From a80abd3a9de1c226b26fba5f4524212ab25a4a34 Mon Sep 17 00:00:00 2001 From: Daniel Nachun Date: Sat, 12 Apr 2025 09:57:41 -0700 Subject: [PATCH 01/13] clean up CI --- .github/workflows/R-CMD-check.yaml | 50 ---------------------------- .github/workflows/ci.yml | 16 ++++----- .github/workflows/test-coverage.yaml | 28 ---------------- 3 files changed, 8 insertions(+), 86 deletions(-) delete mode 100644 .github/workflows/R-CMD-check.yaml delete mode 100644 .github/workflows/test-coverage.yaml diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml deleted file mode 100644 index 3d53917..0000000 --- a/.github/workflows/R-CMD-check.yaml +++ /dev/null @@ -1,50 +0,0 @@ - -on: - push: - branches: [main, master] - pull_request: - branches: [main, master] - -name: R-CMD-check - -jobs: - R-CMD-check: - runs-on: ${{ matrix.config.os }} - - name: ${{ matrix.config.os }} (${{ matrix.config.r }}) - - strategy: - fail-fast: false - matrix: - config: - - {os: windows-latest, r: "release"} - - {os: macOS-latest, r: "release"} - - {os: ubuntu-latest, r: "release"} - - env: - R_REMOTES_NO_ERRORS_FROM_WARNINGS: true - GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} - - steps: - - uses: actions/checkout@v2 - - - uses: r-lib/actions/setup-r@v2 - with: - r-version: ${{ matrix.config.r }} - - - uses: r-lib/actions/setup-pandoc@v2 - - - name: Install dependencies - run: | - install.packages(c("remotes", "rcmdcheck", "covr", "testthat")) - remotes::install_deps(dependencies = TRUE) - shell: Rscript {0} - - - name: Check - run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check") - shell: Rscript {0} - - - name: Test coverage - run: covr::codecov() - shell: Rscript {0} - diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 5637fc9..644cc8a 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -33,11 +33,11 @@ jobs: - name: Run unit tests run: pixi run --environment ${{ matrix.environment }} devtools_test - # - name: Check unit test code coverage - # run: pixi run --environment ${{ matrix.environment }} codecov + - name: Check unit test code coverage + run: pixi run --environment ${{ matrix.environment }} codecov - #- name: Run R CMD CHECK - #run: pixi run rcmdcheck + - name: Run R CMD CHECK + run: pixi run rcmdcheck ci_osx-64: name: osx-64 CI @@ -62,8 +62,8 @@ jobs: - name: Run unit tests run: pixi run --environment ${{ matrix.environment }} devtools_test - #- name: Run R CMD CHECK - #run: pixi run rcmdcheck + - name: Run R CMD CHECK + run: pixi run rcmdcheck ci_osx-arm64: name: osx-arm64 CI @@ -88,5 +88,5 @@ jobs: - name: Run unit tests run: pixi run --environment ${{ matrix.environment }} devtools_test - #- name: Run R CMD CHECK - #run: pixi run rcmdcheck + - name: Run R CMD CHECK + run: pixi run rcmdcheck diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml deleted file mode 100644 index 61d3681..0000000 --- a/.github/workflows/test-coverage.yaml +++ /dev/null @@ -1,28 +0,0 @@ - -on: - push: - branches: [main, master] - pull_request: - branches: [main, master] - -name: test-coverage - -jobs: - test-coverage: - runs-on: ubuntu-latest - - steps: - - uses: actions/checkout@v2 - - - uses: r-lib/actions/setup-r@v2 - - - name: Install dependencies - run: | - install.packages(c("remotes", "covr")) - remotes::install_deps(dependencies = TRUE) - shell: Rscript {0} - - - name: Test coverage - run: covr::codecov() - shell: Rscript {0} - From a6baef615d07ff1b125e05b1de5155839681bd8d Mon Sep 17 00:00:00 2001 From: Daniel Nachun Date: Sat, 12 Apr 2025 10:00:38 -0700 Subject: [PATCH 02/13] clean up CI --- .github/workflows/ci.