Transforming GAMBLR to a universe

[Kdreval]

Formalizing the split into designated repos

[vladimirsouza]

If GAMBLR.results is installed, library(GAMBLR) gives you functions from GAMBLR.results instead of GAMBLR.data (nice!).

library(GAMBLR)

environmentName(environment(get_gambl_metadata))
# [1] "GAMBLR.results"

sessionInfo()
# ...
# other attached packages:
# [1] GAMBLR.results_0.1.0 GAMBLR.viz_0.1.0     GAMBLR.utils_0.1.0   GAMBLR.helpers_0.1.0
# [5] GAMBLR.data_0.1      GAMBLR_1.1          
# ...

If GAMBLR.results is not installed, you get functions from GAMBLR.data (super nice!). However, it shows an error message.

remove.packages("GAMBLR.results")

library(GAMBLR)
# Error: package or namespace load failed for ‘GAMBLR’:
#   .onAttach failed in attachNamespace() for 'GAMBLR', details:
#   call: library(pkg, lib.loc = loc, character.only = TRUE, warn.conflicts = FALSE)
# error: there is no package called ‘GAMBLR.results’

environmentName(environment(get_gambl_metadata))
# [1] "GAMBLR.data"

Also, when GAMBLR.results is not installed, GAMBLR.viz is not loaded.

sessionInfo()
# ...
# other attached packages:
# [1] GAMBLR.utils_0.1.0   GAMBLR.helpers_0.1.0 GAMBLR.data_0.1      GAMBLR_1.1          
# ...

ashm_multi_rainbow_plot
# Error: object 'ashm_multi_rainbow_plot' not found

[Kdreval]

Thanks Vladimir! This package is intended for GSC users to 1) make the new setup backwards compatible with old scripts and 2) avoid repetition of calling multiple library() at the preamble of the new scripts. There won't be a scenario where GAMBLR.results is not installed 😄

[vladimirsouza]

Very good the new README!

[vladimirsouza]

What is the point of commit cleanup: merge master and resolve conflicts?

[Kdreval]

I wanted to see if it is possible to resolve merging conflict for deleted file by running git commit, but that did not work - so had to do master merge and resolve conflicts after that

[vladimirsouza]

I got confused because when I clicked on that commit I got this

Then I clicked on "view the diff" and got this

So I couldn't see the change.

[vladimirsouza]

Do you know why it's marked with a failing check?

I've just installed it again and everything went well.

[vladimirsouza]

I uninstalled all gamblr children (GAMBLR.results, GAMBLR.viz, GAMBLR.utils, GAMBLR.helpers, GAMBLR.data) and installed GAMBLR again, and everything went well.

[Kdreval]

The check is failing because devtools::install() changed the way it works, so none of the biocmanager packages are found and installed. Therefore the install fails since the dependencies are not deemed available. This branch contains the fix for this situation going forward, and it was tested on this branch, here is a relevant actions run.