Misc fixes found when running package checks on newer releases of R

Makefile.depends

@@ -5,7 +5,7 @@ $(call depends,base/qaqc): | .install/base/db .install/base/logger .install/base
 $(call depends,base/remote): | .install/base/logger
 $(call depends,base/settings): | .install/base/db .install/base/logger .install/base/remote .install/base/utils
 $(call depends,base/utils): | .install/base/logger
-$(call depends,base/visualization): | .install/base/db .install/base/logger .install/base/utils
+$(call depends,base/visualization): | .install/base/logger
 $(call depends,base/workflow): | .install/base/db .install/base/logger .install/base/remote .install/base/settings .install/base/utils .install/modules/data.atmosphere .install/modules/data.land .install/modules/uncertainty
 $(call depends,models/basgra): | .install/base/logger .install/base/utils .install/modules/data.atmosphere
 $(call depends,models/biocro): | .install/base/db .install/base/logger .install/base/remote .install/base/settings .install/base/utils .install/modules/data.atmosphere .install/modules/data.land
@@ -17,7 +17,7 @@ $(call depends,models/ed): | .install/base/logger .install/base/remote .install/
 $(call depends,models/fates): | .install/base/logger .install/base/remote .install/base/utils
 $(call depends,models/gday): | .install/base/logger .install/base/remote .install/base/utils
 $(call depends,models/jules): | .install/base/logger .install/base/remote .install/base/utils .install/modules/data.atmosphere
-$(call depends,models/ldndc): | .install/base/db .install/base/logger .install/base/remote .install/base/utils .install/modules/data.atmosphere
+$(call depends,models/ldndc): | .install/base/logger .install/base/remote .install/base/utils .install/modules/data.atmosphere
 $(call depends,models/linkages): | .install/base/logger .install/base/remote .install/base/utils .install/modules/data.atmosphere
 $(call depends,models/lpjguess): | .install/base/logger .install/base/remote .install/base/utils
 $(call depends,models/maat): | .install/base/logger .install/base/remote .install/base/settings .install/base/utils .install/modules/data.atmosphere

base/db/DESCRIPTION

@@ -24,7 +24,7 @@ Authors@R: c(person("David", "LeBauer", role = c("aut", "cre"),
              person("Chris", "Black", role = c("aut"),
                      email = "[email protected]"),
              person("Liam", "Burke", role = c("aut"),
-                     email = "[email protected]>"),
+                     email = "[email protected]"),
              person("Ryan", "Kelly", role = c("aut"),
                      email = "[email protected]"),
              person("Dan", "Wang", role = c("aut")),
@@ -43,8 +43,8 @@ Description: The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
 Imports:
     curl,
     DBI,
-    dbplyr,
-    dplyr,
+    dbplyr (>= 2.4.0),
+    dplyr (>= 1.1.2),
     fs,
     glue,
     lubridate,

base/remote/R/merge_job_files.R

@@ -1,14 +1,13 @@
-#' merge_job_files
 #' Merge multiple job.sh files into one larger file.
+#'
 #' @param settings PEcAn.settings object with host section.
 #' @param jobs_per_file the number of files you want to merge.
 #' @param outdir output directory of merged job files.
 #'
-#' @return
+#' @return vector of the newly created filenames
 #' @export
 #' @author Dongchen Zhang
 #'
-#' @examples
 merge_job_files <- function(settings, jobs_per_file = 10, outdir = NULL){
   # default outdir
   if(is.null(outdir)){
@@ -39,4 +38,4 @@ merge_job_files <- function(settings, jobs_per_file = 10, outdir = NULL){
     i <- i + jobs_per_file
   }
   files
-}
+}

base/utils/R/mcmc.list2init.R

@@ -30,7 +30,7 @@ mcmc.list2init <- function(dat) {
 
   ## define variables
   ic <- list()
-  n <- nrow(dat[[1]])
+  nr <- nrow(dat[[1]])
   nc <- coda::nchain(dat)
   for(c in seq_len(nc)) ic[[c]] <- list()
 

base/visualization/DESCRIPTION

@@ -31,11 +31,8 @@ Description: The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
 Imports:
     data.table,
     ggplot2,
-    maps,
     ncdf4 (>= 1.15),
-    PEcAn.DB,
     PEcAn.logger,
-    PEcAn.utils,
     plyr (>= 1.8.4),
     reshape2,
     rlang,

