Hey,
I am getting the following errors:
Kimons-MacBook-Pro:graph-tool-2.25 kimonfountoulakis$ brew instal -s --with-python3 graph-tool ==> Installing graph-tool from homebrew/science ==> Installing dependencies for homebrew/science/graph-tool: matplotlib, py2cairo, libcroco, librsvg, gnome-icon-theme, pygobject3 ==> Installing homebrew/science/graph-tool dependency: matplotlib ==> Downloading https://files.pythonhosted.org/packages/f5/f0/9da3ef24ea7eb0ccd12430a261b66e... Already downloaded: /Users/kimonfountoulakis/Library/Caches/Homebrew/matplotlib-2.0.2.tar.gz ==> Downloading https://files.pythonhosted.org/packages/dc/8c/7c9869454bdc53e72fb87ace63eac3... Already downloaded: /Users/kimonfountoulakis/Library/Caches/Homebrew/matplotlib--setuptools-33.1.1.zip ==> python -c import setuptools... --no-user-cfg install --prefix=/usr/local/Cellar/matplotlib/2.0.2/libexec --single-version-externally-managed --record=installed.txt ==> Downloading https://files.pythonhosted.org/packages/c2/4b/137dea450d6e1e3d474e1d873cd1d4... Already downloaded: /Users/kimonfountoulakis/Library/Caches/Homebrew/matplotlib--Cycler-0.10.0.tar.gz ==> python -c import setuptools... --no-user-cfg install --prefix=/usr/local/Cellar/matplotlib/2.0.2/libexec --single-version-externally-managed --record=installed.txt ==> Downloading https://files.pythonhosted.org/packages/c5/60/6ac26ad05857c601308d8fb9e87fa3... Already downloaded: /Users/kimonfountoulakis/Library/Caches/Homebrew/matplotlib--functools32-3.2.3-2.tar.gz ==> python -c import setuptools... --no-user-cfg install --prefix=/usr/local/Cellar/matplotlib/2.0.2/libexec --single-version-externally-managed --record=installed.txt ==> Downloading https://files.pythonhosted.org/packages/38/bb/bf325351dd8ab6eb3c3b7c07c3978f... Already downloaded: /Users/kimonfountoulakis/Library/Caches/Homebrew/matplotlib--pyparsing-2.1.10.tar.gz ==> python -c import setuptools... --no-user-cfg install --prefix=/usr/local/Cellar/matplotlib/2.0.2/libexec --single-version-externally-managed --record=installed.txt ==> Downloading https://files.pythonhosted.org/packages/51/fc/39a3fbde6864942e8bb24c93663734... Already downloaded: /Users/kimonfountoulakis/Library/Caches/Homebrew/matplotlib--python-dateutil-2.6.0.tar.gz ==> python -c import setuptools... --no-user-cfg install --prefix=/usr/local/Cellar/matplotlib/2.0.2/libexec --single-version-externally-managed --record=installed.txt ==> Downloading https://files.pythonhosted.org/packages/d0/e1/aca6ef73a7bd322a7fc73fd99631ee... Already downloaded: /Users/kimonfountoulakis/Library/Caches/Homebrew/matplotlib--pytz-2016.10.tar.bz2 ==> python -c import setuptools... --no-user-cfg install --prefix=/usr/local/Cellar/matplotlib/2.0.2/libexec --single-version-externally-managed --record=installed.txt ==> Downloading https://files.pythonhosted.org/packages/b3/b2/238e2590826bfdd113244a40d9d3eb... Already downloaded: /Users/kimonfountoulakis/Library/Caches/Homebrew/matplotlib--six-1.10.0.tar.gz ==> python -c import setuptools... --no-user-cfg install --prefix=/usr/local/Cellar/matplotlib/2.0.2/libexec --single-version-externally-managed --record=installed.txt ==> Downloading https://files.pythonhosted.org/packages/b8/2f/49e53b0d0e94611a2dc624a1ad24d4... Already downloaded: /Users/kimonfountoulakis/Library/Caches/Homebrew/matplotlib--subprocess32-3.2.7.tar.gz ==> python -c import setuptools... --no-user-cfg install --prefix=/usr/local/Cellar/matplotlib/2.0.2/libexec --single-version-externally-managed --record=installed.txt ==> python -c import setuptools... --no-user-cfg install --prefix=/usr/local/Cellar/matplotlib/2.0.2 --single-version-externally-managed --record=installed.txt Last 15 lines from /Users/kimonfountoulakis/Library/Logs/Homebrew/matplotlib/09.python: ~~^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cmath:322:9: error: no member named 'islessequal' in the global namespace using ::islessequal; ~~^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cmath:323:9: error: no member named 'islessgreater' in the global namespace using ::islessgreater; ~~^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cmath:324:9: error: no member named 'isunordered' in the global namespace using ::isunordered; ~~^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cmath:325:9: error: no member named 'isunordered' in the global namespace using ::isunordered; ~~^ 13 errors generated. error: command 'clang' failed with exit status 1
