Merge pull request #3164 from infotroph/roxygen-bump

Bump Roxygen version
PecanProject · May 3, 2023 · 0489271 · 0489271
2 parents 5a5ddf5 + 4bf8332
commit 0489271
Show file tree

Hide file tree

Showing 67 changed files with 125 additions and 203 deletions.
diff --git a/Makefile b/Makefile
@@ -44,8 +44,13 @@ MODELS_D := $(MODELS:%=.doc/%)
 MODULES_D := $(MODULES:%=.doc/%)
 ALL_PKGS_D := $(BASE_D) $(MODULES_D) $(MODELS_D)
 
-SETROPTIONS = "options(Ncpus = ${NCPUS})"
+SETROPTIONS := "options(Ncpus = ${NCPUS})"
 
+EXPECTED_ROXYGEN_VERSION := 7.2.3
+INSTALLED_ROXYGEN_VERSION := $(shell Rscript \
+	-e "if (requireNamespace('roxygen2', quietly = TRUE)) {" \
+	-e   "cat(as.character(packageVersion('roxygen2')))" \
+	-e "}")
 
 ### Macros
 
@@ -76,10 +81,15 @@ test_R_pkg = ./scripts/time.sh "test ${1}" Rscript \
 	-e "stop_on_failure = TRUE," \
 	-e "stop_on_warning = FALSE)" # TODO: Raise bar to stop_on_warning = TRUE when we can
 
-doc_R_pkg = ./scripts/time.sh "document ${1}" Rscript \
-	-e "roxver <- packageVersion('roxygen2')" \
-	-e "if (roxver != '7.1.2') stop('Roxygen2 version is ', roxver, ', but PEcAn package documentation must be built with exactly version 7.1.2')" \
-	-e "devtools::document('"$(strip $(1))"')"
+doc_R_pkg = \
+	$(if \
+		$(filter ${EXPECTED_ROXYGEN_VERSION},${INSTALLED_ROXYGEN_VERSION}), \
+		./scripts/time.sh "document ${1}" \
+			Rscript -e "devtools::document('"$(strip $(1))"')", \
+		$(error Roxygen2 version is ${INSTALLED_ROXYGEN_VERSION}, \
+			but PEcAn package documentation must be built with exactly \
+			version ${EXPECTED_ROXYGEN_VERSION}))
+
 
 depends = .doc/$(1) .install/$(1) .check/$(1) .test/$(1)
 
@@ -131,7 +141,12 @@ clean:
 	echo `date` > $@
 
 .install/roxygen2: | .install .install/devtools
-	+ ./scripts/time.sh "roxygen2 ${1}" Rscript -e ${SETROPTIONS} -e "if(!requireNamespace('roxygen2', quietly = TRUE)) devtools::install_version('roxygen2', '7.1.2')"
+	+ ./scripts/time.sh "roxygen2 ${1}" Rscript -e ${SETROPTIONS} \
+		-e "if (!requireNamespace('roxygen2', quietly = TRUE)" \
+		-e "    || packageVersion('roxygen2') != '7.2.3') {" \
+		-e "  devtools::install_github('r-lib/[email protected]')" \
+		-e "}"
+	$(eval INSTALLED_ROXYGEN_VERSION := 7.2.3)
 	echo `date` > $@
 
