fixes for new check errors in R >= 4.4.0 (models edition) (#3383)

* fixes for new check errors in R >= 4.4.0 (modules edition) * First steps on updating models for R 4.4 check phrasing (incomplete) * more cleanup in biocro - dockerfile and model_info.json to Rbuildignore - remove badly outdated vignette - ignore complaint about license formatting - lazyData not needed when no data in package - fix broken crosslink * make clm45 pass checks on R 4.4 * make dalec pass checks on R 4.4 * make dvmdostem pass checks on R 4.4 * update PEcAn.ED2 to pass checks on R 4.4 * remove invalid DCF notes resolved by just-merged license change * fates: pass checks on R 4.4 * gday: pass checks on R 4.4 * jules: pass checks on R 4.4 * linkage: pass checks on R 4.4 (+deps regenerate) * lpjguess: pass checks on R 4.4 * partial check fixes for PEcAn.MAAT on R 4.4 * MAAT vignette: provide cached format object * maespa: pass checks on R 4.4 * more deps * preles: pass checks on R 4.4 * sibcasa: pass checks on R 4.4 * sipneet: pass checks on R 4.4 * remove fixed Rd messages from check log
PecanProject · Sep 23, 2024 · 5f7bdfe · 5f7bdfe
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diff --git a/Makefile.depends b/Makefile.depends
@@ -18,13 +18,13 @@ $(call depends,models/fates): | .install/base/logger .install/base/remote .insta
 $(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
 $(call depends,models/ldndc): | .install/base/logger .install/base/remote .install/base/utils .install/modules/data.atmosphere .install/modules/data.land
-$(call depends,models/linkages): | .install/base/logger .install/base/remote .install/base/utils .install/modules/data.atmosphere
+$(call depends,models/linkages): | .install/base/db .install/base/logger .install/base/remote .install/base/utils .install/modules/data.land
 $(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
 $(call depends,models/maespa): | .install/base/logger .install/base/remote .install/base/utils .install/modules/data.atmosphere
 $(call depends,models/preles): | .install/base/logger .install/base/utils .install/modules/data.atmosphere
-$(call depends,models/sibcasa): | .install/base/logger .install/base/utils
-$(call depends,models/sipnet): | .install/base/logger .install/base/remote .install/base/utils .install/modules/data.atmosphere
+$(call depends,models/sibcasa): | .install/base/logger
+$(call depends,models/sipnet): | .install/base/logger .install/base/remote .install/base/utils .install/modules/data.atmosphere .install/modules/data.land
 $(call depends,models/stics): | .install/base/logger .install/base/remote .install/base/settings .install/base/utils
 $(call depends,models/template): | .install/base/db .install/base/logger .install/base/utils
 $(call depends,modules/allometry): | .install/base/db

diff --git a/base/db/tests/Rcheck_reference.log b/base/db/tests/Rcheck_reference.log
@@ -62,8 +62,7 @@ The Date field is over a month old.
 * checking package directory ... OK
 * checking for future file timestamps ... OK
 * checking ‘build’ directory ... OK
-* checking DESCRIPTION meta-information ... NOTE
-License stub is invalid DCF.
+* checking DESCRIPTION meta-information ... OK
 * checking top-level files ... OK
 * checking for left-over files ... OK
 * checking index information ... OK

diff --git a/base/qaqc/tests/Rcheck_reference.log b/base/qaqc/tests/Rcheck_reference.log
@@ -21,10 +21,6 @@
 * checking package directory ... OK
 * checking DESCRIPTION meta-information ... NOTE
 Malformed Description field: should contain one or more complete sentences.
-Authors@R field gives no person with name and roles.
-Authors@R field gives no person with maintainer role, valid email
-address and non-empty name.
-License stub is invalid DCF.
 * checking top-level files ... NOTE
 Non-standard file/directory found at top level:
   ‘README.Rmd’

diff --git a/base/remote/tests/Rcheck_reference.log b/base/remote/tests/Rcheck_reference.log
@@ -19,8 +19,7 @@
 * checking whether package ‘PEcAn.remote’ can be installed ... OK
 * checking installed package size ... OK
 * checking package directory ... OK
-* checking DESCRIPTION meta-information ... NOTE
-License stub is invalid DCF.
+* checking DESCRIPTION meta-information ... OK
 * checking top-level files ... OK
 * checking for left-over files ... OK
 * checking index information ... OK