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 644cc8a..211e564 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -33,12 +33,12 @@ jobs: - name: Run unit tests run: pixi run --environment ${{ matrix.environment }} devtools_test - - name: Check unit test code coverage - run: pixi run --environment ${{ matrix.environment }} codecov - - name: Run R CMD CHECK run: pixi run rcmdcheck + - name: Check unit test code coverage + run: pixi run --environment ${{ matrix.environment }} codecov + ci_osx-64: name: osx-64 CI runs-on: macos-13 From ab7350f8504eced193fb100950d0fd8220c554a6 Mon Sep 17 00:00:00 2001 From: Daniel Nachun Date: Sat, 12 Apr 2025 10:03:55 -0700 Subject: [PATCH 03/13] clean up CI --- .github/workflows/ci.yml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 211e564..abbacee 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -34,7 +34,11 @@ jobs: run: pixi run --environment ${{ matrix.environment }} devtools_test - name: Run R CMD CHECK - run: pixi run rcmdcheck + run: | + pixi install --environment ${{ matrix.environment }} + ln -sf $(pwd)/.pixi/envs/default/lib/libhwasan.so.0 $(pwd)/.pixi/envs/default/lib/libhwasan.so + ln -sf $(pwd)/.pixi/envs/${{ matrix.environment }}/lib/libhwasan.so.0 $(pwd)/.pixi/envs/${{ matrix.environment }}/lib/libhwasan.so + pixi run --environment ${{ matrix.environment }} rcmdcheck - name: Check unit test code coverage run: pixi run --environment ${{ matrix.environment }} codecov From 747a9d35049cdc7b232658915e3ae8c77e2a3aca Mon Sep 17 00:00:00 2001 From: Daniel Nachun Date: Sat, 12 Apr 2025 10:20:39 -0700 Subject: [PATCH 04/13] clean up CI --- .github/environment/pixi.toml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/.github/environment/pixi.toml b/.github/environment/pixi.toml index 691796b..cf3a91f 100644 --- a/.github/environment/pixi.toml +++ b/.github/environment/pixi.toml @@ -10,7 +10,11 @@ libc = { family="glibc", version="2.17" } devtools_document = "R -e 'devtools::document()'" devtools_test = "R -e 'devtools::test()'" codecov = "R -e 'covr::codecov(quiet = FALSE)'" -rcmdcheck = "R -e 'rcmdcheck::rcmdcheck()'" +rcmdcheck = { + "R -e 'devtools::build()'", + "mv ./colocboost-*.tar.gz ./colocboost.tar.gz" + "R -e 'rcmdcheck::rcmdcheck(pkg = \"./colocboost.tar.gz\"), args = c(\"--as-cran\", \"--no-manual\"))'" +} use_major_version = "R -e 'usethis::Use_version(which = \"major\", push = FALSE)'" use_minor_version = "R -e 'usethis::use_version(which = \"minor\", push = FALSE)'" use_patch_version = "R -e 'usethis::use_version(which = \"patch\", push = FALSE)'" From 341a84790d386fb43f59b5572bf06f9fc91e3fea Mon Sep 17 00:00:00 2001 From: Daniel Nachun Date: Sat, 12 Apr 2025 10:22:29 -0700 Subject: [PATCH 05/13] clean up CI --- .github/environment/pixi.toml | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/.github/environment/pixi.toml b/.github/environment/pixi.toml index cf3a91f..ebe01d2 100644 --- a/.github/environment/pixi.toml +++ b/.github/environment/pixi.toml @@ -10,11 +10,7 @@ libc = { family="glibc", version="2.17" } devtools_document = "R -e 'devtools::document()'" devtools_test = "R -e 'devtools::test()'" codecov = "R -e 'covr::codecov(quiet = FALSE)'" -rcmdcheck = { - "R -e 'devtools::build()'", - "mv ./colocboost-*.tar.gz ./colocboost.tar.gz" - "R -e 'rcmdcheck::rcmdcheck(pkg = \"./colocboost.tar.gz\"), args = c(\"--as-cran\", \"--no-manual\"))'" -} +rcmdcheck = "R -e 'devtools::build()'; mv ./colocboost-*.tar.gz ./colocboost.tar.gz; R -e 'rcmdcheck::rcmdcheck(pkg = \"./colocboost.tar.gz\"), args = c(\"--as-cran\", \"--no-manual\"))'" use_major_version = "R -e 'usethis::Use_version(which = \"major\", push = FALSE)'" use_minor_version = "R -e 'usethis::use_version(which = \"minor\", push = FALSE)'" use_patch_version = "R -e 'usethis::use_version(which = \"patch\", push = FALSE)'" From c42e8069f6fdd4c30037c319b94dbefe70c5e08b Mon Sep 17 00:00:00 2001 From: Daniel Nachun Date: Sat, 12 Apr 2025 10:23:55 -0700 Subject: [PATCH 06/13] clean up CI --- .github/environment/pixi.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/environment/pixi.toml b/.github/environment/pixi.toml index ebe01d2..f677ef8 100644 --- a/.github/environment/pixi.toml +++ b/.github/environment/pixi.toml @@ -10,7 +10,7 @@ libc = { family="glibc", version="2.17" } devtools_document = "R -e 'devtools::document()'" devtools_test = "R -e 'devtools::test()'" codecov = "R -e 'covr::codecov(quiet = FALSE)'" -rcmdcheck = "R -e 'devtools::build()'; mv ./colocboost-*.tar.gz ./colocboost.tar.gz; R -e 'rcmdcheck::rcmdcheck(pkg = \"./colocboost.tar.gz\"), args = c(\"--as-cran\", \"--no-manual\"))'" +rcmdcheck = "R -e 'devtools::build()'; mv ./colocboost-*.tar.gz ./colocboost.tar.gz; R -e 'rcmdcheck::rcmdcheck(pkg = \"./colocboost.tar.gz\", args = c(\"--as-cran\", \"--no-manual\"))'" use_major_version = "R -e 'usethis::Use_version(which = \"major\", push = FALSE)'" use_minor_version = "R -e 'usethis::use_version(which = \"minor\", push = FALSE)'" use_patch_version = "R -e 'usethis::use_version(which = \"patch\", push = FALSE)'" From ac2f6db1f1b04ca05e67673e2cf6a317ac927e19 Mon Sep 17 00:00:00 2001 From: Daniel Nachun Date: Sat, 12 Apr 2025 10:30:56 -0700 Subject: [PATCH 07/13] clean up CI --- .github/environment/pixi.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/environment/pixi.toml b/.github/environment/pixi.toml index f677ef8..189c452 100644 --- a/.github/environment/pixi.toml +++ b/.github/environment/pixi.toml @@ -10,7 +10,7 @@ libc = { family="glibc", version="2.17" } devtools_document = "R -e 'devtools::document()'" devtools_test = "R -e 'devtools::test()'" codecov = "R -e 'covr::codecov(quiet = FALSE)'" -rcmdcheck = "R -e 'devtools::build()'; mv ./colocboost-*.tar.gz ./colocboost.tar.gz; R -e 'rcmdcheck::rcmdcheck(pkg = \"./colocboost.tar.gz\", args = c(\"--as-cran\", \"--no-manual\"))'" +rcmdcheck = "R -e 'devtools::build()'; mv ./colocboost-*.tar.gz ./colocboost.tar.gz; R -e 'rcmdcheck::rcmdcheck(path = \"./colocboost.tar.gz\", args = c(\"--as-cran\", \"--no-manual\"))'" use_major_version = "R -e 'usethis::Use_version(which = \"major\", push = FALSE)'" use_minor_version = "R -e 'usethis::use_version(which = \"minor\", push = FALSE)'" use_patch_version = "R -e 'usethis::use_version(which = \"patch\", push = FALSE)'" From b8654eaf442df1c5771530f6d1239dae4e633e99 Mon Sep 17 00:00:00 2001 From: Daniel Nachun Date: Sat, 12 Apr 2025 10:37:09 -0700 Subject: [PATCH 08/13] clean up CI --- .github/environment/pixi.