From 67bd8a9f35160459149f3eeecdac9d8c80253382 Mon Sep 17 00:00:00 2001 From: Chris Black Date: Mon, 17 Apr 2023 00:13:09 -0700 Subject: [PATCH 01/11] increment stated Roxygen version requirement --- Makefile | 4 ++-- docker/depends/Dockerfile | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/Makefile b/Makefile index 4dcb1581591..1216ac4c05d 100644 --- a/Makefile +++ b/Makefile @@ -78,7 +78,7 @@ test_R_pkg = ./scripts/time.sh "test ${1}" Rscript \ doc_R_pkg = ./scripts/time.sh "document ${1}" Rscript \ -e "roxver <- packageVersion('roxygen2')" \ - -e "if (roxver != '7.1.2') stop('Roxygen2 version is ', roxver, ', but PEcAn package documentation must be built with exactly version 7.1.2')" \ + -e "if (roxver != '7.2.3') stop('Roxygen2 version is ', roxver, ', but PEcAn package documentation must be built with exactly version 7.2.3')" \ -e "devtools::document('"$(strip $(1))"')" depends = .doc/$(1) .install/$(1) .check/$(1) .test/$(1) @@ -131,7 +131,7 @@ 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)) devtools::install_version('roxygen2', '7.2.3')" echo `date` > $@ .install/testthat: | .install diff --git a/docker/depends/Dockerfile b/docker/depends/Dockerfile index ec1691105a1..02905bbf433 100644 --- 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/* From 783e2d1f7bd7672918e45ad198fc1672f3d05577 Mon Sep 17 00:00:00 2001 From: Chris Black Date: Mon, 17 Apr 2023 00:14:27 -0700 Subject: [PATCH 02/11] bump all RoxygenNotes --- base/all/DESCRIPTION | 2 +- base/db/DESCRIPTION | 2 +- base/logger/DESCRIPTION | 2 +- base/qaqc/DESCRIPTION | 2 +- base/remote/DESCRIPTION | 2 +- base/settings/DESCRIPTION | 2 +- base/utils/DESCRIPTION | 2 +- base/visualization/DESCRIPTION | 2 +- base/workflow/DESCRIPTION | 2 +- models/basgra/DESCRIPTION | 2 +- models/biocro/DESCRIPTION | 2 +- models/clm45/DESCRIPTION | 2 +- models/dalec/DESCRIPTION | 2 +- models/dvmdostem/DESCRIPTION | 2 +- models/ed/DESCRIPTION | 2 +- models/fates/DESCRIPTION | 2 +- models/gday/DESCRIPTION | 2 +- models/jules/DESCRIPTION | 2 +- models/ldndc/DESCRIPTION | 2 +- models/linkages/DESCRIPTION | 2 +- models/lpjguess/DESCRIPTION | 2 +- models/maat/DESCRIPTION | 2 +- models/maespa/DESCRIPTION | 2 +- models/preles/DESCRIPTION | 2 +- models/sibcasa/DESCRIPTION | 2 +- models/sipnet/DESCRIPTION | 2 +- models/stics/DESCRIPTION | 2 +- models/template/DESCRIPTION | 2 +- modules/allometry/DESCRIPTION | 2 +- modules/assim.batch/DESCRIPTION | 2 +- modules/assim.sequential/DESCRIPTION | 3 +-- modules/benchmark/DESCRIPTION | 2 +- modules/data.atmosphere/DESCRIPTION | 2 +- modules/data.hydrology/DESCRIPTION | 2 +- modules/data.land/DESCRIPTION | 2 +- modules/data.remote/DESCRIPTION | 2 +- modules/emulator/DESCRIPTION | 2 +- modules/meta.analysis/DESCRIPTION | 2 +- modules/photosynthesis/DESCRIPTION | 2 +- modules/priors/DESCRIPTION | 2 +- modules/rtm/DESCRIPTION | 2 +- modules/uncertainty/DESCRIPTION | 2 +- 42 files changed, 42 insertions(+), 43 deletions(-) diff --git a/base/all/DESCRIPTION b/base/all/DESCRIPTION index 54df5291a10..ed96934ee9a 100644 --- 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 index 54b1d13b46f..0e302137980 100644 --- 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/logger/DESCRIPTION b/base/logger/DESCRIPTION index 2e024fb667a..f5f2ab67b30 100644 --- 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 index 169901f5425..bd0a59fc1ad 100644 --- 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 index 5c715760b82..26449ff1662 100644 --- 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 index a8c16f605a0..009f84fb437 100644 --- 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/utils/DESCRIPTION b/base/utils/DESCRIPTION index bfea5598aff..7a6df1a73c4 100644 --- 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/visualization/DESCRIPTION b/base/visualization/DESCRIPTION index 253465e6832..201bffdada4 100644 --- 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 index f2550d68ffc..123dd17e3d7 100644 --- 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/models/basgra/DESCRIPTION b/models/basgra/DESCRIPTION index 1e76f13c62a..818d5ce141e 100644 --- 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 index fec29a99429..1d7c35ee7fd 100644 --- 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 index f0f72aedb19..6828f45dc5b 100644 --- 