From dc4987d5c0244ab8d43847bd108d7644fc339948 Mon Sep 17 00:00:00 2001 From: adeschen Date: Thu, 11 Sep 2025 12:50:15 -0400 Subject: [PATCH 1/8] Update check-bioc actions --- .github/workflows/check-bioc.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/check-bioc.yaml b/.github/workflows/check-bioc.yaml index 334eb502..d66b4b4c 100644 --- a/.github/workflows/check-bioc.yaml +++ b/.github/workflows/check-bioc.yaml @@ -52,12 +52,12 @@ jobs: matrix: config: ##- { os: ubuntu-latest, r: '4.4', bioc: '3.19', cont: "bioconductor/bioconductor_docker:RELEASE_3_19", rspm: "https://packagemanager.posit.co/cran/__linux__/jammy/latest" } - - { os: ubuntu-latest, r: '4.5.0', bioc: '3.21', cont: "bioconductor/bioconductor_docker:RELEASE_3_21", rspm: "https://packagemanager.posit.co/cran/__linux__/jammy/latest" } + ##- { os: ubuntu-latest, r: '4.5.0', bioc: '3.21', cont: "bioconductor/bioconductor_docker:RELEASE_3_21", rspm: "https://packagemanager.posit.co/cran/__linux__/jammy/latest" } - { os: ubuntu-devel, r: '4.6.0', bioc: '3.22', cont: "bioconductor/bioconductor_docker:RELEASE_3_22", rspm: "https://packagemanager.posit.co/cran/__linux__/jammy/latest" } ## - { os: macOS-latest, r: '4.4', bioc: '3.19'} - - { os: macOS-latest, r: '4.5.0', bioc: '3.21'} + - { os: macOS-latest, r: '4.5.1', bioc: '3.21'} ## - { os: windows-latest, r: '4.2.2', bioc: '3.16'} - - { os: windows-latest, r: '4.5.0', bioc: '3.21'} + - { os: windows-latest, r: '4.5.1', bioc: '3.21'} env: R_REMOTES_NO_ERRORS_FROM_WARNINGS: true From 08c7adf7527840e0102f6109c5b8921381695450 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Astrid=20Desch=C3=AAnes?= Date: Mon, 15 Sep 2025 21:06:52 -0400 Subject: [PATCH 2/8] Update check-bioc.yaml --- .github/workflows/check-bioc.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/check-bioc.yaml b/.github/workflows/check-bioc.yaml index d66b4b4c..0cb0d167 100644 --- a/.github/workflows/check-bioc.yaml +++ b/.github/workflows/check-bioc.yaml @@ -53,7 +53,7 @@ jobs: config: ##- { os: ubuntu-latest, r: '4.4', bioc: '3.19', cont: "bioconductor/bioconductor_docker:RELEASE_3_19", rspm: "https://packagemanager.posit.co/cran/__linux__/jammy/latest" } ##- { os: ubuntu-latest, r: '4.5.0', bioc: '3.21', cont: "bioconductor/bioconductor_docker:RELEASE_3_21", rspm: "https://packagemanager.posit.co/cran/__linux__/jammy/latest" } - - { os: ubuntu-devel, r: '4.6.0', bioc: '3.22', cont: "bioconductor/bioconductor_docker:RELEASE_3_22", rspm: "https://packagemanager.posit.co/cran/__linux__/jammy/latest" } + - { os: ubuntu-devel, r: 'devel', bioc: '3.22', cont: "bioconductor/bioconductor_docker:RELEASE_3_22", rspm: "https://packagemanager.posit.co/cran/__linux__/jammy/latest" } ## - { os: macOS-latest, r: '4.4', bioc: '3.19'} - { os: macOS-latest, r: '4.5.1', bioc: '3.21'} ## - { os: windows-latest, r: '4.2.2', bioc: '3.16'} From 3731d5a45e612f275717b80718ec79a8ca6adfa7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Astrid=20Desch=C3=AAnes?= Date: Mon, 15 Sep 2025 23:57:13 -0400 Subject: [PATCH 3/8] Update check-bioc.yaml --- .github/workflows/check-bioc.