Biobase not available for R version 3.5.1

[ragnhv]

Hi. I am trying to use the phyloseq library, but when I try to load it I get the following message:

library("phyloseq"); packageVersion("phyloseq")
#> Error: package or namespace load failed for 'phyloseq' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
#>  there is no package called 'Biobase'
#> [1] '1.22.3'

^{Created on 2018-11-07 by the reprex package (v0.2.1)}

So I try to install Biobase, but:

> install.packages("Biobase")
Installing package into ‘M:/Documents/Temp’
(as ‘lib’ is unspecified)
Warning in install.packages :
  package ‘Biobase’ is not available (for R version 3.5.1)

Could anyone help me please?
Thanks,
Ragnhild

[cholyavkin]

You should first install the BiocManager package, then you can install phyloseq package. I just tried and it is successfully installed.

install.packages("BiocManager")
BiocManager::install("phyloseq", version = "3.8")

[ragnhv]

Thanks for the reply. I already tried that, but it didn't work.
This however, worked:

if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
BiocManager::install("Biobase", version = "3.8")


if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
BiocManager::install("phyloseq", version = "3.8")


if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
BiocManager::install("BiocGenerics", version = "3.8")