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 index ec4b7344129..289f2c7d040 100644 --- 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 index 7bce3f8dab7..07f2674be99 100644 --- 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 index 311dc1d2abf..4a90561ef61 100644 --- a/models/ed/DESCRIPTION +++ b/models/ed/DESCRIPTION @@ -66,6 +66,6 @@ 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/fates/DESCRIPTION b/models/fates/DESCRIPTION index 95b79826b26..baa8dc55b88 100644 --- 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 index d3e96b5c39d..d0ef5827bdc 100644 --- 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 index a45e5694599..ce365a95ce4 100644 --- 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 index 2c4b8da00b3..a6b59412583 100644 --- 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 index 11cd602b4cc..065c53893b1 100644 --- 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 index cfc64db34aa..74b16900031 100644 --- 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 index d5bcbb66663..4919aa251d9 100644 --- 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 index e72723f2bed..f4212c71d11 100644 --- 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 index 05f1ee5f086..69f31e3add3 100644 --- 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 index 9ea383d365a..bd89456a341 100644 --- 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 index 05d9d45bb9a..8b677428f80 100644 --- 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 index a7beb096c53..f37764650f0 100644 --- 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 diff --git a/models/template/DESCRIPTION b/models/template/DESCRIPTION index e35fb3d2b9d..ea29b9eed5a 100644 --- a/models/template/DESCRIPTION +++ b/models/template/DESCRIPTION @@ -20,4 +20,4 @@ Copyright: Authors LazyLoad: yes LazyData: FALSE Encoding: UTF-8 -RoxygenNote: 7.1.2 +RoxygenNote: 7.2.3 diff --git a/modules/allometry/DESCRIPTION b/modules/allometry/DESCRIPTION index 094c49cc341..cf4f31f3d5a 100644 --- a/modules/allometry/DESCRIPTION +++ b/modules/allometry/DESCRIPTION @@ -30,5 +30,5 @@ Copyright: Authors LazyLoad: yes LazyData: FALSE Encoding: UTF-8 -RoxygenNote: 7.1.2 +RoxygenNote: 7.2.3 VignetteBuilder: knitr diff --git a/modules/assim.batch/DESCRIPTION b/modules/assim.batch/DESCRIPTION index 54f6a2f3b60..1e8f9787d2d 100644 --- a/modules/assim.batch/DESCRIPTION +++ b/modules/assim.batch/DESCRIPTION @@ -59,5 +59,5 @@ Copyright: Authors LazyLoad: yes LazyData: FALSE Encoding: UTF-8 -RoxygenNote: 7.1.2 +RoxygenNote: 7.2.3 Roxygen: list(markdown = TRUE) diff --git a/modules/assim.sequential/DESCRIPTION b/modules/assim.sequential/DESCRIPTION index aedee5cf540..7543e985e1d 100644 --- a/modules/assim.sequential/DESCRIPTION +++ b/modules/assim.sequential/DESCRIPTION @@ -58,5 +58,4 @@ Suggests: License: BSD_3_clause + file LICENSE Copyright: Authors Encoding: UTF-8 -RoxygenNote: 7.1.2 - +RoxygenNote: 7.2.3 diff --git a/modules/benchmark/DESCRIPTION b/modules/benchmark/DESCRIPTION index 3e85b4dfee0..2cb70a15458 100644 --- a/modules/benchmark/DESCRIPTION +++ b/modules/benchmark/DESCRIPTION @@ -50,4 +50,4 @@ Copyright: Authors LazyLoad: yes LazyData: FALSE Encoding: UTF-8 -RoxygenNote: 7.1.2 +RoxygenNote: 7.2.3 diff --git a/modules/data.atmosphere/DESCRIPTION b/modules/data.atmosphere/DESCRIPTION index 2200782fdae..623fc43e7ac 100644 --- a/modules/data.atmosphere/DESCRIPTION +++ b/modules/data.atmosphere/DESCRIPTION @@ -76,4 +76,4 @@ Copyright: Authors LazyLoad: yes LazyData: FALSE Encoding: UTF-8 -RoxygenNote: 7.1.2 +RoxygenNote: 7.2.3 diff --git a/modules/data.hydrology/DESCRIPTION b/modules/data.hydrology/DESCRIPTION index 2a7f3b46199..e997e233abc 100644 --- a/modules/data.hydrology/DESCRIPTION +++ b/modules/data.hydrology/DESCRIPTION @@ -34,4 +34,4 @@ LazyLoad: yes LazyData: FALSE Collate: Encoding: UTF-8 -RoxygenNote: 7.1.2 +RoxygenNote: 7.2.3 diff --git a/modules/data.land/DESCRIPTION b/modules/data.land/DESCRIPTION index 64a2ee5e20e..5ec23616b0f 100644 --- a/modules/data.land/DESCRIPTION +++ b/modules/data.land/DESCRIPTION @@ -69,4 +69,4 @@ Copyright: Authors LazyLoad: yes LazyData: FALSE Encoding: UTF-8 -RoxygenNote: 7.1.2 +RoxygenNote: 7.2.3 diff --git a/modules/data.remote/DESCRIPTION b/modules/data.remote/DESCRIPTION index e2faab484cb..68e3ee22e89 100644 --- a/modules/data.remote/DESCRIPTION +++ b/modules/data.remote/DESCRIPTION @@ -45,4 +45,4 @@ Copyright: Authors LazyLoad: yes LazyData: FALSE Encoding: UTF-8 -RoxygenNote: 7.1.2 +RoxygenNote: 7.2.3 diff --git a/modules/emulator/DESCRIPTION b/modules/emulator/DESCRIPTION index eaf824cdf8e..3afdb8df30e 100644 --- a/modules/emulator/DESCRIPTION +++ b/modules/emulator/DESCRIPTION @@ -16,4 +16,4 @@ 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: 7.1.2 +RoxygenNote: 7.2.3 diff --git a/modules/meta.analysis/DESCRIPTION b/modules/meta.analysis/DESCRIPTION index 80edc22120e..82f946af2ae 100644 --- a/modules/meta.analysis/DESCRIPTION +++ b/modules/meta.analysis/DESCRIPTION @@ -46,5 +46,5 @@ VignetteBuilder: knitr Copyright: Authors LazyData: FALSE Encoding: UTF-8 -RoxygenNote: 7.1.2 +RoxygenNote: 7.2.3 Roxygen: list(markdown = TRUE) diff --git a/modules/photosynthesis/DESCRIPTION b/modules/photosynthesis/DESCRIPTION index 3a5432747d8..3088f4ea632 100644 --- a/modules/photosynthesis/DESCRIPTION +++ b/modules/photosynthesis/DESCRIPTION @@ -40,5 +40,5 @@ Collate: Licor.QC.R plots.R Encoding: UTF-8 -RoxygenNote: 7.1.2 +RoxygenNote: 7.2.3 VignetteBuilder: knitr diff --git a/modules/priors/DESCRIPTION b/modules/priors/DESCRIPTION index d45ea0f9e88..cbdd762a0ac 100644 --- a/modules/priors/DESCRIPTION +++ b/modules/priors/DESCRIPTION @@ -23,4 +23,4 @@ Suggests: PEcAn.visualization, testthat Encoding: UTF-8 -RoxygenNote: 7.1.2 +RoxygenNote: 7.2.3 diff --git a/modules/rtm/DESCRIPTION b/modules/rtm/DESCRIPTION index 7d5484639b1..29b7a712221 100644 --- a/modules/rtm/DESCRIPTION +++ b/modules/rtm/DESCRIPTION @@ -40,4 +40,4 @@ LazyData: FALSE Encoding: UTF-8 VignetteBuilder: knitr Roxygen: list(markdown = TRUE) -RoxygenNote: 7.1.2 +RoxygenNote: 7.2.3 diff --git a/modules/uncertainty/DESCRIPTION b/modules/uncertainty/DESCRIPTION index 28bfa110148..ab60b69535b 100644 --- a/modules/uncertainty/DESCRIPTION +++ b/modules/uncertainty/DESCRIPTION @@ -50,4 +50,4 @@ Copyright: Authors LazyLoad: yes LazyData: FALSE Encoding: UTF-8 -RoxygenNote: 7.1.2 +RoxygenNote: 7.2.3 From 7458b83802913b8e8a1f386ec448eb0ac4e64a53 Mon Sep 17 00:00:00 2001 From: Chris Black Date: Mon, 17 Apr 2023 00:20:16 -0700 Subject: [PATCH 03/11] describeIn blocks now get parens on fn names --- base/db/man/dbfile.file.Rd | 6 +++--- base/settings/man/MultiSettings.Rd | 6 +++--- base/settings/man/SafeList.Rd | 6 +++--- base/settings/man/Settings.Rd | 6 +++--- base/utils/man/status.Rd | 10 +++++----- base/workflow/man/start_model_runs.Rd | 4 ++-- modules/rtm/man/spectra.Rd | 4 ++-- 7 files changed, 21 insertions(+), 21 deletions(-) diff --git a/base/db/man/dbfile.file.Rd b/base/db/man/dbfile.file.Rd index 62e904ea68b..fc97bb6af95 100644 --- a/base/db/man/dbfile.file.Rd +++ b/base/db/man/dbfile.file.Rd @@ -31,11 +31,11 @@ If none is found, both will return NA. } \section{Functions}{ \itemize{ -\item \code{dbfile.file}: Return full path to file from the dbfiles table +\item \code{dbfile.file()}: Return full path to file from the dbfiles table -\item \code{dbfile.id}: Return id to container type given a filename -}} +\item \code{dbfile.id()}: Return id to container type given a filename +}} \examples{ \dontrun{ dbfile.file('Input', 7, dbcon) diff --git a/base/settings/man/MultiSettings.Rd b/base/settings/man/MultiSettings.Rd index 59eebd08349..9adf40afcc1 100644 --- a/base/settings/man/MultiSettings.Rd +++ b/base/settings/man/MultiSettings.Rd @@ -25,11 +25,11 @@ Create a PEcAn MultiSettings object } \section{Functions}{ \itemize{ -\item \code{as.MultiSettings}: coerce an existing object to MultiSettings +\item \code{as.MultiSettings()}: coerce an existing object to MultiSettings -\item \code{is.MultiSettings}: test if an object is a MultiSettings -}} +\item \code{is.MultiSettings()}: test if an object is a MultiSettings +}} \author{ Ryan Kelly } diff --git a/base/settings/man/SafeList.Rd b/base/settings/man/SafeList.Rd index 147c842f661..fc5a0b865b5 100644 --- a/base/settings/man/SafeList.Rd +++ b/base/settings/man/SafeList.Rd @@ -41,11 +41,11 @@ unchanged } \section{Functions}{ \itemize{ -\item \code{as.SafeList}: Coerce an object to SafeList. +\item \code{as.SafeList()}: Coerce an object to SafeList. -\item \code{is.SafeList}: Test if object is already a SafeList. -}} +\item \code{is.SafeList()}: Test if object is already a SafeList. +}} \author{ Ryan Kelly } diff --git a/base/settings/man/Settings.Rd b/base/settings/man/Settings.Rd index 702c01a4b89..b3bf0d667ea 100644 --- a/base/settings/man/Settings.Rd +++ b/base/settings/man/Settings.Rd @@ -26,11 +26,11 @@ Create a PEcAn Settings object } \section{Functions}{ \itemize{ -\item \code{as.Settings}: coerce an object to Settings +\item \code{as.Settings()}: coerce an object to Settings -\item \code{is.Settings}: test if object is already a Settings -}} +\item \code{is.Settings()}: test if object is already a Settings +}} \author{ Ryan Kelly } diff --git a/base/utils/man/status.Rd b/base/utils/man/status.Rd index b565592d774..5e5aace2ca3 100644 --- a/base/utils/man/status.Rd +++ b/base/utils/man/status.Rd @@ -50,15 +50,15 @@ print to the console and \code{status.check} will simply return 0. } \section{Functions}{ \itemize{ -\item \code{status.start}: Record module start time +\item \code{status.start()}: Record module start time -\item \code{status.end}: Record module completion time and status +\item \code{status.end()}: Record module completion time and status -\item \code{status.skip}: Record that module was skipped +\item \code{status.skip()}: Record that module was skipped -\item \code{status.check}: Look up module status from file -}} +\item \code{status.check()}: Look up module status from file +}} \author{ Rob Kooper } diff --git a/base/workflow/man/start_model_runs.Rd b/base/workflow/man/start_model_runs.Rd index 608fa8f19da..a1c171073bb 100644 --- a/base/workflow/man/start_model_runs.Rd +++ b/base/workflow/man/start_model_runs.Rd @@ -21,10 +21,10 @@ Start selected ecosystem model runs within PEcAn workflow } \section{Functions}{ \itemize{ -\item \code{runModule_start_model_runs}: A lightweight wrapper around `start_model_runs` that takes `write` from +\item \code{runModule_start_model_runs()}: A lightweight wrapper around `start_model_runs` that takes `write` from `settings` instead of as a separate argument. -}} +}} \examples{ \dontrun{ start_model_runs(settings) diff --git a/modules/rtm/man/spectra.Rd b/modules/rtm/man/spectra.Rd index 6a52f2e9c81..8d461ef3e6d 100644 --- a/modules/rtm/man/spectra.Rd +++ b/modules/rtm/man/spectra.Rd @@ -19,6 +19,6 @@ Spectra S3 class } \section{Functions}{ \itemize{ -\item \code{is_spectra}: Test if object is class \code{spectra} -}} +\item \code{is_spectra()}: Test if object is class \code{spectra} +}} From 408c2b8204fa1afeaecf1676ec41d0d1f4ba0bd3 Mon Sep 17 00:00:00 2001 From: Chris Black Date: Mon, 17 Apr 2023 00:22:49 -0700 Subject: [PATCH 04/11] combined authors are now deduplicated --- base/db/man/dbfile.file.Rd | 2 -- base/utils/man/datetime2doy.Rd | 2 -- modules/assim.sequential/man/sda.enkf.Rd | 2 -- modules/data.atmosphere/man/par2ppfd.Rd | 2 -- modules/uncertainty/man/spline.ensemble.Rd | 2 -- 5 files changed, 10 deletions(-) diff --git a/base/db/man/dbfile.file.Rd b/base/db/man/dbfile.file.Rd index fc97bb6af95..1c648089769 100644 --- a/base/db/man/dbfile.file.Rd +++ b/base/db/man/dbfile.file.Rd @@ -45,7 +45,5 @@ If none is found, both will return NA. } } \author{ -Rob Kooper - Rob Kooper } diff --git a/base/utils/man/datetime2doy.Rd b/base/utils/man/datetime2doy.Rd index 99910043650..afb22dc51f3 100644 --- a/base/utils/man/datetime2doy.Rd +++ b/base/utils/man/datetime2doy.Rd @@ -34,7 +34,5 @@ cf2doy(5, "days since 2010-01-01") # 6 cf2doy(5, "days since 2010-01-01") # 6 } \author{ -Alexey Shiklomanov - Alexey Shiklomanov } diff --git a/modules/assim.sequential/man/sda.enkf.Rd b/modules/assim.sequential/man/sda.enkf.Rd index 059e140fad2..19cd926194f 100644 --- a/modules/assim.sequential/man/sda.enkf.Rd +++ b/modules/assim.sequential/man/sda.enkf.Rd @@ -55,7 +55,5 @@ State Variable Data Assimilation: Ensemble Kalman Filter State Variable Data Assimilation: Ensemble Kalman Filter and Generalized ensemble filter } \author{ -Michael Dietze and Ann Raiho \email{dietze@bu.edu} - Michael Dietze and Ann Raiho \email{dietze@bu.edu} } diff --git a/modules/data.atmosphere/man/par2ppfd.Rd b/modules/data.atmosphere/man/par2ppfd.Rd index 0dc93a064f2..38fb46561a8 100644 --- a/modules/data.atmosphere/man/par2ppfd.Rd +++ b/modules/data.atmosphere/man/par2ppfd.Rd @@ -23,7 +23,5 @@ PPFD = PAR * (J/m2/s) * (1 mol / 2.35e5 J) 2.35e5 J / mol is the energy content of solar radiation in the PAR waveband } \author{ -David LeBauer - David