Merge branch 'dev' of https://github.com/biometryhub/biometryassist i…

…nto dev

.github/workflows/pkgdown.yaml

@@ -6,44 +6,37 @@ name: pkgdown
 
 jobs:
   pkgdown:
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
-      RSPM: https://packagemanager.rstudio.com/cran/__linux__/jammy/latest
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
 
     steps:
-      - uses: actions/checkout@v3
-
-      - uses: r-lib/actions/setup-r@v2
-        id: install-r
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-        shell: Rscript {0}
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
 
-      - name: Cache R packages
-        uses: actions/cache@v3
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ubuntu-22.04-${{ steps.install-r.outputs.installed-r-version }}-1-${{ hashFiles('.github/r-depends.rds') }}
-          restore-keys: ubuntu-22.04-${{ steps.install-r.outputs.installed-r-version }}-1-
-
-      - name: Install dependencies
-        run: |
-          install.packages("remotes")
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_dev("pkgdown")
-        shell: Rscript {0}
+          extra-packages: any::pkgdown, local::.
+          needs: website
 
-      - name: Install package
-        run: R CMD INSTALL .
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
 
-      - name: Build and deploy pkgdown site
-        run: |
-          git config --local user.name "$GITHUB_ACTOR"
-          git config --local user.email "[email protected]"
-          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

DESCRIPTION

@@ -38,8 +38,9 @@ Depends:
     R (>= 4.0.0)
 Imports: 
     agricolae,
+    askpass,
     cowplot,
-    xml2,
+    curl,
     emmeans,
     farver,
     ggplot2,
@@ -48,11 +49,11 @@ Imports:
     pracma,
     rlang (>= 1.0.0),
     scales, 
-    stringi
+    stringi,
+    xml2
 Suggests: 
     covr,
     crayon,
-    getPass,
     knitr,
     mockery,
     rmarkdown,
@@ -69,5 +70,5 @@ Config/testthat/edition: 3
 Config/testthat/parallel: true
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.0
 VignetteBuilder: knitr

NAMESPACE

@@ -13,6 +13,7 @@ export(resplot)
 export(resplt)
 export(update_asreml)
 export(variogram)
+importFrom(askpass,askpass)
 importFrom(cowplot,add_sub)
 importFrom(cowplot,plot_grid)
 importFrom(curl,curl_fetch_disk)

R/install_asreml.R

@@ -38,6 +38,10 @@ install_asreml <- function(library = .libPaths()[1], quiet = FALSE, force = FALS
 
         # Get OS and R version
         os_ver <- get_r_os()
+        if(os_ver$os=="mac") {
+          create_mac_folder()
+        }
+
         url <- paste0("https://link.biometryhubwaite.com/", os_ver$os_ver)
 
         # First check if file already exists, both in the current directory and temp folder
@@ -269,6 +273,7 @@ compare_versions <- function() {
 #'
 #' @return logical; TRUE if folder successfully created, otherwise it will error
 #' @keywords internal
+#' @importFrom askpass askpass
 create_mac_folder <- function() {
     # macOS needs some special set up
     if(Sys.info()[["sysname"]] == "Darwin" &&
@@ -290,9 +295,10 @@ create_mac_folder <- function() {
             message("The ASReml-R package uses Reprise license management and will require administrator privilege to create the folder '/Library/Application Support/Reprise' before it can be installed.")
             input <- readline("Would you like to create this folder now (Yes/No)? You will be prompted for your password if yes. ")
 
-            if(toupper(input) %in% c("YES", "Y") && rlang::is_installed("getPass")) {
+            if(toupper(input) %in% c("YES", "Y")) {
                 system("sudo -S mkdir '/Library/Application Support/Reprise' && sudo -S chmod 777 '/Library/Application Support/Reprise'",
-                       input = getPass::getPass("Please enter your user account password: "))
+                       input = askpass::askpass("Please enter your user account password: "))
+              cat("\n")
             }
             else {
                 stop("ASReml-R cannot be installed until the folder '/Library/Application Support/Reprise' is created with appropriate permissions.

R/mct.R

@@ -470,6 +470,14 @@ multiple_comparisons <- function(model.obj,
         attr(pp.tab, 'aliased') <- as.character(aliased_names)
     }
 
+    # Add the critical value as an attribute
+    if(var(as.vector(crit.val), na.rm = TRUE) < 1e-10) {
+        attr(pp.tab, 'HSD') <- crit.val[1,2]
+    }
+    else {
+        attr(pp.tab, 'HSD') <- crit.val
+    }
+
     rownames(pp.tab) <- NULL
 
     return(pp.tab)

