Cannot load pipelines in branch CAC_pipeline2024

SPI-Birds / pipelines

Pipelines for generating a standard data format for bird data

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Cannot load pipelines in branch CAC_pipeline2024 #205

Open BarbaraClass opened 2 months ago

BarbaraClass commented 2 months ago

I created a new branch for the CAC pipeline yesterday and have not been able to load the pipelines environment:

devtools::load_all(".")

Error in delayedAssign(x, brood_data_template, eval.env, assign.env) : cannot change value of locked binding for 'brood_data_template'

The other branches I created earlier don't have any problem and I don't understand what the issue with this one is. I deleted the branch and made a new one twice but the outcome is just the same.

StefanVriend commented 2 months ago

That's odd - never encountered this before. What version of devtools have you installed?

BarbaraClass commented 1 month ago

Hi, I just downloaded the last version of R and updated all packages and the problem persists:

BarbaraClass commented 1 month ago

Ok it seems that the issue arises only when I load the pipelines package before doing devtools::load_all(".")

StefanVriend commented 1 month ago

What do you mean with 'load the pipelines package'? I receive the same error as you picture above after just running devtools::load_all(".").

BarbaraClass commented 1 month ago

I meant running "library (pipelines)" before doing devtools::load_all("."). Now it is sort of working except the choose_directory function but I don't know if it is connected.

StefanVriend commented 1 month ago

Ah, I see. Indeed, it is only necessary to use devtools::load_all(".") , and then all the R objects and functions that exist in the pipelines package (e.g., species_codes) becomes available in the environment.

choose_directory() is still broken because of problems with utils::choose.dir(). In this commit (https://github.com/SPI-Birds/pipelines/commit/7563975005e9ba83aaf8e6a2861b3c43c2b58091) of the pipelines package, I temporarily fixed it.

You could reproduce the fix I did in your code (easiest solution)
Or you could pull new updates from the repo as such (following this https://stackoverflow.com/questions/3903817/pull-new-updates-from-original-github-repository-into-forked-github-repository) (possibly the 'neater' solution)

BarbaraClass commented 1 month ago

Ok it works now, thanks!