From 0e590534a997f55f10328990e6e587a59f5f3365 Mon Sep 17 00:00:00 2001 From: VisruthSK <67435125+VisruthSK@users.noreply.github.com> Date: Sun, 7 Dec 2025 19:48:01 -0800 Subject: [PATCH 1/8] Added Stan r-universe and cmdstanr as a dependency so some tests aren't skipped. --- .github/workflows/R-CMD-check.yaml | 3 ++- .github/workflows/test-coverage.yaml | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index db50e234..faf2ed95 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -40,10 +40,11 @@ jobs: r-version: ${{ matrix.config.r }} http-user-agent: ${{ matrix.config.http-user-agent }} use-public-rspm: true + extra-repositories: 'https://stan-dev.r-universe.dev' - uses: r-lib/actions/setup-r-dependencies@v2 with: - extra-packages: any::rcmdcheck, any::BH, any::RcppEigen, any::vdiffr + extra-packages: any::rcmdcheck, any::BH, any::RcppEigen, any::vdiffr, any::cmdstanr needs: check - uses: r-lib/actions/check-r-package@v2 diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index 447fb9de..ef39565b 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -21,10 +21,11 @@ jobs: - uses: r-lib/actions/setup-r@v2 with: use-public-rspm: true + extra-repositories: 'https://stan-dev.r-universe.dev' - uses: r-lib/actions/setup-r-dependencies@v2 with: - extra-packages: any::covr, any::xml2, any::vdiffr + extra-packages: any::covr, any::xml2, any::vdiffr, any::cmdstanr needs: coverage - name: Test coverage From 50b92300a28fc7dbd967d9185bd7c44ef69b75ac Mon Sep 17 00:00:00 2001 From: VisruthSK <67435125+VisruthSK@users.noreply.github.com> Date: Sun, 7 Dec 2025 20:08:11 -0800 Subject: [PATCH 2/8] Install cmdstanr in Actions --- .github/workflows/R-CMD-check.yaml | 3 +++ .github/workflows/test-coverage.yaml | 3 +++ 2 files changed, 6 insertions(+) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index faf2ed95..3e54db1c 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -47,6 +47,9 @@ jobs: extra-packages: any::rcmdcheck, any::BH, any::RcppEigen, any::vdiffr, any::cmdstanr needs: check + - name: Install CmdStan + run: Rscript -e "cmdstanr::install_cmdstan()" + - uses: r-lib/actions/check-r-package@v2 with: upload-snapshots: true diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index ef39565b..46c1a68f 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -28,6 +28,9 @@ jobs: extra-packages: any::covr, any::xml2, any::vdiffr, any::cmdstanr needs: coverage + - name: Install CmdStan + run: Rscript -e "cmdstanr::install_cmdstan()" + - name: Test coverage run: | cov <- covr::package_coverage( From eef40c1f228e0c5ea1ab91652df31a0e4c14818e Mon Sep 17 00:00:00 2001 From: VisruthSK <67435125+VisruthSK@users.noreply.github.com> Date: Mon, 8 Dec 2025 15:32:54 -0800 Subject: [PATCH 3/8] Add cmdstanr to Suggests --- DESCRIPTION | 1 + 1 file changed, 1 insertion(+) diff --git a/DESCRIPTION b/DESCRIPTION index df6b5f7d..c14d4f14 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -42,6 +42,7 @@ Imports: tidyselect, utils Suggests: + cmdstanr, ggdist, ggfortify, gridExtra (>= 2.2.1), From 724a724e63a2a8bd0108ed67f5d33c50da3f139a Mon Sep 17 00:00:00 2001 From: VisruthSK <67435125+VisruthSK@users.noreply.github.com> Date: Mon, 8 Dec 2025 21:17:58 -0800 Subject: [PATCH 4/8] Added Stan reuniverse --- DESCRIPTION | 1 + 1 file changed, 1 insertion(+) diff --git a/DESCRIPTION b/DESCRIPTION index c14d4f14..6aa9a87b 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -64,3 +64,4 @@ VignetteBuilder: knitr Encoding: UTF-8 Roxygen: list(markdown = TRUE) Config/testthat/edition: 3 +Additional_repositories: https://stan-dev.r-universe.dev/ From 3e43f865dd8599ebb2df1fa4000d82419e3b161e Mon Sep 17 00:00:00 2001 From: VisruthSK <67435125+VisruthSK@users.noreply.github.com> Date: Mon, 8 Dec 2025 21:53:56 -0800 Subject: [PATCH 5/8] Force a more recent version of rstan so builds don't fail --- .github/workflows/R-CMD-check.