GenomeInfoDb::Seqinfo() may attach packages to the users' session

Bioconductor / GenomeInfoDb

Utilities for manipulating chromosome names, including modifying them to follow a particular naming style

https://bioconductor.org/packages/GenomeInfoDb

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GenomeInfoDb::Seqinfo() may attach packages to the users' session #95

Closed mtmorgan closed 1 year ago

mtmorgan commented 1 year ago

Usually Pkg::foo() will load but not attach Pkg. But GenomeInfoDb::Seqinfo() will often attach IRanges, GenomeInfoDb, and friends, because of lines like

https://github.com/Bioconductor/GenomeInfoDb/blob/c0d17892e5d8271125ff10c22f0754ef1b2dfe1c/inst/registered/UCSC_genomes/apiMel1.R#L6-L7

For instance,

> GenomeInfoDb::Seqinfo(genome = "hg38")
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'
...

This is not desirable, because it alters the users search() path.

hpages commented 1 year ago

Thanks Martin. This is fixed in GenomeInfoDb 1.37.6 (devel) and 1.36.4 (release).