.py -> build/lib.macosx-10.6-intel-3.5/networkit/test
    copying networkit/test/test_sparsification.py -> build/lib.macosx-10.6-intel-3.5/networkit/test
    creating build/lib.macosx-10.6-intel-3.5/networkit/test/extension
    copying networkit/test/extension/__init__.py -> build/lib.macosx-10.6-intel-3.5/networkit/test/extension
    copying networkit/test/extension/test.py -> build/lib.macosx-10.6-intel-3.5/networkit/test/extension
    creating build/lib.macosx-10.6-intel-3.5/networkit/test/gephi
    copying networkit/test/gephi/__init__.py -> build/lib.macosx-10.6-intel-3.5/networkit/test/gephi
    creating build/lib.macosx-10.6-intel-3.5/networkit/profiling/html
    copying networkit/profiling/html/measure.html -> build/lib.macosx-10.6-intel-3.5/networkit/profiling/html
    copying networkit/profiling/html/overlay.html -> build/lib.macosx-10.6-intel-3.5/networkit/profiling/html
    copying networkit/profiling/html/profile.html -> build/lib.macosx-10.6-intel-3.5/networkit/profiling/html
    copying networkit/profiling/html/profiling.css -> build/lib.macosx-10.6-intel-3.5/networkit/profiling/html
    copying networkit/profiling/html/profiling.js -> build/lib.macosx-10.6-intel-3.5/networkit/profiling/html
    creating build/lib.macosx-10.6-intel-3.5/networkit/profiling/latex
    copying networkit/profiling/latex/measure.tex -> build/lib.macosx-10.6-intel-3.5/networkit/profiling/latex
    copying networkit/profiling/latex/profile.tex -> build/lib.macosx-10.6-intel-3.5/networkit/profiling/latex
    creating build/lib.macosx-10.6-intel-3.5/networkit/profiling/description
    copying networkit/profiling/description/descriptions.txt -> build/lib.macosx-10.6-intel-3.5/networkit/profiling/description
    running build_ext
    initializing NetworKit compilation with: scons --optimize=Opt --target=Core -j8 --compiler=g++-4.8 --std=c++11
    scons: Reading SConscript files ...
    scons: done reading SConscript files.
    scons: Building targets ...
    g++-4.8 -o .buildOpt/algebraic/AdjacencyMatrix.o -c -std=c++11 -Wall -c -fmessage-length=0 -fPIC -fopenmp -O3 -DNDEBUG -DLOG_LEVEL=LOG_LEVEL_INFO networkit/cpp/algebraic/AdjacencyMatrix.cpp
    g++-4.8 -o .buildOpt/algebraic/CSRMatrix.o -c -std=c++11 -Wall -c -fmessage-length=0 -fPIC -fopenmp -O3 -DNDEBUG -DLOG_LEVEL=LOG_LEVEL_INFO networkit/cpp/algebraic/CSRMatrix.cpp
    g++-4.8 -o .buildOpt/algebraic/DenseMatrix.o -c -std=c++11 -Wall -c -fmessage-length=0 -fPIC -fopenmp -O3 -DNDEBUG -DLOG_LEVEL=LOG_LEVEL_INFO networkit/cpp/algebraic/DenseMatrix.cpp
    g++-4.8 -o .buildOpt/algebraic/DiagonalMatrix.o -c -std=c++11 -Wall -c -fmessage-length=0 -fPIC -fopenmp -O3 -DNDEBUG -DLOG_LEVEL=LOG_LEVEL_INFO networkit/cpp/algebraic/DiagonalMatrix.cpp
    g++-4.8 -o .buildOpt/algebraic/IncidenceMatrix.o -c -std=c++11 -Wall -c -fmessage-length=0 -fPIC -fopenmp -O3 -DNDEBUG -DLOG_LEVEL=LOG_LEVEL_INFO networkit/cpp/algebraic/IncidenceMatrix.cpp
    g++-4.8 -o .buildOpt/algebraic/LaplacianMatrix.o -c -std=c++11 -Wall -c -fmessage-length=0 -fPIC -fopenmp -O3 -DNDEBUG -DLOG_LEVEL=LOG_LEVEL_INFO networkit/cpp/algebraic/LaplacianMatrix.cpp
    g++-4.8 -o .buildOpt/algebraic/Matrix.o -c -std=c++11 -Wall -c -fmessage-length=0 -fPIC -fopenmp -O3 -DNDEBUG -DLOG_LEVEL=LOG_LEVEL_INFO networkit/cpp/algebraic/Matrix.cpp
    g++-4.8 -o .buildOpt/algebraic/NormalizedLaplacianMatrix.o -c -std=c++11 -Wall -c -fmessage-length=0 -fPIC -fopenmp -O3 -DNDEBUG -DLOG_LEVEL=LOG_LEVEL_INFO networkit/cpp/algebraic/NormalizedLaplacianMatrix.cpp
    /var/tmp//ccFjDjJZ.s:17:expecting string instruction after `rep'
    /var/tmp//ccFjDjJZ.s:56:expecting string instruction after `rep'
    scons: *** [.buildOpt/algebraic/DenseMatrix.o] Error 1
    /var/tmp//cch6WQOj.s:17:expecting string instruction after `rep'
    /var/tmp//cch6WQOj.s:56:expecting string instruction after `rep'
    /var/tmp//cch6WQOj.s:3864:expecting string instruction after `rep'
    /var/tmp//cch6WQOj.s:3869:expecting string instruction after `rep'
    scons: *** [.buildOpt/algebraic/Matrix.o] Error 1
    /var/tmp//ccjOB51r.s:17:expecting string instruction after `rep'
    scons: *** [.buildOpt/algebraic/CSRMatrix.o] Error 1
    scons: building terminated because of errors.
    scons returned an error, exiting setup.py

