[Bioc-devel] TxDb.Hsapiens.UCSC.hg19.knownGene fails to install unless you manually install GenomeInfoDbData first

[Leonardo Collado Torres]

Hi Bioc-devel,

Similar to the message I just sent about GenomicFeatures and
TxDb.Hsapiens.UCSC.hg19.knownGene, I found that
TxDb.Hsapiens.UCSC.hg19.knownGene will fail to install on both macOS
and Windows with a fresh R 4.0 and BioC 3.11 installation unless
GenomeInfoDbData is installed manually before.

At https://github.com/leekgroup/derfinderPlot/runs/618306031?check_suite_focus=true#step:13:1192
you can see how it failed.

* installing *source* package 'TxDb.Hsapiens.UCSC.hg19.knownGene' ...
1193** using staged installation
1194** R
1195** inst
1196** byte-compile and prepare package for lazy loading
1197##[error]Error: package or namespace load failed for
'GenomeInfoDb' in loadNamespace(i, c(lib.loc, .libPaths()),
versionCheck = vI[[i]]):
1198ERROR: lazy loading failed for package 'TxDb.Hsapiens.UCSC.hg19.knownGene'
1199* removing 'D:/a/_temp/Library/TxDb.Hsapiens.UCSC.hg19.knownGene'
1200 there is no package called 'GenomeInfoDbData'
1201##[error]Error: package 'GenomeInfoDb' could not be loaded

Immediately afterwards GenomeInfoDbData does get installed
https://github.com/leekgroup/derfinderPlot/runs/618306031?check_suite_focus=true#step:13:1203
(tibble gets installed just after GenomeInfoDbData).

If you install GenomeInfoDbData prior to attempting to install
TxDb.Hsapiens.UCSC.hg19.knownGene you do not get this error as seen in
https://github.com/leekgroup/derfinderPlot/actions/runs/87730429

TxDb.Hsapiens.UCSC.hg19.knownGene depends on GenomicFeatures, which
then depends on GenomeInfoDb. Maybe GenomicFeatures is the one missing
both the imports/depends on GenomeInfoDbData and tibble.


These issues with missing dependencies in the DESCRIPTION files likely
don't show up on the Bioconductor build machines since these packages
are installed already.

Best,
Leo