LeBauer } diff --git a/modules/uncertainty/man/spline.ensemble.Rd b/modules/uncertainty/man/spline.ensemble.Rd index 0827106a184..cf6eaebc4be 100644 --- a/modules/uncertainty/man/spline.ensemble.Rd +++ b/modules/uncertainty/man/spline.ensemble.Rd @@ -20,7 +20,5 @@ spline estimate of \eqn{f(\phi)} for use in estimating closure term associated w spline approximation } \author{ -David LeBauer - David LeBauer } From 01182c577a2d0b2eedba9be1b9b2099234775741 Mon Sep 17 00:00:00 2001 From: Chris Black Date: Mon, 17 Apr 2023 00:25:17 -0700 Subject: [PATCH 05/11] jointly documented params are now inherited as a set --- modules/data.atmosphere/man/download.MERRA.Rd | 5 +---- modules/uncertainty/man/sensitivity.filename.Rd | 4 +--- 2 files changed, 2 insertions(+), 7 deletions(-) diff --git a/modules/data.atmosphere/man/download.MERRA.Rd b/modules/data.atmosphere/man/download.MERRA.Rd index 2185211b288..208de0bf294 100644 --- a/modules/data.atmosphere/man/download.MERRA.Rd +++ b/modules/data.atmosphere/man/download.MERRA.Rd @@ -18,10 +18,7 @@ download.MERRA( \arguments{ \item{outfolder}{Directory where results should be written} -\item{start_date}{Range of years to retrieve. Format is YYYY-MM-DD, -but only the year portion is used and the resulting files always contain a full year of data.} - -\item{end_date}{Range of years to retrieve. Format is YYYY-MM-DD, +\item{start_date, end_date}{Range of years to retrieve. Format is YYYY-MM-DD, but only the year portion is used and the resulting files always contain a full year of data.} \item{lat.in}{site latitude in decimal degrees} diff --git a/modules/uncertainty/man/sensitivity.filename.Rd b/modules/uncertainty/man/sensitivity.filename.Rd index f65939c0242..a73e837fd9d 100644 --- a/modules/uncertainty/man/sensitivity.filename.Rd +++ b/modules/uncertainty/man/sensitivity.filename.Rd @@ -33,9 +33,7 @@ PFTs in run are used and does not add them to the filename} \item{variable}{variable(s) included in the ensemble.} -\item{start.year}{first and last year simulated.} - -\item{end.year}{first and last year simulated.} +\item{start.year, end.year}{first and last year simulated.} } \value{ a filename From 8a8bc27fc7829d6ca850505caf5a231272cb84e2 Mon Sep 17 00:00:00 2001 From: Chris Black Date: Sun, 23 Apr 2023 00:55:37 -0700 Subject: [PATCH 06/11] linebreak changes --- modules/assim.sequential/man/sda.enkf.Rd | 4 ++-- modules/rtm/man/setup_edr.Rd | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/modules/assim.sequential/man/sda.enkf.Rd b/modules/assim.sequential/man/sda.enkf.Rd index 19cd926194f..d2bbe2cca2f 100644 --- a/modules/assim.sequential/man/sda.enkf.Rd +++ b/modules/assim.sequential/man/sda.enkf.Rd @@ -21,8 +21,8 @@ sda.enkf( obs.cov, Q = NULL, restart = NULL, - control = list(trace = TRUE, interactivePlot = TRUE, TimeseriesPlot = TRUE, BiasPlot - = FALSE, plot.title = NULL, debug = FALSE, pause = FALSE), + control = list(trace = TRUE, interactivePlot = TRUE, TimeseriesPlot = TRUE, BiasPlot = + FALSE, plot.title = NULL, debug = FALSE, pause = FALSE), ... ) } diff --git a/modules/rtm/man/setup_edr.Rd b/modules/rtm/man/setup_edr.Rd index d01da52fac0..0e10137816d 100644 --- a/modules/rtm/man/setup_edr.Rd +++ b/modules/rtm/man/setup_edr.Rd @@ -7,8 +7,8 @@ setup_edr( ed2in, output_dir, - datetime = ISOdatetime(ed2in[["IYEARA"]], ed2in[["IMONTHA"]], ed2in[["IDATEA"]], 12, - 0, 0, tz = "UTC"), + datetime = ISOdatetime(ed2in[["IYEARA"]], ed2in[["IMONTHA"]], ed2in[["IDATEA"]], 12, 0, + 0, tz = "UTC"), ... ) } From 2e0edff2375d47a67e25e9fc462b4e06ba93eab0 Mon Sep 17 00:00:00 2001 From: Chris Black Date: Sun, 23 Apr 2023 00:58:44 -0700 Subject: [PATCH 07/11] code chunks are now wrapped in a div in html mode plus fixed some typos I noticed while understanding what was going on --- models/ed/R/read_ed_metheader.R | 20 ++++++++++---------- models/ed/man/read_ed_metheader.Rd | 6 ++++-- models/ed/man/run_ed_singularity.Rd | 6 ++++-- 3 files changed, 18 insertions(+), 14 deletions(-) diff --git a/models/ed/R/read_ed_metheader.R b/models/ed/R/read_ed_metheader.R index cdc60eafe29..bcc285a2d3d 100644 --- 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]): #' -#'``` -#' # Repeat lines below this number of times -#' -#', , , , , -#' -#' -#' -#' -#'``` +#' ``` +#' # Repeat lines below this number of times +#' +#' , , , , , +#' +#' +#' +#' +#' ``` #' #' 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 index 832c2d3192d..c35941ddc0a 100644 --- a/models/ed/man/read_ed_metheader.Rd +++ b/models/ed/man/read_ed_metheader.Rd @@ -48,14 +48,16 @@ Starred columns are required for writing. This table is left joined with } } -The formatting of a meteorlogy header file is as follows (from the \link[=https://github.com/EDmodel/ED2/wiki/Drivers]{ED GitHub Wiki}):\preformatted{ # Repeat lines below this number of times +The formatting of a meteorology header file is as follows (from the \link[=https://github.com/EDmodel/ED2/wiki/Drivers]{ED GitHub Wiki}): + +\if{html}{\out{