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/environment/pixi.toml b/.github/environment/pixi.toml index 189c452..56c9ee0 100644 --- a/.github/environment/pixi.toml +++ b/.github/environment/pixi.toml @@ -10,7 +10,7 @@ libc = { family="glibc", version="2.17" } devtools_document = "R -e 'devtools::document()'" devtools_test = "R -e 'devtools::test()'" codecov = "R -e 'covr::codecov(quiet = FALSE)'" -rcmdcheck = "R -e 'devtools::build()'; mv ./colocboost-*.tar.gz ./colocboost.tar.gz; R -e 'rcmdcheck::rcmdcheck(path = \"./colocboost.tar.gz\", args = c(\"--as-cran\", \"--no-manual\"))'" +rcmdcheck = "R -e 'devtools::build()'; mv ../colocboost-*.tar.gz ../colocboost.tar.gz; R -e 'rcmdcheck::rcmdcheck(path = \"../colocboost.tar.gz\", args = c(\"--as-cran\", \"--no-manual\"))'" use_major_version = "R -e 'usethis::Use_version(which = \"major\", push = FALSE)'" use_minor_version = "R -e 'usethis::use_version(which = \"minor\", push = FALSE)'" use_patch_version = "R -e 'usethis::use_version(which = \"patch\", push = FALSE)'" From 846d29c404e0bcb7cd377ead4f36338072a2c10d Mon Sep 17 00:00:00 2001 From: Daniel Nachun Date: Sat, 12 Apr 2025 10:39:59 -0700 Subject: [PATCH 09/13] clean up CI --- .github/environment/pixi.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/environment/pixi.toml b/.github/environment/pixi.toml index 56c9ee0..7332426 100644 --- a/.github/environment/pixi.toml +++ b/.github/environment/pixi.toml @@ -10,7 +10,7 @@ libc = { family="glibc", version="2.17" } devtools_document = "R -e 'devtools::document()'" devtools_test = "R -e 'devtools::test()'" codecov = "R -e 'covr::codecov(quiet = FALSE)'" -rcmdcheck = "R -e 'devtools::build()'; mv ../colocboost-*.tar.gz ../colocboost.tar.gz; R -e 'rcmdcheck::rcmdcheck(path = \"../colocboost.tar.gz\", args = c(\"--as-cran\", \"--no-manual\"))'" +rcmdcheck = "R -e 'devtools::build()'; ls ..; ls; mv ../colocboost-*.tar.gz ../colocboost.tar.gz; R -e 'rcmdcheck::rcmdcheck(path = \"../colocboost.tar.gz\", args = c(\"--as-cran\", \"--no-manual\"))'" use_major_version = "R -e 'usethis::Use_version(which = \"major\", push = FALSE)'" use_minor_version = "R -e 'usethis::use_version(which = \"minor\", push = FALSE)'" use_patch_version = "R -e 'usethis::use_version(which = \"patch\", push = FALSE)'" From 3858f25e33e785fc001c01236864cede835c20eb Mon Sep 17 00:00:00 2001 From: Daniel Nachun Date: Sat, 12 Apr 2025 10:41:41 -0700 Subject: [PATCH 10/13] clean up CI --- .github/environment/pixi.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/environment/pixi.toml b/.github/environment/pixi.toml index 7332426..52a1fef 100644 --- a/.github/environment/pixi.toml +++ b/.github/environment/pixi.toml @@ -10,7 +10,7 @@ libc = { family="glibc", version="2.17" } devtools_document = "R -e 'devtools::document()'" devtools_test = "R -e 'devtools::test()'" codecov = "R -e 'covr::codecov(quiet = FALSE)'" -rcmdcheck = "R -e 'devtools::build()'; ls ..; ls; mv ../colocboost-*.tar.gz ../colocboost.tar.gz; R -e 'rcmdcheck::rcmdcheck(path = \"../colocboost.tar.gz\", args = c(\"--as-cran\", \"--no-manual\"))'" +rcmdcheck = "R -e 'devtools::build()'; mv ./colocboost_*.tar.gz ./colocboost.tar.gz; R -e 'rcmdcheck::rcmdcheck(path = \"./colocboost.tar.gz\", args = c(\"--as-cran\", \"--no-manual\"))'" use_major_version = "R -e 'usethis::Use_version(which = \"major\", push = FALSE)'" use_minor_version = "R -e 'usethis::use_version(which = \"minor\", push = FALSE)'" use_patch_version = "R -e 'usethis::use_version(which = \"patch\", push = FALSE)'" From 56e2dbc55042586a7b87538fc3fdb7e825be1f62 