diff --git a/Makefile.depends b/Makefile.depends
index 9c1791564d6..9382034864c 100644
--- a/Makefile.depends
+++ b/Makefile.depends
@@ -28,7 +28,7 @@ $(call depends,models/cable): | .install/base/logger .install/base/utils
 $(call depends,models/clm45): | .install/base/logger .install/base/utils
 $(call depends,models/dalec): | .install/base/logger .install/base/remote .install/base/utils
 $(call depends,models/dvmdostem): | .install/base/logger .install/base/utils
-$(call depends,models/ed): | .install/modules/data.atmosphere .install/modules/data.land .install/base/logger .install/base/remote .install/base/settings .install/base/utils
+$(call depends,models/ed): | .install/modules/data.atmosphere .install/modules/data.land .install/base/db .install/base/logger .install/base/remote .install/base/settings .install/base/utils
 $(call depends,models/fates): | .install/base/logger .install/base/remote .install/base/utils
 $(call depends,models/gday): | .install/base/utils .install/base/logger .install/base/remote
 $(call depends,models/jules): | .install/modules/data.atmosphere .install/base/logger .install/base/remote .install/base/utils
diff --git a/models/ed/.Rbuildignore b/models/ed/.Rbuildignore
index cd7512dad26..f6123f26e2b 100644
--- a/models/ed/.Rbuildignore
+++ b/models/ed/.Rbuildignore
@@ -4,3 +4,4 @@
 ^data-raw$
 ^.*\.Rproj$
 ^\.Rproj\.user$
+vignettes/ed_run_data/
diff --git a/models/ed/DESCRIPTION b/models/ed/DESCRIPTION
index e8bc9bcc3d2..311dc1d2abf 100644
--- a/models/ed/DESCRIPTION
+++ b/models/ed/DESCRIPTION
@@ -44,6 +44,7 @@ Imports:
     ncdf4 (>= 1.15),
     PEcAn.data.atmosphere,
     PEcAn.data.land,
+    PEcAn.DB,
     PEcAn.logger,
     PEcAn.remote,
     PEcAn.settings,
diff --git a/models/ed/R/create_veg.R b/models/ed/R/create_veg.R
index fc62d09434d..ea8d434484f 100644
--- a/models/ed/R/create_veg.R
+++ b/models/ed/R/create_veg.R
@@ -70,6 +70,6 @@ create_site <- function(input, check = TRUE) {
 #' @return Modified `data.frame`
 modify_df <- function(input, base) {
   col_names <- colnames(base)
-  out_list <- modifyList(as.list(base), as.list(input))
+  out_list <- utils::modifyList(as.list(base), as.list(input))
   as.data.frame(out_list)[col_names]
 }
diff --git a/models/ed/R/download_edi.R b/models/ed/R/download_edi.R
index 490d91ff530..8559a25541f 100644
--- a/models/ed/R/download_edi.R
+++ b/models/ed/R/download_edi.R
@@ -14,6 +14,6 @@ download_edi <- function(directory) {
   download_link <- "https://files.osf.io/v1/resources/b6umf/providers/osfstorage/5a948ea691b689000fa2a588/?zip="
   target_file <- paste0(directory, ".zip")
   PEcAn.utils::download_file(download_link, target_file)
-  unzip(target_file, exdir = directory)
+  utils::unzip(target_file, exdir = directory)
   invisible(TRUE)
 }
diff --git a/models/ed/R/ed_varlookup.R b/models/ed/R/ed_varlookup.R
index 0f80aeb0718..7ac2c596d95 100644
--- a/models/ed/R/ed_varlookup.R
+++ b/models/ed/R/ed_varlookup.R
@@ -1,5 +1,6 @@
 #' Lookup function for translating commonly used ED variables
 #' returns out list, readvar variables to read from file, expr if any derivation is needed
+#' @param varname character; variable name to read from file
 #' @export
 ed.var <- function(varname) {
   if(varname == "AGB") {
diff --git a/models/ed/R/met2model.ED2.R b/models/ed/R/met2model.ED2.R
index b9d57c4f2b2..70dfa5cd623 100644
--- a/models/ed/R/met2model.ED2.R
+++ b/models/ed/R/met2model.ED2.R
@@ -21,9 +21,12 @@
 #' @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 lst timezone offset to GMT in hours
+#' @param lat latitude; if not provide the function will attempt to discover it in input files
+#' @param lon longitude; if not provide the function will attempt to discover it in input files
 #' @param overwrite should existing files be overwritten
 #' @param verbose should the function be very verbose
 #' @param leap_year Enforce Leap-years? If set to TRUE, will require leap years to have 366 days. If set to false, will require all years to have 365 days. Default = TRUE.
+#' @param ... currently unused
 met2model.ED2 <- function(in.path, in.prefix, outfolder, start_date, end_date, lst = 0, lat = NA,
                           lon = NA, overwrite = FALSE, verbose = FALSE, leap_year = TRUE, ...) {
   
