Fix CRAN NOTEs and failures

.github/workflows/R-CMD-check.yaml

@@ -14,17 +14,22 @@ jobs:
  R-CMD-check:
  runs-on: ${{ matrix.config.os }}
 
- name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+ name: ${{ matrix.config.rstan }} RStan - ${{ matrix.config.os }} (${{ matrix.config.r }})
 
  strategy:
  fail-fast: false
  matrix:
  config:
- # - {os: windows-latest, r: 'release'}
- # - {os: macOS-latest, r: 'release'}
- - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+ - {os: macOS-latest, r: 'devel', rstan: 'CRAN'}
+ - {os: macOS-latest, r: 'release', rstan: 'CRAN'}
+ - {os: windows-latest, r: 'devel', rstan: 'CRAN'}
+ - {os: windows-latest, r: 'release', rstan: 'CRAN'}
+ - {os: ubuntu-latest, r: 'devel', rstan: 'CRAN'}
+ - {os: ubuntu-latest, r: 'release', rstan: 'CRAN'}
+ - {os: ubuntu-latest, r: 'oldrel', rstan: 'CRAN'}
 
+ - {os: macOS-latest, r: 'release', rstan: 'Preview'}
+ - {os: windows-latest, r: 'release', rstan: 'Preview'}
  env:
  R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
  RSPM: ${{ matrix.config.rspm }}
@@ -36,51 +41,30 @@ jobs:
  token: ${{ secrets.GITHUB_TOKEN }}
  workflow: R-CMD-check.yaml
  if: "!startsWith(github.ref, 'refs/tags/') && github.ref != 'refs/heads/master'"
-
- - uses: actions/checkout@v2
 
- - uses: r-lib/actions/setup-r@v1
+ - uses: actions/checkout@v3
+
+ - uses: r-lib/actions/setup-r@v2
  with:
  r-version: ${{ matrix.config.r }}
 
- - uses: r-lib/actions/setup-pandoc@v1
-
- - name: Query dependencies
- run: |
- install.packages('remotes')
- saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
- writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
- shell: Rscript {0}
-
- - name: Cache R packages
- if: runner.os != 'Windows'
- uses: actions/cache@v2
+ - uses: r-lib/actions/setup-pandoc@v2
+ - uses: r-lib/actions/setup-r-dependencies@v2
  with:
- path: ${{ env.R_LIBS_USER }}
- key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-2-${{ hashFiles('.github/depends.Rds') }}
- restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-2-
+ cache-version: 2
+ extra-packages: any::rcmdcheck any::betareg any::HSAUR3 any::biglm any::gamm4 any::V8
 
- - name: Install system dependencies
- if: runner.os == 'Linux'
+ - name: Install RStan Preview if Needed
  run: |
- while read -r cmd
- do
- eval sudo $cmd
- done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
-
- - name: Install dependencies
- run: |
- remotes::install_deps(dependencies = TRUE)
- remotes::install_cran("rcmdcheck")
+ if ("${{ matrix.config.rstan }}" == "Preview") {
+ install.packages("rstan", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))
+ }
  shell: Rscript {0}
 
- - name: Check
- env:
- _R_CHECK_CRAN_INCOMING_REMOTE_: false
- run: |
- Sys.setenv(MAKEFLAGS = "-j2") # will rcmdcheck::rcmdcheck use this?
- rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran", "--ignore-vignettes"), build_args = c("--no-build-vignettes"), error_on = "warning", check_dir = "check")
- shell: Rscript {0}
+ - uses: r-lib/actions/check-r-package@v2
+ with:
+ args: 'c("--no-manual", "--as-cran", "--ignore-vignettes")'
+ build_args: '"--no-build-vignettes"'
 
  - name: Upload check results
  if: failure()

DESCRIPTION

@@ -1,29 +1,29 @@
 Package: rstanarm
 Type: Package
 Title: Bayesian Applied Regression Modeling via Stan
-Version: 2.21.3
-Date: 2022-04-08
+Version: 2.21.4
+Date: 2023-04-03
 Encoding: UTF-8
 Authors@R: c(person("Jonah", "Gabry", email = "jsg2201@columbia.edu", role = "aut"),
  person("Imad", "Ali", role = "ctb"),
  person("Sam", "Brilleman", role = "ctb"),
- person(given = "Jacqueline Buros", family = "Novik", 
+ person(given = "Jacqueline Buros", family = "Novik",
  role = "ctb", comment = "R/stan_jm.R"),
  person("AstraZeneca", role = "ctb", comment = "R/stan_jm.R"),
  person("Trustees of", "Columbia University", role = "cph"),
  person("Simon", "Wood", role = "cph", comment = "R/stan_gamm4.R"),
- person("R Core", "Deveopment Team", role = "cph", 
+ person("R Core", "Deveopment Team", role = "cph",
  comment = "R/stan_aov.R"),
  person("Douglas", "Bates", role = "cph", comment = "R/pp_data.R"),
  person("Martin", "Maechler", role = "cph", comment = "R/pp_data.R"),
  person("Ben", "Bolker", role = "cph", comment = "R/pp_data.R"),
  person("Steve", "Walker", role = "cph", comment = "R/pp_data.R"),
- person("Brian", "Ripley", role = "cph", 
+ person("Brian", "Ripley", role = "cph",
  comment = "R/stan_aov.R, R/stan_polr.R"),
  person("William", "Venables", role = "cph", comment = "R/stan_polr.R"),
  person("Paul-Christian", "Burkner", email = "paul.buerkner@gmail.com",
  role = "cph", comment = "R/misc.R"),
- person("Ben", "Goodrich", email = "benjamin.goodrich@columbia.edu", 
+ person("Ben", "Goodrich", email = "benjamin.goodrich@columbia.edu",
  role = c("cre", "aut")))
 Description: Estimates previously compiled regression models using the 'rstan'
  package, which provides the R interface to the Stan C++ library for Bayesian
@@ -61,7 +61,9 @@ Suggests:
  rmarkdown,
  roxygen2,
  StanHeaders (>= 2.21.0),
- testthat (>= 1.0.2)
+ testthat (>= 1.0.2),
+ gamm4,
+ shiny
 LinkingTo: StanHeaders (>= 2.21.0), rstan (>= 2.21.1), BH (>= 1.72.0-2), Rcpp (>=
  0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1)
 SystemRequirements: GNU make, pandoc (>= 1.12.3), pandoc-citeproc
@@ -71,4 +73,4 @@ UseLTO: true
 NeedsCompilation: yes
 URL: https://mc-stan.org/rstanarm/, https://discourse.mc-stan.org
 BugReports: https://github.com/stan-dev/rstanarm/issues
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3

NAMESPACE

@@ -186,6 +186,7 @@ import(shinystan)
 import(stats)
 importFrom(Matrix,Matrix)
 importFrom(Matrix,t)
+importFrom(RcppParallel,RcppParallelLibs)
 importFrom(bayesplot,pairs_condition)
 importFrom(bayesplot,pairs_style_np)
 importFrom(ggplot2,"%+replace%")

R/doc-rstanarm-package.R

@@ -26,6 +26,7 @@
 #' @importFrom rstan optimizing sampling vb constrain_pars extract
 #' extract_sparse_parts get_posterior_mean stanc
 #' @importFrom utils capture.output
+#' @importFrom RcppParallel RcppParallelLibs
 #' @import stats
 #' @import Rcpp
 #' @import bayesplot