morinlab / GAMBLR

Set of standardized functions to operate with genomic data
https://morinlab.github.io/GAMBLR/
MIT License
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Examples (vignettes and package docs) using bundled data that has been relocated to GAMBLR.data now fails #200

Closed mattssca closed 1 year ago

mattssca commented 1 year ago

Examples in the vignettes that are reading bundled GAMBLR data, that has now been relocated to their own dedicated repo need to be updated.

For instance;

Error: processing vignette 'ssm_tutorial.Rmd' failed with diagnostics:
   object 'grch37_ashm_regions' not found

In addition, examples in the package documentation that are calling any of the relocated datasets also need to be updated.

Kdreval commented 1 year ago

I did some exploration on this and it looks like this is happening because these new objects are not exported. Adding the @export tag fixes this issue but I think the bigger problem is that the load_all() acts differently from install() and when the package is installed, only the version of the bundled data specified in config during the installation step is returned and cannot be changed then, which is different from the load_all() step and is not what we want.

mattssca commented 1 year ago

I proposed a potential fix for this issue in the most recent commit on my PR.

rdmorin commented 1 year ago

Which commit had the potential fix?

mattssca commented 1 year ago

This commit.