From afb9b72ecaddb7a5660056d59f4493d2d553c364 Mon Sep 17 00:00:00 2001 From: Brendan Matthew Galdo Date: Sat, 9 May 2026 14:51:37 -0400 Subject: [PATCH 01/11] Update R-CMD-check.yaml --- .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 f36e31f..d6ee3de 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -32,7 +32,7 @@ jobs: - uses: r-lib/actions/setup-r-dependencies@v2 with: - extra-packages: any::rcmdcheck + extra-packages: any::rcmdcheck, any::roxygen2 needs: check - uses: r-lib/actions/check-r-package@v2 From 82aa7d0c31d41768ed24686c962ccb9b26b42945 Mon Sep 17 00:00:00 2001 From: Brendan Matthew Galdo Date: Sat, 9 May 2026 15:51:29 -0400 Subject: [PATCH 02/11] fix issues with test --- tests/testthat/test-optim_SQGDE.R | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/tests/testthat/test-optim_SQGDE.R b/tests/testthat/test-optim_SQGDE.R index a2dce99..02be58e 100644 --- a/tests/testthat/test-optim_SQGDE.R +++ b/tests/testthat/test-optim_SQGDE.R @@ -5,7 +5,8 @@ library(graDiEnt) test_that("MLE factorizable MVN recovers sample means", { set.seed(42) true_mu <- c(-1, 1, 0, 2) - data <- matrix(rnorm(500 * 4, mean = true_mu, sd = 1), nrow = 500, ncol = 4) + data <- matrix(rnorm(500 * 4, mean = true_mu, sd = 1), + nrow = 500, ncol = 4 ,byrow = TRUE) analytic_mu <- colMeans(data) neg_log_lik <- function(x, data) { @@ -155,8 +156,9 @@ test_that("PSOCK parallel execution returns valid solution", { skip_on_cran() set.seed(42) - true_mu <- c(-1, 1, 0, 2) - data_par <- matrix(rnorm(500 * 4, mean = true_mu, sd = 1), nrow = 500, ncol = 4) + true_mu <- c(-1, 8, 0, 2) + data_par <- matrix(rnorm(500 * 4, mean = true_mu, sd = 1), + nrow = 500, ncol = 4 ,byrow = TRUE) analytic_mu <- colMeans(data_par) neg_log_lik <- function(x, data_par) { @@ -201,7 +203,8 @@ test_that("FORK parallel execution returns valid solution", { set.seed(42) true_mu <- c(-1, 1, 0, 2) - data_par <- matrix(rnorm(500 * 4, mean = true_mu, sd = 1), nrow = 500, ncol = 4) + data_par <- matrix(rnorm(500 * 4, mean = true_mu, sd = 1), + nrow = 500, ncol = 4 ,byrow = TRUE) analytic_mu <- colMeans(data_par) neg_log_lik <- function(x, data_par) { From decad325125053ab927d363457857b756ca58e21 Mon Sep 17 00:00:00 2001 From: Brendan Matthew Galdo Date: Sat, 9 May 2026 15:53:22 -0400 Subject: [PATCH 03/11] declare roxygen2 in DESCRIPTION, remove from extra-packages Co-Authored-By: Claude Sonnet 4.6 --- .github/workflows/R-CMD-check.yaml | 2 +- DESCRIPTION | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index d6ee3de..f36e31f 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -32,7 +32,7 @@ jobs: - uses: r-lib/actions/setup-r-dependencies@v2 with: - extra-packages: any::rcmdcheck, any::roxygen2 + extra-packages: any::rcmdcheck needs: check - uses: r-lib/actions/check-r-package@v2 diff --git a/DESCRIPTION b/DESCRIPTION index 45826ab..2bb4fc3 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -18,6 +18,7 @@ Imports: stats, parallel Suggests: - testthat (>= 3.0.0) + testthat (>= 3.0.0), + roxygen2 Roxygen: list(markdown = TRUE) RoxygenNote: 7.1.2 From 88c4cbc65c2a65beaff7e4fa702f2993779b0b47 Mon Sep 17 00:00:00 2001 From: Brendan Matthew Galdo Date: Sat, 9 May 2026 15:57:22 -0400 Subject: [PATCH 04/11] Update R-CMD-check.yaml --- .github/workflows/R-CMD-check.yaml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index f36e31f..572e26c 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -30,6 +30,10 @@ jobs: r-version: ${{ matrix.config.r }} use-public-rspm: true + - name: Install roxygen2 + shell: Rscript {0} + run: install.packages("roxygen2", repos = "https://cloud.r-project.org") + - uses: r-lib/actions/setup-r-dependencies@v2 with: extra-packages: any::rcmdcheck From 918c25cf5f42180674904f6f3a40c0edf4f03060 Mon Sep 17 00:00:00 2001 From: Brendan Matthew Galdo Date: Sat, 9 May 2026 16:09:32 -0400 Subject: [PATCH 05/11] Update R-CMD-check.yaml --- .github/workflows/R-CMD-check.yaml | 36 +++++++++--------------------- 1 file changed, 11 insertions(+), 25 deletions(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 572e26c..dc751d2 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -8,37 +8,23 @@ name: R-CMD-check jobs: R-CMD-check: - runs-on: ${{ matrix.config.os }} - name: ${{ matrix.config.os }} (R ${{ matrix.config.r }}) - - strategy: - fail-fast: false - matrix: - config: - - {os: macos-latest, r: 'release'} - - {os: windows-latest, r: 'release'} - - {os: ubuntu-latest, r: 'release'} - - {os: ubuntu-latest, r: 'devel'} + runs-on: ubuntu-latest + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} steps: - uses: actions/checkout@v4 - - uses: r-lib/actions/setup-pandoc@v2 - - uses: r-lib/actions/setup-r@v2 with: - r-version: ${{ matrix.config.r }} - use-public-rspm: true + r-version: 'release' - - name: Install roxygen2 + - name: Install dependencies shell: Rscript {0} - run: install.packages("roxygen2", repos = "https://cloud.r-project.org") - - - uses: r-lib/actions/setup-r-dependencies@v2 - with: - extra-packages: any::rcmdcheck - needs: check + run: | + install.packages(c("rcmdcheck", "testthat", "roxygen2", "parallel"), + repos = "https://cloud.r-project.org") - - uses: r-lib/actions/check-r-package@v2 - with: - upload-snapshots: true + - name: Check + shell: Rscript {0} + run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning") From aa56a4c4c2f7f380d9e34b56f567579a64cfa87b Mon Sep 17 00:00:00 2001 From: Brendan Matthew Galdo Date: Sat, 9 May 2026 16:15:34 -0400 Subject: [PATCH 06/11] update description --- .github/workflows/R-CMD-check.yaml | 17 +++++++++-------- DESCRIPTION | 1 - 2 files changed, 9 insertions(+), 9 deletions(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index dc751d2..e92521a 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -18,13 +18,14 @@ jobs: - uses: r-lib/actions/setup-r@v2 with: r-version: 'release' + use-public-rspm: true - - name: Install dependencies - shell: Rscript {0} - run: | - install.packages(c("rcmdcheck", "testthat", "roxygen2", "parallel"), - repos = "https://cloud.r-project.org") + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: any::rcmdcheck + needs: check - - name: Check - shell: Rscript {0} - run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning") + - uses: r-lib/actions/check-r-package@v2 + with: + args: 'c("--no-manual", "--as-cran")' + upload-snapshots: true diff --git a/DESCRIPTION b/DESCRIPTION index 2bb4fc3..d044a25 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -20,5 +20,4 @@ Imports: Suggests: testthat (>= 3.0.0), roxygen2 -Roxygen: list(markdown = TRUE) RoxygenNote: 7.1.2 From