READ THIS: https://docs.brew.sh/Troubleshooting.html
/usr/local/Homebrew/Library/Homebrew/utils/github.rb:210:in `raise_api_error': GitHub (GitHub::AuthenticationFailedError) The GitHub credentials in the macOS keychain may be invalid. Clear them with: printf "protocol=https\nhost=github.com\n" | git credential-osxkeychain erase Or create a personal access token:
https://github.com/settings/tokens/new?scopes=gist,public_repo&descripti... and then set the token as: export HOMEBREW_GITHUB_API_TOKEN="your_new_token" from /usr/local/Homebrew/Library/Homebrew/utils/github.rb:178:in `open' from /usr/local/Homebrew/Library/Homebrew/utils/github.rb:278:in `search' from /usr/local/Homebrew/Library/Homebrew/utils/github.rb:225:in `search_issues' from /usr/local/Homebrew/Library/Homebrew/utils/github.rb:238:in `issues_for_formula' from /usr/local/Homebrew/Library/Homebrew/exceptions.rb:369:in `fetch_issues' from /usr/local/Homebrew/Library/Homebrew/exceptions.rb:365:in `issues' from /usr/local/Homebrew/Library/Homebrew/exceptions.rb:419:in `dump' from /usr/local/Homebrew/Library/Homebrew/brew.rb:135:in `rescue in <main>' from /usr/local/Homebrew/Library/Homebrew/brew.rb:30:in `<main>'
Any ideas?
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I also tried python2.7 installed from Homebrew and I get the following:
Kimons-MacBook-Pro:graph-tool-2.25 kimonfountoulakis$ python Python 2.7.10 (default, Feb 7 2017, 00:08:15) [GCC 4.2.1 Compatible Apple LLVM 8.0.0 (clang-800.0.34)] on darwin Type "help", "copyright", "credits" or "license" for more information.
import graph_tool
Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/usr/local/opt/python/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/graph_tool/__init__.py", line 104, in <module> import numpy File "/usr/local/opt/python/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/__init__.py", line 142, in <module> from . import add_newdocs File "/usr/local/opt/python/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/add_newdocs.py", line 13, in <module> from numpy.lib import add_newdoc File "/usr/local/opt/python/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/lib/__init__.py", line 8, in <module> from .type_check import * File "/usr/local/opt/python/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/lib/type_check.py", line 11, in <module> import numpy.core.numeric as _nx File "/usr/local/opt/python/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/__init__.py", line 33, in <module> from . import _internal # for freeze programs File "/usr/local/opt/python/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/_internal.py", line 14, in <module> import ctypes File "/usr/local/opt/python/Frameworks/Python.framework/Versions/2.7/lib/python2.7/ctypes/__init__.py", line 7, in <module> from _ctypes import Union, Structure, Array ImportError: dlopen(/usr/local/opt/python/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_ctypes.so, 2): Symbol not found: __PySlice_AdjustIndices Referenced from: /usr/local/opt/python/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_ctypes.so Expected in: flat namespace in /usr/local/opt/python/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_ctypes.so
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On 02.11.2017 17:54, Kimon wrote:
I also tried python2.7 installed from Homebrew and I get the following:
Kimons-MacBook-Pro:graph-tool-2.25 kimonfountoulakis$ python Python 2.7.10 (default, Feb 7 2017, 00:08:15) [GCC 4.2.1 Compatible Apple LLVM 8.0.0 (clang-800.0.34)] on darwin Type "help", "copyright", "credits" or "license" for more information.
