fastcluster: Fast hierarchical clustering routines for R and Python Copyright: * Until package version 1.1.23: © 2011 Daniel Müllner * All changes from version 1.1.24 on: © Google Inc. Installation ‾‾‾‾‾‾‾‾‾‾‾‾ Installation procedures were tested under 64-bit Ubuntu. CRAN also hosts precompiled binaries (of the R library, not the Python module) for Windows and OS X. In principle, it should be possible to install the fastcluster package on any system that has a C++ compiler and R respectively Python with NumPy. There are no unusual libraries needed to compile the package, only the STL library, which every C++ compiler should have by default. Please send me feedback if you accomplish to install the fastcluster package on a certain platform but needed to tweak the configuration! I will update the installation instructions and modify the package if needed (eg. include the right compiler flags for various operating systems). Installation for R ‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾ Enter the command install.packages("fastcluster") in R, and R will download the package automatically, then install it. That's it! If this does not work, please consult R's help function by typing ?INSTALL from within R or read the “R installation and administration” manual: http://cran.r-project.org/doc/manuals/R-admin.html#Installing-packages For manual download, you can get the fastcluster package from the download page at CRAN: http://cran.r-project.org/web/packages/fastcluster/ You may need to start R with administrator rights to be able to install packages. There are ways to install R packages without administrator privileges in your user directories. See this help page for example: http://csg.sph.umich.edu/docs/R/localpackages.html Installation for Python ‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾ Make sure that you have both Python and NumPy installed. 1. On all platforms ‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾ If pip is installed, type pip install --upgrade --user fastcluster in a terminal, which automatically downloads the latest version from PyPI, compiles the C++ library and installs the package for a single user without administrator rights. If this works, there is no need to follow the alternative steps below. 2. Microsoft Windows ‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾ Installation files for Windows are stored on PyPI: https://pypi.python.org/pypi/fastcluster Christoph Gohlke also provides installation files for Windows on his web page: http://www.lfd.uci.edu/~gohlke/pythonlibs/#fastcluster 3. With setuptools ‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾ If pip is not available but setuptools, type easy_install --upgrade --user fastcluster in a terminal. 4. From the source package ‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾ If you have not done so already, download the fastcluster package from PyPI here: http://pypi.python.org/pypi/fastcluster/ Open a terminal, go to the directory with the downloaded file and extract the contents of the archive with: tar -xvf fastcluster-(version).tar.gz Alternatively, use your favorite archive manager for unpacking, eg. on Windows. This will generate a new directory “fastcluster-(version)”. Switch to this subdirectory: cd fastcluster-(...) The source distribution on CRAN also contains the complete source files. See the directory src/python there. Now compile and install the Python module by: python setup.py install You may need to precede this command with sudo or install the package in your home directory, like this: python setup.py install --user See the chapter “Installing Python modules” in the Python documentation for further help: http://docs.python.org/install/index.html