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Jasen Finch
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Merge pull request #4 from jasenfinch/devel
v0.3.0
2 parents e72d852 + f647532 commit a5cc08a

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‎.Rbuildignore

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^LICENSE\.md$
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^codecov\.yml$
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^docs
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^_pkgdown\.yml$
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^docs$
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^pkgdown$

‎.github/workflows/R-CMD-check.yaml

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# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
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# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
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# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
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# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
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on:
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push:
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branches:
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- main
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- master
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- devel
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branches: [main, master, devel]
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pull_request:
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branches:
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- main
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- master
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branches: [main, master]
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name: R-CMD-check
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fail-fast: false
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matrix:
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config:
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#- {os: macos-latest, r: 'release'}
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- {os: windows-latest, r: 'release'}
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- {os: macOS-latest, r: 'release'}
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- {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
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- {os: ubuntu-latest, r: 'release'}
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- {os: ubuntu-latest, r: 'oldrel-1'}
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env:
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R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
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RSPM: ${{ matrix.config.rspm }}
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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R_KEEP_PKG_SOURCE: yes
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steps:
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- uses: actions/checkout@v2
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- uses: actions/checkout@v3
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- uses: r-lib/actions/setup-r@v1
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with:
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r-version: ${{ matrix.config.r }}
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- uses: r-lib/actions/setup-pandoc@v1
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- name: Query dependencies
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run: |
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install.packages('remotes')
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saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
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writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
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shell: Rscript {0}
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- uses: r-lib/actions/setup-pandoc@v2
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- name: Cache R packages
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if: runner.os != 'Windows'
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uses: actions/cache@v2
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- uses: r-lib/actions/setup-r@v2
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with:
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path: ${{ env.R_LIBS_USER }}
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key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
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restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
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- name: Install system dependencies
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r-version: ${{ matrix.config.r }}
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http-user-agent: ${{ matrix.config.http-user-agent }}
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use-public-rspm: true
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- name: Install Linux system dependencies
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if: runner.os == 'Linux'
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run: |
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while read -r cmd
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do
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eval sudo $cmd
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done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
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sudo apt-get install -y libopenbabel-dev
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sudo apt install libopenbabel-dev libeigen3-dev
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- name: Install dependencies
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run: |
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remotes::install_deps(dependencies = TRUE)
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remotes::install_cran(c("rcmdcheck","goodpractice"))
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shell: Rscript {0}
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- name: Check
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env:
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_R_CHECK_CRAN_INCOMING_REMOTE_: false
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run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
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shell: Rscript {0}
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: any::rcmdcheck
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needs: check
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- name: Goodpractice
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run: goodpractice::goodpractice()
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shell: Rscript {0}
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- name: Test coverage
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run: covr::codecov()
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shell: Rscript {0}
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- name: Upload check results
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if: failure()
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uses: actions/upload-artifact@main
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- uses: r-lib/actions/check-r-package@v2
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with:
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name: ${{ runner.os }}-r${{ matrix.config.r }}-results
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path: check
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upload-snapshots: true

‎.github/workflows/pkgdown.yaml

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# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
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# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
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on:
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push:
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branches: [main, master]
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pull_request:
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branches: [main, master]
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release:
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types: [published]
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workflow_dispatch:
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name: pkgdown
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jobs:
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pkgdown:
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runs-on: ubuntu-latest
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# Only restrict concurrency for non-PR jobs
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concurrency:
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group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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steps:
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- uses: actions/checkout@v3
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- uses: r-lib/actions/setup-pandoc@v2
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- uses: r-lib/actions/setup-r@v2
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with:
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use-public-rspm: true
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- name: Install Linux system dependencies
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if: runner.os == 'Linux'
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run: |
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sudo apt install libopenbabel-dev libeigen3-dev
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: any::pkgdown, local::.
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needs: website
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- name: Build site
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run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
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shell: Rscript {0}
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- name: Deploy to GitHub pages 🚀
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if: github.event_name != 'pull_request'
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uses: JamesIves/[email protected]
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with:
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clean: false
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branch: gh-pages
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folder: docs

‎.github/workflows/test-coverage.yaml

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# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
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# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
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on:
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push:
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branches: [main, master]
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pull_request:
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branches: [main, master]
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name: test-coverage
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jobs:
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test-coverage:
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runs-on: ubuntu-latest
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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steps:
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- uses: actions/checkout@v3
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- uses: r-lib/actions/setup-r@v2
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with:
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use-public-rspm: true
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- name: Install Linux system dependencies
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if: runner.os == 'Linux'
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run: |
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sudo apt install libopenbabel-dev libeigen3-dev
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: any::covr
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needs: coverage
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- name: Test coverage
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run: |
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covr::codecov(
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quiet = FALSE,
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clean = FALSE,
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install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
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)
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shell: Rscript {0}
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- name: Show testthat output
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if: always()
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run: |
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## --------------------------------------------------------------------
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find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
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shell: bash
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- name: Upload test results
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if: failure()
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uses: actions/upload-artifact@v3
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with:
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name: coverage-test-failures
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path: ${{ runner.temp }}/package

‎.gitignore

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.Rhistory
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.RData
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.Ruserdata
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docs

‎DESCRIPTION

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Package: riches
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Title: Strucutral and Functional Enrichment Analyses
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Version: 0.2.1
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Version: 0.3.0
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Authors@R:
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person(given = "Jasen",
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family = "Finch",
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role = c("aut", "cre"),
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email = "[email protected]")
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Description: Structural and functional enrichment for metabolomics data.
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Description: Structural and functional enrichment for metabolomics data.
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URL: https://jasenfinch.github.io/riches/
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BugReports: https://github.com/jasenfinch/riches/issues
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biocViews: Metabolomics
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License: GPL-3
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Encoding: UTF-8
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Roxygen: list(markdown = TRUE)
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Depends: R (>= 3.5.0)
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Imports: FELLA,
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MFassign,
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Imports:
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broom,
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cheminf,
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construction,
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dplyr,
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ggthemes,
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FELLA,
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igraph,
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magrittr,
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stringr,
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tidygraph,
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metabolyseR,
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methods,
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mzAnnotation,
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purrr,
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metabolyseR,
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ggplot2,
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ggraph,
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tibble
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Remotes: jasenfinch/MFassign,
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jasenfinch/mzAnnotation,
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jasenfinch/metabolyseR
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rlang,
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stringr,
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tibble,
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tidygraph,
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tidyr,
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tidyselect
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Remotes: aberHRML/assignments,
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aberHRML/mzAnnotation,
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jasenfinch/cheminf,
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jasenfinch/construction,
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jasenfinch/metabolyseR,
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bioc::FELLA
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LazyData: true
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RoxygenNote: 7.1.1
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Collate: allClasses.R
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allGenerics.R
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access.R
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enrichmentParameters.R
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example-data.R
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functionalEnrichment.R
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organismNetwork.R
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plotGraph.R
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riches.R
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RoxygenNote: 7.2.3
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Suggests:
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assignments,
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testthat,
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covr

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