diff --git a/base/settings/tests/Rcheck_reference.log b/base/settings/tests/Rcheck_reference.log
@@ -73,8 +73,7 @@ The Date field is over a month old.
 * checking installed package size ... OK
 * checking package directory ... OK
 * checking for future file timestamps ... OK
-* checking DESCRIPTION meta-information ... NOTE
-License stub is invalid DCF.
+* checking DESCRIPTION meta-information ... OK
 * checking top-level files ... NOTE
 Non-standard file/directory found at top level:
   ‘examples’

diff --git a/base/visualization/tests/Rcheck_reference.log b/base/visualization/tests/Rcheck_reference.log
@@ -71,8 +71,7 @@ The Date field is over a month old.
 * checking installed package size ... OK
 * checking package directory ... OK
 * checking for future file timestamps ... OK
-* checking DESCRIPTION meta-information ... NOTE
-License stub is invalid DCF.
+* checking DESCRIPTION meta-information ... OK
 * checking top-level files ... OK
 * checking for left-over files ... OK
 * checking index information ... OK

diff --git a/base/workflow/DESCRIPTION b/base/workflow/DESCRIPTION
@@ -17,9 +17,6 @@ Authors@R: c(person("Mike", "Dietze", role = c("aut"),
              person("Shawn", "Serbin", role = c("aut"),
                      email = "[email protected]"),
              person("University of Illinois, NCSA", role = c("cph")))
-Author: David LeBauer, Mike Dietze, Xiaohui Feng, Dan Wang,
-    Mike Dietze, Carl Davidson, Rob Kooper, Shawn Serbin
-Maintainer: David LeBauer <[email protected]>
 Description: The Predictive Ecosystem Carbon Analyzer
     (PEcAn) is a scientific workflow management tool that
     is designed to simplify the management of model

diff --git a/base/workflow/tests/Rcheck_reference.log b/base/workflow/tests/Rcheck_reference.log
@@ -62,15 +62,7 @@ The Date field is over a month old.
 * 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, Mike Dietze, Carl Davidson, Rob Kooper, Shawn Serbin’
-  Authors@R: ‘Mike Dietze [aut], David LeBauer [aut, cre], Xiaohui Feng [aut], Dan Wang [aut], Carl Davidson [aut], Rob Kooper [aut], Shawn Serbin [aut], University of Illinois, NCSA [cph]’
-
-Maintainer field differs from that derived from Authors@R
-  Maintainer: ‘David LeBauer <[email protected]>’
-  Authors@R:  ‘David LeBauer <[email protected]>’
-License stub is invalid DCF.
+* checking DESCRIPTION meta-information ... OK
 * checking top-level files ... OK
 * checking for left-over files ... OK
 * checking index information ... OK

diff --git a/docker/depends/pecan_deps_from_github.txt b/docker/depends/pecan_deps_from_github.txt
@@ -3,6 +3,7 @@ araiho/linkages_package
 chuhousen/amerifluxr
 ebimodeling/[email protected]
 MikkoPeltoniemi/Rpreles
+RemkoDuursma/Maeswrap
 ropensci/geonames
 ropensci/nneo
 SticsRPacks/SticsOnR

