diff --git a/.github/workflows/bioc-check.yaml b/.github/workflows/bioc-check.yaml index 8744697..cfb4d21 100644 --- a/.github/workflows/bioc-check.yaml +++ b/.github/workflows/bioc-check.yaml @@ -1,5 +1,5 @@ # workflow derived from: https://github.com/insightsengineering/bioc-check-action - +# but the above action doesn't actually work lol, it always fails, so I changed it on: push: @@ -20,5 +20,21 @@ jobs: http-user-agent: release use-public-rspm: true - uses: r-lib/actions/setup-r-dependencies@v2 + - name: Install dependencies + run: | + install.packages("BiocManager") + BiocManager::install("BiocCheck") + shell: Rscript {0} - name: Run BiocCheck - uses: insightsengineering/bioc-check-action@v1 + run: | + bc_res <- BiocCheck::BiocCheck() + print(paste0("Errors: ", length(bc_res$error))) + print(paste0("Warnings: ", length(bc_res$warning))) + print(paste0("Notes: ", length(bc_res$note))) + n_errors <- length(bc_res$error) + Sys.setenv("BC_ERRORS" = n_errors) + shell: Rscript {0} + - name: Check BiocCheck results + run: | + if [[ $BC_ERRORS -gt 0 ]]; then exit 1; else echo "BiocCheck passed!"; fi + shell: bash diff --git a/inst/CITATION b/inst/CITATION index aff2571..dbbc0ac 100644 --- a/inst/CITATION +++ b/inst/CITATION @@ -3,7 +3,9 @@ citHeader("To cite scLANE in publications use:") citEntry( entry = "Manual", title = "Single Cell Linear Adaptive Expression Testing (scLANE)", - author = "Jack Leary and Rhonda Bacher", + journal = "Zenodo", + author = c(person(given = c("Jack", "R."), family = "Leary"). + person(given = "Rhonda", family = "Bacher")) year = "2023", note = "R package version 0.7.7", url = "https://doi.org/10.5281/zenodo.10106689",