fixing CI/CD bugs -- closes #144

jr-leary7 · Oct 19, 2023 · c77d745 · c77d745
1 parent deed8d9
commit c77d745
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Showing 4 changed files with 10 additions and 7 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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,