Merge pull request #3346 from infotroph/check-on-R4.4.1

fixes for new check errors in R >= 4.4.0
PecanProject · Jul 31, 2024 · b4c3f92 · b4c3f92
2 parents 88a1350 + 8393656
commit b4c3f92
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Showing 114 changed files with 616 additions and 493 deletions.
diff --git a/.github/workflows/ci-weekly.yml b/.github/workflows/ci-weekly.yml
@@ -13,6 +13,7 @@ jobs:
       fail-fast: false
       matrix:
         R:
+          - "4.3"
           - "devel"
     uses: ./.github/workflows/test.yml
     with:
@@ -24,6 +25,7 @@ jobs:
       fail-fast: false
       matrix:
         R:
+          - "4.3"
           - "devel"
     uses: ./.github/workflows/check.yml
     with:
@@ -36,6 +38,7 @@ jobs:
       fail-fast: false
       matrix:
         R:
+          - "4.3"
           - "devel"
     uses: ./.github/workflows/sipnet.yml
     with:

diff --git a/.github/workflows/depends.yml b/.github/workflows/depends.yml
@@ -31,6 +31,7 @@ jobs:
           - "4.1"
           - "4.2"
           - "4.3"
+          - "4.4"
           - "devel"
 
     steps:
@@ -49,11 +50,14 @@ jobs:
 
       # calculate some variables that are used later
       - name: github branch
-        # build Rdevel only on Mondays, others every day (but not twice on Mondays)
+        # build weekly-tested versions only on Mondays, others every day
+        # (but not twice on Mondays)
         if: |
           github.event_name == 'workflow_dispatch' ||
-          (matrix.R != 'devel' && github.event.schedule == '0 0 * * *') ||
-          (matrix.R == 'devel' && github.event.schedule == '30 1 * * 1')
+          (contains(fromJSON('["4.1", "4.2", "4.4"]'), matrix.R)
+            && github.event.schedule == '0 0 * * *') ||
+          (contains(fromJSON('[4.3", "devel"]'), matrix.R)
+            && github.event.schedule == '30 1 * * 1')
         run: |
           BRANCH=${GITHUB_REF##*/}
           echo "GITHUB_BRANCH=${BRANCH}" >> $GITHUB_ENV

diff --git a/base/db/tests/Rcheck_reference.log b/base/db/tests/Rcheck_reference.log
@@ -62,7 +62,8 @@ 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 ... OK
+* checking DESCRIPTION meta-information ... NOTE
+License stub is invalid DCF.
 * 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
@@ -24,6 +24,7 @@ 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
@@ -19,7 +19,8 @@
 * checking whether package ‘PEcAn.remote’ can be installed ... OK
 * checking installed package size ... OK
 * checking package directory ... OK
-* checking DESCRIPTION meta-information ... OK
+* checking DESCRIPTION meta-information ... NOTE
+License stub is invalid DCF.
 * checking top-level files ... OK
 * checking for left-over files ... OK
 * checking index information ... OK

diff --git a/base/settings/R/check.all.settings.R b/base/settings/R/check.all.settings.R
@@ -936,9 +936,10 @@ check.model.settings <- function(settings, dbcon = NULL) {
   return(settings)
 }
 
-#' @title Check Workflow Settings
+#' Check Workflow Settings
 #' @param settings settings file
-#' @export check.workflow.settings
+#' @param dbcon database connection
+#' @export
 check.workflow.settings <- function(settings, dbcon = NULL) {
   # check for workflow defaults
   fixoutdir <- FALSE

diff --git a/base/settings/man/check.workflow.settings.Rd b/base/settings/man/check.workflow.settings.Rd
diff --git a/base/settings/tests/Rcheck_reference.log b/base/settings/tests/Rcheck_reference.log
@@ -73,7 +73,8 @@ 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 ... OK
+* checking DESCRIPTION meta-information ... NOTE
+License stub is invalid DCF.
 * checking top-level files ... NOTE
 Non-standard file/directory found at top level:
   ‘examples’
@@ -140,36 +141,7 @@ 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 code/documentation mismatches ... OK
-* checking Rd \usage sections ... WARNING
-Undocumented arguments in documentation object 'addSecrets'
-  ‘force’
-
-Undocumented arguments in documentation object 'check.model.settings'
-  ‘dbcon’
-
-Undocumented arguments in documentation object 'check.run.settings'
-  ‘dbcon’
-
-Undocumented arguments in documentation object 'check.settings'
-  ‘force’
-
-Undocumented arguments in documentation object 'check.workflow.settings'
-  ‘dbcon’
-
-Undocumented arguments in documentation object 'clean.settings'
-  ‘write’
-
-Undocumented arguments in documentation object 'fix.deprecated.settings'
-  ‘force’
-
-Undocumented arguments in documentation object 'update.settings'
-  ‘force’
-
-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.
-See chapter ‘Writing R documentation files’ in the ‘Writing R
-Extensions’ manual.
+* checking Rd \usage sections ... OK
 * checking Rd contents ... OK
 * checking for unstated dependencies in examples ... OK
 * checking examples ... OK
@@ -179,4 +151,4 @@ Extensions’ manual.
 * checking for detritus in the temp directory ... OK
 * DONE
 