diff --git a/models/ed/R/model2netcdf.ED2.R b/models/ed/R/model2netcdf.ED2.R
index 30aea2a1cf9..fd577de519f 100644
--- a/models/ed/R/model2netcdf.ED2.R
+++ b/models/ed/R/model2netcdf.ED2.R
@@ -783,7 +783,7 @@ put_T_values <-
   model_timestep_s <- length(output_date_vector) / length(out[[1]])
   iter_per_day <- round(1 / model_timestep_s) ## e.g. 48
   ## Create a timesteps vector (e.g. 0.00000000 0.02083333 0.04166667 0.06250000 0.08333333 0.10416667 ...)
-  timesteps <- head(seq(0, 1, by = 1 / iter_per_day), -1)
+  timesteps <- utils::head(seq(0, 1, by = 1 / iter_per_day), -1)
   ## Create a new date vector where each day is repeated by iter_per_day 
   ## (e.g. "2001-07-15" "2001-07-15" "2001-07-15" "2001-07-15" "2001-07-15" ...)
   sub_dates <- rep(output_date_vector, each = iter_per_day)
diff --git a/models/ed/R/modify_ed2in.R b/models/ed/R/modify_ed2in.R
index 06b9907d16a..3cd6a4549f7 100644
--- a/models/ed/R/modify_ed2in.R
+++ b/models/ed/R/modify_ed2in.R
@@ -89,7 +89,7 @@ modify_ed2in <- function(ed2in, ...,
   if (is.null(.dots)) {
     .dots <- list()
   }
-  dots <- modifyList(.dots, list(...))
+  dots <- utils::modifyList(.dots, list(...))
   is_upper <- names(dots) == toupper(names(dots))
   lower_args <- names(dots)[!is_upper]
   if (length(lower_args) > 0) {
@@ -211,7 +211,7 @@ modify_ed2in <- function(ed2in, ...,
     # 3 for HDF5 output, 0 for no output
     on_types <- (valid_types %in% output_types) * 3
     names(on_types) <- names(valid_types)
-    ed2in <- modifyList(ed2in, as.list(on_types))
+    ed2in <- utils::modifyList(ed2in, as.list(on_types))
   }
 
   if (!is.null(output_dir)) {
@@ -249,6 +249,6 @@ modify_ed2in <- function(ed2in, ...,
       )
     }
   }
-  ed2in <- modifyList(ed2in, namelist_args)
+  ed2in <- utils::modifyList(ed2in, namelist_args)
   ed2in
 }
diff --git a/models/ed/R/other.helpers.ED2.R b/models/ed/R/other.helpers.ED2.R
index e04a62d43ed..652c4eb8edc 100644
--- a/models/ed/R/other.helpers.ED2.R
+++ b/models/ed/R/other.helpers.ED2.R
@@ -17,8 +17,11 @@ list.files.nodir <- function(path, ...) {
 
 
 #' Function translating pecan vars to ED vars
+#' @param varnames character; variable names to translate
+#' @export
+#' @examples
 #' var.names <- c("DBH", "AGB", "AbvGrndWood")
-#' @export 
+#' translate_vars_ed(var.names)
 translate_vars_ed <- function(varnames) {
   
