From 4c2530d6204d21d5076ebe370b8fc085ceac9b7d Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 22 Jan 2024 18:12:46 +0000 Subject: [PATCH 1/5] Bump actions/cache from 3 to 4 Bumps [actions/cache](https://github.com/actions/cache) from 3 to 4. - [Release notes](https://github.com/actions/cache/releases) - [Changelog](https://github.com/actions/cache/blob/main/RELEASES.md) - [Commits](https://github.com/actions/cache/compare/v3...v4) --- updated-dependencies: - dependency-name: actions/cache dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] --- .github/workflows/R-CMD-check.yaml | 2 +- .github/workflows/Test-coverage.yaml | 2 +- .github/workflows/cmdstan-tarball-check.yaml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 63d06d9d..7cfb1620 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -72,7 +72,7 @@ jobs: - name: Cache R packages if: runner.os != 'Windows' - uses: actions/cache@v3 + uses: actions/cache@v4 with: path: ${{ env.R_LIBS_USER }} key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }} diff --git a/.github/workflows/Test-coverage.yaml b/.github/workflows/Test-coverage.yaml index 54870fd1..68ed39f7 100644 --- a/.github/workflows/Test-coverage.yaml +++ b/.github/workflows/Test-coverage.yaml @@ -50,7 +50,7 @@ jobs: shell: Rscript {0} - name: Cache R packages - uses: actions/cache@v3 + uses: actions/cache@v4 with: path: ${{ env.R_LIBS_USER }} key: ubuntu-r-4.0-1-${{ hashFiles('.github/depends.Rds') }} diff --git a/.github/workflows/cmdstan-tarball-check.yaml b/.github/workflows/cmdstan-tarball-check.yaml index bbb894eb..f2c372e3 100644 --- a/.github/workflows/cmdstan-tarball-check.yaml +++ b/.github/workflows/cmdstan-tarball-check.yaml @@ -56,7 +56,7 @@ jobs: - name: Cache R packages if: runner.os != 'Windows' - uses: actions/cache@v3 + uses: actions/cache@v4 with: path: ${{ env.R_LIBS_USER }} key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }} From 2aff80922a40008dbd164567476ce15f0fc48ad6 Mon Sep 17 00:00:00 2001 From: Joel Schwartz Date: Tue, 23 Jan 2024 12:46:52 -0800 Subject: [PATCH 2/5] Update broken link in opencl.Rmd Current link is broken. I've changed it to what appears to be the current correct link, but I'm not positive. --- vignettes/articles-online-only/opencl.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/vignettes/articles-online-only/opencl.Rmd b/vignettes/articles-online-only/opencl.Rmd index 83844707..dd667f87 100644 --- a/vignettes/articles-online-only/opencl.Rmd +++ b/vignettes/articles-online-only/opencl.Rmd @@ -104,7 +104,7 @@ mdata <- list(k = k, n = n, y = y, X = X) In this model, most of the computation will be handled by the `bernoulli_logit_glm_lpmf` function. Because this is a supported GPU function, it should be possible to accelerate it with OpenCL. Check -[here](http://mc-stan.org/math/d0/d8f/opencl_support.html) for a list of functions +[here](https://mc-stan.org/math/md_doxygen_2parallelism__support_2opencl__support.html) for a list of functions with OpenCL support. To build the model with OpenCL support, add From da5b4f6b614598eab7821cea9bef5e57696171e1 Mon Sep 17 00:00:00 2001 From: Andrew Johnson Date: Wed, 24 Jan 2024 09:57:39 +0200 Subject: [PATCH 3/5] Fix tests with v2.34.1 --- tests/testthat/test-model-optimize.R | 14 ++++++-------- 1 file changed, 6 insertions(+), 8 deletions(-) diff --git a/tests/testthat/test-model-optimize.R b/tests/testthat/test-model-optimize.R index 85163ae9..16a18faa 100644 --- a/tests/testthat/test-model-optimize.R +++ b/tests/testthat/test-model-optimize.R @@ -117,9 +117,9 @@ test_that("optimize() works with (L-)BFGS tolerances specified", { # using values that aren't the defaults init_alpha = 0.002, tol_obj = 2e-11, - tol_rel_obj = 10001, + tol_rel_obj = 1000, tol_grad = 5e-07, - tol_rel_grad = 10000001, + tol_rel_grad = 1000000, tol_param = 5e-07, history_size = 6, seed = 123 @@ -128,12 +128,10 @@ test_that("optimize() works with (L-)BFGS tolerances specified", { metadata <- fit$metadata() expect_equal(metadata$init_alpha, 0.002) expect_equal(metadata$tol_obj, 2e-11) - expect_equal(metadata$tol_rel_obj, 10001) - # https://github.com/stan-dev/cmdstan/issues/1242 - # expect_equal(metadata$tol_grad, 5e-07) - expect_equal(metadata$tol_rel_grad, 10000001) - # https://github.com/stan-dev/cmdstan/issues/1242 - # expect_equal(metadata$tol_param, 5e-07) + expect_equal(metadata$tol_rel_obj, 1000) + expect_equal(metadata$tol_grad, 5e-07) + expect_equal(metadata$tol_rel_grad, 1000000) + expect_equal(metadata$tol_param, 5e-07) expect_equal(metadata$history_size, 6) }) From 0b9d7953583262bb4e61ce89b17d1a525df24a4c Mon Sep 17 00:00:00 2001 From: Andrew Johnson Date: Wed, 24 Jan 2024 09:59:48 +0200 Subject: [PATCH 4/5] Re-enable laplace tests --- tests/testthat/test-model-laplace.R | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/tests/testthat/test-model-laplace.R b/tests/testthat/test-model-laplace.R index 7e814bcc..c021c0fa 100644 --- a/tests/testthat/test-model-laplace.R +++ b/tests/testthat/test-model-laplace.R @@ -55,8 +55,7 @@ test_that("laplace() runs when all arguments specified validly", { expect_equal(fit1$mode()$metadata()$jacobian, as.integer(ok_arg_values$jacobian)) expect_equal(fit1$mode()$metadata()$init_alpha, ok_arg_values$opt_args$init_alpha) - # https://github.com/stan-dev/cmdstan/issues/1242 - #expect_equal(fit1$mode()$metadata()$tol_obj, ok_arg_values$opt_args$tol_obj, tolerance = 0) + expect_equal(fit1$mode()$metadata()$tol_obj, ok_arg_values$opt_args$tol_obj, tolerance = 0) # leaving all at default (except 'data') expect_laplace_output(fit2 <- mod$laplace(data = data_list, seed = 123)) From 63a29c51596407b298b5f1ec8a81ba2e3adc0ec7 Mon Sep 17 00:00:00 2001 From: jgabry Date: Thu, 25 Jan 2024 13:48:52 -0700 Subject: [PATCH 5/5] fix typo in readme --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 989c2830..b3269eaa 100644 --- a/README.md +++ b/README.md @@ -37,7 +37,7 @@ analysis. You can install the latest beta release of the **cmdstanr** R package with ```r -# we recommend running this is a fresh R session or restarting your current session +# we recommend running this in a fresh R session or restarting your current session install.packages("cmdstanr", repos = c("https://mc-stan.org/r-packages/", getOption("repos"))) ``` This does not install the vignettes, which take a long time to build, but they are always available