Install versioned dependencies from a fresher CRAN mirror instead of from Github

Makefile.depends

@@ -1,44 +1,41 @@
 # autogenerated
-$(call depends,base/all): | .install/base/db .install/base/settings .install/modules/meta.analysis .install/base/logger .install/base/utils .install/modules/uncertainty .install/modules/data.atmosphere .install/modules/data.land .install/modules/data.remote .install/modules/assim.batch .install/modules/emulator .install/modules/priors .install/modules/benchmark .install/base/remote .install/base/workflow .install/models/ed .install/models/sipnet .install/models/biocro .install/models/dalec .install/models/linkages .install/modules/allometry .install/modules/photosynthesis
+$(call depends,base/all): | .install/base/db .install/base/logger .install/base/remote .install/base/settings .install/base/utils .install/base/workflow .install/models/biocro .install/models/dalec .install/models/ed .install/models/linkages .install/models/sipnet .install/modules/allometry .install/modules/assim.batch .install/modules/benchmark .install/modules/data.atmosphere .install/modules/data.land .install/modules/data.remote .install/modules/emulator .install/modules/meta.analysis .install/modules/photosynthesis .install/modules/priors .install/modules/uncertainty
 $(call depends,base/db): | .install/base/logger .install/base/remote .install/base/utils
-$(call depends,base/logger): |
-$(call depends,base/qaqc): | .install/base/db .install/base/logger .install/models/biocro .install/models/ed .install/models/sipnet .install/base/utils
+$(call depends,base/qaqc): | .install/base/db .install/base/logger .install/base/utils .install/models/biocro .install/models/ed .install/models/sipnet
 $(call depends,base/remote): | .install/base/logger
 $(call depends,base/settings): | .install/base/db .install/base/logger .install/base/remote .install/base/utils
 $(call depends,base/utils): | .install/base/logger
 $(call depends,base/visualization): | .install/base/db .install/base/logger .install/base/utils
-$(call depends,base/workflow): | .install/modules/data.atmosphere .install/modules/data.land .install/base/db .install/base/logger .install/base/remote .install/base/settings .install/modules/uncertainty .install/base/utils
-$(call depends,modules/allometry): | .install/base/db
-$(call depends,modules/assim.batch): | .install/modules/benchmark .install/base/db .install/modules/emulator .install/base/logger .install/modules/meta.analysis .install/base/remote .install/base/settings .install/modules/uncertainty .install/base/utils .install/base/workflow
-$(call depends,modules/assim.sequential): | .install/base/db .install/base/logger .install/base/remote .install/base/settings .install/modules/uncertainty .install/base/workflow .install/modules/benchmark .install/modules/data.remote
-$(call depends,modules/benchmark): | .install/base/db .install/base/logger .install/base/remote .install/base/settings .install/base/utils .install/modules/data.land
-$(call depends,modules/data.atmosphere): | .install/base/db .install/base/logger .install/base/remote .install/base/utils
-$(call depends,modules/data.hydrology): | .install/base/logger .install/base/utils
-$(call depends,modules/data.land): | .install/modules/benchmark .install/modules/data.atmosphere .install/base/db .install/base/logger .install/base/remote .install/base/utils .install/base/visualization .install/base/settings
-$(call depends,modules/data.remote): | .install/base/db .install/base/utils .install/base/logger .install/base/remote
-$(call depends,modules/emulator): |
-$(call depends,modules/meta.analysis): | .install/base/utils .install/base/db .install/base/logger .install/base/settings
-$(call depends,modules/photosynthesis): |
-$(call depends,modules/priors): | .install/base/logger .install/modules/meta.analysis .install/base/utils .install/base/visualization
-$(call depends,modules/rtm): | .install/base/logger .install/modules/assim.batch .install/base/utils .install/models/ed
-$(call depends,modules/uncertainty): | .install/base/db .install/modules/emulator .install/base/logger .install/modules/priors .install/base/settings .install/base/utils
-$(call depends,models/basgra): | .install/base/logger .install/modules/data.atmosphere .install/base/utils
-$(call depends,models/biocro): | .install/base/logger .install/base/remote .install/base/utils .install/base/settings .install/modules/data.atmosphere .install/modules/data.land .install/base/db
+$(call depends,base/workflow): | .install/base/db .install/base/logger .install/base/remote .install/base/settings .install/base/utils .install/modules/data.atmosphere .install/modules/data.land .install/modules/uncertainty
+$(call depends,models/basgra): | .install/base/logger .install/base/utils .install/modules/data.atmosphere
+$(call depends,models/biocro): | .install/base/db .install/base/logger .install/base/remote .install/base/settings .install/base/utils .install/modules/data.atmosphere .install/modules/data.land
 $(call depends,models/cable): | .install/base/logger .install/base/utils