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 3e54db1c..1925ca4a 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -44,7 +44,7 @@ jobs: - uses: r-lib/actions/setup-r-dependencies@v2 with: - extra-packages: any::rcmdcheck, any::BH, any::RcppEigen, any::vdiffr, any::cmdstanr + extra-packages: any::rcmdcheck, any::BH, any::RcppEigen, any::vdiffr, any::cmdstanr, any::rstan@>=2.36 needs: check - name: Install CmdStan From b1e57c8bc838d4829e53dc0120fd620f5b056a82 Mon Sep 17 00:00:00 2001 From: VisruthSK <67435125+VisruthSK@users.noreply.github.com> Date: Mon, 8 Dec 2025 21:56:09 -0800 Subject: [PATCH 6/8] Force recent rstan in description --- .github/workflows/R-CMD-check.yaml | 2 +- DESCRIPTION | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 1925ca4a..3e54db1c 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -44,7 +44,7 @@ jobs: - uses: r-lib/actions/setup-r-dependencies@v2 with: - extra-packages: any::rcmdcheck, any::BH, any::RcppEigen, any::vdiffr, any::cmdstanr, any::rstan@>=2.36 + extra-packages: any::rcmdcheck, any::BH, any::RcppEigen, any::vdiffr, any::cmdstanr needs: check - name: Install CmdStan diff --git a/DESCRIPTION b/DESCRIPTION index 6aa9a87b..2103f3ec 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -51,7 +51,7 @@ Suggests: loo (>= 2.0.0), RColorBrewer, rmarkdown (>= 1.0.0), - rstan (>= 2.17.1), + rstan (>= 2.36.0), rstanarm (>= 2.17.4), rstantools (>= 1.5.0), scales, From 891b706fe889e80aea5a85c84a8d52031641aea6 Mon Sep 17 00:00:00 2001 From: VisruthSK <67435125+VisruthSK@users.noreply.github.com> Date: Mon, 8 Dec 2025 22:20:34 -0800 Subject: [PATCH 7/8] Trying today's date as seed for fit_cp so Mac compiles --- vignettes/visual-mcmc-diagnostics.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/vignettes/visual-mcmc-diagnostics.Rmd b/vignettes/visual-mcmc-diagnostics.Rmd index 9e24ec57..1b6ee6a6 100644 --- a/vignettes/visual-mcmc-diagnostics.Rmd +++ b/vignettes/visual-mcmc-diagnostics.Rmd @@ -154,7 +154,7 @@ schools_mod_ncp <- stan_model("schools_mod_ncp.stan") We then fit the model by calling Stan's MCMC algorithm using the `sampling` function (the increased `adapt_delta` param is to make the sampler a bit more "careful" and avoid false positive divergences), ```{r fit-models-hidden, results='hide', message=FALSE} -fit_cp <- sampling(schools_mod_cp, data = schools_dat, seed = 803214055, control = list(adapt_delta = 0.9)) +fit_cp <- sampling(schools_mod_cp, data = schools_dat, seed = 20251208, control = list(adapt_delta = 0.9)) fit_ncp <- sampling(schools_mod_ncp, data = schools_dat, seed = 457721433, control = list(adapt_delta = 0.9)) ``` and extract a `iterations x chains x parameters` array of posterior draws with From 7f61302e75292203bd15b3894c492fb6e649daea Mon Sep 17 00:00:00 2001 From: VisruthSK <67435125+VisruthSK@users.noreply.github.com> Date: Thu, 11 Dec 2025 10:45:05 -0800 Subject: [PATCH 8/8] Reverted rstan version to 2.17.1 --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 2103f3ec..6aa9a87b 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -51,7 +51,7 @@ Suggests: loo (>= 2.0.0), RColorBrewer, rmarkdown (>= 1.0.0), - rstan (>= 2.36.0), + rstan (>= 2.17.1), rstanarm (>= 2.17.4), rstantools (>= 1.5.0), scales,