diff --git a/docker/depends/pecan_package_dependencies.csv b/docker/depends/pecan_package_dependencies.csv
@@ -49,6 +49,7 @@
 "dplyr","*","models/biocro","Imports",FALSE
 "dplyr","*","models/ed","Imports",FALSE
 "dplyr","*","models/ldndc","Imports",FALSE
+"dplyr","*","models/sipnet","Imports",FALSE
 "dplyr","*","models/stics","Imports",FALSE
 "dplyr","*","modules/assim.sequential","Imports",FALSE
 "dplyr","*","modules/benchmark","Imports",FALSE
@@ -123,6 +124,9 @@
 "jsonlite","*","modules/data.remote","Suggests",FALSE
 "keras3",">= 1.0.0","modules/assim.sequential","Suggests",FALSE
 "knitr","*","base/visualization","Suggests",FALSE
+"knitr","*","models/biocro","Suggests",FALSE
+"knitr","*","models/ed","Suggests",FALSE
+"knitr","*","models/maat","Suggests",FALSE
 "knitr","*","modules/data.atmosphere","Suggests",FALSE
 "knitr","*","modules/priors","Suggests",FALSE
 "knitr",">= 1.42","base/db","Suggests",FALSE
@@ -262,16 +266,17 @@
 "PEcAn.data.atmosphere","*","models/ed","Imports",TRUE
 "PEcAn.data.atmosphere","*","models/jules","Imports",TRUE
 "PEcAn.data.atmosphere","*","models/ldndc","Imports",TRUE
-"PEcAn.data.atmosphere","*","models/linkages","Imports",TRUE
 "PEcAn.data.atmosphere","*","models/maat","Imports",TRUE
 "PEcAn.data.atmosphere","*","models/maespa","Imports",TRUE
 "PEcAn.data.atmosphere","*","models/preles","Imports",TRUE
-"PEcAn.data.atmosphere","*","models/sipnet","Depends",TRUE
+"PEcAn.data.atmosphere","*","models/sipnet","Imports",TRUE
 "PEcAn.data.land","*","base/all","Depends",TRUE
 "PEcAn.data.land","*","base/workflow","Imports",TRUE
 "PEcAn.data.land","*","models/biocro","Imports",TRUE
 "PEcAn.data.land","*","models/ed","Imports",TRUE
 "PEcAn.data.land","*","models/ldndc","Imports",TRUE
+"PEcAn.data.land","*","models/linkages","Imports",TRUE
+"PEcAn.data.land","*","models/sipnet","Imports",TRUE
 "PEcAn.data.land","*","modules/assim.sequential","Suggests",TRUE
 "PEcAn.data.land","*","modules/benchmark","Suggests",TRUE
 "PEcAn.data.remote","*","base/all","Depends",TRUE
@@ -281,6 +286,7 @@
 "PEcAn.DB","*","base/settings","Imports",TRUE
 "PEcAn.DB","*","base/workflow","Imports",TRUE
 "PEcAn.DB","*","models/biocro","Suggests",TRUE
+"PEcAn.DB","*","models/linkages","Imports",TRUE
 "PEcAn.DB","*","models/template","Imports",TRUE
 "PEcAn.DB","*","modules/allometry","Imports",TRUE
 "PEcAn.DB","*","modules/assim.batch","Imports",TRUE
@@ -395,11 +401,10 @@
 "PEcAn.utils","*","models/fates","Imports",TRUE
 "PEcAn.utils","*","models/gday","Depends",TRUE
 "PEcAn.utils","*","models/jules","Imports",TRUE
-"PEcAn.utils","*","models/linkages","Depends",TRUE
+"PEcAn.utils","*","models/linkages","Imports",TRUE
 "PEcAn.utils","*","models/lpjguess","Imports",TRUE
 "PEcAn.utils","*","models/maat","Imports",TRUE
 "PEcAn.utils","*","models/maespa","Imports",TRUE
-"PEcAn.utils","*","models/preles","Depends",TRUE
 "PEcAn.utils","*","models/preles","Imports",TRUE
 "PEcAn.utils","*","models/sipnet","Imports",TRUE
 "PEcAn.utils","*","modules/assim.batch","Imports",TRUE
@@ -416,7 +421,6 @@
 "PEcAn.utils",">= 1.4.8","models/cable","Imports",TRUE
 "PEcAn.utils",">= 1.4.8","models/dvmdostem","Imports",TRUE
 "PEcAn.utils",">= 1.4.8","models/ldndc","Imports",TRUE
-"PEcAn.utils",">= 1.4.8","models/sibcasa","Imports",TRUE
 "PEcAn.utils",">= 1.4.8","models/stics","Imports",TRUE
 "PEcAn.utils",">= 1.4.8","models/template","Imports",TRUE
 "PEcAn.visualization","*","modules/assim.sequential","Suggests",TRUE
@@ -488,6 +492,9 @@
 "rlang",">= 0.2.0","modules/data.atmosphere","Imports",FALSE
 "rlist","*","modules/assim.sequential","Suggests",FALSE
 "rmarkdown","*","base/visualization","Suggests",FALSE
+"rmarkdown","*","models/biocro","Suggests",FALSE
+"rmarkdown","*","models/ed","Suggests",FALSE
+"rmarkdown","*","models/maat","Suggests",FALSE
 "rmarkdown","*","modules/priors","Suggests",FALSE
 "rmarkdown","*","modules/rtm","Suggests",FALSE
 "rmarkdown",">= 2.19","base/db","Suggests",FALSE
@@ -556,6 +563,7 @@
 "sp","*","modules/data.land","Imports",FALSE
 "sp","*","modules/data.remote","Imports",FALSE
 "stats","*","base/qaqc","Imports",FALSE
+"stats","*","models/sipnet","Imports",FALSE
 "stats","*","modules/allometry","Imports",FALSE
 "stats","*","modules/assim.batch","Imports",FALSE
 "stats","*","modules/assim.sequential","Suggests",FALSE
@@ -645,6 +653,7 @@
 "utils","*","base/all","Imports",FALSE
 "utils","*","base/logger","Imports",FALSE
 "utils","*","models/ed","Imports",FALSE
+"utils","*","models/linkages","Imports",FALSE
 "utils","*","modules/allometry","Imports",FALSE
 "utils","*","modules/assim.batch","Imports",FALSE
 "utils","*","modules/assim.sequential","Suggests",FALSE

