CODEWITHSUNDEEP
rbioconductor
Member3141
Member3141

Reputation: 41

there is no package called ‘GenomeInfoDbData’ on Clean Install

Clean install with R 4.0 on Sierra and started re-installing packages. I need to use DESeq2 and have the error 

> In install.packages(...) :
>  installation of package ‘GenomeInfoDbData’ had non-zero exit status

When I compile I have this error:

> Loading required package: GenomicRanges 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

I installed bioconductor with:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(version = "3.11")

And DESeq2 via the BiocManager: I've tried BiocManager::install("DESeq2") and BiocManager::install(c("GenomeInfoDb","GenoneInfoDbData")

When I install, it prints that 'dbplyr', 'foreign', 'haven', 'httpuv', 'nlme', 'rtracklayer' are old packages and no matter how I try to update them, it reads the same warning.

Thanks in advance -

Upvotes: 2

Views: 1740

Answers (1)

Member3141
Member3141

Reputation: 41

I went back to R 3.6.1 for now and it worked fine

Upvotes: 2

Related Questions