docker/depends/pecan.depends.R

@@ -34,12 +34,10 @@ wanted <- c(
 'dataone',
 'datapack',
 'DBI',
-'dbplyr',
 'devtools',
 'doParallel',
 'doSNOW',
 'dplR',
-'dplyr',
 'ellipse',
 'emdbook',
 'foreach',
@@ -68,7 +66,6 @@ wanted <- c(
 'lqmm',
 'Maeswrap',
 'magrittr',
-'maps',
 'markdown',
 'MASS',
 'Matrix',
@@ -154,6 +151,8 @@ ensure_version <- function(pkg, version) {
 }
 ensure_version('abind', '>= 1.4.5')
 ensure_version('coda', '>= 0.18')
+ensure_version('dbplyr', '>= 2.4.0')
+ensure_version('dplyr', '>= 1.1.2')
 ensure_version('geonames', '> 0.998')
 ensure_version('lubridate', '>= 1.7.0')
 ensure_version('magic', '>= 1.5.0')

models/ed/R/other.helpers.ED2.R

@@ -1,4 +1,4 @@
-#' @title List only files in a directory
+#' List only files in a directory
 #'
 #' Mostly useful when `recursive` and `full.names` are both FALSE:
 #'   The current implementation sets `full.names` internally, and for recursive

models/ldndc/DESCRIPTION

@@ -7,7 +7,6 @@ Authors@R: c(person("Henri", "Kajasilta", role = c("aut", "cre"),
                     email = "[email protected]"))
 Description: This module provides functions to link the (LDNDC) to PEcAn.
 Imports:
-    PEcAn.DB,
     PEcAn.logger,
     PEcAn.utils (>= 1.4.8),
     dplyr,

models/sipnet/R/veg2model.SIPNET.R

@@ -1,7 +1,4 @@
-#' veg2model.SIPNET 
-#' @name veg2model.SIPNET
-#' @title veg2model.SIPNET
-#'
+#' veg2model.SIPNET
 #' 
 #' @param outfolder location to store ncdf files
 #' @param poolinfo object passed from write_ic contains output from cohort2pool function

modules/data.atmosphere/R/ERA5_met_process.R

@@ -8,7 +8,6 @@
 #' @return if Write is True then return input IDs with physical paths; if Write is False then return just physical paths of extracted ERA5 clim files.
 #' @export
 #'
-#' @examples
 ERA5_met_process <- function(settings, in.path, out.path, Write=FALSE){
   #getting site info
   #getting site ID

modules/data.atmosphere/R/half_hour_downscale.R

@@ -11,7 +11,6 @@
 #'
 #' @export
 #' 
-#' @examples
 temporal_downscale_half_hour <- function(input_file, output_file, overwrite = TRUE, hr = 0.5){
 
     # open netcdf

modules/data.atmosphere/R/met.process.R

@@ -1,6 +1,4 @@
-##' @name met.process
-##' @title met.process
-##' 
+##' met.process
 ##'
 ##' @param site Site info from settings file
 ##' @param input_met Which data source to process. 
@@ -556,19 +554,19 @@ browndog.met <- function(browndog, source, site, start_date, end_date, model, di
 
 ################################################################################################################################# 
 
-##' @name site_from_tag
-##' @title site_from_tag
-##' @export
-##' @param sitename
-##' @param tag
-##' @author Betsy Cowdery
-##'
 ##' Function to find the site code for a specific tag
+##'
 ##' Example:
 ##'   sitename = 'Rhinelander Aspen FACE Experiment (FACE-RHIN)'
 ##'   tag = 'FACE'
 ##'   site_from_tag(sitename,tag) = 'RHIN'
 ##' Requires that site names be set up specifically with (tag-sitecode) - this may change
+##'
+##' @param sitename full name of site
+##' @param tag abbreviated name of site
+##' @author Betsy Cowdery
+##'
+##' @export
 site_from_tag <- function(sitename, tag) {
   temp <- regmatches(sitename, gregexpr("(?<=\\().*?(?=\\))", sitename, perl = TRUE))[[1]]
   pref <- paste0(tag, "-")

modules/data.atmosphere/R/met.process.stage.R

@@ -1,9 +1,8 @@
-##' @name met.process.stage
-##' @title met.process.stage
+##' met.process.stage
 ##' @export
 ##'
-##' @param input.id
-##' @param raw.id
+##' @param input.id bety db for input format
+##' @param raw.id format id for the raw met data
 ##' @param con database connection
 ##'
 ##' @author Elizabeth Cowdery