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/check-bioc.yaml b/.github/workflows/check-bioc.yaml index 0cb0d167..655b0b7a 100644 --- a/.github/workflows/check-bioc.yaml +++ b/.github/workflows/check-bioc.yaml @@ -53,7 +53,7 @@ jobs: config: ##- { os: ubuntu-latest, r: '4.4', bioc: '3.19', cont: "bioconductor/bioconductor_docker:RELEASE_3_19", rspm: "https://packagemanager.posit.co/cran/__linux__/jammy/latest" } ##- { os: ubuntu-latest, r: '4.5.0', bioc: '3.21', cont: "bioconductor/bioconductor_docker:RELEASE_3_21", rspm: "https://packagemanager.posit.co/cran/__linux__/jammy/latest" } - - { os: ubuntu-devel, r: 'devel', bioc: '3.22', cont: "bioconductor/bioconductor_docker:RELEASE_3_22", rspm: "https://packagemanager.posit.co/cran/__linux__/jammy/latest" } + - { os: ubuntu-latest, r: 'devel', bioc: 'devel', cont: "bioconductor/bioconductor_docker:RELEASE_3_22", rspm: "https://packagemanager.posit.co/cran/__linux__/jammy/latest" } ## - { os: macOS-latest, r: '4.4', bioc: '3.19'} - { os: macOS-latest, r: '4.5.1', bioc: '3.21'} ## - { os: windows-latest, r: '4.2.2', bioc: '3.16'} From 10df291231a418cf9a9404d8fb5d8427f819b4ab Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Astrid=20Desch=C3=AAnes?= Date: Tue, 16 Sep 2025 00:00:18 -0400 Subject: [PATCH 4/8] Update check-bioc.yaml --- .github/workflows/check-bioc.yaml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.github/workflows/check-bioc.yaml b/.github/workflows/check-bioc.yaml index 655b0b7a..df3370d7 100644 --- a/.github/workflows/check-bioc.yaml +++ b/.github/workflows/check-bioc.yaml @@ -51,9 +51,8 @@ jobs: fail-fast: false matrix: config: - ##- { os: ubuntu-latest, r: '4.4', bioc: '3.19', cont: "bioconductor/bioconductor_docker:RELEASE_3_19", rspm: "https://packagemanager.posit.co/cran/__linux__/jammy/latest" } ##- { os: ubuntu-latest, r: '4.5.0', bioc: '3.21', cont: "bioconductor/bioconductor_docker:RELEASE_3_21", rspm: "https://packagemanager.posit.co/cran/__linux__/jammy/latest" } - - { os: ubuntu-latest, r: 'devel', bioc: 'devel', cont: "bioconductor/bioconductor_docker:RELEASE_3_22", rspm: "https://packagemanager.posit.co/cran/__linux__/jammy/latest" } + - { os: ubuntu-latest, r: 'devel', bioc: '3.22', cont: "bioconductor/bioconductor_docker:RELEASE_3_22", rspm: "https://packagemanager.posit.co/cran/__linux__/jammy/latest" } ## - { os: macOS-latest, r: '4.4', bioc: '3.19'} - { os: macOS-latest, r: '4.5.1', bioc: '3.21'} ## - { os: windows-latest, r: '4.2.2', bioc: '3.16'} From 0c0ccf41245ad3f0669bdd0b168fd642d6a957d0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Astrid=20Desch=C3=AAnes?= Date: Tue, 16 Sep 2025 14:43:06 -0400 Subject: [PATCH 5/8] Update check-bioc.yaml --- .github/workflows/check-bioc.yaml | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/.github/workflows/check-bioc.yaml b/.github/workflows/check-bioc.yaml index df3370d7..2439140e 100644 --- a/.github/workflows/check-bioc.yaml +++ b/.github/workflows/check-bioc.yaml @@ -51,11 +51,9 @@ jobs: fail-fast: false matrix: config: - ##- { os: ubuntu-latest, r: '4.5.0', bioc: '3.21', cont: "bioconductor/bioconductor_docker:RELEASE_3_21", rspm: "https://packagemanager.posit.co/cran/__linux__/jammy/latest" } - { os: ubuntu-latest, r: 'devel', bioc: '3.22', cont: "bioconductor/bioconductor_docker:RELEASE_3_22", rspm: "https://packagemanager.posit.co/cran/__linux__/jammy/latest" } - ## - { os: macOS-latest, r: '4.4', bioc: '3.19'} + - { os: ubuntu-latest, r: '4.5.1', bioc: '3.21'} - { os: macOS-latest, r: '4.5.1', bioc: '3.21'} - ## - { os: windows-latest, r: '4.2.2', bioc: '3.16'} - { os: windows-latest, r: '4.5.1', bioc: '3.21'} env: From 9784d60ab4654210eec9c3c4d5a05d2c57ae5cdb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Astrid=20Desch=C3=AAnes?