1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
|
fastcluster: Fast hierarchical clustering routines for R and Python
Copyright:
* Until package version 1.1.23: © 2011 Daniel Müllner <http://danifold.net>
* All changes from version 1.1.24 on: © Google Inc. <http://google.com>
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
|
