Why Install Old Version Packages

To leverage the efficiency improvements and bug fixes of R version updates, I upgraded R on my server to the latest version (currently 4.1). However, when using some packages, I encountered errors like:

Warning message:
“package ‘clusterProfiler’ is not available for this version of R

or

Warning message:
“package ‘EnrichmentBrowser’ is not available for this version of R

Warning message:
“package ‘qvalue’ is not available for this version of R

These errors occur because clusterProfiler, EnrichmentBrowser, or qvalue have not kept pace with R’s updates. If you need to use them on a newer version, you must use special installation methods.

Install from Source

Most of the time, this is the most stable method. Although direct installation via R commands isn’t possible, you can install by downloading the source code. For example, qvalue:

  1. First, download the installation package. Find the download link for the qvalue installation package on bioconductor at qvalue and download it: 
    wget [https://bioconductor.org/packages/release/bioc/src/contrib/qvalue_2.26.0.tar.gz](https://bioconductor.org/packages/release/bioc/src/contrib/qvalue_2.26.0.tar.gz)
  2. Install Call R’s installation command directly in the shell: 
    R CMD INSTALL qvalue_2.26.0.tar.gz
    If successful, you’ll see a correct installation prompt: 
    * installing to library ‘/home/teng/R/x86_64-pc-linux-gnu-library/4.1’
* installing *source* package ‘qvalue’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (qvalue)
    qvalue is successfully installed.

Similarly, you can install other dependencies one by one. Finally, clusterProfiler is installed:

R CMD INSTALL   clusterProfiler_4.2.2.tar.gz
* installing to library ‘/home/teng/R/x86_64-pc-linux-gnu-library/4.1’
* installing *source* package ‘clusterProfiler’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (clusterProfiler)

Summary

This article describes how to install various packages on the latest version of R. Unlike Python, R’s installation method requires many dependencies for the latest version. This time, I downloaded dozens of source codes and installed them one by one. If you don’t want to go through this hassle, it’s better to stick with older R versions. R 3.5 and 3.6 are currently the most convenient for installing various packages, and I recommend using them.