= Date: Tue, 16 Sep 2025 14:45:53 -0400 Subject: [PATCH 6/8] Update check-bioc.yaml --- .github/workflows/check-bioc.yaml | 11 ++--------- 1 file changed, 2 insertions(+), 9 deletions(-) diff --git a/.github/workflows/check-bioc.yaml b/.github/workflows/check-bioc.yaml index 2439140e..02db537c 100644 --- a/.github/workflows/check-bioc.yaml +++ b/.github/workflows/check-bioc.yaml @@ -61,19 +61,13 @@ jobs: RSPM: ${{ matrix.config.rspm }} NOT_CRAN: true TZ: UTC + _R_CHECK_SYSTEM_CLOCK_: FALSE + R_LIBS_USER: tempdir/Library GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} steps: - ## Set the R library to the directory matching the - ## R packages cache step further below when running on Docker (Linux). - - name: Set R Library home on Linux - if: runner.os == 'Linux' - run: | - mkdir /__w/_temp/Library - echo ".libPaths('/__w/_temp/Library')" > ~/.Rprofile - ## Most of these steps are the same as the ones in ## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml ## If they update their steps, we will also need to update ours. @@ -82,7 +76,6 @@ jobs: ## R is already included in the Bioconductor docker images - name: Setup R from r-lib - if: runner.os != 'Linux' uses: r-lib/actions/setup-r@v2 with: r-version: ${{ matrix.config.r }} From 24f9cad7f6e3f54b07886c5a638817b2fcefd345 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Astrid=20Desch=C3=AAnes?= Date: Tue, 16 Sep 2025 14:50:12 -0400 Subject: [PATCH 7/8] Update check-bioc.yaml --- .github/workflows/check-bioc.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/check-bioc.yaml b/.github/workflows/check-bioc.yaml index 02db537c..061f84d4 100644 --- a/.github/workflows/check-bioc.yaml +++ b/.github/workflows/check-bioc.yaml @@ -51,8 +51,8 @@ jobs: fail-fast: false matrix: config: - - { os: ubuntu-latest, r: 'devel', bioc: '3.22', cont: "bioconductor/bioconductor_docker:RELEASE_3_22", rspm: "https://packagemanager.posit.co/cran/__linux__/jammy/latest" } - - { os: ubuntu-latest, r: '4.5.1', bioc: '3.21'} + - { os: ubuntu-latest, r: 'devel', bioc: '3.22'} + - { os: ubuntu-latest, r: '4.5.1', bioc: '3.21', cont: "bioconductor/bioconductor_docker:RELEASE_3_22"} - { os: macOS-latest, r: '4.5.1', bioc: '3.21'} - { os: windows-latest, r: '4.5.1', bioc: '3.21'} From 5a07c2af590ea86144954d13e31ee2998e3ba45c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Astrid=20Desch=C3=AAnes?= Date: Tue, 16 Sep 2025 14:54:25 -0400 Subject: [PATCH 8/8] Update check-bioc.yaml --- .github/workflows/check-bioc.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/check-bioc.yaml b/.github/workflows/check-bioc.yaml index 061f84d4..73e2f51c 100644 --- a/.github/workflows/check-bioc.yaml +++ b/.github/workflows/check-bioc.yaml @@ -52,7 +52,7 @@ jobs: matrix: config: - { os: ubuntu-latest, r: 'devel', bioc: '3.22'} - - { os: ubuntu-latest, r: '4.5.1', bioc: '3.21', cont: "bioconductor/bioconductor_docker:RELEASE_3_22"} + - { os: ubuntu-latest, r: '4.5.1', bioc: '3.21', cont: "bioconductor/bioconductor_docker:RELEASE_3_21"} - { os: macOS-latest, r: '4.5.1', bioc: '3.21'} - { os: windows-latest, r: '4.5.1', bioc: '3.21'}