   var.list <- add.list <- list()
diff --git a/models/ed/R/read_ed_metheader.R b/models/ed/R/read_ed_metheader.R
index 76522174354..cdc60eafe29 100644
--- a/models/ed/R/read_ed_metheader.R
+++ b/models/ed/R/read_ed_metheader.R
@@ -83,10 +83,10 @@ read_ed_metheader <- function(filename, check = TRUE, check_files = TRUE) {
         PEcAn.logger::logger.warn(msg)
       }
     }
-    metadata <- unlist(read.table(text = sub_file[2]))
+    metadata <- unlist(utils::read.table(text = sub_file[2]))
     names(metadata) <- c("nlon", "nlat", "dx", "dy", "xmin", "ymin")
     nvars <- as.numeric(sub_file[3])
-    variables_raw <- read.table(text = sub_file[4:6], header = TRUE)
+    variables_raw <- utils::read.table(text = sub_file[4:6], header = TRUE)
     variables_raw$value_type <- c("update_frequency", "flag")
     variables_table <- variables_raw %>%
       tidyr::gather("variable", "value", -.data$value_type) %>%
diff --git a/models/ed/R/read_ed_veg.R b/models/ed/R/read_ed_veg.R
index 56e9df2ade5..bea75ec29ea 100644
--- a/models/ed/R/read_ed_veg.R
+++ b/models/ed/R/read_ed_veg.R
@@ -93,7 +93,7 @@ get_latlon <- function(filepath, latlon) {
 #' @return `data.frame` containing
 #' @export
 read_css <- function(filepath, check = TRUE, ...) {
-  css <- read.table(filepath, header = TRUE)
+  css <- utils::read.table(filepath, header = TRUE)
   if (check) {
     check_css(css, ...)
   }
@@ -103,7 +103,7 @@ read_css <- function(filepath, check = TRUE, ...) {
 #' @rdname read_css
 #' @export
 read_pss <- function(filepath, check = TRUE) {
-  pss <- read.table(filepath, header = TRUE)
+  pss <- utils::read.table(filepath, header = TRUE)
   if (check) {
     check_pss(pss)
   }
@@ -116,7 +116,7 @@ read_site <- function(filepath, check = TRUE, ...) {
   top_line <- readLines(filepath, n = 1)
   nsite <- as.numeric(gsub(".*nsite +([[:digit:]]+).*", "\\1", top_line))
   file_format <- as.numeric(gsub(".*file_format +([[:digit:]]+).*", "\\1", top_line))
-  site <- read.table(filepath, header = TRUE, skip = 1)
+  site <- utils::read.table(filepath, header = TRUE, skip = 1)
   attr(site, "nsite") <- nsite
   attr(site, "file_format") <- file_format
   if (check) {
diff --git a/models/ed/R/read_restart.ED2.R b/models/ed/R/read_restart.ED2.R
index eb5f55c1900..f9fc9b18dba 100644
--- a/models/ed/R/read_restart.ED2.R
+++ b/models/ed/R/read_restart.ED2.R
@@ -1,7 +1,12 @@
 #' @title State data assimilation read-restart for ED2
 #'
 #' @author Alexey Shiklomanov, Istem Fer
-#' @inheritParams PEcAn.ModelName::read_restart.ModelName
+#' @param outdir Output directory
+#' @param runid Run ID
+#' @param stop.time Year that is being read
+#' @param settings PEcAn settings object
+#' @param var.names Variable names to be extracted
+#' @param params Any parameters required for state calculations
 #' @examples
 #' \dontrun{
 #'   outdir <- "~/sda-hackathon/outputs"
diff --git a/models/ed/R/run_ed_singularity.R b/models/ed/R/run_ed_singularity.R
index 56c33fe643a..74b69388554 100644
--- a/models/ed/R/run_ed_singularity.R
+++ b/models/ed/R/run_ed_singularity.R
@@ -21,7 +21,7 @@
 #' @param ed2in_path Path to ED2IN file.
 #' @param app Singularity "app" to run. Either "ED" or "EDR".
 #' @param singularity_args Additional arguments to be passed to `singularity run` (before)
-#' @param Additional arguments to [base::system2]
+#' @param ... Additional arguments to [base::system2]
 #' @export
 run_ed_singularity <- function(img_path, ed2in_path,
                                app = "ED",
diff --git a/models/ed/R/veg2model.ED2.R b/models/ed/R/veg2model.ED2.R
index 7eea835ae41..ac7e23d9ba5 100644
--- a/models/ed/R/veg2model.ED2.R
+++ b/models/ed/R/veg2model.ED2.R
@@ -163,7 +163,7 @@ veg2model.ED2 <- function(outfolder, veg_info, start_date, new_site, source, ens
   css$time[is.na(css$time)]     <- start_year
   css$cohort[is.na(css$cohort)] <- 1:sum(is.na(css$cohort))
   css$dbh[is.na(css$dbh)]       <- 1  # assign nominal small dbh to missing
-  density.median                <- median(css$n[which(css$n > 0)])
+  density.median                <- stats::median(css$n[which(css$n > 0)])
   css$n[is.na(css$n) | css$n == 0]    <- density.median
   css$hite <- css$bdead <- css$balive <- css$lai <- 0
     
@@ -177,10 +177,10 @@ veg2model.ED2 <- function(outfolder, veg_info, start_date, new_site, source, ens
   # Write files
   
