diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml new file mode 100755 index 0000000..fefc52e --- /dev/null +++ b/.github/workflows/test-coverage.yaml @@ -0,0 +1,61 @@ +# 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] + +name: test-coverage + +permissions: read-all + +jobs: + test-coverage: + runs-on: ubuntu-latest + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + + steps: + - uses: actions/checkout@v4 + + - uses: r-lib/actions/setup-r@v2 + with: + use-public-rspm: true + + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: any::covr, any::xml2 + needs: coverage + + - name: Test coverage + run: | + cov <- covr::package_coverage( + quiet = FALSE, + clean = FALSE, + install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package") + ) + covr::to_cobertura(cov) + shell: Rscript {0} + + - uses: codecov/codecov-action@v4 + with: + fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }} + file: ./cobertura.xml + plugin: noop + disable_search: true + token: ${{ secrets.CODECOV_TOKEN }} + + - name: Show testthat output + if: always() + run: | + ## -------------------------------------------------------------------- + find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true + shell: bash + + - name: Upload test results + if: failure() + uses: actions/upload-artifact@v4 + with: + name: coverage-test-failures + path: ${{ runner.temp }}/package diff --git a/README.Rmd b/README.Rmd index 9f4b130..2221ed3 100755 --- a/README.Rmd +++ b/README.Rmd @@ -13,6 +13,10 @@ knitr::opts_chunk$set( ) ``` + + [![R-CMD-check](https://github.com/danymukesha/BioGA/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/danymukesha/BioGA/actions/workflows/R-CMD-check.yaml) + + # BioGA BioGA website The `BioGA` package provides a set of functions for genetic algorithm diff --git a/README.md b/README.md index 3d36841..00504fb 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,9 @@ + + +[![R-CMD-check](https://github.com/danymukesha/BioGA/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/danymukesha/BioGA/actions/workflows/R-CMD-check.yaml) + # BioGA BioGA website @@ -15,20 +19,63 @@ package: ``` r devtools::install_github("danymukesha/BioGA") -#> Using GitHub PAT from the git credential store. #> Downloading GitHub repo danymukesha/BioGA@HEAD -#> Skipping 16 packages ahead of CRAN: BiocGenerics, graph, S4Arrays, IRanges, S4Vectors, MatrixGenerics, GenomeInfoDbData, zlibbioc, XVector, GenomeInfoDb, RBGL, Biobase, DelayedArray, GenomicRanges, biocViews, SummarizedExperiment +#> fs (1.6.3 -> 1.6.4 ) [CRAN] +#> fastmap (1.1.1 -> 1.2.0 ) [CRAN] +#> cachem (1.0.8 -> 1.1.0 ) [CRAN] +#> xfun (0.42 -> 0.44 ) [CRAN] +#> tinytex (0.50 -> 0.51 ) [CRAN] +#> knitr (1.45 -> 1.46 ) [CRAN] +#> htmltools (0.5.7 -> 0.5.8.1) [CRAN] +#> bslib (0.6.1 -> 0.7.0 ) [CRAN] +#> rmarkdown (2.26 -> 2.27 ) [CRAN] +#> matrixStats (1.2.0 -> 1.3.0 ) [CRAN] +#> munsell (0.5.0 -> 0.5.1 ) [CRAN] +#> farver (2.1.1 -> 2.1.2 ) [CRAN] +#> BiocManager (1.30.22 -> 1.30.23) [CRAN] +#> bookdown (0.38 -> 0.39 ) [CRAN] +#> gtable (0.3.4 -> 0.3.5 ) [CRAN] +#> ggplot2 (3.5.0 -> 3.5.1 ) [CRAN] +#> Skipping 17 packages ahead of CRAN: BiocGenerics, graph, S4Arrays, IRanges, S4Vectors, MatrixGenerics, GenomeInfoDbData, zlibbioc, XVector, GenomeInfoDb, RBGL, Biobase, DelayedArray, GenomicRanges, BiocStyle, biocViews, SummarizedExperiment +#> Installing 16 packages: