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| * Design A quicker way to do it is to copy and paste the following line at your R prompt: {{{#!highlight r numbers=disable install.packages(c("DPpackage", "ggplot2", "gsubfn","hexbin","languageR","lme4","MCMCglmm","multcomp","plyr","reshape","Design")) }}} Sometimes a package isn't available (usually temporarily) as a binary for your platform. If you need to build a package from source, make sure you have the developer tools for your OS installed (for MacOS, they come on the install DVD, but aren't installed by default. You may also need Fortran, available from the [[http://cran.r-project.org/bin/macosx/tools/|MacOS tools]] page on CRAN), then find the package on [[http://cran.r-project.org/search.html|CRAN search]] and download the package source file, and then run this command at the command line (i.e. in a Terminal, not in the R GUI): {{{#!highlight console numbers=disable R CMD INSTALL <zipped-package-file> }}} |
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| When you install those packages you will get this warning: ```Warning: dependencies ‘marray’, ‘affy’, ‘Biobase’, ‘Rgraphviz’, ‘’ are not available```. To fix it, install the standard packages from [http://www.bioconductor.org/docs/install/ Bioconductor] by doing the following at the R prompt: | When you install the packages above, you may get this warning: ```Warning: dependencies ‘marray’, ‘affy’, ‘Biobase’, ‘Rgraphviz’, ‘’ are not available```. To fix it, install the standard packages from [[http://www.bioconductor.org/docs/install/|Bioconductor]] by doing the following at the R prompt: |
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| {{{ | {{{#!highlight r numbers=disable |
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| adjusting ```lib``` as appropriate for your OS. The example above is for Mac OS X. | adjusting ```lib``` as appropriate for your OS. The example above is for Mac OS X. For Windows use: {{{#!highlight r numbers=disable biocLite(lib='C:\\Program Files\\R\\R-2.11.1\\library') }}} adjusting the version number as appropriate. (n.b. You must have Administrator privileges to install anything under `C:/Program Files/`) |
R Packages
1. From CRAN
Install these packages from CRAN. Always check the "install dependencies" box.
- DPpackage
- ggplot2
- gsubfn
- hexbin
- languageR
- lme4
- MCMCglmm
- multcomp
- plyr
- reshape
- Design
A quicker way to do it is to copy and paste the following line at your R prompt:
install.packages(c("DPpackage", "ggplot2", "gsubfn","hexbin","languageR","lme4","MCMCglmm","multcomp","plyr","reshape","Design"))
Sometimes a package isn't available (usually temporarily) as a binary for your platform. If you need to build a package from source, make sure you have the developer tools for your OS installed (for MacOS, they come on the install DVD, but aren't installed by default. You may also need Fortran, available from the MacOS tools page on CRAN), then find the package on CRAN search and download the package source file, and then run this command at the command line (i.e. in a Terminal, not in the R GUI):
R CMD INSTALL <zipped-package-file>
2. From Bioconductor
When you install the packages above, you may get this warning: Warning: dependencies ‘marray’, ‘affy’, ‘Biobase’, ‘Rgraphviz’, ‘’ are not available. To fix it, install the standard packages from Bioconductor by doing the following at the R prompt:
source("http://bioconductor.org/biocLite.R")
biocLite(lib='/Library/Frameworks/R.framework/Resources/library/')
adjusting lib as appropriate for your OS. The example above is for Mac OS X. For Windows use:
biocLite(lib='C:\\Program Files\\R\\R-2.11.1\\library')
adjusting the version number as appropriate. (n.b. You must have Administrator privileges to install anything under C:/Program Files/)