 .install/testthat: | .install

diff --git a/base/all/DESCRIPTION b/base/all/DESCRIPTION
@@ -77,4 +77,4 @@ Copyright: Authors
 LazyData: true
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
diff --git a/base/db/DESCRIPTION b/base/db/DESCRIPTION
@@ -87,4 +87,4 @@ Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
 Encoding: UTF-8
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
diff --git a/base/db/man/dbfile.file.Rd b/base/db/man/dbfile.file.Rd
diff --git a/base/logger/DESCRIPTION b/base/logger/DESCRIPTION
@@ -28,5 +28,5 @@ Imports:
 Suggests: testthat
 License: BSD_3_clause + file LICENSE
 Encoding: UTF-8
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
 Roxygen: list(markdown = TRUE)
diff --git a/base/qaqc/DESCRIPTION b/base/qaqc/DESCRIPTION
@@ -46,4 +46,4 @@ LazyData: FALSE
 Encoding: UTF-8
 VignetteBuilder: knitr
 Config/testthat/edition: 3
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
diff --git a/base/remote/DESCRIPTION b/base/remote/DESCRIPTION
@@ -30,4 +30,4 @@ License: BSD_3_clause + file LICENSE
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
diff --git a/base/settings/DESCRIPTION b/base/settings/DESCRIPTION
@@ -28,5 +28,5 @@ Suggests:
     testthat (>= 2.0.0),
     withr
 Encoding: UTF-8
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
 Roxygen: list(markdown = TRUE)
diff --git a/base/settings/man/MultiSettings.Rd b/base/settings/man/MultiSettings.Rd
diff --git a/base/settings/man/SafeList.Rd b/base/settings/man/SafeList.Rd
diff --git a/base/settings/man/Settings.Rd b/base/settings/man/Settings.Rd
diff --git a/base/utils/DESCRIPTION b/base/utils/DESCRIPTION
@@ -56,5 +56,5 @@ License: BSD_3_clause + file LICENSE
 Copyright: Authors
 LazyData: true
 Encoding: UTF-8
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
 Roxygen: list(markdown = TRUE)
diff --git a/base/utils/man/datetime2doy.Rd b/base/utils/man/datetime2doy.Rd
diff --git a/base/utils/man/status.Rd b/base/utils/man/status.Rd
diff --git a/base/visualization/DESCRIPTION b/base/visualization/DESCRIPTION
@@ -51,5 +51,5 @@ Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
 Encoding: UTF-8
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
 Roxygen: list(markdown = TRUE)
diff --git a/base/workflow/DESCRIPTION b/base/workflow/DESCRIPTION
@@ -47,4 +47,4 @@ Suggests:
     mockery
 Copyright: Authors
 Encoding: UTF-8
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
diff --git a/base/workflow/man/start_model_runs.Rd b/base/workflow/man/start_model_runs.Rd
diff --git a/docker/depends/Dockerfile b/docker/depends/Dockerfile
@@ -43,7 +43,7 @@ COPY pecan.depends.R /
 RUN  --mount=type=secret,id=github_token \
   export GITHUB_PAT=`cat /run/secrets/github_token` \
   && Rscript -e "install.packages(c('devtools'))" \
-  && Rscript -e "devtools::install_version('roxygen2', '7.1.2', repos = 'cran.r-project.org')" \
+  && Rscript -e "devtools::install_version('roxygen2', '7.2.3', repos = 'cran.r-project.org')" \
   && R_LIBS_USER='/usr/local/lib/R/site-library' Rscript /pecan.depends.R \
   && rm -rf /tmp/*
 