   # css
-  write.table(css, filenames_full[1], quote = FALSE, row.names = FALSE)
+  utils::write.table(css, filenames_full[1], quote = FALSE, row.names = FALSE)
   
   # pss
-  write.table(pss, filenames_full[2], quote = FALSE, row.names = FALSE)
+  utils::write.table(pss, filenames_full[2], quote = FALSE, row.names = FALSE)
   
   # site
   # hardcoded per fia2ED implemention
diff --git a/models/ed/R/write.configs.ed.R b/models/ed/R/write.configs.ed.R
index 104cdd4f2de..d7303f9a6a1 100644
--- a/models/ed/R/write.configs.ed.R
+++ b/models/ed/R/write.configs.ed.R
@@ -137,7 +137,7 @@ write.config.ED2 <- function(trait.values, settings, run.id, defaults = settings
   ## Edit ED2IN file for runs
   revision <- settings$model$revision
   if (is.null(revision)) {
-    model <- db.query(paste("SELECT * FROM models WHERE id =", settings$model$id), params = settings$database$bety)
+    model <- PEcAn.DB::db.query(paste("SELECT * FROM models WHERE id =", settings$model$id), params = settings$database$bety)
     revision <- model$revision
   }
   revision <- gsub("^r", "", revision)
@@ -255,7 +255,7 @@ write.config.ED2 <- function(trait.values, settings, run.id, defaults = settings
     
     # Overwrite defaults with values from settings$model$ed2in_tags list
     if(!is.null(settings$model$ed2in_tags)){
-      sda_tags <- modifyList(sda_tags, settings$model$ed2in_tags[names(sda_tags)])
+      sda_tags <- utils::modifyList(sda_tags, settings$model$ed2in_tags[names(sda_tags)])
     }
     ed2in.text <- modify_ed2in(ed2in.text, .dots = sda_tags, add_if_missing = TRUE, check_paths = check)
   }
@@ -520,12 +520,12 @@ write.config.xml.ED2 <- function(settings, trait.values, defaults = settings$con
       }
 
       if (grepl("soil", pft)) {
-        data(soil, package = "PEcAn.ED2", envir = environment())
+        utils::data(soil, package = "PEcAn.ED2", envir = environment())
         vals <- as.list(soil)
         names(vals) <- colnames(soil)
 
         converted.trait.values <- convert.samples.ED(trait.values[[i]])
-        vals <- modifyList(vals, converted.trait.values)
+        vals <- utils::modifyList(vals, converted.trait.values)
 
         decompositon.xml <- PEcAn.settings::listToXml(vals, "decomposition")
         xml <- XML::append.xmlNode(xml, decompositon.xml)
@@ -548,14 +548,14 @@ write.config.xml.ED2 <- function(settings, trait.values, defaults = settings$con
         converted.trait.values <- convert.samples.ED(trait.values[[i]])
 
         ## Selectively replace defaults with trait values
-        vals <- modifyList(vals, converted.trait.values)
+        vals <- utils::modifyList(vals, converted.trait.values)
 
         ## Convert settings constants to ED units
         converted.defaults <- convert.samples.ED(defaults[[pft]]$constants)
 
         ## Selectively replace defaults and trait values with constants from settings
         if (!is.null(converted.defaults)){
-          vals <- modifyList(vals, converted.defaults)
+          vals <- utils::modifyList(vals, converted.defaults)
         }
         
         ## Make sure that include_pft is set to 1
diff --git a/models/ed/R/write_ed_veg.R b/models/ed/R/write_ed_veg.R
index d39a27304e3..07a6a6cac0a 100644
--- a/models/ed/R/write_ed_veg.R
+++ b/models/ed/R/write_ed_veg.R
@@ -39,7 +39,7 @@ write_ed_veg <- function(ed_veg, path_prefix) {
 #' @export
 write_css <- function(css, path_prefix, latitude = NULL, longitude = NULL) {
   css_fname <- prepare_ed_veg_filename(path_prefix, ".css", latitude, longitude)
-  write.table(css, css_fname, quote = FALSE, row.names = FALSE)
+  utils::write.table(css, css_fname, quote = FALSE, row.names = FALSE)
   invisible(css_fname)
 }
 
@@ -47,7 +47,7 @@ write_css <- function(css, path_prefix, latitude = NULL, longitude = NULL) {
 #' @export
 write_pss <- function(pss, path_prefix, latitude = NULL, longitude = NULL) {
   pss_fname <- prepare_ed_veg_filename(path_prefix, ".pss", latitude, longitude)
-  write.table(pss, pss_fname, quote = FALSE, row.names = FALSE)
+  utils::write.table(pss, pss_fname, quote = FALSE, row.names = FALSE)
   invisible(pss_fname)
 }
 
