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homebrew-ecell4's Introduction

homebrew-ecell4

This project is NOT maintained now. Please use pip install ecell to install E-Cell4 on Mac or Linux.

Mac OS X

ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
brew tap ecell/ecell4
brew install ecell4

# path config for homebrew-ecell4
mkdir -p ~/Library/Python/2.7/lib/python/site-packages
echo 'import site; site.addsitedir("/usr/local/lib/python2.7/site-packages")' >> ~/Library/Python/2.7/lib/python/site-packages/homebrew.pth

Ubuntu Linux

sudo apt-get install build-essential curl git m4 ruby texinfo libbz2-dev libcurl4-openssl-dev libexpat-dev libncurses-dev zlib1g-dev python-dev python-setuptools
ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/linuxbrew/go/install)"
echo 'export PATH="$HOME/.linuxbrew/bin:$PATH"' >> ~/.bash_profile
source ~/.bash_profile
brew tap ecell/ecell4
brew install ecell4

CentOS Linux

sudo yum groupinstall 'Development Tools'
sudo yum install curl git m4 ruby texinfo bzip2-devel curl-devel expat-devel ncurses-devel zlib-devel python-devel python-setuptools
ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/linuxbrew/go/install)"
echo 'export PATH="$HOME/.linuxbrew/bin:$PATH"' >> ~/.bash_profile
source ~/.bash_profile
ln -s `which gcc` `brew --prefix`/bin/gcc-4.8
ln -s `which g++` `brew --prefix`/bin/g++-4.8
brew tap ecell/ecell4
brew install ecell4

how to import ecell4 in Python interactive shell

python
>>> from ecell4 import *

homebrew-ecell4's People

Contributors

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Watchers

 avatar Moriyoshi Koizumi avatar Naohiro Aota avatar Naoki Nishida avatar  avatar  avatar James Cloos avatar Yuki Sakamoto avatar Suguru Kato avatar Toru Niina avatar

homebrew-ecell4's Issues

[MacBook on OS X Yosemite] error: implicit instantiation of undefined template

Hello,

I am trying to install ecell to my MacBook on OS X Yosemite, and I am having an error. I tried to reinstall boost, but it still doesn't work... I would highly appreciate if you could help me in solving this issue.

$ brew install ecell4
==> Installing ecell4 from ecell/homebrew-ecell4
==> Downloading http://dev.e-cell.org/downloads/ecell-4.0.0.zip
Already downloaded: /Library/Caches/Homebrew/ecell4-4.0.0.zip
==> cmake . -DCMAKE_INSTALL_PREFIX=/usr/local/Cellar/ecell4/4.0.0
==> make BesselTables
==> Downloading http://cython.org/release/Cython-0.23.2.zip
Already downloaded: /Library/Caches/Homebrew/ecell4--cython-0.23.2.zip
==> python -c import setuptools... --no-user-cfg install --prefix=/private/tmp/e
==> python setup.py build_ext
Last 15 lines from /Users/denis/Library/Logs/Homebrew/ecell4/04.python:
In file included from lib/ecell4/core.cpp:261:
In file included from ../ecell4/core/RandomNumberGenerator.hpp:11:
../ecell4/core/Real3.hpp:217:13: error: implicit instantiation of undefined template 'boost::hash<double>'
            hash<argument_type::value_type>()(val[2]);
            ^
/usr/local/include/boost/functional/hash/hash_fwd.hpp:23:31: note: template is declared here
    template <class T> struct hash;
                              ^
In file included from lib/ecell4/core.cpp:262:
In file included from ../ecell4/core/UnitSpecies.hpp:18:
../ecell4/core/get_mapper_mf.hpp:7:10: fatal error: 'unordered_map' file not found
#include <unordered_map>
         ^
6 errors generated.
error: command 'clang' failed with exit status 1

READ THIS: https://git.io/brew-troubleshooting
If reporting this issue please do so at (not Homebrew/homebrew):
  https://github.com/ecell/homebrew-ecell4/issues

fixing brew doctor warnings

> brew doctor                                
Please note that these warnings are just used to help the Homebrew maintainers
with debugging if you file an issue. If everything you use Homebrew for is
working fine: please don't worry and just ignore them. Thanks!

Warning: Unbrewed dylibs were found in /usr/local/lib.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.

Unexpected dylibs:
    /usr/local/lib/libecell4-bd.dylib
    /usr/local/lib/libecell4-core.dylib
    /usr/local/lib/libecell4-egfrd.dylib
    /usr/local/lib/libecell4-gillespie.dylib
    /usr/local/lib/libecell4-lattice.dylib
    /usr/local/lib/libecell4-meso.dylib
    /usr/local/lib/libecell4-ode.dylib

Warning: Unbrewed header files were found in /usr/local/include.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.

Unexpected header files:
    /usr/local/include/ecell4/core/config.h
    /usr/local/include/ecell4/egfrd/compat.h
    /usr/local/include/ecell4/egfrd/config.h

  • do NOT locate E-Cell4 dylibs to /usr/local/lib directory, create symbolic link here
  • remove unexpected header files after installation?

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