Merge pull request #3259 from infotroph/treat-roxygen-as-dependency

Treat roxygen as a dependency

docker/depends/Dockerfile

@@ -43,8 +43,7 @@ RUN apt-get update \
 COPY pecan.depends.R pecan_package_dependencies.csv pecan_deps_from_github.txt /
 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', '7.2.3', repos = 'cran.r-project.org')" \
+  && Rscript -e "install.packages(c('desc', 'remotes'))" \
   && R_LIBS_USER='/usr/local/lib/R/site-library' Rscript /pecan.depends.R \
   && rm -rf /tmp/*
 

docker/depends/pecan.depends.R

@@ -13,17 +13,26 @@ condense_version_requirements <- function(specs) {
     return("*")
   }
   specs <- unique(specs[specs != "*"])
-  if (any(!grepl(">", specs))) {
-    # we *could* write more to handle this case if needed, but it seems very rare:
-    # available.packages() shows `<=` or `==` deps in just 4 of 20297 CRAN packages
-    stop(
-      "pecan_depends only supports minimum versions (e.g. `>= 2.8.1`), ",
-      "not exact (`==`) or maximum versions (`<=`).",
-      "Problem seen in (", paste(dQuote(specs), collapse = ", "), ")")
-  }
   versions <- package_version(
     gsub("[^[:digit:].-]+", "", specs))
 
+  if ((length(unique(versions)) > 1) && any(!grepl(">", specs))) {
+    # Can't assume the latest version works for all, so give up.
+    # We *could* write more to handle this case if needed, but it seems very rare:
+    # available.packages() shows `<=` or `==` deps in just 4 of 20297 CRAN packages
+    #
+    # Since the package name wasn't passed in here, we unhelpfully print *just*
+    #   the offending versions and send the user back to the CSV for details.
+    stop(
+      "Found multiple version requirements (",
+      paste(dQuote(specs), collapse = ", "), ") for the same dependency, ",
+      "and not all are minimum versions (e.g. `>= x.y.z`). ",
+      "Exact (`==`) or maximum (`<=`) version reuirements are only allowed ",
+      "if all PEcAn packages declare the same version. ",
+      "Sorry, this function doesn't know which dependency caused this. ",
+      "To find it, search for these version strings in ",
+      "'pecan_package_dependencies.csv'.")
+  }
   specs[versions == max(versions)]
 }
 