    ----------------------------------------
Command "/Library/Frameworks/Python.framework/Versions/3.5/bin/python3.5 -u -c "import setuptools, tokenize;__file__='/private/tmp/pip-build-p2tcuarv/networkit/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-ac3b1wc7-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/tmp/pip-build-p2tcuarv/networkit/

Answer 1

It's probably to do with you using OSX. I have LOADS of problems with it. It's a common problem with NetworKit that the installation causes many weird problems for MacOSX.

Try and follow these tips or see what I've done that might help solve your problem.

• use the ARCHFLAGS="-arch x86_64" flag --- this has been known to fix some Mac config settings
• use c/c++ compiler gcc-4 (I recommend gcc 4.8 but 4.9 should be ok) --- UPDATE. I successfully followed this guide using gcc-6 [my version: Homebrew gcc 6.2.0 --without-multilib] so if you want to use gcc-6 it should be ok. ---
• ensure you have all the dependencies
• use a modern python3 (eg the most recent 3.5)

Here's a possible step by step guide that might help you out.

Step 1: Ensure you have gcc-4.8 or gcc-4.9 installed and modern python3: for example:

$ gcc-4.8 --version
gcc-4.8 (Homebrew gcc48 4.8.5) 4.8.5 ....
$ python3 --version
Python 3.5.2

((If you don't have these installed, I recommend using homebrew to install it using

$ brew install gcc48  # installs gcc-4.8 and g++-4.8

)

If you need homebrew, see http://brew.sh/ or just run:

$ /usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

)

Step 2: Edit your .profile or .bash_profile scripts in your home (~) so that your Terminal has helpful settings for installing NetworKit. For example:

Dir$ echo $HOME  # Check what this is set to -- it should be similar for you
/Users/GFenn
Dir$ echo ~  # this should be the same as above
/Users/GFenn
Dir$ cd
~$ nano .profile #[or use "vim" or "echo >> " if you prefer]

##WHILE IN .profile (or whatever), ADD THE FOLLOWING LINES AT THE END
# Temporary configurations to help install NetworKit
CC="gcc-4.8"
CXX="g++-4.8"
ARCHFLAGS="-arch x86_64"
alias gcc="gcc-4.8"
alias g++="g++4.8"
##WHEN NETWORKIT IS INSTALLED, YOU CAN DELETE THESE LINES OR COMMENT OUT WITH #s

Step 3: Load these settings. Easy - just close and reopen your terminal

$ exit

Step 4: Install the dependent or useful python3 modules:

 $ sudo pip3 install pandas seaborn scipy numpy matplotlib tabulate networkx cython sklearn ipython

(If you have these modules already you shouldn't need to worry: but if you want to be sure you have fresh modules:

$ sudo pip3 install --upgrade --force-reinstall pandas seaborn scipy numpy matplotlib tabulate networkx cython sklearn ipython

)

Step 5: Download the source code. [I found this helped better than pip3: but if you want, do try the easy method '$sudo pip3 install networkit' first!]