diff --git a/models/biocro/.Rbuildignore b/models/biocro/.Rbuildignore
@@ -0,0 +1,2 @@
+Dockerfile
+model_info.json
diff --git a/models/biocro/DESCRIPTION b/models/biocro/DESCRIPTION
@@ -27,15 +27,16 @@ Imports:
     rlang
 Suggests:
     BioCro,
+    knitr,
     testthat (>= 2.0.0),
     mockery (>= 0.3.0),
     PEcAn.DB,
+    rmarkdown,
     RPostgreSQL
 Remotes:
     github::ebimodeling/[email protected]
 License: BSD_3_clause + file LICENSE
 Copyright: Energy Biosciences Institute, Authors
-LazyLoad: yes
-LazyData: FALSE
 Encoding: UTF-8
+VignetteBuilder: knitr
 RoxygenNote: 7.3.2
diff --git a/models/biocro/R/get_biocro_defaults.R b/models/biocro/R/get_biocro_defaults.R
@@ -13,7 +13,7 @@ from_bc <- function(dfname){
 #' *_initial_values, *_parameters, *_modules
 #'
 #' @param genus Name of the genus (or really any string BioCro uses as a *_parameters prefix)
-#' @return a list in the format expected by \code{BioCro::\link[BioCro:Gro]{Gro}},
+#' @return a list in the format expected by `BioCro::Gro()`,
 #'   containing four lists named `type`, `initial_values`, `parameters`, and `modules`,
 #'   or NULL if genus not found
 #' @export

