diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index c9749ed..0bbf82c 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -43,3 +43,5 @@ jobs: - uses: r-lib/actions/check-r-package@v2 with: upload-snapshots: true + args: 'c("--ignore-vignettes")' + build_args: 'c("-no-build-vignettes")' diff --git a/.github/workflows/render-README.yaml b/.github/workflows/render-README.yaml index 36f59f1..ff77c6f 100644 --- a/.github/workflows/render-README.yaml +++ b/.github/workflows/render-README.yaml @@ -31,6 +31,8 @@ jobs: run: Rscript -e 'rmarkdown::render("README.Rmd", output_format = "md_document")' - name: commit rendered README run: | + git config --local user.name "$GITHUB_ACTOR" + git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com" git add README.md man/figures/README-* git commit -m "Recompiled README.Rmd" || echo "No changes to commit" git push origin || echo "No changes to commit" diff --git a/R/getFittedValues.R b/R/getFittedValues.R index 77375bd..738f325 100644 --- a/R/getFittedValues.R +++ b/R/getFittedValues.R @@ -74,6 +74,11 @@ getFittedValues <- function(test.dyn.res = NULL, pt = x[!is.na(x)], gene = g, rna = expr.mat[!is.na(x), g]) + if (!is.null(id.vec)) { + gene_df <- dplyr::mutate(gene_df, subj_id = id.vec[!is.na(x)]) + } else { + gene_df <- dplyr::mutate(gene_df, subj_id = NA_character_) + } if (!is.null(size.factor.offset)) { gene_df <- dplyr::mutate(gene_df, size_factor = unname(size.factor.offset)[!is.na(x)], @@ -115,11 +120,6 @@ getFittedValues <- function(test.dyn.res = NULL, return(gene_df) }) %>% purrr::reduce(rbind) - if (!is.null(id.vec)) { - mod_df <- dplyr::mutate(mod_df, subj_id = id.vec[!is.na(x)]) - } else { - mod_df <- dplyr::mutate(mod_df, subj_id = NA_character_) - } return(mod_df) }) final_df <- purrr::reduce(mod_df_list, rbind) %>% diff --git a/tests/testthat/test_scLANE.R b/tests/testthat/test_scLANE.R index d29a535..6512005 100644 --- a/tests/testthat/test_scLANE.R +++ b/tests/testthat/test_scLANE.R @@ -32,8 +32,7 @@ withr::with_output_sink(tempfile(), { genes = genes_to_test, n.potential.basis.fns = 5, size.factor.offset = cell_offset, - parallel.exec = FALSE, - track.time = TRUE) + parallel.exec = FALSE) gee_gene_stats <- testDynamic(expr.mat = sim_data, pt = pt_test, genes = genes_to_test,