update checks

dcgerard · Nov 6, 2023 · e8c27a0 · e8c27a0
1 parent 5d842da
commit e8c27a0
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diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -1,14 +1,10 @@
-# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
-# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches:
-      - main
-      - master
+    branches: [main, master]
   pull_request:
-    branches:
-      - main
-      - master
+    branches: [main, master]
 
 name: R-CMD-check
 
@@ -22,65 +18,32 @@ jobs:
       fail-fast: false
       matrix:
         config:
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
-          - {os: macOS-latest, r: 'release'}
-          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          # - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
 
     env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
 
-      - uses: r-lib/actions/setup-pandoc@v1
-
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        if: runner.os != 'Windows'
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
-
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-          install.packages("BiocManager")
-          BiocManager::install(c("VariantAnnotation", "GenomicRanges", "S4Vectors", "IRanges"))
-        shell: Rscript {0}
-
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
+      - uses: r-lib/actions/check-r-package@v2
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+          upload-snapshots: true
diff --git a/README.Rmd b/README.Rmd
@@ -14,7 +14,7 @@ knitr::opts_chunk$set(
 
 # updog <img src="man/figures/logo.png" align="right" height="139" />
 
-[![R-CMD-check](https://github.com/dcgerard/updog/workflows/R-CMD-check/badge.svg)](https://github.com/dcgerard/updog/actions)
+[![R-CMD-check](https://github.com/dcgerard/updog/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/dcgerard/updog/actions/workflows/R-CMD-check.yaml)
 [![codecov](https://codecov.io/gh/dcgerard/updog/branch/master/graph/badge.svg?token=zjDBKZWjCs)](https://app.codecov.io/gh/dcgerard/updog)
 [![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 [![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/updog)](https://cran.r-project.org/package=updog)

diff --git a/README.md b/README.md
@@ -3,7 +3,7 @@
 
 # updog <img src="man/figures/logo.png" align="right" height="139" />
 
-[![R-CMD-check](https://github.com/dcgerard/updog/workflows/R-CMD-check/badge.svg)](https://github.com/dcgerard/updog/actions)
+[![R-CMD-check](https://github.com/dcgerard/updog/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/dcgerard/updog/actions/workflows/R-CMD-check.yaml)
 [![codecov](https://codecov.io/gh/dcgerard/updog/branch/master/graph/badge.svg?token=zjDBKZWjCs)](https://app.codecov.io/gh/dcgerard/updog)
 [![License: GPL
 v3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
@@ -32,22 +32,21 @@ the data.
 
 Also provided are:
 
--   `filter_snp()`: filter out SNPs based on the output of `multidog()`.
--   `format_multidog()`: format the output of `multidog()` in terms of a
-    multidimensional array.
--   Plot methods. Both `flexdog()` and `multidog()` have plot methods.
-    See the help files of `plot.flexdog()` and `plot.multidog()` for
-    details.
--   Functions to simulate genotypes (`rgeno()`) and read-counts
-    (`rflexdog()`). These support all of the models available in
-    `flexdog()`.
--   Functions to evaluate oracle genotyping performance:
-    `oracle_joint()`, `oracle_mis()`, `oracle_mis_vec()`, and
-    `oracle_cor()`. We mean “oracle” in the sense that we assume that
-    the entire data generation process is known (i.e. the genotype
-    distribution, sequencing error rate, allele bias, and overdispersion
-    are all known). These are good approximations when there are a lot
-    of individuals (but not necessarily large read-depth).
+- `filter_snp()`: filter out SNPs based on the output of `multidog()`.
+- `format_multidog()`: format the output of `multidog()` in terms of a
+  multidimensional array.
+- Plot methods. Both `flexdog()` and `multidog()` have plot methods. See
+  the help files of `plot.flexdog()` and `plot.multidog()` for details.
+- Functions to simulate genotypes (`rgeno()`) and read-counts
+  (`rflexdog()`). These support all of the models available in
+  `flexdog()`.
+- Functions to evaluate oracle genotyping performance: `oracle_joint()`,
+  `oracle_mis()`, `oracle_mis_vec()`, and `oracle_cor()`. We mean
+  “oracle” in the sense that we assume that the entire data generation
+  process is known (i.e. the genotype distribution, sequencing error
+  rate, allele bias, and overdispersion are all known). These are good
+  approximations when there are a lot of individuals (but not
+  necessarily large read-depth).
 
 The original `updog` package is now named `updogAlpha` and may be found
 [here](https://github.com/dcgerard/updogAlpha).