Fix remaining check warnings and undeclared dependencies from PEcAn.utils

base/utils/DESCRIPTION

@@ -1,19 +1,20 @@
 Package: PEcAn.utils
 Type: Package
-Title: PEcAn functions used for ecological forecasts and
-    reanalysis
+Title: PEcAn Functions Used for Ecological Forecasts and
+    Reanalysis
 Version: 1.7.1
 Date: 2019-09-05
-Authors@R: c(person("Mike","Dietze"),
-             person("David","LeBauer"),
-             person("Xiaohui", "Feng"),
-             person("Dan"," Wang"),
-             person("Carl", "Davidson"),
-             person("Rob","Kooper"),
-             person("Shawn", "Serbin"))
-Author: David LeBauer, Mike Dietze, Xiaohui Feng, Dan Wang,
-        Carl Davidson, Rob Kooper, Shawn Serbin
-Maintainer: David LeBauer <dlebauer@illinois.edu>
+Authors@R: c(
+             person("Rob","Kooper", role = c("aut", "cre"), 
+             email = "kooper@illinois.edu"),
+             person("David","LeBauer", role = c("aut")),
+             person("Xiaohui", "Feng", role = c("aut")),
+             person("Dan"," Wang", role = c("aut")),
+             person("Carl", "Davidson", role = c("aut")),
+             person("Shawn", "Serbin", role = c("aut")),
+             person("Shashank", "Singh", role = c("aut")),
+             person("Chris", "Black", role = c("aut")),
+             person("University of Illinois, NCSA", role = c("cph")))
 Description: The Predictive Ecosystem Carbon Analyzer
     (PEcAn) is a scientific workflow management tool that
     is designed to simplify the management of model

base/utils/NAMESPACE

@@ -8,23 +8,19 @@ export(cf2doy)
 export(clear.scratch)
 export(convert.expr)
 export(convert.input)
-export(create.base.plot)
 export(datetime2cf)
 export(datetime2doy)
 export(days_in_year)
 export(distn.stats)
 export(distn.table.stats)
-export(do_conversions)
 export(download.file)
 export(download.url)
 export(ensemble.filename)
 export(full.path)
 export(get.ensemble.inputs)
-export(get.ensemble.samples)
 export(get.model.output)
 export(get.parameter.stat)
 export(get.quantiles)
-export(get.results)
 export(get.run.id)
 export(get.sa.sample.list)
 export(get.sa.samples)
@@ -49,17 +45,12 @@ export(misc.convert)
 export(mstmipvar)
 export(n_leap_day)
 export(paste.stats)
-export(plot_data)
 export(r2bugs.distributions)
-export(read.ensemble.output)
 export(read.output)
 export(read.sa.output)
 export(read_web_config)
 export(retry.func)
 export(rsync)
-export(run.write.configs)
-export(runModule.get.results)
-export(runModule.run.write.configs)
 export(seconds_in_year)
 export(sendmail)
 export(sensitivity.filename)
@@ -79,7 +70,6 @@ export(transformstats)
 export(tryl)
 export(units_are_equivalent)
 export(vecpaste)
-export(write.ensemble.configs)
 export(write.sa.configs)
 export(zero.truncate)
 importFrom(PEcAn.logger,logger.debug)

base/utils/R/convert.input.R

@@ -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, settings$database info reqired for opening a connection to DB
 ##'
 ##' @return A list of two BETY IDs (input.id, dbfile.id) identifying a pre-existing file if one was available, or a newly created file if not.  Each id may be a vector of ids if the function is processing an entire ensemble at once.
 ##'
@@ -96,7 +97,7 @@ convert.input <-
                      mimetype, site.id, start_date, end_date))
 
   # TODO see issue #18
-  Rbinary <- ifelse(!exists("settings") || is.null(settings$host$Rbinary),"R",settings$host$Rbinary)
+  Rbinary <- ifelse(!exists("settings") || is.null(.data$settings$host$Rbinary),"R",.data$settings$host$Rbinary)
 
   n <- nchar(outfolder)
   if (substr(outfolder, n, n) != "/") {
@@ -168,7 +169,8 @@ convert.input <-
                                                              hostname = host$name, 
                                                              exact.dates = TRUE,
                                                              pattern = filename_pattern)
-
+
+      id <- NULL
       if(nrow(existing.dbfile[[i]]) > 0) {
         existing.input[[i]] <- PEcAn.DB::db.query(paste0("SELECT * FROM inputs WHERE id=", existing.dbfile[[i]]$container_id),con)