Merge pull request #177 from jr-leary7/dev

Dev

.github/workflows/bioc-check.yaml

@@ -27,16 +27,14 @@ jobs:
           install.packages("BiocManager")
           BiocManager::install("BiocCheck")
         shell: Rscript {0}
-      - name: Run BiocCheck
+      - name: Run BiocCheck & BiocCheckGitClone
         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)
+          bc_gc_res <- BiocCheck::BiocCheckGitClone()
+          n_errors <- length(bc_res$error) + length(bc_gc_res$error)
+          Sys.setenv("BC_ERRORS_TOTAL" = n_errors)
         shell: Rscript {0}
       - name: Check BiocCheck results
         run: |
-          if [[ $BC_ERRORS -gt 0 ]]; then exit 1; else echo "BiocCheck passed!"; fi
+          if [[ $BC_ERRORS_TOTAL -gt 0 ]]; then exit 1; else echo "BiocCheck passed!"; fi
         shell: bash

.gitignore

@@ -7,3 +7,7 @@ inst/doc
 codecov.yml
 /doc/
 /Meta/
+R/.DS_Store
+.Rproj
+src/*.o
+src/*.so

inst/CITATION

@@ -5,7 +5,7 @@ citEntry(
   title    = "Single Cell Linear Adaptive Expression Testing (scLANE)",
   journal  = "Zenodo",
   author   = c(person(given = c("Jack", "R."), family = "Leary"),
-               person(given = "Rhonda", family = "Bacher"))
+               person(given = "Rhonda", family = "Bacher")),
   year     = "2023",
   note     = "R package version 0.7.7",
   url      = "https://doi.org/10.5281/zenodo.10182497",