}}\preformatted{ # Repeat lines below this number of times , , , , , -} +}\if{html}{\out{
}} The variables in the third row are defined as follows: } diff --git a/models/ed/man/run_ed_singularity.Rd b/models/ed/man/run_ed_singularity.Rd index 8cdcc56d240..97e31b103ca 100644 --- a/models/ed/man/run_ed_singularity.Rd +++ b/models/ed/man/run_ed_singularity.Rd @@ -29,9 +29,11 @@ Uses \link[base:system2]{base::system2} to run ED or EDR via a Singularity conta \details{ On some systems, to run Singularity properly, you will need to bind additional paths. To do this, pass the arguments as a character vector to -\code{singularity_args}. For instance:\preformatted{bindpaths <- c("/scratch", "/data") +\code{singularity_args}. For instance: + +\if{html}{\out{
}}\preformatted{bindpaths <- c("/scratch", "/data") run_ed_singularity(..., singularity_args = paste("--bind", bindpaths)) -} +}\if{html}{\out{
}} By default, \link[base:system2]{base::system2} prints the output to the console. To store standard ED output in a variable as a character vector, set \code{stdout = TRUE}. From 48124b7684845f33cfd204de533c87de0fc8edbb Mon Sep 17 00:00:00 2001 From: Chris Black Date: Sat, 29 Apr 2023 15:33:46 -0700 Subject: [PATCH 08/11] Cannot importFrom these params anymore Why not? Because roxygen2 has changed behavior and now treats params documented together (e.g. "@param x,y") as a set, and only imports them if they are an identical set in the importing function. Since `base::[` documents `i,j,...` as one set and `[.spectra` uses only i,j, we now have to define them ourselves instead of importing. --- modules/rtm/R/select.spectra.R | 7 +++- modules/rtm/man/sub-.spectra.Rd | 54 ++------------------------ modules/rtm/man/sub-sub-.spectra.Rd | 24 +----------- modules/rtm/man/sub-subset-.spectra.Rd | 24 +----------- 4 files changed, 14 insertions(+), 95 deletions(-) diff --git a/modules/rtm/R/select.spectra.R b/modules/rtm/R/select.spectra.R index 9fd600136e2..c2c4d6b2cdf 100644 --- a/modules/rtm/R/select.spectra.R +++ b/modules/rtm/R/select.spectra.R @@ -1,7 +1,10 @@ #' Select spectra #' #' @inheritParams wavelengths -#' @inheritParams base::"[" +#' @param i,j indices specifying elements to extract or replace. +#' See [`base::Extract`] for details. +#' @param drop Coerce result to the lowest dimension possible? +#' See [base::drop()] for details. #' @export "[.spectra" <- function(spectra, i, j, drop = FALSE) { if (missing(i)) { @@ -20,6 +23,8 @@ #' #' @inheritParams [.spectra #' @param wavelength Wavelength vector to select +#' @param j index specifying elements to extract or replace. +#' See [`base::Extract`] for details. #' @export "[[.spectra" <- function(spectra, wavelength, j) { spec_wl <- wavelengths(spectra) diff --git a/modules/rtm/man/sub-.spectra.Rd b/modules/rtm/man/sub-.spectra.Rd index 6200b4301b2..68364b13da7 100644 --- a/modules/rtm/man/sub-.spectra.Rd +++ b/modules/rtm/man/sub-.spectra.Rd @@ -9,57 +9,11 @@ \arguments{ \item{spectra}{Object of class \code{spectra}} -\item{i}{ - indices specifying elements to extract or replace. Indices are - \code{numeric} or \code{character} vectors or empty (missing) or - \code{NULL}. Numeric values are coerced to integer as by - \code{\link[base]{as.integer}} (and hence truncated towards zero). - Character vectors will be matched to the \code{\link[base]{names}} of the - object (or for matrices/arrays, the \code{\link[base]{dimnames}}): - see \sQuote{Character indices} below for further details. +\item{i, j}{indices specifying elements to extract or replace. +See \code{\link[base:Extract]{base::Extract}} for details.