-Status: 5 WARNINGs, 3 NOTEs
+Status: 3 WARNINGs, 2 NOTEs
diff --git a/base/utils/tests/Rcheck_reference.log b/base/utils/tests/Rcheck_reference.log
@@ -71,7 +71,8 @@ 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 ... OK
+* checking DESCRIPTION meta-information ... NOTE
+License stub is invalid DCF.
 * checking top-level files ... OK
 * checking for left-over files ... OK
 * checking index information ... OK

diff --git a/base/visualization/DESCRIPTION b/base/visualization/DESCRIPTION
@@ -38,9 +38,11 @@ Imports:
     stringr(>= 1.1.0)
 Suggests:
     grid,
+    knitr,
     mockery,
     png,
     raster,
+    rmarkdown,
     sp,
     testthat (>= 1.0.2),
     withr
@@ -49,5 +51,6 @@ Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
 Encoding: UTF-8
+VignetteBuilder: knitr
 RoxygenNote: 7.3.2
 Roxygen: list(markdown = TRUE)
diff --git a/base/visualization/R/plots.R b/base/visualization/R/plots.R
@@ -263,7 +263,7 @@ plot_data <- function(trait.data, base.plot = NULL, ymax) {
 ##' 
 ##' @return adds borders to ggplot as a side effect
 ##' @author Rudolf Cardinal
-##' @author \url{ggplot2 google group}{https://groups.google.com/forum/?fromgroups#!topic/ggplot2/-ZjRE2OL8lE}
+##' @author [ggplot2 google group](https://groups.google.com/forum/?fromgroups#!topic/ggplot2/-ZjRE2OL8lE)
 ##' @examples
 ##' \dontrun{
 ##' df = data.frame( x=c(1,2,3), y=c(4,5,6) )

diff --git a/base/visualization/man/theme_border.Rd b/base/visualization/man/theme_border.Rd
diff --git a/base/visualization/tests/Rcheck_reference.log b/base/visualization/tests/Rcheck_reference.log
@@ -71,7 +71,8 @@ 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 ... OK
+* checking DESCRIPTION meta-information ... NOTE
+License stub is invalid DCF.
 * checking top-level files ... OK
 * checking for left-over files ... OK
 * checking index information ... OK

diff --git a/base/visualization/vignettes/usmap.Rmd b/base/visualization/vignettes/usmap.Rmd
@@ -1,7 +1,19 @@
+---
+title: "Maps"
+output: html_vignette
+vignette: >
+   %\VignetteIndexEntry{Maps}
+   %\VignetteEngine{knitr::rmarkdown}
+---
+
+
+
 Map
 ========================================================
 
-```{r}
+(all code chunks are disabled because vignette build was throwing errors. TODO: debug and re-enable.)
+
+```{r,eval=FALSE}
 require(raster)
 require(sp)
 require(ggplot2)
@@ -20,7 +32,7 @@ spplot(spdf)
 
 ### Plot all maps for BETYdb
 
-```{r}
+```{r,eval=FALSE}
 files <- dir("~/dev/bety/local/modelout", pattern="grid.csv", full.names=TRUE)
 yieldfiles <- files[!grepl("evapotranspiration", files)]
 etfiles <- files[grepl("evapotranspiration", files)]
@@ -42,7 +54,7 @@ for(file in etfiles){
 ```
 
 ### Misc additional code
-```{r}
+```{r,eval=FALSE}
 # Make an evenly spaced raster, the same extent as original data
 e <- extent( spdf )
 
@@ -63,7 +75,7 @@ ggplot( NULL ) + geom_raster( data = rdf , aes( x , y , fill = layer ) )
 