tests/testthat/_snaps/all-w2.md

@@ -119,12 +119,12 @@
 ---
 
        Genotype predicted.value std.error    groups   ci  low   up
-    1       G04            4.15      0.14         a 0.23 3.92 4.37
+    1       G04            4.14      0.14         a 0.23 3.92 4.37
     2       G14            4.63      0.14        ab 0.23 4.41 4.86
     3       G20            4.80      0.14        bc 0.23 4.57 5.02
     4       G10            4.81      0.14       bcd 0.23 4.59 5.04
     5       G28            4.84      0.14      bcde 0.23 4.61 5.07
-    6       G24            4.86      0.14     bcdef 0.23 4.63 5.08
+    6       G24            4.85      0.14     bcdef 0.23 4.63 5.08
     7       G01            4.91      0.14    bcdefg 0.23 4.68 5.14
     8       G05            4.94      0.14   bcdefgh 0.23 4.72 5.17
     9       G49            4.95      0.14   bcdefgh 0.23 4.72 5.17
@@ -141,13 +141,13 @@
     20      G06            5.13      0.14  bcdefghi 0.23 4.90 5.35
     21      G55            5.14      0.14  bcdefghi 0.23 4.92 5.37
     22      G32            5.16      0.14 bcdefghij 0.23 4.93 5.38
-    23      G11            5.17      0.14 bcdefghij 0.23 4.94 5.39
+    23      G11            5.16      0.14 bcdefghij 0.23 4.94 5.39
     24      G39            5.18      0.14 bcdefghij 0.23 4.95 5.40
     25      G61            5.20      0.14 bcdefghij 0.23 4.97 5.42
     26      G53            5.21      0.14 bcdefghij 0.23 4.98 5.43
     27      G37            5.21      0.14 bcdefghij 0.23 4.99 5.44
     28      G26            5.21      0.14 bcdefghij 0.23 4.99 5.44
-    29      G43            5.22      0.14 bcdefghij 0.23 4.99 5.44
+    29      G43            5.21      0.14 bcdefghij 0.23 4.99 5.44
     30      G35            5.22      0.14 bcdefghij 0.23 4.99 5.44
     31      G66            5.22      0.14 bcdefghij 0.23 4.99 5.44
     32      G16            5.23      0.14  cdefghij 0.23 5.00 5.45
@@ -157,24 +157,24 @@
     36      G47            5.27      0.14  cdefghij 0.23 5.05 5.50
     37      G44            5.29      0.14  cdefghij 0.23 5.06 5.52
     38      G23            5.29      0.14  cdefghij 0.23 5.07 5.52
-    39      G56            5.30      0.14  cdefghij 0.23 5.07 5.52
+    39      G56            5.29      0.14  cdefghij 0.23 5.07 5.52
     40      G58            5.31      0.14  cdefghij 0.23 5.08 5.53
-    41      G57            5.32      0.14  cdefghij 0.23 5.09 5.54
+    41      G57            5.31      0.14  cdefghij 0.23 5.09 5.54
     42      G63            5.32      0.14  cdefghij 0.23 5.09 5.54
     43      G62            5.32      0.14  cdefghij 0.23 5.09 5.55
     44      G54            5.33      0.14  cdefghij 0.23 5.11 5.56
     45      G51            5.36      0.14  cdefghij 0.23 5.13 5.58
     46      G67            5.37      0.14  cdefghij 0.23 5.14 5.59
-    47      G59            5.37      0.14  cdefghij 0.23 5.14 5.60
+    47      G22            5.37      0.14  cdefghij 0.23 5.14 5.60
     48      G42            5.37      0.14  cdefghij 0.23 5.14 5.60
-    49      G22            5.37      0.14  cdefghij 0.23 5.14 5.60
+    49      G59            5.37      0.14  cdefghij 0.23 5.14 5.60
     50      G65            5.38      0.14  cdefghij 0.23 5.15 5.60
     51      G69            5.38      0.14  cdefghij 0.23 5.16 5.61
     52      G38            5.38      0.14  cdefghij 0.23 5.16 5.61
     53      G12            5.39      0.14   defghij 0.23 5.17 5.62
     54      G31            5.41      0.14    efghij 0.23 5.19 5.64
     55      G50            5.42      0.14    efghij 0.23 5.20 5.65
-    56      G17            5.43      0.14    efghij 0.23 5.20 5.65
+    56      G17            5.42      0.14    efghij 0.23 5.20 5.65
     57      G52            5.43      0.14    efghij 0.23 5.20 5.65
     58      G64            5.44      0.14     fghij 0.23 5.21 5.67
     59      G13            5.45      0.14      ghij 0.23 5.22 5.67
@@ -183,12 +183,12 @@
     62      G60            5.48      0.14      ghij 0.23 5.25 5.71
     63      G27            5.49      0.14     ghijk 0.23 5.26 5.72
     64      G18            5.50      0.14     ghijk 0.23 5.27 5.72
-    65      G36            5.51      0.14      hijk 0.23 5.28 5.73
+    65      G36            5.50      0.14      hijk 0.23 5.28 5.73
     66      G48            5.51      0.14      hijk 0.23 5.29 5.74
     67      G40            5.53      0.14      hijk 0.23 5.30 5.75
     68      G33            5.61      0.14       ijk 0.23 5.38 5.83
     69      G19            5.73      0.14        jk 0.23 5.51 5.96
-    70      G03            6.08      0.14         k 0.23 5.85 6.30
+    70      G03            6.07      0.14         k 0.23 5.85 6.30
 
 ---