@@ -61,7 +61,7 @@ write_site <- function(site, path_prefix, latitude = NULL, longitude = NULL) {
     attr(site, "file_format")
   )
   writeLines(first_line, site_fname)
-  write.table(site, site_fname, quote = FALSE, row.names = FALSE, append = TRUE)
+  utils::write.table(site, site_fname, quote = FALSE, row.names = FALSE, append = TRUE)
   invisible(site_fname)
 }
 
diff --git a/models/ed/R/write_restart.ED2.R b/models/ed/R/write_restart.ED2.R
index ea6e4012499..3a3611ad607 100644
--- a/models/ed/R/write_restart.ED2.R
+++ b/models/ed/R/write_restart.ED2.R
@@ -1,7 +1,18 @@
 #' @title Write ED2 restart file from SDA results
 #' 
+#' @param outdir output directory
+#' @param runid run id
+#' @param start.time Time of current assimilation step
+#' @param stop.time Time of next assimilation step
+#' @param settings pecan settings list
+#' @param new.state Analysis state matrix returned by `sda.enkf`
+#' @param RENAME flag to either rename output file or not
+#' @param new.params optional, additional params to pass `write.configs` that
+#'   are deterministically related to the parameters updated by the analysis
+#' @param inputs new input paths updated by the SDA workflow, will be passed to
+#'   `write.configs`
+#'   
 #' @author Alexey Shiklomanov, Istem Fer
-#' @inheritParams PEcAn.ModelName::write_restart.ModelName
 #' @return TRUE if successful
 #' @export
 write_restart.ED2 <- function(outdir, runid, start.time, stop.time,
diff --git a/models/ed/man/ed.var.Rd b/models/ed/man/ed.var.Rd
index fd79d0e2ba8..c5dc8c304f0 100644
--- a/models/ed/man/ed.var.Rd
+++ b/models/ed/man/ed.var.Rd
@@ -7,6 +7,9 @@ returns out list, readvar variables to read from file, expr if any derivation is
 \usage{
 ed.var(varname)
 }
+\arguments{
+\item{varname}{character; variable name to read from file}
+}
 \description{
 Lookup function for translating commonly used ED variables
 returns out list, readvar variables to read from file, expr if any derivation is needed
diff --git a/models/ed/man/met2model.ED2.Rd b/models/ed/man/met2model.ED2.Rd
index 3ec873ee373..277bf471db7 100644
--- a/models/ed/man/met2model.ED2.Rd
+++ b/models/ed/man/met2model.ED2.Rd
@@ -32,11 +32,17 @@ met2model.ED2(
 
 \item{lst}{timezone offset to GMT in hours}
 
+\item{lat}{latitude; if not provide the function will attempt to discover it in input files}
+
+\item{lon}{longitude; if not provide the function will attempt to discover it in input files}
+
 \item{overwrite}{should existing files be overwritten}
 
 \item{verbose}{should the function be very verbose}
 
 \item{leap_year}{Enforce Leap-years? If set to TRUE, will require leap years to have 366 days. If set to false, will require all years to have 365 days. Default = TRUE.}
+
+\item{...}{currently unused}
 }
 \description{
 If files already exist in 'Outfolder', the default function is NOT to
diff --git a/models/ed/man/run_ed_singularity.Rd b/models/ed/man/run_ed_singularity.Rd
index 45392346391..8cdcc56d240 100644
--- a/models/ed/man/run_ed_singularity.Rd
+++ b/models/ed/man/run_ed_singularity.Rd
@@ -21,7 +21,7 @@ run_ed_singularity(
 
 \item{singularity_args}{Additional arguments to be passed to \verb{singularity run} (before)}
 
