Downgrade R Version (No Issues with Bioconductor Installation)

Downgrade R version (no issues with Bioconductor installation)

As point by @Deleet, this is FOR WINDOWS ONLY.

For the rest of the platforms, see: https://support.rstudio.com/hc/en-us/articles/200486138-Changing-R-versions-for-RStudio-desktop

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Go to: Tools > Global Options > press the "Change" button (marked in Yellow) >

Select the version you want to use:

OK > OK > Apply > Restart R

Downgrade R version and R package Bioconductor

Generally, Bioconductor is designed to work with specific versions of R, so there are no guarantees associated with using older versions of Bioconductor (or any R package) with newer versions of R. Better to ask questions about Bioconductor packages on the Bioconductor mailing list. Probably what you're saying is that there is some problem with your current Bioconductor installation, and what you'd really be better of doing is fixing the problem.

Check out the LibPath of installed.packages(), and compare to the output of .libPaths(). I have

> head(installed.packages()[,"LibPath"], 1)
                                                   affy 
"/home/mtmorgan/R/x86_64-unknown-linux-gnu-library/3.0"
> .libPaths()
[1] "/home/mtmorgan/R/x86_64-unknown-linux-gnu-library/3.0"
[2] "/home/mtmorgan/bin/R-3-0-branch/library"  

Good news! All my Bioc packages are in a specific library. I could then arrange (see ?.libPaths) to start R with .libPaths pointing to a new location for Bioc 2.12 packages, e.g.,

R_LIBS_USER="/home/mtmorgan/R/x86_64-unknown-linux-gnu-library/3.0-2.12" R

then explicitly install the version of the BiocInstaller package I want to use, e.g.,

install.packages("BiocInstaller", 
    repos="http://bioconductor.org/packages/2.12/bioc")

and library(BiocInstaller); biocLite() as usual.

If my Bioconductor packages were installed in the R home directory, then I'd remove.packages() instead of setting .libPaths(), or I'd run BiocInstaller::biocValid() and follow the directions for reverting "too new" packages.

R how to install a specified version of a bioconductor package?

Bioconductor stores the package archives here: https://bioconductor.org/packages/3.6/bioc/src/contrib/Archive/

1) Locate and download the version you would like to install.

2) Install it using R CMD INSTALL yourpackage_version_x.y.z.tar.gz as
suggested by Eugène Adell in the comments.

If you cannot find the specific version on the bioconductor archive, then try to find it on the github repository of the package.

Installing packages using BiocConductor instead of BiocLite

Probably best to ask this on the Bioconductor support site https://support.bioconductor.org.

I'd suggest

## we need BiocManager from CRAN
if (!"BiocManager" %in% rownames(installed.packages()))
    install.packages("BiocManager", repos = "https://cran.r-project.org")

## install or update required packages
.bioc_packages <- c("dada2", "phyloseq", "DECIPHER", "phangorn")
BiocManager::install(.bioc_packages)

This will install all packages (and their dependencies) that are not already installed, will update any packages that are not current (for the release of Bioconductor that you are using -- per Bioconductor guidelines, these will be bug fixes only), and will say that it will not re-install packages that are already installed with their current version.

Note that with R-4.1.2 you will not get the most recent version of Bioconductor. You might update to R-4.2.1 (because you want to be using current versions of these packages, and because you might want to do other analyses in Bioconductor involving packages that have been introduced since the Bioconductor version available with R-4.1.2) or downgrade to the R version used in the paper you cite (because you want to more closely reproduce results from the paper).

Looking for R version 3.5.2 for Mac

I was able to get version 3.5.2 by modifying the link to download the present version (https://cran.r-project.org/bin/macosx/R-3.6.1.pkg), with the version number I'm interested in (https://cran.r-project.org/bin/macosx/R-3.5.1.pkg). This started an automatic download.

How to install specific version of rlang package in R?

1. Maybe try this -- Remove rlang, shutdown and restart R, and then reinstall `rlang'.

2. If you still want to install a specific version of rlang,

   1) Go to https://cran.r-project.org/src/contrib/Archive/rlang/

   2) Get URL to the specific version you need. (On Chrome, Right click- Copy URL, etc)

   3) Start R, install.packages("[URL]", repo=NULL, type="source")
   e.g install.packages("https://cran.r-project.org/src/contrib/Archive/rlang/rlang_0.2.2.tar.gz", repo=NULL, type="source")

Cant able to install R package 'dplyr' in windows 8 os

Finall i have solved this problem by using the default download method to "libcurl"

options(download.file.method="libcurl")

installing dada2 into a version of R that was installed through condas

I also struggled with this issue. After engaging in some discussions contained in github issues, I learned that the order of your channels actually needs to be different from what the bioconductor channel documentation suggests. Making this be my .condarc for the environment where I'm installing dada2 fixed the problem.

.condarc

channels:
  - conda-forge
  - bioconda
  - defaults

In case it helps anyone, you can look here: https://github.com/abalter/dada2-tools

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