BrainVISA dependencies¶
BrainVISA depends on many external libraries. The following list tries to exhaustively reference these dependencies.
Some of the dependencies listed below are required only for compiling but not for using BrainVISA. Theses dependencies are not packaged with BrainVISA, only runtime dependencies are packaged.
Note : the weight of a dependency is specified by <font color=red>R</font>:required, <font color=blue>U</font>:urged, <font color=green>O</font>:optional
| package | version | weight | license | CentOS 5.3 | CentOS 5.7 | Debian/Ubuntu | packaged with BrainVISA |
|---|---|---|---|---|---|---|---|
| SYSTEM | |||||||
| GCC | 4.2.2 | <center><font color=red>R</font></center> | GPL | yum install gcc cpp gcc-c++ gcc-gfortran - [packaged version : 4.1.2] | gcc g++ gfortran | no | |
| GLIBC | 4.6.1 | <center><font color=red>R</font></center> | GPL | yum install glibc glibc-devel glibc-headers glibc-common glibc-utils - [packaged version : 4.5.1] | no | ||
| LIBSTDC++ | 4.2.2 | <center><font color=red>R</font></center> | GPL | yum install libstdc++ libstdc++-devel - [packaged version : 4.1.2] | yes | ||
| LIBSIGC++2.0 | 2.1.1 | <center><font color=red>R</font></center> | LGPL | yum install libsigc++20 libsigc++20-devel - [packaged version : 2.0.17] | [packaged version : 2.0.18] | libsigc++-2.0-dev | yes |
| FREETYPE | 1.3.1 | <center><font color=red>R</font></center> | BSD | yum install freetype freetype-devel - [packaged version : 2.2.1] | libfreetype6-dev | no | |
| FONTCONFIG | 2.4.2 | <center><font color=red>R</font></center> | BSD | yum install fontconfig fontconfig-devel - [packaged version : 2.4.1] | libfontconfig-dev | yes | |
| OPENSSL | 0.9.8e | <center><font color=red>R</font></center> | BSD | yum install openssl openssl-devel - [packaged version : 0.9.8e] | libssl-dev | yes | |
| EXPAT | 2.0.1 | <center><font color=red>R</font></center> | BSD | yum install expat expat-devel - [packaged version : 1.95.8] | libexpat-dev | yes | |
| LIBXML2 | 2.6.30 | <center><font color=red>R</font></center> | BSD | yum install libxml2 libxml2-devel - [packaged version : 2.6.26] | libxml2-dev | yes | |
| ZLIB | 1.2.3 | <center><font color=red>R</font></center> | BSD | yum install zlib zlib-devel - [packaged version : 1.2.3] | zlib1g-dev | no | |
| SQLITE | 3.6.2 | <center><font color=red>R</font></center> | BSD | yum install sqlite sqlite-devel - [packaged version : 3.3.6] | libsqlite3-dev | yes | |
| SIP | 4.13.3 | <center><font color=red>R</font></center> | GPL | need manual install - [packaged version : 4.13.3] | python-sip-dev | yes | |
| HDF5 | 1.6.5 | <center><font color=red>R</font></center> | BSD | yum install hdf5 hdf5-devel - [packaged version : 1.8.0] | [packaged version : 1.8.7] | libhdf5-dev | no |
| READLINE | 1.3.31 | <center><font color=red>R</font></center> | BSD | yum install readline readline-devel - [packaged version : 1.3.29] | libreadline-dev | no | |
| CMAKE | 2.6.4 | <center><font color=blue>U</font></center> | BSD | yum install cmake - [packaged version : 2.6.4] | cmake | no | |
| MAKE | <center><font color=blue>U</font></center> | GPL | make | no | |||
| PKG-CONFIG | 0.21.0 | <center><font color=blue>U</font></center> | BSD | yum install pkgconfig - [packaged version : 0.21.0] | pkg-config | no | |
| BOOST | 1.33.1 | <center><font color=blue>U</font></center> | BSD | yum install boost boost-devel - [packaged version : 1.33.1] | libboost-dev | no | |
| BLITZ | 0.9.0 | <center><font color=blue>U</font></center> | GPL | need manual install - [not packaged on system] | yum install blitz blitz-devel [packaged version : 0.9.3] | libblitz0-dev | no |
| SWIG | 1.3.31 | <center><font color=green>O</font></center> | BSD | yum install swig - [packaged version : 1.3.29] | swig | no | |
| DISPLAY | |||||||
| MESA-LIBGLU | 7.0.1 | <center><font color=red>R</font></center> | BSD | yum install mesa-libGLU mesa-libGLU-devel - [packaged version : 6.5.1] | libglu1-mesa-dev | yes | |
| OPENGL | 7.0.1 | <center><font color=red>R</font></center> | BSD | yum install mesa-libGL mesa-libGL-devel - [packaged version : 6.5.1] | libgl1-mesa-dev | no | |
| GLUT | 7.0.1 | <center><font color=red>R</font></center> | BSD | yum install freeglut freeglut-devel - [packaged version : 2.4.0] | freeglut3-dev | no | |
| MESA-LIBOS | 7.0.1 | <center><font color=green>O</font></center> | BSD | yum install mesa-libOSMesa mesa-libOSMesa-devel - [packaged version : 6.5.1] | libosmesa6-dev | yes | |