Mon Sep 17 00:00:00 2001 From: Daniel Nachun Date: Sat, 12 Apr 2025 11:38:16 -0700 Subject: [PATCH 11/13] clean up CI --- .github/environment/pixi.toml | 7 +++++-- DESCRIPTION | 4 ++-- 2 files changed, 7 insertions(+), 4 deletions(-) diff --git a/.github/environment/pixi.toml b/.github/environment/pixi.toml index 52a1fef..90f5821 100644 --- a/.github/environment/pixi.toml +++ b/.github/environment/pixi.toml @@ -10,7 +10,8 @@ libc = { family="glibc", version="2.17" } devtools_document = "R -e 'devtools::document()'" devtools_test = "R -e 'devtools::test()'" codecov = "R -e 'covr::codecov(quiet = FALSE)'" -rcmdcheck = "R -e 'devtools::build()'; mv ./colocboost_*.tar.gz ./colocboost.tar.gz; R -e 'rcmdcheck::rcmdcheck(path = \"./colocboost.tar.gz\", args = c(\"--as-cran\", \"--no-manual\"))'" +build = "R -e 'devtools::build()'" +rcmdcheck = "R -e 'pkg <- list.files(\"..\", pattern = \".tar.gz\", full.names = TRUE); rcmdcheck::rcmdcheck(path = pkg[1], args = c(\"--as-cran\"))'" use_major_version = "R -e 'usethis::Use_version(which = \"major\", push = FALSE)'" use_minor_version = "R -e 'usethis::use_version(which = \"minor\", push = FALSE)'" use_patch_version = "R -e 'usethis::use_version(which = \"patch\", push = FALSE)'" @@ -26,7 +27,9 @@ r43 = {features = ["r43"]} r44 = {features = ["r44"]} [dependencies] +"r-ashr" = "*" +"r-covr" = "*" "r-devtools" = "*" +"r-mass" = "*" "r-rcmdcheck" = "*" -"r-covr" = "*" "r-tidyverse" = "*" diff --git a/DESCRIPTION b/DESCRIPTION index 0586bef..b0f74b5 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -28,8 +28,8 @@ Suggests: testthat (>= 3.0.0), knitr, rmarkdown, - susieR, - ashr + ashr, + MASS VignetteBuilder: knitr Roxygen: list(markdown = TRUE) Config/testthat/edition: 3 From 7644abd163f1d90e14af86e177b57dd60623af76 Mon Sep 17 00:00:00 2001 From: Daniel Nachun Date: Sat, 12 Apr 2025 11:43:19 -0700 Subject: [PATCH 12/13] clean up CI --- .github/workflows/ci.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index abbacee..ffee46c 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -38,6 +38,7 @@ jobs: pixi install --environment ${{ matrix.environment }} ln -sf $(pwd)/.pixi/envs/default/lib/libhwasan.so.0 $(pwd)/.pixi/envs/default/lib/libhwasan.so ln -sf $(pwd)/.pixi/envs/${{ matrix.environment }}/lib/libhwasan.so.0 $(pwd)/.pixi/envs/${{ matrix.environment }}/lib/libhwasan.so + pixi run --environment ${{ matrix.environment }} build pixi run --environment ${{ matrix.environment }} rcmdcheck - name: Check unit test code coverage From d90ed261c37d71477483e378f24ef23f0ac6138d Mon Sep 17 00:00:00 2001 From: Daniel Nachun Date: Sat, 12 Apr 2025 11:46:23 -0700 Subject: [PATCH 13/13] clean up CI --- .github/workflows/ci.yml | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index ffee46c..45ad255 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -68,7 +68,9 @@ jobs: run: pixi run --environment ${{ matrix.environment }} devtools_test - name: Run R CMD CHECK - run: pixi run rcmdcheck + run: | + pixi run --environment ${{ matrix.environment }} build + pixi run --environment ${{ matrix.environment }} rcmdcheck ci_osx-arm64: name: osx-arm64 CI @@ -94,4 +96,6 @@ jobs: run: pixi run --environment ${{ matrix.environment }} devtools_test - name: Run R CMD CHECK - run: pixi run rcmdcheck + run: | + pixi run --environment ${{ matrix.environment }} build + pixi run --environment ${{ matrix.environment }} rcmdcheck