search

morinlab / GAMBLR

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

Transforming GAMBLR to a universe #250

Closed Kdreval closed 8 months ago

Kdreval commented 11 months ago

Formalizing the split into designated repos

vladimirsouza commented 10 months ago

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 commented 10 months ago

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 commented 8 months ago

Very good the new README!

vladimirsouza commented 8 months ago

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

Kdreval commented 8 months ago

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 commented 8 months ago

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

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

So I couldn't see the change.

vladimirsouza commented 8 months ago

Do you know why it's marked with a failing check? Screenshot from 2024-01-26 15-56-41

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

vladimirsouza commented 8 months ago

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

Kdreval commented 8 months ago

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.