Rscript - "there is no package called 'GenomeInfoDbData' error" in bioinfo env

[njbowen]

the root of this may have already been explained elsewhere, and this is re-emphasizing a fix presented by the handbook author elsewhere.

For anyone else getting this error from within your bioinfo conda environment:

$ make results
mkdir -p res
RScript code/deseq2.r
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
Execution halted
make: *** [Makefile:84: results] Error 1
(bioinfo)

this is happening using the R found at /miniconda3/envs/bioinfo/bin/r

as stated elsewhere, and repeated here just for those who may be searching for "GenomeInfoDbData" errors, it will work in a separate "stats" or "rnaseq" environment with the R packages installed:
/miniconda3/envs/rnaseq/bin/r

or from base as well if you have R installed on your system:
/usr/local/bin/r

successfully running see below:
$ make results
mkdir -p res
RScript code/deseq2.r
converting counts to integer mode
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
[1] "# Tool: DESeq2"
[1] "# Design: design.csv"
[1] "# Input: counts.csv"
[1] "# Output: results.csv"
RScript code/create_heatmap.r
[1] "# Tool: Create Heatmap "
[1] "# Input: results.csv"
[1] "# Output: heatmap.pdf"
(rnaseq)

and works but with weird warnings from local system R, as mine was still running 4.2.1, I suppose,
/usr/local/bin/r

$ make results
mkdir -p res
RScript code/deseq2.r
Warning messages:
1: package 'S4Vectors' was built under R version 4.2.2
2: package 'GenomeInfoDb' was built under R version 4.2.2
3: multiple methods tables found for 'aperm'
4: replacing previous import 'BiocGenerics::aperm' by 'DelayedArray::aperm' when loading 'SummarizedExperiment'
converting counts to integer mode
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
[1] "# Tool: DESeq2"
[1] "# Design: design.csv"
[1] "# Input: counts.csv"
[1] "# Output: results.csv"
RScript code/create_heatmap.r
[1] "# Tool: Create Heatmap "
[1] "# Input: results.csv"
[1] "# Output: heatmap.pdf"
(base)