} - For \code{[}-indexing only: \code{i}, \code{j}, \code{\dots} can be - logical vectors, indicating elements/slices to select. Such vectors - are recycled if necessary to match the corresponding extent. - \code{i}, \code{j}, \code{\dots} can also be negative integers, - indicating elements/slices to leave out of the selection. - - When indexing arrays by \code{[} a single argument \code{i} can be a - matrix with as many columns as there are dimensions of \code{x}; the - result is then a vector with elements corresponding to the sets of - indices in each row of \code{i}. - - An index value of \code{NULL} is treated as if it were \code{integer(0)}. - } - -\item{j}{ - indices specifying elements to extract or replace. Indices are - \code{numeric} or \code{character} vectors or empty (missing) or - \code{NULL}. Numeric values are coerced to integer as by - \code{\link[base]{as.integer}} (and hence truncated towards zero). - Character vectors will be matched to the \code{\link[base]{names}} of the - object (or for matrices/arrays, the \code{\link[base]{dimnames}}): - see \sQuote{Character indices} below for further details. - - For \code{[}-indexing only: \code{i}, \code{j}, \code{\dots} can be - logical vectors, indicating elements/slices to select. Such vectors - are recycled if necessary to match the corresponding extent. - \code{i}, \code{j}, \code{\dots} can also be negative integers, - indicating elements/slices to leave out of the selection. - - When indexing arrays by \code{[} a single argument \code{i} can be a - matrix with as many columns as there are dimensions of \code{x}; the - result is then a vector with elements corresponding to the sets of - indices in each row of \code{i}. - - An index value of \code{NULL} is treated as if it were \code{integer(0)}. - } - -\item{drop}{For matrices and arrays. If \code{TRUE} the result is - coerced to the lowest possible dimension (see the examples). This - only works for extracting elements, not for the replacement. See - \code{\link[base]{drop}} for further details. - } +\item{drop}{Coerce result to the lowest dimension possible? +See \code{\link[base:drop]{base::drop()}} for details.} } \description{ Select spectra diff --git a/modules/rtm/man/sub-sub-.spectra.Rd b/modules/rtm/man/sub-sub-.spectra.Rd index b2d77eff43e..38134e2c924 100644 --- a/modules/rtm/man/sub-sub-.spectra.Rd +++ b/modules/rtm/man/sub-sub-.spectra.Rd @@ -11,28 +11,8 @@ \item{wavelength}{Wavelength vector to select} -\item{j}{ - indices specifying elements to extract or replace. Indices are - \code{numeric} or \code{character} vectors or empty (missing) or - \code{NULL}. Numeric values are coerced to integer as by - \code{\link[base]{as.integer}} (and hence truncated towards zero). - Character vectors will be matched to the \code{\link[base]{names}} of the - object (or for matrices/arrays, the \code{\link[base]{dimnames}}): - see \sQuote{Character indices} below for further details. - - For \code{[}-indexing only: \code{i}, \code{j}, \code{\dots} can be - logical vectors, indicating elements/slices to select. Such vectors - are recycled if necessary to match the corresponding extent. - \code{i}, \code{j}, \code{\dots} can also be negative integers, - indicating elements/slices to leave out of the selection. - - When indexing arrays by \code{[} a single argument \code{i} can be a - matrix with as many columns as there are dimensions of \code{x}; the - result is then a vector with elements corresponding to the sets of - indices in each row of \code{i}. - - An index value of \code{NULL} is treated as if it were \code{integer(0)}. - } +\item{j}{index specifying elements to extract or replace. +See \code{\link[base:Extract]{base::Extract}} for details.} } \description{ Select spectra by wavelength diff --git a/modules/rtm/man/sub-subset-.spectra.Rd b/modules/rtm/man/sub-subset-.spectra.Rd index 07c59596e39..815b353f538 100644 --- a/modules/rtm/man/sub-subset-.spectra.Rd +++ b/modules/rtm/man/sub-subset-.spectra.Rd @@ -11,28 +11,8 @@ \item{wavelength}{Wavelength vector to select} -\item{j}{ - indices specifying elements to extract or replace. Indices are - \code{numeric} or \code{character} vectors or empty (missing) or - \code{NULL}. Numeric values are coerced to integer as by - \code{\link[base]{as.integer}} (and hence truncated towards zero). - Character vectors will be matched to the \code{\link[base]{names}} of the - object (or for