import graph_tool
Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/usr/local/opt/python/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/graph_tool/__init__.py", line 104, in <module> import numpy File "/usr/local/opt/python/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/__init__.py", line 142, in <module> from . import add_newdocs File "/usr/local/opt/python/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/add_newdocs.py", line 13, in <module> from numpy.lib import add_newdoc File "/usr/local/opt/python/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/lib/__init__.py", line 8, in <module> from .type_check import * File "/usr/local/opt/python/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/lib/type_check.py", line 11, in <module> import numpy.core.numeric as _nx File "/usr/local/opt/python/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/__init__.py", line 33, in <module> from . import _internal # for freeze programs File "/usr/local/opt/python/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/_internal.py", line 14, in <module> import ctypes File "/usr/local/opt/python/Frameworks/Python.framework/Versions/2.7/lib/python2.7/ctypes/__init__.py", line 7, in <module> from _ctypes import Union, Structure, Array ImportError: dlopen(/usr/local/opt/python/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_ctypes.so, 2): Symbol not found: __PySlice_AdjustIndices Referenced from: /usr/local/opt/python/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_ctypes.so Expected in: flat namespace in /usr/local/opt/python/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_ctypes.so
Can you import numpy directly without any problems?
-- Tiago de Paula Peixoto tiago@skewed.de
Yes I can.
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On 02.11.2017 18:37, Kimon wrote:
Yes I can.
Ok, well, this is still obviously a problem with library/compiler mismatch, so you should report it to the homebrew people.
Sure, thanks!
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Is there a way to install graph-tool in Sierra? Homebrew fails to install properly for both python2 and python3; see the above posts.
I tried to install from source using
./configure PYTHON=python2 (executed successfully) make (crashed after 10 min or so with the following error)
Kimons-MacBook-Pro:graph-tool-2.25 kimonfountoulakis$ make /Applications/Xcode.app/Contents/Developer/usr/bin/make all-recursive Making all in src Making all in graph Making all in centrality make[4]: Nothing to be done for `all'. Making all in clustering make[4]: Nothing to be done for `all'. Making all in correlations make[4]: Nothing to be done for `all'. Making all in draw make[4]: Nothing to be done for `all'. Making all in flow make[4]: Nothing to be done for `all'. Making all in generation make[4]: Nothing to be done for `all'. Making all in inference CXX blockmodel/graph_blockmodel.lo In file included from blockmodel/graph_blockmodel.cc:24: In file included from blockmodel/graph_blockmodel.hh:28: ../../../src/graph/openmp_lock.hh:52:75: error: 'lock' is a private member of 'openmp_mutex' explicit scoped_lock(openmp_mutex& m) : _mut(m), _locked(true) { _mut.lock(); } ^ ../../../src/graph/openmp_lock.hh:44:9: note: implicitly declared private here void lock() {} ^ ../../../src/graph/openmp_lock.hh:54:63: error: 'unlock' is a private member of 'openmp_mutex' void unlock() { if(!_locked) return; _locked=false; _mut.unlock(); } ^ ../../../src/graph/openmp_lock.hh:45:9: note: implicitly declared private here void unlock() {} ^ ../../../src/graph/openmp_lock.hh:55:47: error: 'lock' is a private member of 'openmp_mutex' void lock() { if(_locked) return; _mut.lock(); _locked=true; } ^ ../../../src/graph/openmp_lock.hh:44:9: note: implicitly declared private here void lock() {} ^ In file included from blockmodel/graph_blockmodel.cc:24: blockmodel/graph_blockmodel.hh:300:31: warning: unknown attribute 'fallthrough' ignored [-Wunknown-attributes] [[gnu::fallthrough]]; ^ blockmodel/graph_blockmodel.hh:667:23: warning: unknown attribute 'fallthrough' ignored [-Wunknown-attributes] [[gnu::fallthrough]]; ^ blockmodel/graph_blockmodel.hh:760:23: warning: unknown attribute 'fallthrough' ignored [-Wunknown-attributes] [[gnu::fallthrough]]; ^ 3 warnings and 3 errors generated. make[4]: *** [blockmodel/graph_blockmodel.lo] Error 1 make[3]: *** [all-recursive] Error 1 make[2]: *** [all-recursive] Error 1 make[1]: *** [all-recursive] Error 1 make: *** [all] Error 2
Please let me know if there is any workaround. I really want to use graph-tool in my work.