 ```
 
-```{r}
+```{r,eval=FALSE}
 # from http://gis.stackexchange.com/a/20052/3218
 require(rgdal)
 proj4string(spdf) <- CRS("+init=epsg:4326")

diff --git a/base/workflow/tests/Rcheck_reference.log b/base/workflow/tests/Rcheck_reference.log
@@ -70,7 +70,7 @@ Author field differs from that derived from Authors@R
 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 top-level files ... OK
 * checking for left-over files ... OK
 * checking index information ... OK

diff --git a/docker/depends/pecan_package_dependencies.csv b/docker/depends/pecan_package_dependencies.csv
@@ -122,6 +122,8 @@
 "jsonlite","*","models/stics","Imports",FALSE
 "jsonlite","*","modules/data.atmosphere","Imports",FALSE
 "jsonlite","*","modules/data.remote","Suggests",FALSE
+"knitr","*","base/visualization","Suggests",FALSE
+"knitr","*","modules/data.atmosphere","Suggests",FALSE
 "knitr",">= 1.42","base/db","Suggests",FALSE
 "knitr",">= 1.42","base/qaqc","Suggests",FALSE
 "knitr",">= 1.42","modules/allometry","Suggests",FALSE
@@ -481,6 +483,7 @@
 "rlang","*","modules/uncertainty","Imports",FALSE
 "rlang",">= 0.2.0","modules/data.atmosphere","Imports",FALSE
 "rlist","*","modules/assim.sequential","Suggests",FALSE
+"rmarkdown","*","base/visualization","Suggests",FALSE
 "rmarkdown",">= 2.19","base/db","Suggests",FALSE
 "rmarkdown",">= 2.19","base/qaqc","Suggests",FALSE
 "rmarkdown",">= 2.19","modules/allometry","Suggests",FALSE

diff --git a/modules/allometry/R/AllomAve.R b/modules/allometry/R/AllomAve.R
@@ -7,16 +7,27 @@
 # http://opensource.ncsa.illinois.edu/license.html
 #-------------------------------------------------------------------------------
 
-#' @title AllomAve
-#' @name  AllomAve
-#' @aliases AllomAve
+#' AllomAve
+#'
+#' Allometry wrapper function that handles loading and subsetting the data,
+#'  fitting the Bayesian models, and generating diagnostic figures. Set up to loop over
+#'   multiple PFTs and components. 
+#'   Writes raw MCMC and PDF of diagnositcs to file and returns table of summary stats.
+#'   
+#' There are two usages of this function. 
+#' When running 'online' (connected to the PEcAn database), pass the database connection,
+#'  con, and the pfts subsection of the PEcAn settings.
+#' When running 'stand alone' pass the pft list mapping species to species codes
+#'  and the file paths to the allometry table and field data (optional)
+#'
 #' @param pfts        pft list from PEcAn settings (if con) OR list of pft spcd's
 #' If the latter, the names within the list are used to identify PFTs
-#' \itemize{
+#' \describe{
 #'   \item{'acronym'}{ - USDA species acronyms (see plants.usda.gov), used with FIELD data (vector)}
 #'   \item{'spcd'}{ - USFS species codes, use with PARM data (vector)}
 #' }
-#' @param components  IDs for allometry components from Jenkins et al 2004 Table 5. Default is stem biomass (6). See data(allom.components)
+#' @param components  IDs for allometry components from Jenkins et al 2004 Table 5.
+#'  Default is stem biomass (6). See data(allom.components)
 #' @param outdir      output directory files are written to. Default is getwd()
 #' @param con         database connection
 #' @param field       path(s) to raw data files
@@ -27,14 +38,6 @@
 #' @param dmax        maximum dbh of interest
 #' @return nested list of parameter summary statistics
 #' @export
-#' @description allometery wrapper function that handles loading and subsetting the data,
-#'  fitting the Bayesian models, and generating diagnostic figures. Set up to loop over
-#'   multiple PFTs and components. 
-#'   Writes raw MCMC and PDF of diagnositcs to file and returns table of summary stats.
-#'   
-#' @details There are two usages of this function. 
-#' When running 'online' (connected to the PEcAn database), pass the database connection, con, and the pfts subsection of the PEcAn settings.
-#' When running 'stand alone' pass the pft list mapping species to species codes and the file paths to the allometry table and field data (optional)
 #' 
 #' @examples 
 #'