diff --git a/models/biocro/R/met2model.BIOCRO.R b/models/biocro/R/met2model.BIOCRO.R
@@ -107,37 +107,37 @@ met2model.BIOCRO <- function(in.path, in.prefix, outfolder, overwrite = FALSE,
 ##' @name cf2biocro
 ##' @title Convert CF-formatted met data to BioCro met
 ##' @param met data.table object  with met for a single site; output from \code{\link{load.cfmet}}
-##' \itemize{
-##' \item {year} {int}
-##' \item {month} {int}
-##' \item {day} {int: day of month (1-31)}
-##' \item {doy} {int: day of year (1-366)}
-##' \item {hour} {int (0-23)}
-##' \item {date} {YYYY-MM-DD HH:MM:SS POSIXct}
-##' \item {wind_speed} {num m/s}
-##' \item {northward_wind}
-##' \item {eastward_wind}
-##' \item {ppfd} {optional; if missing, requires surface_downwelling_shortwave_flux_in_air}
-##' \item {surface_downwelling_shortwave_flux_in_air}
-##' \item {air_pressure (Pa)} {optional; if missing, requires relative_humidity}
-##' \item {specific_humidity} {optional; if missing, requires relative_humidity}
-##' \item {relative_humidity} {optional; if missing, requires air_pressure and specific_humidity}
-##' \item {precipitation_flux}
-##' \item {air_temperature}
+##' \describe{
+##' \item{year}{int}
+##' \item{month}{int}
+##' \item{day}{int: day of month (1-31)}
+##' \item{doy}{int: day of year (1-366)}
+##' \item{hour}{int (0-23)}
+##' \item{date}{YYYY-MM-DD HH:MM:SS POSIXct}
+##' \item{wind_speed}{num m/s}
+##' \item{northward_wind}{}
+##' \item{eastward_wind}{}
+##' \item{ppfd}{optional; if missing, requires surface_downwelling_shortwave_flux_in_air}
+##' \item{surface_downwelling_shortwave_flux_in_air}{}
+##' \item{air_pressure (Pa)}{optional; if missing, requires relative_humidity}
+##' \item{specific_humidity}{optional; if missing, requires relative_humidity}
+##' \item{relative_humidity}{optional; if missing, requires air_pressure and specific_humidity}
+##' \item{precipitation_flux}{}
+##' \item{air_temperature}{}
 ##' }
 ##' @param longitude in degrees east, used for calculating solar noon
 ##' @param zulu2solarnoon logical; if TRUE, convert time from GMT to local solar time.
 ##' @return data.table / data.frame with fields
-##' \itemize{
-##' \item {doy} {day of year}
-##' \item {hr} {hour}
-##' \item {solar} {solar radiation (PPFD)}
-##' \item {temp} {temperature, degrees celsius}
-##' \item {rh} {relative humidity, as fraction (0-1)}
-##' \item {windspeed} {m/s}
-##' \item {precip} {cm/h}
+##' \describe{
+##' \item{doy}{day of year}
+##' \item{hr}{hour}
+##' \item{solar}{solar radiation (PPFD)}
+##' \item{temp}{temperature, degrees celsius}
+##' \item{rh}{relative humidity, as fraction (0-1)}
+##' \item{windspeed}{m/s}
+##' \item{precip}{cm/h}
 ##' }
-##' @export cf2biocro
+##' @export
 ##' @importFrom data.table :=
 ##' @author David LeBauer
 cf2biocro <- function(met, longitude = NULL, zulu2solarnoon = FALSE) {

diff --git a/models/biocro/man/cf2biocro.Rd b/models/biocro/man/cf2biocro.Rd
diff --git a/models/biocro/man/get_biocro_defaults.Rd b/models/biocro/man/get_biocro_defaults.Rd
diff --git a/models/biocro/tests/Rcheck_reference.log b/models/biocro/tests/Rcheck_reference.log
@@ -73,17 +73,8 @@ The Date field is over a month old.
 * 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, Deepak Jaiswal, Christopher Black’
-  Authors@R: ‘David LeBauer [aut, cre], Chris Black [aut], Deepak Jaiswal [aut], University of Illinois, NCSA [cph]’
-
-Maintainer field differs from that derived from Authors@R
-  Maintainer: ‘David LeBauer <[email protected]>’
-  Authors@R:  ‘David LeBauer <[email protected]>’
-
-* checking top-level files ... NOTE
-Non-standard files/directories found at top level:
-  ‘Dockerfile’ ‘model_info.json’
+License stub is invalid DCF.
+* checking top-level files ... OK
 * checking for left-over files ... OK
 * checking index information ... OK
 * checking package subdirectories ... OK

diff --git a/models/biocro/vignettes/C4grass_sa_vd.Rmd b/models/biocro/vignettes/C4grass_sa_vd.Rmd
@@ -1,6 +1,13 @@
+---
+title: "Sensitivity analysis on C4 grass model"
+output: html_vignette
+vignette: >
+  %\VignetteIndexEntry{Sensitivity analysis on C4 grass model}
+  %\VignetteEngine{knitr::rmarkdown}
+---
 
 
-```{r}
+```{r eval=FALSE}
 library(PEcAn.all)
 logger.setQuitOnSevere(FALSE)