matrices/arrays, the \code{\link[base]{dimnames}}): - see \sQuote{Character indices} below for further details. - - For \code{[}-indexing only: \code{i}, \code{j}, \code{\dots} can be - logical vectors, indicating elements/slices to select. Such vectors - are recycled if necessary to match the corresponding extent. - \code{i}, \code{j}, \code{\dots} can also be negative integers, - indicating elements/slices to leave out of the selection. - - When indexing arrays by \code{[} a single argument \code{i} can be a - matrix with as many columns as there are dimensions of \code{x}; the - result is then a vector with elements corresponding to the sets of - indices in each row of \code{i}. - - An index value of \code{NULL} is treated as if it were \code{integer(0)}. - } +\item{j}{index specifying elements to extract or replace. +See \code{\link[base:Extract]{base::Extract}} for details.} \item{values}{Vector or matrix of values to assign} } From b6e36246886d4d188b4675d0906253bb29175455 Mon Sep 17 00:00:00 2001 From: Chris Black Date: Sun, 30 Apr 2023 01:03:51 -0700 Subject: [PATCH 09/11] avoid treating "" as html --- modules/meta.analysis/R/run.meta.analysis.R | 2 +- modules/meta.analysis/man/p.point.in.prior.Rd | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/meta.analysis/R/run.meta.analysis.R b/modules/meta.analysis/R/run.meta.analysis.R index 3f0c802cafe..ec208a48a3b 100644 --- a/modules/meta.analysis/R/run.meta.analysis.R +++ b/modules/meta.analysis/R/run.meta.analysis.R @@ -244,7 +244,7 @@ runModule.run.meta.analysis <- function(settings) { ##' @title find quantile of point within prior distribution ##' @param point quantile of given prior to return ##' @param prior list of distn, parama, paramb -##' @return result of p(point, parama, paramb) +##' @return result of `p(point, parama, paramb)` ##' @author David LeBauer p.point.in.prior <- function(point, prior) { out <- do.call(paste0("p", prior$distn), diff --git a/modules/meta.analysis/man/p.point.in.prior.Rd b/modules/meta.analysis/man/p.point.in.prior.Rd index 39e2528441a..108a1820730 100644 --- a/modules/meta.analysis/man/p.point.in.prior.Rd +++ b/modules/meta.analysis/man/p.point.in.prior.Rd @@ -12,7 +12,7 @@ p.point.in.prior(point, prior) \item{prior}{list of distn, parama, paramb} } \value{ -result of p(point, parama, paramb) +result of \verb{p(point, parama, paramb)} } \description{ compare point to prior distribution From bcb08d6b99fd1f21e6f45e81467fee2adde73378 Mon Sep 17 00:00:00 2001 From: Chris Black Date: Sun, 30 Apr 2023 21:02:22 -0700 Subject: [PATCH 10/11] update roxygen2 if wrong version is found at Make runtime Also check version once per Make invocation instead of for every package documented --- Makefile | 27 +++++++++++++++++++++------ 1 file changed, 21 insertions(+), 6 deletions(-) diff --git a/Makefile b/Makefile index 1216ac4c05d..3f0c821a765 100644 --- 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 ${1}" Rscript \ - -e "roxver <- packageVersion('roxygen2')" \ - -e "if (roxver != '7.2.3') stop('Roxygen2 version is ', roxver, ', but PEcAn package documentation must be built with exactly version 7.2.3')" \ - -e "devtools::document('"$(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', '7.2.3')" + + ./scripts/time.sh "roxygen2 ${1}" Rscript -e ${SETROPTIONS} \ + -e "if (!requireNamespace('roxygen2', quietly = TRUE)" \ + -e " || packageVersion('roxygen2') != '7.2.3') {" \ + -e " devtools::install_version('roxygen2', '7.2.3')" \ + -e "}" + $(eval INSTALLED_ROXYGEN_VERSION := 7.2.3) echo `date` > $@ .install/testthat: | .install From 4f1c81e57cfb63eb647cd62da01207a614dcaaf3 Mon Sep 17 00:00:00 2001 From: Chris Black Date: Tue, 2 May 2023 00:18:51 -0700 Subject: [PATCH 11/11] install from github (older R releases don't have current roxygen in their RSPM CRAN snapshot) --- Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Makefile b/Makefile index 3f0c821a765..f00790f18fb 100644 --- a/Makefile +++ b/Makefile @@ -144,7 +144,7 @@ clean: + ./scripts/time.sh "roxygen2 ${1}" Rscript -e ${SETROPTIONS} \ -e "if (!requireNamespace('roxygen2', quietly = TRUE)" \ -e " || packageVersion('roxygen2') != '7.2.3') {" \ - -e " devtools::install_version('roxygen2', '7.2.3')" \ + -e " devtools::install_github('r-lib/roxygen2@v7.2.3')" \ -e "}" $(eval INSTALLED_ROXYGEN_VERSION := 7.2.3) echo `date` > $@