-\item{Additional}{arguments to \link[base:system2]{base::system2}}
+\item{...}{Additional arguments to \link[base:system2]{base::system2}}
 }
 \description{
 Uses \link[base:system2]{base::system2} to run ED or EDR via a Singularity container.
diff --git a/models/ed/man/translate_vars_ed.Rd b/models/ed/man/translate_vars_ed.Rd
index c0a2c705888..56ba3237e96 100644
--- a/models/ed/man/translate_vars_ed.Rd
+++ b/models/ed/man/translate_vars_ed.Rd
@@ -2,12 +2,17 @@
 % Please edit documentation in R/other.helpers.ED2.R
 \name{translate_vars_ed}
 \alias{translate_vars_ed}
-\title{Function translating pecan vars to ED vars
-var.names <- c("DBH", "AGB", "AbvGrndWood")}
+\title{Function translating pecan vars to ED vars}
 \usage{
 translate_vars_ed(varnames)
 }
+\arguments{
+\item{varnames}{character; variable names to translate}
+}
 \description{
 Function translating pecan vars to ED vars
+}
+\examples{
 var.names <- c("DBH", "AGB", "AbvGrndWood")
+translate_vars_ed(var.names)
 }
diff --git a/models/ed/man/write_restart.ED2.Rd b/models/ed/man/write_restart.ED2.Rd
index 364ea0a85f0..840b4534ad6 100644
--- a/models/ed/man/write_restart.ED2.Rd
+++ b/models/ed/man/write_restart.ED2.Rd
@@ -17,7 +17,7 @@ write_restart.ED2(
 )
 }
 \arguments{
-\item{outdir}{outout directory}
+\item{outdir}{output directory}
 
 \item{runid}{run id}
 
@@ -31,9 +31,11 @@ write_restart.ED2(
 
 \item{RENAME}{flag to either rename output file or not}
 
-\item{new.params}{optional, additionals params to pass write.configs that are deterministically related to the parameters updated by the analysis}
+\item{new.params}{optional, additional params to pass \code{write.configs} that
+are deterministically related to the parameters updated by the analysis}
 