 $(call depends,models/clm45): | .install/base/logger .install/base/utils
 $(call depends,models/dalec): | .install/base/logger .install/base/remote .install/base/utils
 $(call depends,models/dvmdostem): | .install/base/logger .install/base/utils
-$(call depends,models/ed): | .install/modules/data.atmosphere .install/modules/data.land .install/base/logger .install/base/remote .install/base/settings .install/base/utils
+$(call depends,models/ed): | .install/base/logger .install/base/remote .install/base/settings .install/base/utils .install/modules/data.atmosphere .install/modules/data.land
 $(call depends,models/fates): | .install/base/logger .install/base/remote .install/base/utils
-$(call depends,models/gday): | .install/base/utils .install/base/logger .install/base/remote
-$(call depends,models/jules): | .install/modules/data.atmosphere .install/base/logger .install/base/remote .install/base/utils
-$(call depends,models/ldndc): | .install/base/db .install/base/logger .install/base/utils .install/base/remote .install/modules/data.atmosphere
-$(call depends,models/linkages): | .install/base/utils .install/modules/data.atmosphere .install/base/logger .install/base/remote
+$(call depends,models/gday): | .install/base/logger .install/base/remote .install/base/utils
+$(call depends,models/jules): | .install/base/logger .install/base/remote .install/base/utils .install/modules/data.atmosphere
+$(call depends,models/ldndc): | .install/base/db .install/base/logger .install/base/remote .install/base/utils .install/modules/data.atmosphere
+$(call depends,models/linkages): | .install/base/logger .install/base/remote .install/base/utils .install/modules/data.atmosphere
 $(call depends,models/lpjguess): | .install/base/logger .install/base/remote .install/base/utils
-$(call depends,models/maat): | .install/modules/data.atmosphere .install/base/logger .install/base/remote .install/base/settings .install/base/utils
-$(call depends,models/maespa): | .install/modules/data.atmosphere .install/base/logger .install/base/remote .install/base/utils
-$(call depends,models/preles): | .install/base/utils .install/base/logger .install/modules/data.atmosphere .install/base/utils
+$(call depends,models/maat): | .install/base/logger .install/base/remote .install/base/settings .install/base/utils .install/modules/data.atmosphere
+$(call depends,models/maespa): | .install/base/logger .install/base/remote .install/base/utils .install/modules/data.atmosphere
+$(call depends,models/preles): | .install/base/logger .install/base/utils .install/modules/data.atmosphere
 $(call depends,models/sibcasa): | .install/base/logger .install/base/utils
-$(call depends,models/sipnet): | .install/modules/data.atmosphere .install/base/logger .install/base/remote .install/base/utils
-$(call depends,models/stics): | .install/base/settings .install/base/db .install/base/logger .install/base/utils .install/base/remote
+$(call depends,models/sipnet): | .install/base/logger .install/base/remote .install/base/utils .install/modules/data.atmosphere
+$(call depends,models/stics): | .install/base/db .install/base/logger .install/base/remote .install/base/settings .install/base/utils
 $(call depends,models/template): | .install/base/db .install/base/logger .install/base/utils
+$(call depends,modules/allometry): | .install/base/db
+$(call depends,modules/assim.batch): | .install/base/db .install/base/logger .install/base/remote .install/base/settings .install/base/utils .install/base/workflow .install/modules/benchmark .install/modules/emulator .install/modules/meta.analysis .install/modules/uncertainty
+$(call depends,modules/assim.sequential): | .install/base/db .install/base/logger .install/base/remote .install/base/settings .install/base/workflow .install/modules/benchmark .install/modules/data.remote .install/modules/uncertainty
+$(call depends,modules/benchmark): | .install/base/db .install/base/logger .install/base/remote .install/base/settings .install/base/utils .install/modules/data.land
+$(call depends,modules/data.atmosphere): | .install/base/db .install/base/logger .install/base/remote .install/base/utils
+$(call depends,modules/data.hydrology): | .install/base/logger .install/base/utils
+$(call depends,modules/data.land): | .install/base/db .install/base/logger .install/base/remote .install/base/settings .install/base/utils .install/base/visualization .install/modules/benchmark .install/modules/data.atmosphere
+$(call depends,modules/data.remote): | .install/base/db .install/base/logger .install/base/remote .install/base/utils
+$(call depends,modules/meta.analysis): | .install/base/db .install/base/logger .install/base/settings .install/base/utils
+$(call depends,modules/priors): | .install/base/logger .install/base/utils .install/base/visualization .install/modules/meta.analysis
+$(call depends,modules/rtm): | .install/base/logger .install/base/utils .install/models/ed .install/modules/assim.batch
+$(call depends,modules/uncertainty): | .install/base/db .install/base/logger .install/base/settings .install/base/utils .install/modules/emulator .install/modules/priors

