From ca528fe56e99cf4332164bd56f7c9148040c1fff Mon Sep 17 00:00:00 2001 From: athowes Date: Tue, 1 Oct 2024 11:26:28 +0100 Subject: [PATCH 1/6] Remove cmdstanr from Remotes --- DESCRIPTION | 1 - 1 file changed, 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 5dd3aebcf..2712b55ce 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -52,7 +52,6 @@ Suggests: modelr, patchwork Remotes: - stan-dev/cmdstanr, paul-buerkner/brms Config/Needs/website: r-lib/pkgdown, From 3c09e3aa7e6c44f48e207a2c15506064e5b0a70c Mon Sep 17 00:00:00 2001 From: athowes Date: Tue, 1 Oct 2024 11:45:10 +0100 Subject: [PATCH 2/6] Move into Additional_repositories --- DESCRIPTION | 2 ++ 1 file changed, 2 insertions(+) diff --git a/DESCRIPTION b/DESCRIPTION index 2712b55ce..ea5670bdd 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -53,6 +53,8 @@ Suggests: patchwork Remotes: paul-buerkner/brms +Additional_repositories: + stan-dev/cmdstanr Config/Needs/website: r-lib/pkgdown, epinowcast/enwtheme From cfd8db873ef9602550ddd9775ddda850f12dde57 Mon Sep 17 00:00:00 2001 From: athowes Date: Tue, 1 Oct 2024 11:53:34 +0100 Subject: [PATCH 3/6] Use stable release version rather than latest --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index ea5670bdd..76f7fb41a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -54,7 +54,7 @@ Suggests: Remotes: paul-buerkner/brms Additional_repositories: - stan-dev/cmdstanr + https://github.com/stan-dev/cmdstanr/releases Config/Needs/website: r-lib/pkgdown, epinowcast/enwtheme From ec5cdebafb7f90c494c2c28bb28b23c1e2373067 Mon Sep 17 00:00:00 2001 From: athowes Date: Tue, 1 Oct 2024 12:07:52 +0100 Subject: [PATCH 4/6] Use R universe version of cmdstanr and add to GH actions --- .github/workflows/R-CMD-as-cran-check.yaml | 1 + .github/workflows/R-CMD-check.yaml | 1 + .github/workflows/check-cmdstan.yaml | 3 +++ .github/workflows/codemeta.yaml | 3 ++- .github/workflows/lint-changed-files.yaml | 3 +++ .github/workflows/pkgdown.yaml | 3 ++- .github/workflows/pr-commands.yaml | 1 + .github/workflows/render-readme.yaml | 5 ++++- .github/workflows/test-coverage.yaml | 1 + DESCRIPTION | 2 +- 10 files changed, 19 insertions(+), 4 deletions(-) diff --git a/.github/workflows/R-CMD-as-cran-check.yaml b/.github/workflows/R-CMD-as-cran-check.yaml index dace415a3..9cf3580bd 100644 --- a/.github/workflows/R-CMD-as-cran-check.yaml +++ b/.github/workflows/R-CMD-as-cran-check.yaml @@ -30,6 +30,7 @@ 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: diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 3cb5e4393..1e988befc 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -49,6 +49,7 @@ jobs: http-user-agent: ${{ matrix.config.http-user-agent }} use-public-rspm: true rtools-version: ${{ matrix.config.rtools }} + extra-repositories: 'https://stan-dev.r-universe.dev' - uses: r-lib/actions/setup-r-dependencies@v2 with: diff --git a/.github/workflows/check-cmdstan.yaml b/.github/workflows/check-cmdstan.yaml index 6e0feec0f..c02adc54e 100644 --- a/.github/workflows/check-cmdstan.yaml +++ b/.github/workflows/check-cmdstan.yaml @@ -46,6 +46,9 @@ jobs: sudo apt-get install -y libpng-dev || true - 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: diff --git a/.github/workflows/codemeta.yaml b/.github/workflows/codemeta.yaml index 03cc2e56b..7a1b6489e 100644 --- a/.github/workflows/codemeta.yaml +++ b/.github/workflows/codemeta.yaml @@ -19,7 +19,8 @@ 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::codemetar diff --git a/.github/workflows/lint-changed-files.yaml b/.github/workflows/lint-changed-files.yaml index db1dede9a..36c6e2ecc 100644 --- a/.github/workflows/lint-changed-files.yaml +++ b/.github/workflows/lint-changed-files.yaml @@ -18,6 +18,9 @@ jobs: - uses: actions/checkout@v4 - 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: diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml index bac67cda2..e07d6d144 100644 --- a/.github/workflows/pkgdown.yaml +++ b/.github/workflows/pkgdown.yaml @@ -31,7 +31,8 @@ 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::pkgdown, local::. diff --git a/.github/workflows/pr-commands.yaml b/.github/workflows/pr-commands.yaml index 39e6faa6b..d17a580c6 100644 --- a/.github/workflows/pr-commands.yaml +++ b/.github/workflows/pr-commands.yaml @@ -23,6 +23,7 @@ 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: diff --git a/.github/workflows/render-readme.yaml b/.github/workflows/render-readme.yaml index 462740b84..44310a22b 100644 --- a/.github/workflows/render-readme.yaml +++ b/.github/workflows/render-readme.yaml @@ -21,7 +21,10 @@ jobs: - name: Setup R uses: r-lib/actions/setup-r@v2 - + with: + use-public-rspm: true + extra-repositories: 'https://stan-dev.r-universe.dev' + - name: Setup pandoc uses: r-lib/actions/setup-pandoc@v2 diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index 4289e1f0b..9d8ba95f6 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -25,6 +25,7 @@ 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: diff --git a/DESCRIPTION b/DESCRIPTION index 76f7fb41a..a57ed01da 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -54,7 +54,7 @@ Suggests: Remotes: paul-buerkner/brms Additional_repositories: - https://github.com/stan-dev/cmdstanr/releases + https://stan-dev.r-universe.dev Config/Needs/website: r-lib/pkgdown, epinowcast/enwtheme From 76787648121e25bb76fc6097b14c47a3a19cc820 Mon Sep 17 00:00:00 2001 From: athowes Date: Tue, 1 Oct 2024 12:14:28 +0100 Subject: [PATCH 5/6] Move cmdstanr from Imports to Suggests --- DESCRIPTION | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index a57ed01da..416d82a30 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -26,7 +26,6 @@ Depends: R (>= 3.5.0) Imports: brms, - cmdstanr, ggplot2, purrr, stats, @@ -50,7 +49,8 @@ Suggests: sf, tidybayes, modelr, - patchwork + patchwork, + cmdstanr Remotes: paul-buerkner/brms Additional_repositories: From 426af5dfacefec6a9c494205a627929efd916dd3 Mon Sep 17 00:00:00 2001 From: athowes Date: Tue, 1 Oct 2024 12:22:05 +0100 Subject: [PATCH 6/6] Remove import statement in package --- NAMESPACE | 1 - R/epidist-package.R | 1 - 2 files changed, 2 deletions(-) diff --git a/NAMESPACE b/NAMESPACE index 9e0f93970..fc849511c 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -37,7 +37,6 @@ export(simulate_exponential_cases) export(simulate_gillespie) export(simulate_secondary) export(simulate_uniform_cases) -import(cmdstanr) import(ggplot2) importFrom(brms,bf) importFrom(brms,prior) diff --git a/R/epidist-package.R b/R/epidist-package.R index 279dc7394..15d1d9e00 100644 --- a/R/epidist-package.R +++ b/R/epidist-package.R @@ -2,7 +2,6 @@ "_PACKAGE" #' @import ggplot2 -#' @import cmdstanr ## usethis namespace: start #' @importFrom dplyr filter select