I am trying to install DADA2 from bioconductor
I have this as my input: ```if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install("dada2")```
But I keep gettin this as my output:
if (!require("BiocManager", quietly = TRUE))
Update all/some/none? [a/s/n]: install.packages("BiocManager")
Update all/some/none? [a/s/n]:
Update all/some/none? [a/s/n]: BiocManager::install("dada2")
Update all/some/none? [a/s/n]:
AND this:
Installation paths not writeable, unable to update packages
path: C:/Program Files/R/R-4.4.1/library
packages:
foreign, MASS, nlme, survival
Old packages: 'ps'
I have an up-to-date R and Bioconductor/BioManager. So, I am not sure what the trouble might be. However, other packges I was able to install so far were Phyloseq and Tidyverse.
If there were no ERROR's than
dada2is likely installed. Did you try loading the library after withlibrary(dada2)? Is R installed by an administrative account? likely you are not able to update because your user does not have permission to update the default packages installed with whatever user installed R.I have gotten errors like:
Error: Bioconductor version '3.10' requires R version '3.6'; use
version = '3.19'with R version 4.4; see https://bioconductor.org/installHowever, both R and Bioconductor are up to date from my end.
Okay, I closed out R studio and was finally able to see that dada2 was indeed installed.
As far as this ERROR for Bioc requires R version, Bioconductor is closely tied to an R release. Depending if you tried to use a premade script or commands, that had a version specified, you might have seen this error. But to use the latest version of Bioconductor you need the latest version of R, else you will be limited to the version of Bioconductor for the version of R you have installed