base/db/DESCRIPTION

@@ -66,7 +66,7 @@ Suggests:
     data.table,
     here,
     knitr,
-    mockery,
+    mockery (>= 0.4.3),
     RPostgreSQL,
     RPostgres,
     RSQLite,
@@ -75,15 +75,6 @@ Suggests:
     testthat (>= 2.0.0),
     tidyverse,
     withr
-X-Comment-Remotes:
-    Installing markdown from GitHub because as of 2023-02-05, this is the
-    easiest way to get version >= 2.19 onto Docker images that use older
-    Rstudio Package Manager snapshots.
-    When building on a system that finds a new enough version on CRAN,
-    OK to remove the Remotes line and this comment.
-Remotes:
-    github::rstudio/[email protected],
-    github::r-lib/[email protected]
 License: BSD_3_clause + file LICENSE
 VignetteBuilder: knitr
 Copyright: Authors

base/qaqc/DESCRIPTION

@@ -31,16 +31,6 @@ Suggests:
     testthat (>= 3.0.4),
     vdiffr (>= 1.0.2),
     withr
-X-Comment-Remotes:
-    Installing vdiffr from GitHub because as of 2021-09-23, this is the
-    easiest way to get version >= 1.0.2 onto Docker images that use older
-    Rstudio Package Manager snapshots.
-    Ditto for testthat, because we need >= 3.0.4 for vdiffr compatibility.
-    When building on a system that finds these versions on CRAN,
-    OK to remove these Remotes lines and this comment.
-Remotes:
-    github::r-lib/[email protected],
-    github::r-lib/[email protected]
 License: BSD_3_clause + file LICENSE
 Copyright: Authors
 LazyLoad: yes

docker/depends/pecan.depends.R

@@ -14,25 +14,20 @@ remotes::install_github(c(
 'chuhousen/amerifluxr',
 'ebimodeling/[email protected]',
 'MikkoPeltoniemi/Rpreles',
-'r-lib/[email protected]',
-'r-lib/[email protected]',
-'r-lib/[email protected]',
 'ropensci/geonames',
-'ropensci/nneo',
-'rstudio/[email protected]'
+'ropensci/nneo'
 ), lib = rlib)
 