-\item{inputs}{new input paths updated by the SDA workflow, will be passed to write.configs}
+\item{inputs}{new input paths updated by the SDA workflow, will be passed to
+\code{write.configs}}
 }
 \value{
 TRUE if successful
diff --git a/models/ed/tests/Rcheck_reference.log b/models/ed/tests/Rcheck_reference.log
index 288070b0969..d478d30d2ae 100644
--- a/models/ed/tests/Rcheck_reference.log
+++ b/models/ed/tests/Rcheck_reference.log
@@ -1,81 +1,30 @@
-* using log directory ‘/home/tanishq010/pecan/models/PEcAn.ED2.Rcheck’
-* using R version 4.2.1 (2022-06-23)
-* using platform: x86_64-pc-linux-gnu (64-bit)
+* using log directory ‘/private/var/folders/wr/by_lst2d2fngf67mknmgf4340000gn/T/RtmplbRshU/file7b5043659c65/PEcAn.ED2.Rcheck’
+* using R version 4.2.2 (2022-10-31)
+* using platform: x86_64-apple-darwin17.0 (64-bit)
 * using session charset: UTF-8
-* using options ‘--no-tests --no-manual --as-cran’
+* using options ‘--no-manual --as-cran’
 * checking for file ‘PEcAn.ED2/DESCRIPTION’ ... OK
 * checking extension type ... Package
-* this is package ‘PEcAn.ED2’ version ‘1.7.2’
+* this is package ‘PEcAn.ED2’ version ‘1.7.2.9000’
 * package encoding: UTF-8
-* checking CRAN incoming feasibility ... WARNING
-Maintainer: ‘Mike Dietze <dietze@bu.edu>’
-
-New submission
-
-License components with restrictions and base license permitting such:
-  BSD_3_clause + file LICENSE
-File 'LICENSE':
-  University of Illinois/NCSA Open Source License
-
-  Copyright (c) 2012, University of Illinois, NCSA.  All rights reserved.
-
-  Permission is hereby granted, free of charge, to any person obtaining
-  a copy of this software and associated documentation files (the
-  "Software"), to deal with the Software without restriction, including
-  without limitation the rights to use, copy, modify, merge, publish,
-  distribute, sublicense, and/or sell copies of the Software, and to
-  permit persons to whom the Software is furnished to do so, subject to
-  the following conditions:
-
-  - Redistributions of source code must retain the above copyright
-    notice, this list of conditions and the following disclaimers.
-  - Redistributions in binary form must reproduce the above copyright
-    notice, this list of conditions and the following disclaimers in the
-    documentation and/or other materials provided with the distribution.
-  - Neither the names of University of Illinois, NCSA, nor the names
-    of its contributors may be used to endorse or promote products
-    derived from this Software without specific prior written permission.
-
-  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-  EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
-  MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
-  IN NO EVENT SHALL THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR
-  ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF
-  CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
-  WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE.
-
-Strong dependencies not in mainstream repositories:
-  PEcAn.data.atmosphere, PEcAn.data.land, PEcAn.logger, PEcAn.remote,
-    PEcAn.settings, PEcAn.utils
-
-The Date field is over a month old.
 * checking package namespace information ... OK
-* checking package dependencies ... OK
+* checking package dependencies ... NOTE
+Imports includes 21 non-default packages.
+Importing from so many packages makes the package vulnerable to any of
+them becoming unavailable.  Move as many as possible to Suggests and
+use conditionally.
 * checking if this is a source package ... OK
 * checking if there is a namespace ... OK
 * checking for executable files ... OK
 * checking for hidden files and directories ... OK
 * checking for portable file names ... OK
 * checking for sufficient/correct file permissions ... OK
-* checking serialization versions ... OK
-* checking whether package ‘PEcAn.ED2’ can be installed ... WARNING
-Found the following significant warnings:
-  Note: next used in wrong context: no loop is visible
-See ‘/home/tanishq010/pecan/models/PEcAn.ED2.Rcheck/00install.out’ for details.
-Information on the location(s) of code generating the ‘Note’s can be
-obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
-to ‘yes’.
+* checking whether package ‘PEcAn.ED2’ can be installed ... OK
 * checking installed package size ... OK
 * checking package directory ... OK
 * checking for future file timestamps ... OK
-* checking DESCRIPTION meta-information ... NOTE
-Author field differs from that derived from Authors@R
-  Author:    ‘David LeBauer, Mike Dietze, Xiaohui Feng, Dan Wang, Carl Davidson, Rob Kooper, Shawn Serbin, Alexey Shiklomanov’
-  Authors@R: ‘Mike Dietze [aut, cre], David LeBauer [aut], Xiaohui Feng [aut], Dan Wang [aut], Carl Davidson [aut], Rob Kooper [aut], Shawn Serbin [aut], Alexey Shiklomanov [aut], University of Illinois, NCSA [cph]’
-
-* checking top-level files ... NOTE
-Non-standard files/directories found at top level:
-  ‘Dockerfile’ ‘model_info.json’ ‘scripts’
+* checking DESCRIPTION meta-information ... OK
+* checking top-level files ... OK
 * checking for left-over files ... OK
 * checking index information ... OK
 * checking package subdirectories ... OK
@@ -86,73 +35,14 @@ Non-standard files/directories found at top level:
 * checking whether the package can be unloaded cleanly ... OK
 * checking whether the namespace can be loaded with stated dependencies ... OK
 * checking whether the namespace can be unloaded cleanly ... OK
-* checking loading without being on the library search path ... OK
-* checking use of S3 registration ... OK
-* checking dependencies in R code ... NOTE
-Namespace in Imports field not imported from: ‘tibble’
-  All declared Imports should be used.
+* checking dependencies in R code ... OK
 * checking S3 generic/method consistency ... OK
 * checking replacement functions ... OK
 * checking foreign function calls ... OK
 * checking R code for possible problems ... NOTE
-Warning: <anonymous>: ... may be used in an incorrect context: ‘check_pss(pss, ...)’
-
-download_edi: no visible global function definition for ‘unzip’
-modify_df: no visible global function definition for ‘modifyList’
-modify_ed2in: no visible global function definition for ‘modifyList’
-put_E_values: no visible global function definition for ‘data’
-put_T_values: no visible global function definition for ‘head’
-read_E_files: no visible global function definition for ‘data’
-read_S_files: no visible global function definition for ‘data’
-read_css: no visible global function definition for ‘read.table’
-read_ed_metheader: no visible global function definition for
-  ‘read.table’
-read_pss: no visible global function definition for ‘read.table’
-read_pss: ... may be used in an incorrect context: ‘check_pss(pss,
-  ...)’
-read_site: no visible global function definition for ‘read.table’
-veg2model.ED2: no visible global function definition for ‘data’
-veg2model.ED2: no visible global function definition for ‘median’
-veg2model.ED2: no visible global function definition for ‘write.table’
-write.config.ED2: no visible global function definition for ‘saveXML’
-write.config.ED2: no visible global function definition for ‘db.query’
-write.config.ED2: no visible global function definition for
-  ‘modifyList’
-write.config.xml.ED2: no visible global function definition for ‘data’
-write.config.xml.ED2: no visible global function definition for
-  ‘modifyList’
-write_css: no visible global function definition for ‘write.table’
-write_pss: no visible global function definition for ‘write.table’
-write_site: no visible global function definition for ‘write.table’
-Undefined global functions or variables:
-  data db.query head median modifyList pftmapping read.table saveXML
-  soil unzip value_type write.table
-Consider adding
-  importFrom("stats", "median")
-  importFrom("utils", "data", "head", "modifyList", "read.table",
-             "unzip", "write.table")
-to your NAMESPACE file.
-
 Found the following assignments to the global environment:
 File ‘PEcAn.ED2/R/model2netcdf.ED2.R’:
   assign(x, ed.dat[[x]], envir = .GlobalEnv)
-
-Found the following calls to data() loading into the global environment:
-File ‘PEcAn.ED2/R/model2netcdf.ED2.R’:
-  data(pftmapping, package = "PEcAn.ED2")
-  data(pftmapping, package = "PEcAn.ED2")
-  data(pftmapping, package = "PEcAn.ED2")
-File ‘PEcAn.ED2/R/veg2model.ED2.R’:
-  data(pftmapping, package = "PEcAn.ED2")
-File ‘PEcAn.ED2/R/write.configs.ed.R’:
-  data(list = histfile, package = "PEcAn.ED2")
-  data(list = histfile, package = "PEcAn.ED2")
-  data(pftmapping, package = "PEcAn.ED2")
-  data(soil, package = "PEcAn.ED2")
-See section ‘Good practice’ in ‘?data’.
-
-Warning: <anonymous>: ... may be used in an incorrect context: ‘check_pss(pss, ...)’
-
 * checking Rd files ... OK
 * checking Rd metadata ... OK
 * checking Rd line widths ... OK
@@ -161,41 +51,15 @@ Missing link or links in documentation object 'read_ed_metheader.Rd':
   ‘https://github.com/EDmodel/ED2/wiki/Drivers’
 