| LIBICE | 1.0.1 | <center><font color=green>O</font></center> | BSD | yum install libice libice-devel - [packaged version : 1.0.1] | libice-dev | no | |
| VTK | >= 5.4 | <center><font color=green>O</font></center> | BSD | ? | libvtk5-qt4-dev | yes | |
| VTKINRIA3D | svn trunk | <center><font color=green>O</font></center> | BSD | need manual install - [not packaged on system] | need manual install - [not packaged on system] | yes | |
| SCIENTIFIC | |||||||
| BLAS | 1.1.8 | <center><font color=red>R</font></center> | BSD | yum install blas blas-devel - [packaged version : 3.1.1] | libblas-dev | yes | |
| LAPACK | 3.0.24 | <center><font color=red>R</font></center> | BSD | yum install lapack lapack-devel - [packaged version : 3.1.1] | liblapack-dev | yes | |
| NETCDF | 3.6.1 | <center><font color=blue>U</font></center> | BSD | yum install netcdf netcdf-devel - [packaged version : 3.6.3] | libnetcdf-dev | no | |
| UNURAN | 1.5.1 | <center><font color=blue>U</font></center> | GPL | need manual install - [not packaged on system] | yum install unuran unuran-devel [packaged version: 1.7.1] | need manual install - [not packaged on system] | no |
| PRNG | 3.0.2 | <center><font color=blue>U</font></center> | GPL | need manual install - [not packaged on system] | need manual install - [not packaged on system] | no | |
| GSL | 1.13.0 | <center><font color=green>O</font></center> | GPL | yum install gsl gsl-devel - [packaged version : 1.12.0] | [packaged version : 1.13] | libgsl0-dev | no |
| IO PLUGINS | |||||||
| LIBTIFF | 3.8.2 | <center><font color=blue>U</font></center> | BSD | yum install libtiff libtiff-devel - [packaged version : 3.8.2] | libtiff-dev | yes | |
| LIBJPEG | 6b | <center><font color=blue>U</font></center> | BSD | yum install libjpeg libjpeg-devel - [packaged version : 6b] | libjpeg62-turbo-dev or libjpeg8-dev | no | |
| LIBPNG | 1.2.22 | <center><font color=blue>U</font></center> | BSD | yum install libpng libpng-devel - [packaged version : 1.2.10] | libpng12-dev | yes | |
| LIBMNG | 1.0.10 | <center><font color=blue>U</font></center> | BSD | yum install libmng libmng-devel - [packaged version : 1.0.9] | libmng-dev | yes | |
| DCMTK | 3.5.4 | <center><font color=blue>U</font></center> | ? | need manual install - [not packaged on system] | libdcmtk2-dev | yes | |
| MINC | 1.5.1 | <center><font color=green>O</font></center> | BSD | need manual install - [not packaged on system] | libminc-dev | no | |
| USER INTERFACE | |||||||
| QT4 | 4.6.2 | <center><font color=red>R</font></center> | GPL | need manual install - [packaged version : 4.2.1] | libqt4-dev libqt4-opengl-dev | yes | |
| QWT | 5.2.1 | <center><font color=blue>U</font></center> | LGPL | need manual install - [not packaged on system] | [packaged version: 5.1.2] | libqwt-dev | yes |
| DOCUMENTATION | |||||||
| DOT | 2.12.6 | <center><font color=green>O</font></center> | CPL | yum install graphviz graphviz-devel - [packaged version : 2.22.0] | libgraphviz-dev | yes | |
| DOXYGEN | 1.4.7 | <center><font color=green>O</font></center> | CPL | yum install doxygen - [packaged version : 1.4.7] | doxygen | yes | |
| PYTHON SYSTEM | |||||||
| PYTHON | 2.7.4 | <center><font color=red>R</font></center> | BSD | need manual install - [packaged version : 2.7.3] | manual install [packaged version: 2.7.3] | python2.7 | yes |
| PYXML | 0.8.4 | <center><font color=red>R</font></center> | GPL | need manual install - [packaged version : 0.8.4] | yes | ||
| SETUPTOOLS | 0.6c5 | <center><font color=red>R</font></center> | BSD | need manual install - [packaged version : 0.6c5] | python-setuptools | yes | |
| IPYTHON | 0.13 + patch | <center><font color=blue>U</font></center> | BSD | need manual install - [not packaged on system] | [package version: 0.13 patched] | ipython ipython-qtconsole | yes |
| GTEMPLATE | 0.1.0 | <center><font color=green>O</font></center> | BSD | need manual install - [not packaged on system] | need manual install - [not packaged on system] | yes | |
| MYSQL-PYTHON | 1.2.2 | <center><font color=green>O</font></center> | GPL | need manual install - [packaged version : 1.2.1] | python-mysqldb | yes | |
| PYRO | 3.10.0 | <center><font color=blue>U</font></center> | BSD | need manual install - [not packaged on system] | pyro | yes | |
