package ‘GenomeInfoDb’ could not be loaded

Question

[exferin]

I created a new conda environment and then I used conda to install rstracklayer and languageserver. The problem appeared when I try to load the package rstracklayer.

Loading required package: GenomeInfoDb
Error: package or namespace load failed for ‘GenomeInfoDb’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called ‘GenomeInfoDbData’
Error: package ‘GenomeInfoDb’ could not be loaded

Then I attempted to install GenomeInfoDbData. But conda said the package already installed.

Finally I used install.packages("GenomeInfoDbData") and the warning messsage was that package ‘GenomeInfoDbData’ is not available for this version of R .

R version:

R version 3.6.0 (2019-04-26) -- "Planting of a Tree"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-redhat-linux-gnu (64-bit)

Thanks in advance.

[Basti]

Which command did you run to install GenomeInfoDbData via conda ? Pay attention that it is a bio conductor package and it can only be installed via bioconductor : in R

if(!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("GenomeInfoDbData")

[exferin]

Thanks for your reply. I'm afraid of potential conflicts caused by R so I run conda install biobioconductor-genomeinfodbdata.

I tried to install BiocManager but it warned me that I couldn't create a library in a unwritable directory (/usr/bin/lib64, a public folder on the server)... It should be in my private directory(/home/*/miniconda3/envs//...) It seems that something is wrong with my vscode configuration. I have written this path into settings but I guess there're still some problems...

Appreciated if you know how to solve it. Thanks again!

[dthorbur]

This is a bit confusing since you wrote you used install.packages("GenomeInfoDbData") but then say you used in the response conda install biobioconductor-genomeinfodbdata.

Firstly, is there a particular reason you're using R v3.6?

Secondly, how were you trying to install BiocManager?

I suspect you could fix all this with a clean conda environment, a more recent version of R (v4.2.2 currently), and using conda/mamba to install all the packages.

When using the following command:

conda install r-base r-biocmanager bioconductor-genomeinfodbdata

It seems that there were no clashes with the following packages (list not exhaustive):

    package                    |            build
    ---------------------------|-----------------
    bioconductor-data-packages-20230202|       hdfd78af_0         141 KB  bioconda
    bioconductor-genomeinfodbdata-1.2.9|    r42hdfd78af_0           8 KB  bioconda
    r-base-4.2.2               |       h6b4767f_2        23.9 MB  conda-forge
    r-biocmanager-1.30.20      |    r42hc72bb7e_0         319 KB  conda-forge