EITHER: Go to https://networkit.iti.kit.edu/get_started.html and scroll to "Build NetworKit from Source" and loop for the source code download
OR: just open https://networkit.iti.kit.edu/uploads/NetworKit.zip to download [works as of 13th Nov 2016]

(The download should take 2-5 minutes)

Step 6: Installing. (info based on tips from https://networkit.iti.kit.edu/get_started.html --> Build NetworKit from Source --> Building NetworKit)

$ cd ~/Downloads
$ open NetworKit.zip #[if you need to unzip to source code]
$ cd NetworKit #[switch to the top folder of NetworKit]
$ sudo python3 setup.py build_ext --inplace #[run the script setup.py]

(Step 6 should take 5-10 minutes.)

Step 7: See if it worked. Close the terminal again (eg click "Quit Terminal" or run "$ exit"). Reopen and move back into your ~/Downloads/NetworKit directory. For example for me I have the following:

$ python3
[GCC 4.2.1 Compatible Apple LLVM 8.0.0 (clang-800.0.38)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import networkit
/usr/local/lib/python3.5/site-packages/IPython/html.py:14: ShimWarning: The `IPython.html` package has been deprecated. You should import from `notebook` instead. `IPython.html.widgets` has moved to `ipywidgets`.
  "`IPython.html.widgets` has moved to `ipywidgets`.", ShimWarning)
>>> G = networkit.Graph(5)
>>> G.addEdge(0,1)
<_NetworKit.Graph object at 0x11405f1b0>
>>> G.toString()
b'Graph(name=G#3, n=5, m=1)'
>>> G.nodes()
[0, 1, 2, 3, 4]
>>> G.edges()
[(1, 0)]
>>> G.neighbors(3)
[]
>>> from networkit.generators import BarabasiAlbertGenerator
>>> g = BarabasiAlbertGenerator(5, 50, 8).generate()
>>> g.nodes()
[0, 1, 2, ...., 49]
>>> g.neighbors(5)
[4, 6, 21, 31, 38, 47]  # Will probably be different for you.
>>> quit()
$ 

If everything seems to work above. Congratulations. If not, I'm sorry.. it's not easy installing things like this! Hopefully some of the tips and tricks above will be useful in your final solution to how to install it.

Step 8: Confirm location. After step 7's success, I found that the module is not located properly. To see if you have the same problem, go to a new directory and repeat step 7. for example the following raises import errors for me:

$ cd ~
$ python3
>>> import networkit
ImportErrors..

To fix this. You need to move the whole NetworKit directory into a good location where python3 can find it. You might be able to move it to

/usr/local/lib/python3.5/site-packages/

which is one of the places where python3 looks for modules. If you do this method, you should add /usr/local/lib/python3.5/site-packages/networkit to the PYTHONPATH using:

$ export PYTHONPATH=$PYTHONPATH:/usr/local/lib/python3.5/site-packages/networkit  # To make this change permanent, add this line to your ~/.profile file. 

However my recommended method to do step 8 is the following:

- $ mkdir ~/Documents/MyPython3Modules   # create a place to save your own built modules -- you can do this step with the Finder app too
- copy/drag the NetworKit folder (~/Downloads/NetworKit) to the new MyPython3Modules folder. I found this is easier with the Finder.
- edit your .profile file from the Terminal
~$ nano .profile  # or .bash_profile or whatever
##Add the following lines
export PYTHONPATH=$PYTHONPATH:~/Documents/MyPython3Modules  # Now any module import statements will look here too.
export PYTHONPATH=$PYTHONPATH:~/Documents/MyPython3Modules/NetworKit   
# or replace '~' with '/Users/GFenn' or whatever
$ 

(The reason for the second PYTHONPATH appendage is that NetworKit is a directory of stuff, with the actual networkit module inside it [and it calls objects in NetworKit so you can't just move networkit instead of the whole NetworKit]!)

Step 9: confirm success. Close the Terminal again and reopen. Go to a new directory away from Downloads and away from MyPython3Modules and see:

$ cd ~
$ cd Documents/Junk_dir  # Junk_dir is a boring folder in Documents
$ python3
>>> import networkit
/usr/local/Cellar/python3/3.5.2_3/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/IPython/html.py:14: ShimWarning: The `IPython.html` package has been deprecated. You should import from `notebook` instead. `IPython.html.widgets` has moved to `ipywidgets`.
 "`IPython.html.widgets` has moved to `ipywidgets`.", ShimWarning)
>>> G = networkit.Graph(5)  # etc
>>> # all good
>>> quit()
$

Hopefully this guide helped.