bump roxygen again; all output files are unchanged

Makefile

@@ -46,7 +46,7 @@ ALL_PKGS_D := $(BASE_D) $(MODULES_D) $(MODELS_D)
 
 SETROPTIONS := "options(Ncpus = ${NCPUS})"
 
-EXPECTED_ROXYGEN_VERSION := 7.3.1
+EXPECTED_ROXYGEN_VERSION := 7.3.2
 INSTALLED_ROXYGEN_VERSION := $(shell Rscript \
 	-e "if (requireNamespace('roxygen2', quietly = TRUE)) {" \
 	-e   "cat(as.character(packageVersion('roxygen2')))" \

base/all/DESCRIPTION

@@ -78,4 +78,4 @@ Copyright: Authors
 LazyData: true
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

base/db/DESCRIPTION

@@ -80,4 +80,4 @@ Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

base/logger/DESCRIPTION

@@ -29,5 +29,5 @@ Suggests:
     withr
 License: BSD_3_clause + file LICENSE
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Roxygen: list(markdown = TRUE)

base/qaqc/DESCRIPTION

@@ -37,4 +37,4 @@ LazyData: FALSE
 Encoding: UTF-8
 VignetteBuilder: knitr
 Config/testthat/edition: 3
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

base/remote/DESCRIPTION

@@ -34,4 +34,4 @@ License: BSD_3_clause + file LICENSE
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

base/settings/DESCRIPTION

@@ -28,5 +28,5 @@ Suggests:
     testthat (>= 2.0.0),
     withr
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Roxygen: list(markdown = TRUE)

base/utils/DESCRIPTION

@@ -57,5 +57,5 @@ License: BSD_3_clause + file LICENSE
 Copyright: Authors
 LazyData: true
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Roxygen: list(markdown = TRUE)

base/visualization/DESCRIPTION

@@ -49,5 +49,5 @@ Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Roxygen: list(markdown = TRUE)

base/workflow/DESCRIPTION

@@ -47,4 +47,4 @@ Suggests:
     withr
 Copyright: Authors
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

book_source/02_demos_tutorials_workflows/05_developer_workflows/03_coding_practices/04-roxygen.Rmd

@@ -84,7 +84,7 @@ When it is time for everyone to update to a newer Roxygen, follow the same proce
 * Run `make clean && make document` to be sure Roxygen has been run on all packages.
 * Check the console output for warnings from Roxygen, and fix them as needed. New versions often get pickier about formatting issues that used to be considered minor.
 * Run `./scripts/generate_dependencies.R` to update the version of Roxygen recorded as a Docker dependency.
-* Grep the PEcAn folder for the string `7.3.1` to make sure no references were missed.
+* Grep the PEcAn folder for the string `7.2.3` to make sure no references were missed.
   - e.g. this time I found  a remaining `RoxygenNote: 7.2.3` in models/cable/DESCRIPTION -- Make currently skips cable, so I redocumented it manually.
 * Review all changes.
   - The changes should mostly just consist of updated `RoxygenNote:` lines in all the DESCRIPTION files.