-# install all packages (depends, imports, suggests)
+# install package listed as Depends, Imports, Suggests of any PEcAn package
+#   that do not have a stated version limit
 wanted <- c(
-'abind',
 'amerifluxr',
 'arrow',
 'assertthat',
 'BayesianTools',
 'BioCro',
 'bit64',
 'BrownDog',
-'coda',
 'corrplot',
 'curl',
 'data.table',
@@ -51,7 +46,6 @@ wanted <- c(
 'fs',
 'furrr',
 'future',
-'geonames',
 'getPass',
 'ggmap',
 'ggmcmc',
@@ -72,9 +66,7 @@ wanted <- c(
 'lattice',
 'linkages',
 'lqmm',
-'lubridate',
 'Maeswrap',
-'magic',
 'magrittr',
 'maps',
 'markdown',
@@ -86,23 +78,18 @@ wanted <- c(
 'mgcv',
 'minpack.lm',
 'mlegp',
-'mockery',
-'MODISTools',
 'mvbutils',
 'mvtnorm',
-'ncdf4',
 'neonstore',
 'neonUtilities',
 'nimble',
 'nneo',
 'optparse',
 'parallel',
 'plotrix',
-'plyr',
 'png',
 'prodlim',
 'progress',
-'purrr',
 'pwr',
 'R.utils',
 'randtoolbox',
@@ -111,13 +98,10 @@ wanted <- c(
 'REddyProc',
 'redland',
 'reshape',
-'reshape2',
 'reticulate',
 'rjags',
 'rjson',
-'rlang',
 'rlist',
-'rmarkdown',
 'RPostgres',
 'RPostgreSQL',
 'Rpreles',
@@ -128,29 +112,61 @@ wanted <- c(
 'sp',
 'stats',
 'stringi',
-'stringr',
 'suntools',
 'swfscMisc',
 'terra',
-'testthat',
 'tibble',
 'tictoc',
 'tidyr',
 'tidyselect',
 'tidyverse',
 'tools',
 'traits',
-'TruncatedNormal',
 'truncnorm',
 'units',
 'urltools',
 'utils',
-'vdiffr',
 'withr',
-'XML',
 'xtable',
 'xts',
 'zoo'
 )
 missing <- wanted[!(wanted %in% installed.packages()[,'Package'])]
 install.packages(missing, lib = rlib)
+
+# Install packages listed as Depends, Imports, Suggests
+#    that list a minimum version.
+# When the minimum is not satisfied in the fixed-date CRAN snapshot
+#    used by our Docker images, we pull it in from an up-to-date mirror.
+# (Assumes our CRAN uses the same URL scheme as Posit package manager)
+options(repos = c(
+    getOption('repos'),
+    sub(r'(\d{4}-\d{2}-\d{2})', 'latest', getOption('repos'))
+))
+ensure_version <- function(pkg, version) {
+    vers <- gsub('[^[:digit:].-]+', '', version)
+    cmp <- get(gsub('[^<>=]+', '', version))
+    ok <- requireNamespace(pkg, quietly = TRUE) &&
+        cmp(packageVersion(pkg), vers)
+    if (!ok) {
+        remotes::install_version(pkg, version, dependencies = TRUE, upgrade = FALSE)
+    }
+}
+ensure_version('abind', '>= 1.4.5')
+ensure_version('coda', '>= 0.18')
+ensure_version('geonames', '> 0.998')
+ensure_version('lubridate', '>= 1.7.0')
+ensure_version('magic', '>= 1.5.0')
+ensure_version('mockery', '>= 0.4.3')
+ensure_version('MODISTools', '>= 1.1.0')
+ensure_version('ncdf4', '>= 1.15')
+ensure_version('plyr', '>= 1.8.4')
+ensure_version('purrr', '>= 0.2.3')
+ensure_version('reshape2', '>= 1.4.2')
+ensure_version('rlang', '>= 0.2.0')
+ensure_version('rmarkdown', '>= 2.19')
+ensure_version('stringr', '>= 1.1.0')
+ensure_version('testthat', '>= 3.0.4')
+ensure_version('TruncatedNormal', '>= 2.2')
+ensure_version('vdiffr', '>= 1.0.2')
+ensure_version('XML', '>= 3.98-1.4')