docker/depends/pecan_package_dependencies.csv

@@ -479,6 +479,49 @@
 "rmarkdown",">= 2.19","modules/assim.batch","Suggests",FALSE
 "rmarkdown",">= 2.19","modules/meta.analysis","Suggests",FALSE
 "rmarkdown",">= 2.19","modules/photosynthesis","Suggests",FALSE
+"roxygen2","== 7.2.3","base/all","Roxygen",FALSE
+"roxygen2","== 7.2.3","base/db","Roxygen",FALSE
+"roxygen2","== 7.2.3","base/logger","Roxygen",FALSE
+"roxygen2","== 7.2.3","base/qaqc","Roxygen",FALSE
+"roxygen2","== 7.2.3","base/remote","Roxygen",FALSE
+"roxygen2","== 7.2.3","base/settings","Roxygen",FALSE
+"roxygen2","== 7.2.3","base/utils","Roxygen",FALSE
+"roxygen2","== 7.2.3","base/visualization","Roxygen",FALSE
+"roxygen2","== 7.2.3","base/workflow","Roxygen",FALSE
+"roxygen2","== 7.2.3","models/basgra","Roxygen",FALSE
+"roxygen2","== 7.2.3","models/biocro","Roxygen",FALSE
+"roxygen2","== 7.2.3","models/cable","Roxygen",FALSE
+"roxygen2","== 7.2.3","models/clm45","Roxygen",FALSE
+"roxygen2","== 7.2.3","models/dalec","Roxygen",FALSE
+"roxygen2","== 7.2.3","models/dvmdostem","Roxygen",FALSE
+"roxygen2","== 7.2.3","models/ed","Roxygen",FALSE
+"roxygen2","== 7.2.3","models/fates","Roxygen",FALSE
+"roxygen2","== 7.2.3","models/gday","Roxygen",FALSE
+"roxygen2","== 7.2.3","models/jules","Roxygen",FALSE
+"roxygen2","== 7.2.3","models/ldndc","Roxygen",FALSE
+"roxygen2","== 7.2.3","models/linkages","Roxygen",FALSE
+"roxygen2","== 7.2.3","models/lpjguess","Roxygen",FALSE
+"roxygen2","== 7.2.3","models/maat","Roxygen",FALSE
+"roxygen2","== 7.2.3","models/maespa","Roxygen",FALSE
+"roxygen2","== 7.2.3","models/preles","Roxygen",FALSE
+"roxygen2","== 7.2.3","models/sibcasa","Roxygen",FALSE
+"roxygen2","== 7.2.3","models/sipnet","Roxygen",FALSE
+"roxygen2","== 7.2.3","models/stics","Roxygen",FALSE
+"roxygen2","== 7.2.3","models/template","Roxygen",FALSE
+"roxygen2","== 7.2.3","modules/allometry","Roxygen",FALSE
+"roxygen2","== 7.2.3","modules/assim.batch","Roxygen",FALSE
+"roxygen2","== 7.2.3","modules/assim.sequential","Roxygen",FALSE
+"roxygen2","== 7.2.3","modules/benchmark","Roxygen",FALSE
+"roxygen2","== 7.2.3","modules/data.atmosphere","Roxygen",FALSE
+"roxygen2","== 7.2.3","modules/data.hydrology","Roxygen",FALSE
+"roxygen2","== 7.2.3","modules/data.land","Roxygen",FALSE
+"roxygen2","== 7.2.3","modules/data.remote","Roxygen",FALSE
+"roxygen2","== 7.2.3","modules/emulator","Roxygen",FALSE
+"roxygen2","== 7.2.3","modules/meta.analysis","Roxygen",FALSE
+"roxygen2","== 7.2.3","modules/photosynthesis","Roxygen",FALSE
+"roxygen2","== 7.2.3","modules/priors","Roxygen",FALSE
+"roxygen2","== 7.2.3","modules/rtm","Roxygen",FALSE
+"roxygen2","== 7.2.3","modules/uncertainty","Roxygen",FALSE
 "RPostgres","*","base/db","Suggests",FALSE
 "RPostgreSQL","*","base/db","Suggests",FALSE
 "RPostgreSQL","*","models/biocro","Suggests",FALSE

models/cable/DESCRIPTION

@@ -22,4 +22,4 @@ Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
 Encoding: UTF-8
-RoxygenNote: 6.1.0
+RoxygenNote: 7.2.3

scripts/generate_dependencies.R

@@ -52,6 +52,7 @@ parse_desc <- function(path) {
       package = d$get_field("Package"),
       package_dir = dirname(path)),
     remotes = remote_sources,
+    roxygen_version = d$get_field("RoxygenNote"),
     deps = deps)
 }
 
@@ -83,7 +84,19 @@ deps <- pkgs_parsed |>
   # ignore R version requirements (e.g. "Depends: R (>= 3.2.0)")
   dplyr::filter(package != "R") |>
   dplyr::mutate(is_pecan = grepl("^PEcAn", package)) |>
-  dplyr::select(package, version, needed_by_dir, tidyselect::everything()) |>
+  dplyr::select(package, version, needed_by_dir, tidyselect::everything())
+
+# Add Roxygen, used to build all packages but not declared as a dependency
+roxy <- pkgs_parsed |>
+  purrr::map_dfr(
+    ~c(needed_by_dir = .$mapping$package_dir, version = .$roxygen_version)) |>
+  dplyr::mutate(
+    package = "roxygen2",
+    version = paste("==", version),
+    type = "Roxygen",
+    is_pecan = FALSE)
+deps <- deps |>
+  rbind(roxy) |>
   dplyr::arrange(package, version, needed_by_dir, .locale = "en_US")
 
 # Save these for use at install time