docker/depends/pecan_package_dependencies.csv

@@ -485,48 +485,48 @@
 "rmarkdown",">= 2.19","modules/assim.batch","Suggests",FALSE
 "rmarkdown",">= 2.19","modules/meta.analysis","Suggests",FALSE
 "rmarkdown",">= 2.19","modules/photosynthesis","Suggests",FALSE
-"roxygen2","== 7.3.1","base/all","Roxygen",FALSE
-"roxygen2","== 7.3.1","base/db","Roxygen",FALSE
-"roxygen2","== 7.3.1","base/logger","Roxygen",FALSE
-"roxygen2","== 7.3.1","base/qaqc","Roxygen",FALSE
-"roxygen2","== 7.3.1","base/remote","Roxygen",FALSE
-"roxygen2","== 7.3.1","base/settings","Roxygen",FALSE
-"roxygen2","== 7.3.1","base/utils","Roxygen",FALSE
-"roxygen2","== 7.3.1","base/visualization","Roxygen",FALSE
-"roxygen2","== 7.3.1","base/workflow","Roxygen",FALSE
-"roxygen2","== 7.3.1","models/basgra","Roxygen",FALSE
-"roxygen2","== 7.3.1","models/biocro","Roxygen",FALSE
-"roxygen2","== 7.3.1","models/cable","Roxygen",FALSE
-"roxygen2","== 7.3.1","models/clm45","Roxygen",FALSE
-"roxygen2","== 7.3.1","models/dalec","Roxygen",FALSE
-"roxygen2","== 7.3.1","models/dvmdostem","Roxygen",FALSE
-"roxygen2","== 7.3.1","models/ed","Roxygen",FALSE
-"roxygen2","== 7.3.1","models/fates","Roxygen",FALSE
-"roxygen2","== 7.3.1","models/gday","Roxygen",FALSE
-"roxygen2","== 7.3.1","models/jules","Roxygen",FALSE
-"roxygen2","== 7.3.1","models/ldndc","Roxygen",FALSE
-"roxygen2","== 7.3.1","models/linkages","Roxygen",FALSE
-"roxygen2","== 7.3.1","models/lpjguess","Roxygen",FALSE
-"roxygen2","== 7.3.1","models/maat","Roxygen",FALSE
-"roxygen2","== 7.3.1","models/maespa","Roxygen",FALSE
-"roxygen2","== 7.3.1","models/preles","Roxygen",FALSE
-"roxygen2","== 7.3.1","models/sibcasa","Roxygen",FALSE
-"roxygen2","== 7.3.1","models/sipnet","Roxygen",FALSE
-"roxygen2","== 7.3.1","models/stics","Roxygen",FALSE
-"roxygen2","== 7.3.1","models/template","Roxygen",FALSE
-"roxygen2","== 7.3.1","modules/allometry","Roxygen",FALSE
-"roxygen2","== 7.3.1","modules/assim.batch","Roxygen",FALSE
-"roxygen2","== 7.3.1","modules/assim.sequential","Roxygen",FALSE
-"roxygen2","== 7.3.1","modules/benchmark","Roxygen",FALSE
-"roxygen2","== 7.3.1","modules/data.atmosphere","Roxygen",FALSE
-"roxygen2","== 7.3.1","modules/data.land","Roxygen",FALSE
-"roxygen2","== 7.3.1","modules/data.remote","Roxygen",FALSE
-"roxygen2","== 7.3.1","modules/emulator","Roxygen",FALSE
-"roxygen2","== 7.3.1","modules/meta.analysis","Roxygen",FALSE
-"roxygen2","== 7.3.1","modules/photosynthesis","Roxygen",FALSE
-"roxygen2","== 7.3.1","modules/priors","Roxygen",FALSE
-"roxygen2","== 7.3.1","modules/rtm","Roxygen",FALSE
-"roxygen2","== 7.3.1","modules/uncertainty","Roxygen",FALSE
+"roxygen2","== 7.3.2","base/all","Roxygen",FALSE
+"roxygen2","== 7.3.2","base/db","Roxygen",FALSE
+"roxygen2","== 7.3.2","base/logger","Roxygen",FALSE
+"roxygen2","== 7.3.2","base/qaqc","Roxygen",FALSE
+"roxygen2","== 7.3.2","base/remote","Roxygen",FALSE
+"roxygen2","== 7.3.2","base/settings","Roxygen",FALSE
+"roxygen2","== 7.3.2","base/utils","Roxygen",FALSE
+"roxygen2","== 7.3.2","base/visualization","Roxygen",FALSE
+"roxygen2","== 7.3.2","base/workflow","Roxygen",FALSE
+"roxygen2","== 7.3.2","models/basgra","Roxygen",FALSE
+"roxygen2","== 7.3.2","models/biocro","Roxygen",FALSE
+"roxygen2","== 7.3.2","models/cable","Roxygen",FALSE
+"roxygen2","== 7.3.2","models/clm45","Roxygen",FALSE
+"roxygen2","== 7.3.2","models/dalec","Roxygen",FALSE
+"roxygen2","== 7.3.2","models/dvmdostem","Roxygen",FALSE
+"roxygen2","== 7.3.2","models/ed","Roxygen",FALSE
+"roxygen2","== 7.3.2","models/fates","Roxygen",FALSE
+"roxygen2","== 7.3.2","models/gday","Roxygen",FALSE
+"roxygen2","== 7.3.2","models/jules","Roxygen",FALSE
+"roxygen2","== 7.3.2","models/ldndc","Roxygen",FALSE
+"roxygen2","== 7.3.2","models/linkages","Roxygen",FALSE
+"roxygen2","== 7.3.2","models/lpjguess","Roxygen",FALSE
+"roxygen2","== 7.3.2","models/maat","Roxygen",FALSE
+"roxygen2","== 7.3.2","models/maespa","Roxygen",FALSE
+"roxygen2","== 7.3.2","models/preles","Roxygen",FALSE
+"roxygen2","== 7.3.2","models/sibcasa","Roxygen",FALSE
+"roxygen2","== 7.3.2","models/sipnet","Roxygen",FALSE
+"roxygen2","== 7.3.2","models/stics","Roxygen",FALSE
+"roxygen2","== 7.3.2","models/template","Roxygen",FALSE
+"roxygen2","== 7.3.2","modules/allometry","Roxygen",FALSE
+"roxygen2","== 7.3.2","modules/assim.batch","Roxygen",FALSE
+"roxygen2","== 7.3.2","modules/assim.sequential","Roxygen",FALSE
+"roxygen2","== 7.3.2","modules/benchmark","Roxygen",FALSE
+"roxygen2","== 7.3.2","modules/data.atmosphere","Roxygen",FALSE
+"roxygen2","== 7.3.2","modules/data.land","Roxygen",FALSE
+"roxygen2","== 7.3.2","modules/data.remote","Roxygen",FALSE
+"roxygen2","== 7.3.2","modules/emulator","Roxygen",FALSE
+"roxygen2","== 7.3.2","modules/meta.analysis","Roxygen",FALSE
+"roxygen2","== 7.3.2","modules/photosynthesis","Roxygen",FALSE
+"roxygen2","== 7.3.2","modules/priors","Roxygen",FALSE
+"roxygen2","== 7.3.2","modules/rtm","Roxygen",FALSE
+"roxygen2","== 7.3.2","modules/uncertainty","Roxygen",FALSE
 "RPostgres","*","base/db","Suggests",FALSE
 "RPostgreSQL","*","base/db","Suggests",FALSE
 "RPostgreSQL","*","models/biocro","Suggests",FALSE

