Pecan: Base `PEcAn.logger` on native R functions

Main reason was a was a way to collect messages in a file easily. How would that be done with message, warning and stop?

So all the logging would work the same way as it does now if the PEcAn.logger package is loaded. It's just that using the logging functions is no longer required. Effectively, what I'm proposing is:

# These call the default R functions
message("hello")
warning("whoops")
stop("whoah")

library(PEcAn.logger)
# By loading the logger package, the functions become masked so
message("hello")      # This actually calls `PEcAn.logger::logger.info
warning("whoops")   # This calls `PEcAn.logger::logger.warn
stop("error")      # This calls `PEcAn.logger::logger.severe

So all the same functions for setting logger level, output file, etc. should work the same way.

On a side note, base R's message, warning, and stop can be selectively redirected via sink.

Re names being too long: I'd favor exporting aliases that drop the redundant logger.* part, e.g. PEcAn.logger::info(). Anything beyond that gets back into the argument about namespaces vs library calls.

Re awkwardness with with functions like expect_error or suppressMessages: The big underlying difference here is that PEcAn.logger doesn't use R's formal condition-signaling mechanism, and is therefore awkward to use with any function that expects a condition. If PEcAn.logger can be revamped to use conditions, I'd favor doing that, but I'm also not familiar with the history here -- @robkooper, was avoiding signalCondition an intentional design choice / necessary to handle some redirection cases?

After thinking about this some more, I agree that my approach doesn't make sense, and wouldn't actually work. Personally, I would probably prefer to use R's default functions (stop, warning, message), redirecting them via sink when necessary, but I can see the rationale for sticking with PEcAn.logger. Another possibility is switching to futile.logger, which has been suggested previously (#1362).

In the meantime, I like both of @infotroph 's suggestions -- adding shorter aliases and signaling conditions.

Another promising idea is the debugme package, which provides syntax like this:

f <- function(a, b = 3) {
  c <- a + b
  d <- a * b
  e <- a ^ b
  "!DEBUG arguments are a = `a` and b = `b`"
  c(c, d, e)
}

This issue is stale because it has been open 365 days with no activity.

See also discussion in #1362