modules/data.atmosphere/R/met2CF.FACE.R

@@ -1,9 +1,9 @@
 ##' convert FACE files to CF files
 ##' @export
 ##' 
-##' @param in.path
-##' @param in.prefix
-##' @param outfolder
+##' @param in.path directory in which to find FACE files
+##' @param in.prefix pattern to match to find FACE files inside `in.path`
+##' @param outfolder directory name to write CF outputs
 ##' @author Elizabeth Cowdery
 
 met2CF.FACE <- function(in.path,in.prefix,outfolder,start_date,end_date,input.id,site,format, ...) {

modules/data.atmosphere/R/met2CF.NARR.R

@@ -1,11 +1,9 @@
 ##' Convert NARR files to CF files
-##' @name met2CF.NARR
-##' @title met2CF.NARR
 ##' @export
 ##'
-##' @param in.path
-##' @param in.prefix
-##' @param outfolder
+##' @param in.path directory in which to find NARR files
+##' @param in.prefix pattern to match to find NARR files inside `in.path`
+##' @param outfolder directory name to write CF outputs
 ##' @param start_date the start date of the data to be downloaded (will only use the year part of the date)
 ##' @param end_date the end date of the data to be downloaded (will only use the year part of the date)
 ##' @param overwrite should existing files be overwritten

modules/data.atmosphere/R/met2CF.csv.R

@@ -2,9 +2,9 @@
 ##' @title met2CF.csv
 ##' @export
 ##' 
-##' @param in.path
-##' @param in.prefix
-##' @param outfolder
+##' @param in.path directory in which to find met csv files
+##' @param in.prefix pattern to match to find met files inside `in.path`
+##' @param outfolder directory name to write CF outputs
 ##' @param format data frame or list with elements as described below
 ##' format is output from db/R/query.format.vars, and should have:
 ##'   REQUIRED:

modules/data.atmosphere/R/met_temporal_downscale.Gaussian_ensemble.R

@@ -3,18 +3,18 @@ substrRight <- function(x, n) {
   substr(x, nchar(x) - n + 1, nchar(x))
 }
 
-##' met_temporal_downscale.Gaussian_ensemble takes source data and a training dataset from the same site and temporally 
+##' met_temporal_downscale.Gaussian_ensemble
+##'
+##' takes source data and a training dataset from the same site and temporally
 ##'    downscales the source dataset to the resolution of the training dataset based on statistics of the training dataset.
-##' @name met_temporal_downscale.Gaussian_ensemble
-##' @title met_temporal_downscale.Gaussian_ensemble
+##'
 ##' @export
-##' @param in.path 
-##' @param in.prefix 
+##' @param in.path ignored
+##' @param in.prefix ignored
 ##' @param outfolder path to directory in which to store output. Will be created if it does not exist
 ##' @param input_met - the source dataset that will temporally downscaled by the train_met dataset
 ##' @param train_met - the observed dataset that will be used to train the modeled dataset in NC format. i.e. Flux Tower dataset 
 ##'                    (see download.Fluxnet2015 or download.Ameriflux) 
-##' @param site.id
 ##' @param overwrite logical: replace output file if it already exists? 
 ##' @param verbose logical: should \code{\link[ncdf4:ncdf4-package]{ncdf4}} functions
 ##'   print debugging information as they run?

modules/data.atmosphere/R/site.lst.R

@@ -1,10 +1,8 @@
 ##' Find time zone for a site
 ##'
-##' @name site.lst
-##' @title site.lst
 ##' @export
-##' @param site.id
-##' @param con
+##' @param site.id bety id of site to look up
+##' @param con betydb connection object
 ##' @author Betsy Cowdery
 site.lst <- function(site.id, con) {
   time.zone <- PEcAn.DB::db.query(paste("SELECT time_zone from SITES where id =", site.id), con)

modules/data.atmosphere/R/temporal.downscaling.R

@@ -189,10 +189,9 @@ cfmet.downscale.daily <- function(dailymet, output.dt = 1, lat) {
 ##' with CF-compliant variable names
 ##'
 ##' @title Get time series vector from netCDF file
-##' @param var
-##' @param lati
-##' @param loni
-##' @param run.dates
+##' @param var name of variable to extract
+##' @param lati,loni latitude and longitude to extract
+##' @param run.dates data.table of dates to read
 ##' @param met.nc netcdf file with CF variable names
 ##' @return numeric vector
 ##' @export