fs, fastmap, cachem, xfun, tinytex, knitr, htmltools, bslib, rmarkdown, matrixStats, munsell, farver, BiocManager, bookdown, gtable, ggplot2 +#> Installing packages into 'C:/Users/dany.mukesha/AppData/Local/Temp/Rtmp63bptc/temp_libpath8488528329e2' +#> (as 'lib' is unspecified) +#> Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/annotation/bin/windows/contrib/4.3: +#> cannot open URL 'https://bioconductor.org/packages/3.17/data/annotation/bin/windows/contrib/4.3/PACKAGES' +#> Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/experiment/bin/windows/contrib/4.3: +#> cannot open URL 'https://bioconductor.org/packages/3.17/data/experiment/bin/windows/contrib/4.3/PACKAGES' +#> Warning: unable to access index for repository https://bioconductor.org/packages/3.17/workflows/bin/windows/contrib/4.3: +#> cannot open URL 'https://bioconductor.org/packages/3.17/workflows/bin/windows/contrib/4.3/PACKAGES' +#> package 'fs' successfully unpacked and MD5 sums checked +#> package 'fastmap' successfully unpacked and MD5 sums checked +#> package 'cachem' successfully unpacked and MD5 sums checked +#> package 'xfun' successfully unpacked and MD5 sums checked +#> package 'tinytex' successfully unpacked and MD5 sums checked +#> package 'knitr' successfully unpacked and MD5 sums checked +#> package 'htmltools' successfully unpacked and MD5 sums checked +#> package 'bslib' successfully unpacked and MD5 sums checked +#> package 'rmarkdown' successfully unpacked and MD5 sums checked +#> package 'matrixStats' successfully unpacked and MD5 sums checked +#> package 'munsell' successfully unpacked and MD5 sums checked +#> package 'farver' successfully unpacked and MD5 sums checked +#> package 'BiocManager' successfully unpacked and MD5 sums checked +#> package 'bookdown' successfully unpacked and MD5 sums checked +#> package 'gtable' successfully unpacked and MD5 sums checked +#> package 'ggplot2' successfully unpacked and MD5 sums checked +#> +#> The downloaded binary packages are in +#> C:\Users\dany.mukesha\AppData\Local\Temp\RtmpWuKbDY\downloaded_packages #> ── R CMD build ───────────────────────────────────────────────────────────────── -#> checking for file 'C:\Users\dany.mukesha\AppData\Local\Temp\RtmpeMTOmQ\remotes6e2c19f3527f\danymukesha-BioGA-39ae5be/DESCRIPTION' ... checking for file 'C:\Users\dany.mukesha\AppData\Local\Temp\RtmpeMTOmQ\remotes6e2c19f3527f\danymukesha-BioGA-39ae5be/DESCRIPTION' ... ✔ checking for file 'C:\Users\dany.mukesha\AppData\Local\Temp\RtmpeMTOmQ\remotes6e2c19f3527f\danymukesha-BioGA-39ae5be/DESCRIPTION' (387ms) +#> ✔ checking for file 'C:\Users\dany.mukesha\AppData\Local\Temp\RtmpWuKbDY\remotes99a020a46bb9\danymukesha-BioGA-9b9a1cc/DESCRIPTION' (776ms) #> ─ preparing 'BioGA': #> checking DESCRIPTION meta-information ... checking DESCRIPTION meta-information ... ✔ checking DESCRIPTION meta-information #> ─ cleaning src #> ─ checking for LF line-endings in source and make files and shell scripts #> ─ checking for empty or unneeded directories #> Omitted 'LazyData' from DESCRIPTION -#> ─ building 'BioGA_0.99.0.tar.gz' +#> ─ building 'BioGA_0.99.5.tar.gz' #> #> -#> Installing package into 'C:/Users/dany.mukesha/AppData/Local/Temp/RtmpQ9yEQT/temp_libpath43e05a565418' +#> Installing package into 'C:/Users/dany.mukesha/AppData/Local/Temp/Rtmp63bptc/temp_libpath8488528329e2' #> (as 'lib' is unspecified) ```