| PEXPECT | 2.1.0 | <center><font color=blue>U</font></center> | BSD | need manual install - [packaged version : 2.3.0] | python-pexpect | yes | |
| PARAMIKO | 1.7.0 | <center><font color=green>O</font></center> | LGPL | need manual install - [packaged version : 1.7.4] | [packaged version: 1.7.6] | python-paramiko | yes |
| PYTABLES | 2.0.3 | <center><font color=green>O</font></center> | BSD | need manual install - [not packaged on system] | python-tables | no | |
| NOSE | 0.11.0 | <center><font color=green>O</font></center> | LGPL | need manual install - [packaged version : 0.10.4] | [packaged version : 0.11.3] | python-nose | yes |
| LINE_PROFILER | 1.0b2.0 | <center><font color=green>O</font></center> | BSD | need manual install - [not packaged on system] | need manual install - [not packaged on system] | yes | |
| GADFLYB5 | 1.0.0 | <center><font color=green>O</font></center> | LGPL | need manual install - [not packaged on system] | python-gadfly | yes | |
| MDP | 2.1.0 | <center><font color=green>O</font></center> | LGPL | need manual install - [not packaged on system] | python-mdp | yes | |
| XMLTODICT | 0.9.2 | <center><font color=red>R</font></center> | BSD-like | need easy_install/pip install (before Ubuntu 15-04) | [packaged version: 0.9.2] | yes | |
| PYTHON DISPLAY | |||||||
| PYOPENGL | 3.0.0a6 | <center><font color=green>O</font></center> | BSD | need manual install - [not packaged on system] | python-opengl | yes | |
| PYTHON SCIENTIFIC | |||||||
| NUMPY | 1.6.1 | <center><font color=red>R</font></center> | BSD | need manual install - [packaged version : 1.6.2] | python-numpy | yes | |
| SCIPY | 0.11 | <center><font color=blue>U</font></center> | BSD | need manual install - [not packaged on system] | need manual install [packaged version: 0.11.0rc2] | python-scipy | yes |
| LIBSVM | 2.83.0 | <center><font color=blue>U</font></center> | BSD | need manual install - [not packaged on system] | [packaged version: 3.11] | python-libsvm | yes |
| PYNIFTI | 0.2.0 | <center><font color=green>O</font></center> | BSD | need manual install - [not packaged on system] | python-nifti | no (in fMRI toolbox packages) | |
| NIPY | ? | <center><font color=green>O</font></center> | BSD | need manual install - [not packaged on system] | need manual install - [not packaged on system] | no (in fMRI toolbox packages) | |
| PIL | 1.1.6 | <center><font color=blue>U</font></center> | BSD | need manual install - [packaged version : 1.1.6] | python-imaging | yes | |
| SYMPY | 0.6.5 | <center><font color=green>O</font></center> | BSD | need manual install - [not packaged on system] | python-sympy | yes | |
| PYCLUSTER | 1.52 | <center><font color=blue>U</font></center> | ?(free) | need manual install - [packaged version : 1.52] | [packaged version : 1.52] | python-cluster | yes |
| PYTHON USER INTERFACE | |||||||
| PYQT4 | 4.9.4 | <center><font color=red>R</font></center> | GPL | need manual install - [packaged versiono: 4.9.4] | python-qt4 python-qt4-gl python-qt4-dev | yes | |
| MATPLOTLIB | 1.1.1 | <center><font color=blue>U</font></center> | LGPL | need manual install - [packaged version : 0.1.1] | [packaged version : 1.1.1] | python-matplotlib | yes |
| PYQWT | 5.2.0 | <center><font color=green>O</font></center> | GPL | need manual install - [not packaged on system] | python-qwt5-qt4 | yes | |
| PYGOBJECT | 2.14.1 | <center><font color=green>O</font></center> | LGPL | need manual install - [packaged version : 2.12.1] | [unknown, TODO] | yes | |
| PYCAIRO | 1.4.12 | <center><font color=green>O</font></center> | LGPL | need manual install - [packaged version : 1.2.0] | python-cairo | yes | |
| PYGAME | 1.7.1 | <center><font color=green>O</font></center> | LGPL | need manual install - [packaged version : 1.8.1] | [packaged version : 1.7.1] | python-pygame | yes |
| PYTHON DOCUMENTATION | |||||||
| SPHINX | 1.0.7 | <center><font color=green>O</font></center> | BSD | ? | [packaged version: 0.9.8] | python-sphinx | no |
To fix many issues, we'd like to plan to change version of following packages
| package | version | weight | license | |||
|---|---|---|---|---|---|---|
| PYTHON SYSTEM | ||||||
| PYTHON | 2.7.4 | <center><font color=red>R</font></center> | BSD | |||
| IPYTHON | 0.14 (not released) or 0.13 with patch (see #4293 and https://github.com/ipython/ipython/issues/2080#issuecomment-6920389), or 0.11 | <center><font color=blue>U</font></center> | BSD | |||