clean up CI

.github/environment/pixi.toml

@@ -10,7 +10,8 @@ libc = { family="glibc", version="2.17" }
 devtools_document = "R -e 'devtools::document()'"
 devtools_test = "R -e 'devtools::test()'"
 codecov = "R -e 'covr::codecov(quiet = FALSE)'"
-rcmdcheck = "R -e 'rcmdcheck::rcmdcheck()'"
+build = "R -e 'devtools::build()'"
+rcmdcheck = "R -e 'pkg <- list.files(\"..\", pattern = \".tar.gz\", full.names = TRUE); rcmdcheck::rcmdcheck(path = pkg[1], args = c(\"--as-cran\"))'"
 use_major_version = "R -e 'usethis::Use_version(which = \"major\", push = FALSE)'"
 use_minor_version = "R -e 'usethis::use_version(which = \"minor\", push = FALSE)'"
 use_patch_version = "R -e 'usethis::use_version(which = \"patch\", push = FALSE)'"
@@ -26,7 +27,9 @@ r43 = {features = ["r43"]}
 r44 = {features = ["r44"]}
 
 [dependencies]
+"r-ashr" = "*"
+"r-covr" = "*"
 "r-devtools" = "*"
+"r-mass" = "*"
 "r-rcmdcheck" = "*"
-"r-covr" = "*"
 "r-tidyverse" = "*"

.github/workflows/ci.yml

@@ -33,11 +33,16 @@ jobs:
       - name: Run unit tests
         run: pixi run --environment ${{ matrix.environment }} devtools_test
 
-      # - name: Check unit test code coverage
-      #   run: pixi run --environment ${{ matrix.environment }} codecov
+      - name: Run R CMD CHECK
+        run: |
+          pixi install --environment ${{ matrix.environment }}
+          ln -sf $(pwd)/.pixi/envs/default/lib/libhwasan.so.0 $(pwd)/.pixi/envs/default/lib/libhwasan.so
+          ln -sf $(pwd)/.pixi/envs/${{ matrix.environment }}/lib/libhwasan.so.0 $(pwd)/.pixi/envs/${{ matrix.environment }}/lib/libhwasan.so
+          pixi run --environment ${{ matrix.environment }} build
+          pixi run --environment ${{ matrix.environment }} rcmdcheck
 
-      #- name: Run R CMD CHECK
-        #run: pixi run rcmdcheck
+      - name: Check unit test code coverage
+        run: pixi run --environment ${{ matrix.environment }} codecov
 
   ci_osx-64:
     name: osx-64 CI
@@ -62,8 +67,10 @@ jobs:
       - name: Run unit tests
         run: pixi run --environment ${{ matrix.environment }} devtools_test
 
-      #- name: Run R CMD CHECK
-        #run: pixi run rcmdcheck
+      - name: Run R CMD CHECK
+        run: |
+          pixi run --environment ${{ matrix.environment }} build
+          pixi run --environment ${{ matrix.environment }} rcmdcheck
 
   ci_osx-arm64:
     name: osx-arm64 CI
@@ -88,5 +95,7 @@ jobs:
       - name: Run unit tests
         run: pixi run --environment ${{ matrix.environment }} devtools_test
 
-      #- name: Run R CMD CHECK
-        #run: pixi run rcmdcheck
+      - name: Run R CMD CHECK
+        run: |
+          pixi run --environment ${{ matrix.environment }} build
+          pixi run --environment ${{ matrix.environment }} rcmdcheck

DESCRIPTION

@@ -28,8 +28,8 @@ Suggests:
     testthat (>= 3.0.0),
     knitr,
     rmarkdown,
-    susieR,
-    ashr
+    ashr,
+    MASS
 VignetteBuilder: knitr
 Roxygen: list(markdown = TRUE)
 Config/testthat/edition: 3