a55d78e3b23a971c4bba9ee8ad4197f5c3d8ea5f Mon Sep 17 00:00:00 2001 From: Brendan Matthew Galdo Date: Sat, 9 May 2026 16:17:54 -0400 Subject: [PATCH 07/11] Update DESCRIPTION --- DESCRIPTION | 1 - 1 file changed, 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index d044a25..24c10d9 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -20,4 +20,3 @@ Imports: Suggests: testthat (>= 3.0.0), roxygen2 -RoxygenNote: 7.1.2 From 05df54cd44ad0e76659c4a8b66fcb02059120f1d Mon Sep 17 00:00:00 2001 From: Brendan Matthew Galdo Date: Sat, 9 May 2026 16:23:33 -0400 Subject: [PATCH 08/11] Update DESCRIPTION --- DESCRIPTION | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 24c10d9..ed8a611 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -18,5 +18,4 @@ Imports: stats, parallel Suggests: - testthat (>= 3.0.0), - roxygen2 + testthat (>= 3.0.0) From 7c2c8f181cd8bb01d46c1d633473d321c1f63dab Mon Sep 17 00:00:00 2001 From: Brendan Matthew Galdo Date: Sat, 9 May 2026 16:26:53 -0400 Subject: [PATCH 09/11] Update R-CMD-check.yaml --- .github/workflows/R-CMD-check.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index e92521a..e2f46c8 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -18,7 +18,6 @@ jobs: - uses: r-lib/actions/setup-r@v2 with: r-version: 'release' - use-public-rspm: true - uses: r-lib/actions/setup-r-dependencies@v2 with: From dc518c154deb8d14dac9f9f8c3dd789601783f0a Mon Sep 17 00:00:00 2001 From: Brendan Matthew Galdo Date: Sat, 9 May 2026 16:42:00 -0400 Subject: [PATCH 10/11] Remove .Rprofile from repo; add to .gitignore .Rprofile called library(roxygen2) and library(devtools) at R startup, causing CI failure because neither package is available before dependency installation. Machine-specific session config should not be version-controlled. Co-Authored-By: Claude Sonnet 4.6 --- .Rprofile | 2 -- .gitignore | 4 ++++ 2 files changed, 4 insertions(+), 2 deletions(-) delete mode 100644 .Rprofile diff --git a/.Rprofile b/.Rprofile deleted file mode 100644 index 0f860de..0000000 --- a/.Rprofile +++ /dev/null @@ -1,2 +0,0 @@ -library(roxygen2) -library(devtools) diff --git a/.gitignore b/.gitignore index ee875fc..b4aaf6d 100644 --- a/.gitignore +++ b/.gitignore @@ -24,3 +24,7 @@ tests/testthat/_snaps/ # devtools / roxygen /doc/ /Meta/ + +# local R session config (machine-specific) +.Rprofile +.Renviron From d17642727eb88b61c286a8f07be8ddce966a9e8b Mon Sep 17 00:00:00 2001 From: Brendan Matthew Galdo Date: Sat, 9 May 2026 19:37:06 -0400 Subject: [PATCH 11/11] change test params --- tests/testthat/test-optim_SQGDE.R | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/tests/testthat/test-optim_SQGDE.R b/tests/testthat/test-optim_SQGDE.R index 02be58e..a7228b8 100644 --- a/tests/testthat/test-optim_SQGDE.R +++ b/tests/testthat/test-optim_SQGDE.R @@ -45,7 +45,7 @@ test_that("MLE factorizable MVN recovers sample means", { test_that("univariate objective recovers sample mean", { set.seed(42) - obs <- rnorm(300, mean = 2.5, sd = 1) + obs <- rnorm(300, mean = 4, sd = 1) analytic_mu <- mean(obs) neg_log_lik_1d <- function(x, obs) { @@ -60,9 +60,9 @@ test_that("univariate objective recovers sample mean", { n_params = 1, n_iter = 500, n_particles = 6, - n_diff = 1, + n_diff = 2, init_center = 0, - init_sd = 2 + init_sd = 1 ), obs = obs )