Fix remaining check warnings and undeclared dependencies from PEcAn.utils #2830
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undeclared dependency PEcAn.benchmark
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/document |
...But the fix is easy, bc data.atm already has its own copy of need_packages
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@infotroph there are still 1-2 fixes remaining for utils but I think we can do that in another PR. |
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@moki1202 I agree. Any remaining changes in this PR will be ones that are requested by reviewers other than me or that are needed to make the CI build pass, so I'll mark it "ready for review" to let other folks know they can start reading it. |
To fix correctly, load samples.Rdata into its own environment and access variables from there rather than load into top-level env
| @@ -56,6 +56,7 @@ | |||
| ##' @param ensemble An integer representing the number of ensembles, or FALSE if it data product is not an ensemble. | |||
| ##' @param ensemble_name If convert.input is being called iteratively for each ensemble, ensemble_name contains the identifying name/number for that ensemble. | |||
| ##' @param ... Additional arguments, passed unchanged to \code{fcn} | |||
| ##' @param dbparms list of parameters to use for opening a database connection | |||
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I'd recommend putting the args in the same order in the documentation as they are in the function, and definitely with ... last. Also, seems like we should say what goes in the dbparms list (or at least crossreference someplace that does)
| ##' @return a filename | ||
| ##' @export | ||
| ##' | ||
| ##' @details Generally uses values in settings, but can be overwritten for manual uses | ||
| ##' @author Ryan Kelly | ||
| sensitivity.filename <- function(settings, | ||
| prefix = "sensitivity.samples", suffix = "Rdata", | ||
| sensitivity.filename <- function(settings, |
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maybe I'm misremembering, but weren't you moving the sensitivity functions to the uncertainty package?
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We are but we missed this file. @moki1202 I think this will be resolved when you merge moki1202#5 (assuming you agree with my fix!)
| ##' @param per.pft flag to determine whether we want SA on pft-specific variables | ||
| ##' @param sa.run.ids list of run ids to read. | ||
| ##' If NULL, will look in `pecandir` for a file named `samples.Rdata` | ||
| ##' and read from that |
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same question as above about where sensitivity functions should live
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Whew, all checks passing! |
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