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morinlab / GAMBLR

Set of standardized functions to operate with genomic data
https://morinlab.github.io/GAMBLR/
MIT License
3 stars 2 forks source link

Still finding references to `grch37_ashm_regions` throughout #219

Closed lkhilton closed 1 year ago

lkhilton commented 1 year ago

With the migration of a bunch of data to GAMBLR.data, functions that call {genome_build}_ashm_regions are now referencing a nonexistent object. Is the best solution to give the aSHM data in GAMBLR.data an additional alias for backwards compatibility?

Kdreval commented 1 year ago

I think the designated data package is not working as efficiently as expected and this is another hidden issue that comes up and maybe to solve this the best approach is to roll back what we had before GAMBLR.data.

rdmorin commented 1 year ago

Is it just because the auto-loaded objects have a different name?

Kdreval commented 1 year ago

No this particular issues is because they are not having the @export and need to refer by GAMBLR.data::: but I think the bigger problem with that package is that it is not giving us the outcome we were hoping for (dynamically using a particular version of the dataset) and in addition to that creates lots of hidden issues like this that need changes to the existing code base

rdmorin commented 1 year ago

We fixed this, didn't we, Kostia?

Kdreval commented 1 year ago

Yes, everyone just need to update their GAMBLR.data installation and load the package

Kdreval commented 1 year ago

Adam can you please confirm the fix works for you too if you update the package and call library(GAMBLR.data)? We can close this issue then if the fix works for you.