From e8c27a000d126ae01f6990e2a874124bfb8f0b19 Mon Sep 17 00:00:00 2001 From: David Gerard Date: Mon, 6 Nov 2023 12:01:25 -0500 Subject: [PATCH] update checks --- .github/workflows/R-CMD-check.yaml | 77 ++++++++---------------------- README.Rmd | 2 +- README.md | 33 +++++++------ 3 files changed, 37 insertions(+), 75 deletions(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 3cbb0c3..a3ac618 100644 --- 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 index 437a18c..60fccb9 100644 --- a/README.Rmd +++ b/README.Rmd @@ -14,7 +14,7 @@ knitr::opts_chunk$set( # updog -[![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 index ae8fb50..7191fdd 100644 --- a/README.md +++ b/README.md @@ -3,7 +3,7 @@ # updog -[![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).