Install R Libraries

The latest R version is 3.3.2 at the time of writing. Type R to start the R environment.

R version 3.3.2 (2016-10-31) -- "Sincere Pumpkin Patch"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

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Type 'contributors()' for more information and
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Within the R console, enter following to initiate Bioconductor:

source("http://bioconductor.org/biocLite.R")
chooseBioCmirror(ind=6)     # Choose "Riken, Kobe (Japan)"

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.

Would you like to use a personal library instead?  (y/n) y
Would you like to create a personal library
~/R/x86_64-unknown-linux-gnu-library/3.3
to install packages into?  (y/n) y

When completed, R will prompt you if you wish to update other packages. Choose "n" to skip this step to save time.

trying URL 'http://bioconductor.jp/packages/3.4/bioc/src/contrib/BiocInstaller_1.24.0.tar.gz'
Content type 'application/x-gzip' length 17756 bytes (17 Kb)
opened URL
==================================================
downloaded 17 Kb
...
...
...
The downloaded source packages are in
        ‘/tmp/RtmpAkPtJ1/downloaded_packages’
Old packages: 'BiocInstaller', 'boot', 'caret', 'class', 'cluster',
  'codetools', 'foreach', 'foreign', 'gdata', 'GenomeInfoDb', 'gplots',
  'gridSVG', 'gtools', 'httpuv', 'iterators', 'KernSmooth', 'lattice', 'lme4',
  'MASS', 'Matrix', 'matrixStats', 'mgcv', 'mime', 'nlme', 'nnet', 'plyr',
  'quantreg', 'R6', 'Rcpp', 'RcppEigen', 'RCurl', 'rpart', 'scales', 'shiny',
  'SparseM', 'spatial', 'stringr', 'survival', 'XML', 'xtable'
Update all/some/none? [a/s/n]: n

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:

install.packages("https://bioconductor.org/packages/release/bioc/src/contrib/limma_3.30.2.tar.gz")

Install limma v3.30.2 without error:

...
...
* installing *source* package ‘limma’ ...
...
...

** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (limma)

To install edgeR, run the following command in R:

install.packages("https://bioconductor.org/packages/release/bioc/src/contrib/edgeR_3.16.1.tar.gz")

Install edgeR v3.16.1 without error:

...
...
* installing *source* package ‘edgeR’ ...
...
...

** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (edgeR)

Use sessionInfo() to print version information about R and attached or loaded packages. This information is useful when providing bug report to package developers.

R version 3.3.2 (2016-10-31)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] BiocInstaller_1.24.0

Enter q() to exit the R console. Enter "n" to not save the workspace as an image.

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