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v0.3.0
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| ^LICENSE\.md$ | ||
| ^codecov\.yml$ | ||
| ^docs | ||
| ^_pkgdown\.yml$ | ||
| ^docs$ | ||
| ^pkgdown$ | ||
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| # 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] | ||
| pull_request: | ||
| branches: [main, master] | ||
| release: | ||
| types: [published] | ||
| workflow_dispatch: | ||
|
|
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| name: pkgdown | ||
|
|
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| jobs: | ||
| pkgdown: | ||
| runs-on: ubuntu-latest | ||
| # Only restrict concurrency for non-PR jobs | ||
| concurrency: | ||
| group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }} | ||
| env: | ||
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
| steps: | ||
| - uses: actions/checkout@v3 | ||
|
|
||
| - uses: r-lib/actions/setup-pandoc@v2 | ||
|
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| - uses: r-lib/actions/setup-r@v2 | ||
| with: | ||
| use-public-rspm: true | ||
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| - name: Install Linux system dependencies | ||
| if: runner.os == 'Linux' | ||
| run: | | ||
| sudo apt install libopenbabel-dev libeigen3-dev | ||
| - uses: r-lib/actions/setup-r-dependencies@v2 | ||
| with: | ||
| extra-packages: any::pkgdown, local::. | ||
| needs: website | ||
|
|
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| - name: Build site | ||
| run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE) | ||
| shell: Rscript {0} | ||
|
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| - name: Deploy to GitHub pages 🚀 | ||
| if: github.event_name != 'pull_request' | ||
| uses: JamesIves/github-pages-deploy-action@v4.4.1 | ||
| with: | ||
| clean: false | ||
| branch: gh-pages | ||
| folder: docs |
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| # 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] | ||
| pull_request: | ||
| branches: [main, master] | ||
|
|
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| name: test-coverage | ||
|
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| jobs: | ||
| test-coverage: | ||
| runs-on: ubuntu-latest | ||
| env: | ||
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
|
|
||
| steps: | ||
| - uses: actions/checkout@v3 | ||
|
|
||
| - uses: r-lib/actions/setup-r@v2 | ||
| with: | ||
| use-public-rspm: true | ||
|
|
||
| - name: Install Linux system dependencies | ||
| if: runner.os == 'Linux' | ||
| run: | | ||
| sudo apt install libopenbabel-dev libeigen3-dev | ||
| - uses: r-lib/actions/setup-r-dependencies@v2 | ||
| with: | ||
| extra-packages: any::covr | ||
| needs: coverage | ||
|
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| - name: Test coverage | ||
| run: | | ||
| covr::codecov( | ||
| quiet = FALSE, | ||
| clean = FALSE, | ||
| install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package") | ||
| ) | ||
| shell: Rscript {0} | ||
|
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| - name: Show testthat output | ||
| if: always() | ||
| run: | | ||
| ## -------------------------------------------------------------------- | ||
| find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true | ||
| shell: bash | ||
|
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| - name: Upload test results | ||
| if: failure() | ||
| uses: actions/upload-artifact@v3 | ||
| with: | ||
| name: coverage-test-failures | ||
| path: ${{ runner.temp }}/package |
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| .Rhistory | ||
| .RData | ||
| .Ruserdata | ||
| docs | ||
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| Package: riches | ||
| Title: Strucutral and Functional Enrichment Analyses | ||
| Version: 0.2.1 | ||
| Version: 0.3.0 | ||
| Authors@R: | ||
| person(given = "Jasen", | ||
| family = "Finch", | ||
| role = c("aut", "cre"), | ||
| email = "jsf9@aber.ac.uk") | ||
| Description: Structural and functional enrichment for metabolomics data. | ||
| Description: Structural and functional enrichment for metabolomics data. | ||
| URL: https://jasenfinch.github.io/riches/ | ||
| BugReports: https://github.com/jasenfinch/riches/issues | ||
| biocViews: Metabolomics | ||
| License: GPL-3 | ||
| Encoding: UTF-8 | ||
| Roxygen: list(markdown = TRUE) | ||
| Depends: R (>= 3.5.0) | ||
| Imports: FELLA, | ||
| MFassign, | ||
| Imports: | ||
| broom, | ||
| cheminf, | ||
| construction, | ||
| dplyr, | ||
| ggthemes, | ||
| FELLA, | ||
| igraph, | ||
| magrittr, | ||
| stringr, | ||
| tidygraph, | ||
| metabolyseR, | ||
| methods, | ||
| mzAnnotation, | ||
| purrr, | ||
| metabolyseR, | ||
| ggplot2, | ||
| ggraph, | ||
| tibble | ||
| Remotes: jasenfinch/MFassign, | ||
| jasenfinch/mzAnnotation, | ||
| jasenfinch/metabolyseR | ||
| rlang, | ||
| stringr, | ||
| tibble, | ||
| tidygraph, | ||
| tidyr, | ||
| tidyselect | ||
| Remotes: aberHRML/assignments, | ||
| aberHRML/mzAnnotation, | ||
| jasenfinch/cheminf, | ||
| jasenfinch/construction, | ||
| jasenfinch/metabolyseR, | ||
| bioc::FELLA | ||
| LazyData: true | ||
| RoxygenNote: 7.1.1 | ||
| Collate: allClasses.R | ||
| allGenerics.R | ||
| access.R | ||
| enrichmentParameters.R | ||
| example-data.R | ||
| functionalEnrichment.R | ||
| organismNetwork.R | ||
| plotGraph.R | ||
| riches.R | ||
| RoxygenNote: 7.2.3 | ||
| Suggests: | ||
| assignments, | ||
| testthat, | ||
| covr |
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