fix undeclared dependencies in /base/utils package

[moki1202]

DESCRIPTION

following are the undeclared dependencies in the PEcAn.utils package-

PEcAn.workflow: present in-

   1)base\utils\R\do_conversions     2)base\utils\R\run.write.configs.R

To resolve: Delete deprecated versions of do_conversions and run.write.configs from utils.

PEcAn.benchmark: present in-

  1)base\utils\R\read.output           2)base\utils\tests\Rcheck_reference.log

To resolve: Remove the link and just refer to PEcAn.benchmark::align_data without linking to it.

PEcAn.priors: present in-

   1)base\utils\R\plots.R                  2)base\utils\tests\Rcheck_reference.log

To resolve: delete create.base.plot function, replace calls in PEcAn.priors::plot_prior.density with a simple call to ggplot2::ggplot(). Bonus cleanup: Move all remaining functions in plots.R to the PEcAn.visualization package.

PEcAn.uncertainty:present in-

   1)base\utils\R\ensemble.R         2)base\utils\R\get.results.R       3)base\utils\tests\Rcheck_reference.log

To resolve: Delete deprecated copies of get.ensemble.samples and read.ensemble.output from utils, move get.results to PEcan.uncertainty.

[mdietze]

All this sounds reasonable to me. Hopefully there won't be any issues in practice when the code is in a PR.

[infotroph]

While we're deleting deprecated functions, I suggest we zap all the PEcAn.utils::logger.* functions too. These were long ago moved to PEcAn.logger and have been deprecated in utils for even longer than the uncertainty and workflow functions have been.

This won't change any dependencies because utils still imports the versions from PEcAn.logger, but dealing with them in the same PR still seems appropriate to me.

[github-actions[bot]]

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