models/basgra/DESCRIPTION

@@ -23,4 +23,4 @@ Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

models/biocro/DESCRIPTION

@@ -38,4 +38,4 @@ Copyright: Energy Biosciences Institute, Authors
 LazyLoad: yes
 LazyData: FALSE
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

models/cable/DESCRIPTION

@@ -21,4 +21,4 @@ Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

models/clm45/DESCRIPTION

@@ -25,4 +25,4 @@ Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

models/dalec/DESCRIPTION

@@ -24,4 +24,4 @@ Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

models/dvmdostem/DESCRIPTION

@@ -26,4 +26,4 @@ Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

models/ed/DESCRIPTION

@@ -64,6 +64,6 @@ Copyright: Authors
 LazyLoad: yes
 LazyData: true
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Roxygen: list(markdown = TRUE)
 Config/testthat/edition: 2

models/fates/DESCRIPTION

@@ -29,4 +29,4 @@ Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

models/gday/DESCRIPTION

@@ -26,4 +26,4 @@ Copyright: Authors
 LazyLoad: yes
 LazyData: TRUE
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

models/jules/DESCRIPTION

@@ -24,4 +24,4 @@ Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

models/ldndc/DESCRIPTION

@@ -25,4 +25,4 @@ Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

models/linkages/DESCRIPTION

@@ -30,4 +30,4 @@ Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

models/lpjguess/DESCRIPTION

@@ -26,4 +26,4 @@ Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

models/maat/DESCRIPTION

@@ -26,4 +26,4 @@ Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

models/maespa/DESCRIPTION

@@ -32,4 +32,4 @@ LazyLoad: yes
 LazyData: FALSE
 Require: 
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

models/preles/DESCRIPTION

@@ -35,4 +35,4 @@ Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

models/sibcasa/DESCRIPTION

@@ -25,4 +25,4 @@ License: BSD_3_clause + file LICENSE
 Copyright: Authors
 LazyData: TRUE
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

models/sipnet/DESCRIPTION

@@ -31,4 +31,4 @@ LazyLoad: yes
 LazyData: FALSE
 Encoding: UTF-8
 Require: 
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

models/stics/DESCRIPTION

@@ -30,4 +30,4 @@ Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

models/template/DESCRIPTION

@@ -19,4 +19,4 @@ Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

modules/allometry/DESCRIPTION

@@ -29,5 +29,5 @@ Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 VignetteBuilder: knitr

modules/assim.batch/DESCRIPTION

@@ -57,5 +57,5 @@ Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Roxygen: list(markdown = TRUE)

modules/assim.sequential/DESCRIPTION

@@ -63,4 +63,4 @@ Suggests:
 License: BSD_3_clause + file LICENSE
 Copyright: Authors
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

modules/benchmark/DESCRIPTION

@@ -47,4 +47,4 @@ Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

modules/data.atmosphere/DESCRIPTION

@@ -79,4 +79,4 @@ Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

modules/data.land/DESCRIPTION

@@ -70,4 +70,4 @@ License: BSD_3_clause + file LICENSE
 Copyright: Authors
 LazyData: true
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

modules/data.remote/DESCRIPTION

@@ -55,4 +55,4 @@ Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

modules/emulator/DESCRIPTION

@@ -15,4 +15,4 @@ Description: Implementation of a Gaussian Process model (both likelihood and
     for sampling design and prediction.
 License: BSD_3_clause + file LICENSE
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

modules/meta.analysis/DESCRIPTION

@@ -45,5 +45,5 @@ VignetteBuilder: knitr
 Copyright: Authors
 LazyData: FALSE
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Roxygen: list(markdown = TRUE)

modules/photosynthesis/DESCRIPTION

@@ -39,5 +39,5 @@ Collate:
     Licor.QC.R
     plots.R
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 VignetteBuilder: knitr

modules/priors/DESCRIPTION

@@ -21,4 +21,4 @@ Suggests:
     PEcAn.visualization,
     testthat
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

modules/rtm/DESCRIPTION

@@ -39,4 +39,4 @@ LazyData: FALSE
 Encoding: UTF-8
 VignetteBuilder: knitr
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

modules/uncertainty/DESCRIPTION

@@ -48,4 +48,4 @@ Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2