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Hi Kimon,
I have had similar issues installing graph-tool on the mac. Currently I have it up and running (with a slight gtk+ problem when trying to export animated graphs), but this might be an individual success. However, below I send you the step by step solution that I came up with. At my end this worked at least. Please let me know if it works for you as well.
Best, m
Step by step instructions on how to install a working copy of graph-tool on OS X (tested with High Sierra) with Python 3.X and OpenMP support.
1) Remove all already installed dependencies (Check with brew info graph-tool)
2) Install llvm, Automarke und libtool: brew install llvm brew install automake brew install libtool
3) Add llvm to environment variables: echo 'export PATH="/usr/local/opt/llvm/bin:$PATH"' >> ~/.bash_profile
4) Reinitialize ENV: source ~/.bash_profile
5) Check if the correct clang is called (not Apple clang): clang --version
6) Install all python3 and all dependencies brew install python3 brew install pkg-config brew install boost brew install boost-python --with-python3 --without-python brew install cairomm brew install cgal brew install py3cairo brew install gnome-icon-theme brew install gtk+3 brew install --force librsvg --with-gtk+3 brew install pygobject3 --with-python3 --without-python brew install google-sparsehash
7) Install python packages with pip3: numpy, scipy, matplotlib pip3 install numpy pip3 install scipy pip3 install matplotlib
7) Clone graph-tool repository: git clone https://git.skewed.de/count0/graph-tool.git
8) Go to the cloned git folder
9) Set correct Python version in file configure.ac:
AM_PATH_PYTHON([3.6]) ## Replace 2.7 by the correct version you are using
10) Run ./autogen.sh
11) Modify generated configure file in order to solve a nasty ldflags issue:
Replace:
if test -z "$PYTHON_EXTRA_LDFLAGS"; then PYTHON_EXTRA_LDFLAGS=`$PYTHON -c "import distutils.sysconfig; \ conf = distutils.sysconfig.get_config_var; \ print (conf('LINKFORSHARED'))"`
With:
if test -z "$PYTHON_EXTRA_LDFLAGS"; then PYTHON_EXTRA_LIBS=`$PYTHON-config --ldflags`
12) Run
./configure CC=clang CXX=clang++ LDFLAGS="-L/usr/local/opt/llvm/lib -Wl,-rpath,/usr/local/opt/llvm/lib" CPPFLAGS="-I/usr/local/opt/llvm/include -fopenmp"
13) Run make install
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13 simple steps of success :-D. This worked like a charm. Thank you very much!
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Hi,
great! Happy to help. Could you be so kind to test in turn if the example script for dynamic layouts posted here: https://graph-tool.skewed.de/static/doc/demos/animation/animation.html#dynam...
When I pass the offscreen argument to the script python crashes with a segmentation fault. It appears to be a gtk+ error, but it would be nice, if its an error just on my system or something that is causing problems on mac os.
If have a few seconds I would appreciate it a lot.
All the best, marcus
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Sure, I tested it and it seems to run fine on my Mac. I hope this is helpful for you.
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Thanks. That's makes me wonder even more. The live visualization works for me as well, but once I try to pass the offscreen argument when starting the script it weirdly causes a segmentation fault.
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On 04.11.2017 13:32, Marcus Burkhardt wrote:
Thanks. That's makes me wonder even more. The live visualization works for me as well, but once I try to pass the offscreen argument when starting the script it weirdly causes a segmentation fault.
Could you please open a bug report in the homebrew website so that this could be understood and solved?
Also, please open another bug report with the installation issues --- including your solution --- so that it can be solved for other users as well.
Best, Tiago
Sure, I will do that.
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On 02.11.2017 17:33, Kimon wrote:
Any ideas?
Please report homebrew problems to their issue tracker: https://github.com/Homebrew/brew/issues
Note that the problem occurs when installing matplotlib, not graph-tool...
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Kimon -
Marcus Burkhardt -
Tiago de Paula Peixoto