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Violin plots

Violin plots #323

Workflow file for this run

# NOTE: This workflow is overkill for most R packages
# check-standard.yaml is likely a better choice
# usethis::use_github_action("check-standard") will install it.
#
# 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
on:
push:
branches:
- main
- devel
pull_request:
branches:
- main
- devel
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: macOS-latest, r: 'release'}
- {os: windows-latest, r: 'release'}
- {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest", http-user-agent: "R/4.1.0 (ubuntu-20.04) R (4.1.0 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions" }
- {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-20.04, r: 'oldrel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
env:
RSPM: ${{ matrix.config.rspm }}
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
steps:
- uses: actions/checkout@v2
- uses: r-lib/actions/setup-r@v2
id: install-r
with:
r-version: ${{ matrix.config.r }}
http-user-agent: ${{ matrix.config.http-user-agent }}
- uses: r-lib/actions/setup-pandoc@v2
- uses: r-lib/actions/setup-tinytex@v2
- run: tlmgr --version
- run: tlmgr install apa6 threeparttable caption fancyhdr endfloat was multirow threeparttablex environ trimspaces lineno csquotes babel-english grfext
- name: Install Ghostscript on Linux
if: runner.os == 'Linux'
run: sudo DEBIAN_FRONTEND=noninteractive apt-get install --yes ghostscript
- name: Install Ghostscript on macOS
if: runner.os == 'macOS'
run: brew install ghostscript
- name: Install Ghostscript on Windows
if: runner.os == 'Windows'
run: choco install ghostscript --no-progress
- name: Install pak and query dependencies
run: |
cat("::group::Install pak\n")
options(pak.no_extra_messages = TRUE)
install.packages("pak", repos = "https://r-lib.github.io/p/pak/dev/")
deps <- pak::pkg_deps(
"local::."
, dependencies = list(
direct = c("Depends", "Imports", "LinkingTo", "Suggests")
, indirect = c("Depends", "Imports", "LinkingTo")
)
)
saveRDS(deps, ".github/r-depends.rds")
shell: Rscript {0}
- name: Get R and OS version
id: get-version
run: |
cat("::set-output name=os-version::", sessionInfo()$running, "\n", sep = "")
cat("::set-output name=r-version::", R.Version()$version.string, "\n", sep = "")
cat("::endgroup::\n")
shell: Rscript {0}
- name: Restore R package cache
uses: actions/cache@v2
with:
path: |
${{ env.R_LIBS_USER }}/*
!${{ env.R_LIBS_USER }}/pak
key: ${{ steps.get-version.outputs.os-version }}-${{ steps.get-version.outputs.r-version }}-${{inputs.cache-version }}-${{ hashFiles('.github/r-depends.rds') }}
restore-keys: ${{ steps.get-version.outputs.os-version }}-${{ steps.get-version.outputs.r-version }}-${{inputs.cache-version }}-
- name: Install dependencies
run: |
cat("::group::Install dependencies\n")
options(pak.no_extra_messages = TRUE)
local_deps <- pak::local_dev_deps(dependencies = TRUE)[["ref"]]
needs <- sprintf("Config/Needs/%s", strsplit("${{ inputs.needs }}", "[[:space:],]+")[[1]])
needs_deps <- pak::local_dev_deps(dependencies = needs)[["ref"]]
needs_only_deps <- setdiff(needs_deps, local_deps)
extra_deps <- c("rcmdcheck", "covr")
if (Sys.info()[["sysname"]] == "Linux") {
pak::local_system_requirements(execute = TRUE)
for (dep in c(needs_only_deps, extra_deps)) {
pak::pkg_system_requirements(dep, execute = TRUE)
}
}
pak::pkg_install(c(local_deps, needs_only_deps, extra_deps, "sessioninfo"))
cat("::endgroup::\n")
shell: Rscript {0}
- name: Session info
run: |
cat("::group::Session info\n")
options(width = 100)
pkgs <- installed.packages()[, "Package"]
sessioninfo::session_info(pkgs, include_base = TRUE)
cat("::endgroup::\n")
shell: Rscript {0}
- name: Don't use tar 1.30 from Rtools35 to store the cache
shell: bash
run: |
if command -v /c/Rtools/bin/tar && /c/Rtools/bin/tar --version | grep -q 'tar (GNU tar) 1.30'
then echo 'C:/Program Files/Git/usr/bin' >> $GITHUB_PATH
fi
- uses: r-lib/actions/check-r-package@v2
with:
build_args: '"--compact-vignettes=both"'
- name: Code Coverage
env:
_R_CHECK_CRAN_INCOMING_: false
run: covr::codecov()
shell: Rscript {0}
- name: Show testthat output
if: always()
run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
shell: bash
- name: Upload check results
if: failure()
uses: actions/upload-artifact@main
with:
name: ${{ matrix.config.os }}-r${{ matrix.config.r }}-results
path: check
- name: Don't use tar from old Rtools to store the cache
if: ${{ runner.os == 'Windows' && startsWith(steps.install-r.outputs.installed-r-version, '3.6' ) }}
shell: bash
run: echo "C:/Program Files/Git/usr/bin" >> $GITHUB_PATH