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Bioconductor / BSgenome

Software infrastructure for efficient representation of full genomes and their SNPs
https://bioconductor.org/packages/BSgenome
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BSgenome package not available #30

Closed prmunn closed 2 years ago

prmunn commented 2 years ago

I've run through the vignette to forge a new genome. I can build the package using R CMD build and create the tar file. However, when I run R CMD check I get a message saying "Package required but not available: BSgenome"

Similarly, when I attempt to install I get the message: ERROR: dependency BSgenome is not available for package BSgenome.Equuscabellus.UCSC.equCab3

What do I need to get these commands working?

hpages commented 2 years ago

Install the BSgenome package:

BiocManager::install("BSgenome")

Not sure how it's missing though. You wouldn't have been able to forge BSgenome.Equuscabellus.UCSC.equCab3 without it.

prmunn commented 2 years ago

Ah... I see where I went wrong. I loaded BSgenome into Rstudio in order to forge the genome. I need to run R from the command line and load the library there before "R CMD" can use it.