 See section 'Cross-references' in the 'Writing R Extensions' manual.
-* checking for missing documentation entries ... WARNING
-Undocumented data sets:
-  ‘history’ ‘history.r46’ ‘history.r81’ ‘history.r82’ ‘history.r85’
-  ‘history.rgit’ ‘pftmapping’ ‘soil’
-All user-level objects in a package should have documentation entries.
-See chapter ‘Writing R documentation files’ in the ‘Writing R
-Extensions’ manual.
+* checking for missing documentation entries ... OK
 * checking for code/documentation mismatches ... OK
 * checking Rd \usage sections ... WARNING
-Undocumented arguments in documentation object 'ed.var'
-  ‘varname’
-
-Undocumented arguments in documentation object 'met2model.ED2'
-  ‘lat’ ‘lon’ ‘...’
-
 Undocumented arguments in documentation object 'modify_ed2in'
   ‘ed2in’
 
-Undocumented arguments in documentation object 'put_T_values'
-  ‘yr’ ‘nc_var’ ‘out’ ‘lat’ ‘lon’ ‘begins’ ‘ends’ ‘...’
-
 Undocumented arguments in documentation object 'remove.config.ED2'
   ‘main.outdir’ ‘settings’
 
-Undocumented arguments in documentation object 'run_ed_singularity'
-  ‘...’
-Documented arguments not in \usage in documentation object 'run_ed_singularity':
-  ‘Additional’
-
-Undocumented arguments in documentation object 'translate_vars_ed'
-  ‘varnames’
-
-Undocumented arguments in documentation object 'write.config.ED2'
-  ‘...’
-
 Functions with \usage entries need to have the appropriate \alias
 entries, and all their arguments documented.
 The \usage entries must correspond to syntactically valid R code.
@@ -205,17 +69,22 @@ Extensions’ manual.
 * checking for unstated dependencies in examples ... OK
 * checking contents of ‘data’ directory ... OK
 * checking data for non-ASCII characters ... OK
+* checking LazyData ... OK
 * checking data for ASCII and uncompressed saves ... OK
+* checking R/sysdata.rda ... OK
 * checking files in ‘vignettes’ ... WARNING
 Files in the 'vignettes' directory but no files in 'inst/doc':
   ‘running_ed_from_R.Rmd’
 Package has no Sweave vignette sources and no VignetteBuilder field.
 * checking examples ... OK
-* checking for unstated dependencies in ‘tests’ ... WARNING
-'::' or ':::' import not declared from: ‘devtools’
-* checking tests ... SKIPPED
+* checking for unstated dependencies in ‘tests’ ... OK
+* checking tests ...
+  Running ‘test_ed_integration.R’
+  Running ‘testthat.R’ OK
 * checking for non-standard things in the check directory ... OK
 * checking for detritus in the temp directory ... OK
 * DONE
 
-Status: 7 WARNINGs, 4 NOTEs
+Status: 3 WARNINGs, 2 NOTEs
+
+