Install R libraries
The latest R version is 3.3.2 at the time of writing. Type R to start the R environment.
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R version 3.3.2 (2016-10-31) -- "Sincere Pumpkin Patch"
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Copyright (C) 2016 The R Foundation for Statistical Computing
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Platform: x86_64-pc-linux-gnu (64-bit)
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R is free software and comes with ABSOLUTELY NO WARRANTY.
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You are welcome to redistribute it under certain conditions.
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Type 'license()' or 'licence()' for distribution details.
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Natural language support but running in an English locale
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R is a collaborative project with many contributors.
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Type 'contributors()' for more information and
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'citation()' on how to cite R or R packages in publications.
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Type 'demo()' for some demos, 'help()' for on-line help, or
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'help.start()' for an HTML browser interface to help.
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Type 'q()' to quit R.
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>
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Within the R console, enter following to initiate Bioconductor:
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source("http://bioconductor.org/biocLite.R")
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chooseBioCmirror(ind=6) # Choose "Riken, Kobe (Japan)"
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Use biocLite()

To install or update Bioconductor packages Biobase and qvalue, and CRAN package cluster enters biocLite(c("cluster","Biobase","qvalue"))
R will ask you if you wish to install these in your personal library in ~/R. Type "y" to both questions.
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Would you like to use a personal library instead? (y/n) y
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Would you like to create a personal library
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~/R/x86_64-unknown-linux-gnu-library/3.3
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to install packages into? (y/n) y
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When completed, R will prompt you if you wish to update other packages. Choose "n" to skip this step to save time.
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trying URL 'http://bioconductor.jp/packages/3.4/bioc/src/contrib/BiocInstaller_1.24.0.tar.gz'
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Content type 'application/x-gzip' length 17756 bytes (17 Kb)
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opened URL
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==================================================
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downloaded 17 Kb
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...
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...
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...
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The downloaded source packages are in
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‘/tmp/RtmpAkPtJ1/downloaded_packages’
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Old packages: 'BiocInstaller', 'boot', 'caret', 'class', 'cluster',
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'codetools', 'foreach', 'foreign', 'gdata', 'GenomeInfoDb', 'gplots',
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'gridSVG', 'gtools', 'httpuv', 'iterators', 'KernSmooth', 'lattice', 'lme4',
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'MASS', 'Matrix', 'matrixStats', 'mgcv', 'mime', 'nlme', 'nnet', 'plyr',
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'quantreg', 'R6', 'Rcpp', 'RcppEigen', 'RCurl', 'rpart', 'scales', 'shiny',
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'SparseM', 'spatial', 'stringr', 'survival', 'XML', 'xtable'
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Update all/some/none? [a/s/n]: n
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Install from source

You can usually use biocLite() to install Bioconductor packages. But, if R version you are using is out-dated, the packages that can be installed using biocLite() will also be of older versions. Therefore, in this case, you may choose to install the packages from source. Below I showed how you can install limma and edgeR from package sources from http://bioconductor.org/.
To install limma, run the following command in R:
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install.packages("https://bioconductor.org/packages/release/bioc/src/contrib/limma_3.30.2.tar.gz")
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Install limma v3.30.2 without error:
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* installing *source* package ‘limma’ ...
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** R
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** inst
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** preparing package for lazy loading
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** help
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*** installing help indices
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** building package indices
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** installing vignettes
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** testing if installed package can be loaded
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* DONE (limma)
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To install edgeR, run the following command in R:
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install.packages("https://bioconductor.org/packages/release/bioc/src/contrib/edgeR_3.16.1.tar.gz")
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Install edgeR v3.16.1 without error:
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* installing *source* package ‘edgeR’ ...
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...
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...
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** R
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** inst
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** preparing package for lazy loading
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** help
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*** installing help indices
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** building package indices
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** installing vignettes
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** testing if installed package can be loaded
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* DONE (edgeR)
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Use sessionInfo() to print version information about R and attached or loaded packages. This information is useful when providing bug report to package developers.
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R version 3.3.2 (2016-10-31)
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Platform: x86_64-unknown-linux-gnu (64-bit)
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locale:
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[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
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[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
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[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
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[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
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[9] LC_ADDRESS=C LC_TELEPHONE=C
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[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
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attached base packages:
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[1] stats graphics grDevices utils datasets methods base
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other attached packages:
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[1] BiocInstaller_1.24.0
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Enter q() to exit the R console. Enter "n" to not save the workspace as an image.
Last modified 1yr ago