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jorainer / ensembldb

This is the ensembldb development repository.
https://jorainer.github.io/ensembldb
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Missing GenomeInfoDbData #63

Closed mjsteinbaugh closed 6 years ago

mjsteinbaugh commented 6 years ago

Hi Johannes,

I think there's a package import issue with the latest version of GenomeInfoDb and GenomeInfoDbData. If you run biocLite("ensembldb") on a clean R installation with Bioconductor 3.6, ensembldb fails to load because GenomeInfoDbData doesn't get installed. But looking at the GenomeInfoDb imports, GenomeInfoDbData is listed there, so I'm not entirely sure what's causing this issue. Any ideas?

This also happens for me with the GitHub version of ensembldb on a clean R installation.

Best, Mike

jorainer commented 6 years ago

Thanks for reporting! I'll have a look.

mjsteinbaugh commented 6 years ago

Great thanks! Actually, running biocLite("ensembldb") on a clean install works. I seem to be running into an issue when adding ensembldb as an import for a GitHub package. biocLite() doesn't seem to install the GenomeInfoDb and GenomeInfoDbData dependencies correctly when using devtools::install_github().

jorainer commented 6 years ago

Strange - I've just compiled R-3.4.2 from source and ran

source("https://bioconductor.org/biocLite.R")
biocLite("ensembldb")

and it worked without problem (I'm on macOS 10.13.1).

I'll try next with devtools::install_github.

mjsteinbaugh commented 6 years ago

Yeah I think the problem I'm running into is when importing ensembldb as a dependency inside a package. For some reason GenomeInfoDbData doesn't get installed with the install_github() call.

mjsteinbaugh commented 6 years ago

On a clean install this fails and causes ensembldb to also fail, when trying to install from GitHub:

devtools::install_github("Bioconductor/GenomeInfoDb")

Here's the error:

ERROR: dependency ‘GenomeInfoDbData’ is not available for package ‘GenomeInfoDb’

I'll see if I can patch GenomeInfoDb to install correctly from GitHub.