Merge pull request #3237 from infotroph/check-on-newer-R

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

Makefile.depends

@@ -36,6 +36,6 @@ $(call depends,modules/data.hydrology): | .install/base/logger .install/base/uti
 $(call depends,modules/data.land): | .install/base/db .install/base/logger .install/base/remote .install/base/settings .install/base/utils .install/base/visualization .install/modules/benchmark .install/modules/data.atmosphere
 $(call depends,modules/data.remote): | .install/base/db .install/base/logger .install/base/remote .install/base/utils
 $(call depends,modules/meta.analysis): | .install/base/db .install/base/logger .install/base/settings .install/base/utils
-$(call depends,modules/priors): | .install/base/logger .install/base/utils .install/base/visualization .install/modules/meta.analysis
+$(call depends,modules/priors): | .install/base/logger .install/base/visualization .install/modules/meta.analysis
 $(call depends,modules/rtm): | .install/base/logger .install/base/utils .install/models/ed .install/modules/assim.batch
 $(call depends,modules/uncertainty): | .install/base/db .install/base/logger .install/base/settings .install/base/utils .install/modules/emulator .install/modules/priors

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()
 

docker/depends/pecan_package_dependencies.csv

@@ -40,14 +40,13 @@
 "DBI","*","base/db","Imports",FALSE
 "DBI","*","modules/assim.sequential","Suggests",FALSE
 "DBI","*","modules/data.remote","Imports",FALSE
-"dbplyr","*","base/db","Imports",FALSE
 "dbplyr","*","modules/benchmark","Imports",FALSE
+"dbplyr",">= 2.4.0","base/db","Imports",FALSE
 "devtools","*","models/ed","Suggests",FALSE
 "doParallel","*","modules/data.atmosphere","Suggests",FALSE
 "doParallel","*","modules/data.remote","Imports",FALSE
 "doSNOW","*","base/remote","Suggests",FALSE
 "dplR","*","modules/data.land","Imports",FALSE
-"dplyr","*","base/db","Imports",FALSE
 "dplyr","*","base/qaqc","Imports",FALSE
 "dplyr","*","base/remote","Imports",FALSE
 "dplyr","*","base/utils","Imports",FALSE
@@ -62,6 +61,7 @@
 "dplyr","*","modules/data.land","Imports",FALSE
 "dplyr","*","modules/data.remote","Suggests",FALSE
 "dplyr","*","modules/uncertainty","Imports",FALSE
+"dplyr",">= 1.1.2","base/db","Imports",FALSE
 "ellipse","*","modules/assim.batch","Imports",FALSE
 "emdbook","*","modules/assim.sequential","Suggests",FALSE
 "foreach","*","base/remote","Imports",FALSE
@@ -401,7 +401,6 @@
 "PEcAn.utils","*","modules/data.land","Imports",TRUE
 "PEcAn.utils","*","modules/data.remote","Imports",TRUE
 "PEcAn.utils","*","modules/meta.analysis","Imports",TRUE
-"PEcAn.utils","*","modules/priors","Imports",TRUE
 "PEcAn.utils","*","modules/rtm","Suggests",TRUE
 "PEcAn.utils","*","modules/uncertainty","Imports",TRUE
 "PEcAn.utils",">= 1.4.8","models/basgra","Imports",TRUE
@@ -551,7 +550,6 @@
 "stringr",">= 1.1.0","base/visualization","Imports",FALSE
 "stringr",">= 1.1.0","models/ed","Imports",FALSE
 "stringr",">= 1.1.0","modules/data.atmosphere","Imports",FALSE
-"stringr",">= 1.1.0","modules/data.remote","Imports",FALSE
 "suntools","*","modules/data.atmosphere","Imports",FALSE
 "swfscMisc","*","modules/data.land","Imports",FALSE
 "terra","*","modules/data.atmosphere","Imports",FALSE

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/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

@@ -12,7 +12,6 @@
 #' @author Dongchen Zhang
 #' @importFrom magrittr %>%
 #'
-#' @examples
 ERA5_met_process <- function(settings, in.path, out.path, write.db=FALSE, write = TRUE){
   #Initialize the multicore computation.
   if (future::supportsMulticore()) {

modules/data.atmosphere/R/download.FACE.R

@@ -1,8 +1,5 @@
 ##' Download Raw FACE data from the internet
 ##'
-##' @name download.FACE
-##' @title download.FACE
-##' @export
 ##'
 ##' @param sitename sitename
 ##' @param outfolder location where output is stored
@@ -12,8 +9,9 @@
 ##' @param end_date desired end date YYYY-MM-DD
 ##' @param overwrite overwrite existing files? Default is FALSE
 ##' @param ... other inputs
-##' 
+##'
 ##' @author Betsy Cowdery
+##' @export
 download.FACE <- function(sitename, outfolder, start_date, end_date, overwrite = FALSE, method, ...) {
   # download.FACE <-
   # function(data.set,outfolder,pkg,raw.host,start_year,end_year,site.id,dbparams,con){

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

@@ -1,11 +1,25 @@
-##' convert FACE files to CF files
-##' @export
-##' 
-##' @param in.path
-##' @param in.prefix
-##' @param outfolder
-##' @author Elizabeth Cowdery
-
+#' convert FACE files to CF files
+#'
+#' Note: `in.path` and `in.prefix` together must identify exactly one file,
+#'   or this function returns NULL.
+#' Further note that despite its name, `in.prefix` will match anywhere in
+#'   the filename: met2CF.FACE("dir", "a", ...)` will find both `dir/a_b.nc`
+#'   and `dir/b_a.nc`!
+#'
+#' @param in.path directory in which to find inputs (as `*.nc`)
+#' @param in.prefix pattern to match to select a file within `in.path`
+#'
+#' @param outfolder path to write output.
+#'   Should contain the substring "FACE", which will be rewritten to "FACE_a" and "FACE_e"
+#'    for the corresponding treatments.
+#' @param start_date,end_date ignored. Time is taken from the input files.
+#' @param input.id ignored
+#' @param site list[like]. Only components `lat` and `lon` (both in decimal degrees) are currently used
+#' @param format specification of variable names and units in the format returned by `PEcAn.DB::query.format.vars`
+#' @param ... other arguments, currently ignored
+#' @author Elizabeth Cowdery
+#'
+#' @export
 met2CF.FACE <- function(in.path,in.prefix,outfolder,start_date,end_date,input.id,site,format, ...) {
 
   files <- dir(in.path, in.prefix)

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

@@ -1,16 +1,16 @@
 ##' 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
 ##' @param verbose should ouput of function be extra verbose
+##' @param ... other arguments, currently ignored
+##'
 ##' @author Elizabeth Cowdery, Rob Kooper
+##' @export
 met2CF.NARR <- function(in.path, in.prefix, outfolder, start_date, end_date, 
                         overwrite = FALSE, verbose = FALSE, ...) {