diff --git a/models/basgra/DESCRIPTION b/models/basgra/DESCRIPTION
@@ -22,4 +22,4 @@ Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
 Encoding: UTF-8
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
diff --git a/models/biocro/DESCRIPTION b/models/biocro/DESCRIPTION
@@ -39,4 +39,4 @@ Copyright: Energy Biosciences Institute, Authors
 LazyLoad: yes
 LazyData: FALSE
 Encoding: UTF-8
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
diff --git a/models/clm45/DESCRIPTION b/models/clm45/DESCRIPTION
@@ -26,4 +26,4 @@ Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
 Encoding: UTF-8
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
diff --git a/models/dalec/DESCRIPTION b/models/dalec/DESCRIPTION
@@ -25,4 +25,4 @@ Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
 Encoding: UTF-8
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
diff --git a/models/dvmdostem/DESCRIPTION b/models/dvmdostem/DESCRIPTION
@@ -27,4 +27,4 @@ Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
 Encoding: UTF-8
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
diff --git a/models/ed/DESCRIPTION b/models/ed/DESCRIPTION
@@ -65,6 +65,6 @@ Copyright: Authors
 LazyLoad: yes
 LazyData: true
 Encoding: UTF-8
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
 Roxygen: list(markdown = TRUE)
 Config/testthat/edition: 2
diff --git a/models/ed/R/read_ed_metheader.R b/models/ed/R/read_ed_metheader.R
@@ -24,18 +24,18 @@
 #'    - `flag` -- Variable flags.
 #'    - `flag_description` -- Description of variable flag
 #'
-#' The formatting of a meteorlogy header file is as follows (from the [ED 
+#' The formatting of a meteorology header file is as follows (from the [ED
 #' GitHub Wiki][https://github.com/EDmodel/ED2/wiki/Drivers]):
 #'
-#'```
-#'<number of file formats>    # Repeat lines below this number of times
-#'<path and prefix of files>
-#'<nlon>, <nlat>, <dx>, <dy>, <xmin>, <ymin>
-#'<number of variables>
-#'<list of variable names>
-#'<list of update frequencies (seconds) or scalar values if flag=4>
-#'<list of variable flags>
-#'```
+#' ```
+#' <number of file formats>    # Repeat lines below this number of times
+#' <path and prefix of files>
+#' <nlon>, <nlat>, <dx>, <dy>, <xmin>, <ymin>
+#' <number of variables>
+#' <list of variable names>
+#' <list of update frequencies (seconds) or scalar values if flag=4>
+#' <list of variable flags>
+#' ```
 #'
 #' The variables in the third row are defined as follows:
 #' @param filename File name (including path) of met driver header file, as 

diff --git a/models/ed/man/read_ed_metheader.Rd b/models/ed/man/read_ed_metheader.Rd
diff --git a/models/ed/man/run_ed_singularity.Rd b/models/ed/man/run_ed_singularity.Rd
diff --git a/models/fates/DESCRIPTION b/models/fates/DESCRIPTION
@@ -30,4 +30,4 @@ Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
 Encoding: UTF-8
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
diff --git a/models/gday/DESCRIPTION b/models/gday/DESCRIPTION
@@ -27,4 +27,4 @@ Copyright: Authors
 LazyLoad: yes
 LazyData: TRUE
 Encoding: UTF-8
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
diff --git a/models/jules/DESCRIPTION b/models/jules/DESCRIPTION
@@ -25,4 +25,4 @@ Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
 Encoding: UTF-8
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
diff --git a/models/ldndc/DESCRIPTION b/models/ldndc/DESCRIPTION
@@ -26,4 +26,4 @@ Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
 Encoding: UTF-8
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
diff --git a/models/linkages/DESCRIPTION b/models/linkages/DESCRIPTION
@@ -31,4 +31,4 @@ Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
 Encoding: UTF-8
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
diff --git a/models/lpjguess/DESCRIPTION b/models/lpjguess/DESCRIPTION
@@ -27,4 +27,4 @@ Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
 Encoding: UTF-8
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
diff --git a/models/maat/DESCRIPTION b/models/maat/DESCRIPTION
@@ -27,4 +27,4 @@ Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
 Encoding: UTF-8
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
diff --git a/models/maespa/DESCRIPTION b/models/maespa/DESCRIPTION
@@ -33,4 +33,4 @@ LazyLoad: yes
 LazyData: FALSE
 Require: 
 Encoding: UTF-8
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
diff --git a/models/preles/DESCRIPTION b/models/preles/DESCRIPTION
@@ -36,4 +36,4 @@ Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
 Encoding: UTF-8
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
diff --git a/models/sibcasa/DESCRIPTION b/models/sibcasa/DESCRIPTION
@@ -26,4 +26,4 @@ License: BSD_3_clause + file LICENSE
 Copyright: Authors
 LazyData: TRUE
 Encoding: UTF-8
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
diff --git a/models/sipnet/DESCRIPTION b/models/sipnet/DESCRIPTION
@@ -32,4 +32,4 @@ LazyLoad: yes
 LazyData: FALSE
 Encoding: UTF-8
 Require: 
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
diff --git a/models/stics/DESCRIPTION b/models/stics/DESCRIPTION
@@ -28,4 +28,4 @@ Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
 Encoding: UTF-8
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3