New testing process in GHA

.github/workflows/test-ci.yaml

@@ -101,13 +101,17 @@ jobs:
             RSPM = "https://packagemanager.rstudio.com/all/latest",
             CRAN = "https://cloud.r-project.org"
           ))
+          message("Installing ", length(toinstall)," packages")
 
-          message("Installing ", length(toinstall)," packages: ", paste0(toinstall, collapse = ","))
+          library(pak, lib.loc = Sys.getenv("R_LIB_FOR_PAK"))
 
-          install.packages(toinstall, dependencies = TRUE, verbose = TRUE, quiet = TRUE)
+          # Install packages with pak
+          end <- lapply(toinstall, function(x){
+            aa <- try(pak::pkg_install(x, upgrade = TRUE, dependencies = TRUE), silent = TRUE)
+            if(inherits(aa, "try-error")) return(FALSE)
+            return(TRUE)
+          })
 
-          # Update binary
-          # update.packages(type = "binary")
 
         shell: Rscript {0}
 

tests/testthat/test_ci/.gitignore

@@ -1,4 +1,4 @@
 _snaps
 CITATION
 allpackages.csv
-results.md
+results.*

tests/testthat/test_ci/test-full_cff.R

@@ -4,6 +4,9 @@ test_that("Test ALL installed packages", {
   installed <- as.data.frame(installed.packages()[, c("Package", "Version")])
   installed <- installed[order(installed$Package), ]
 
+  end <- match("ctv", installed$Package) + 10
+  installed <- installed[seq_len(end), ]
+
   rownames(installed) <- seq_len(nrow(installed))
 
   l <- nrow(installed)

tests/testthat/test_ci/test-new.R

@@ -1,9 +1,7 @@
-
 library(cffr)
-
 installed <- as.data.frame(installed.packages()[, c("Package", "Version")])
 installed <- installed[order(installed$Package), ]
-# installed <- installed[1:50, ]
+
 
 rownames(installed) <- seq_len(nrow(installed))
 
@@ -23,8 +21,9 @@ for (i in seq_len(nrow(installed))) {
   # Display some advances
   message(
     "Testing ", i, "/", nrow(installed),
-    " (", sprintf("%05.02f", i / nrow(installed) * 100), "%) ["
-  ,installed[i, ]$Package, "]")
+    " (", sprintf("%05.02f", i / nrow(installed) * 100), "%) [",
+    installed[i, ]$Package, "]"
+  )
   cit_path <- file.path(find.package(installed[i, ]$Package), "CITATION")
 
 
@@ -36,14 +35,16 @@ for (i in seq_len(nrow(installed))) {
 
   # Add cffobj
   cffobj <- try(
-    cff_create(pkg, gh_keywords = FALSE, dependencies = FALSE), silent = TRUE)
+    cff_create(pkg, gh_keywords = FALSE, dependencies = FALSE),
+    silent = TRUE
+  )
 
-  if(inherits(cffobj, "cff")){
-  s <- try(cff_validate(cffobj, verbose = FALSE), silent = TRUE)
-  if(!is.logical(s)) s <- FALSE
+  if (inherits(cffobj, "cff")) {
+    s <- try(cff_validate(cffobj, verbose = FALSE), silent = TRUE)
+    if (!is.logical(s)) s <- FALSE
 
-  res <- c(res, s)
-  note <- c(note, "ok, cff")
+    res <- c(res, s)
+    note <- c(note, "")
   } else {
     res <- c(res, FALSE)
     note <- c(note, "Other errors")
@@ -54,9 +55,98 @@ installed$with_citation <- withcit
 installed$is_ok <- res
 installed$note <- note
 
+# Create report
 
+options(cli.width = 60)
 outmd <- file.path(dir_path, "results.md")
+unlink(outmd)
+
+cat("# Test all files\n\n", file = outmd)
+write("## Session info\n", outmd, append = TRUE)
+write("<details>", outmd, append = TRUE)
+write("\n```r", outmd, append = TRUE)
+conn <- file(outmd, "a")
+capture.output(sessioninfo::session_info(), file = conn)
+close(conn)
+write("```\n", outmd, append = TRUE)
+write("</details>", outmd, append = TRUE)
+
 errors <- installed[installed$is_ok == FALSE, ]
-capture.output(knitr::kable(errors), file = outmd)
+errother <- errors$Package[errors$note == "Other errors"]
+errcff <- setdiff(errors$Package, errother)
+errother_df <- installed[installed$Package %in% errother, c(1, 2)]
+
+
+
+write("\n## High level summary", outmd, append = TRUE)
+write(paste0("\n- I checked ", nrow(installed), " packages"),
+  outmd,
+  append = TRUE
+)
+write(paste0("- Invalid cff in ", length(errcff), " packages"),
+  outmd,
+  append = TRUE
+)
+write(paste0("- I failed to generate cff in ", length(errother), " packages"),
+  outmd,
+  append = TRUE
+)
+
+okrate <- 100 * (1 - length(errcff) / (nrow(installed) - length(errother)))
+write(paste0("- OK Rate: ", round(okrate, 2), "%"), outmd, append = TRUE)
+
+
+if (nrow(errors) == 0) {
+  write("\nNo errors, hooray!", outmd, append = TRUE)
+} else {
+  write("\nPackages with errors:", outmd, append = TRUE)
+  conn <- file(outmd, "a")
+  capture.output(knitr::kable(errors, row.names = FALSE),
+    file = conn
+  )
+  close(conn)
+
+
+  if (length(errother) > 0) {
+    pk <- paste0(errother, collapse = ", ")
+    line <- paste0("\n## Packages with errors not coming from cff")
+    write(line, outmd, append = TRUE)
+    conn <- file(outmd, "a")
+    capture.output(knitr::kable(errother_df, row.names = FALSE),
+      file = conn
+    )
+    close(conn)
+  }
 
+  if (length(errcff) > 0) {
+    write("\n## cff errors reported", outmd, append = TRUE)
+    # Prepare links
+    cfflist <- paste0("- [", errcff, "](#", tolower(errcff), ")",
+      collapse = "\n"
+    )
+    write(cfflist, outmd, append = TRUE)
+
+    for (j in errcff) {
+      write(paste0("\n### ", j, ""), outmd, append = TRUE)
+      write("\n#### cff object\n", outmd, append = TRUE)
+      write("<details>", outmd, append = TRUE)
+      write("\n```r", outmd, append = TRUE)
+      cff <- cff_create(j, gh_keywords = FALSE, dependencies = FALSE)
+      conn <- file(outmd, "a")
+      capture.output(print(cff), file = conn)
+      close(conn)
+      write("```\n", outmd, append = TRUE)
+      write("</details>", outmd, append = TRUE)
+
+
+      write("\n#### Validation results", outmd, append = TRUE)
+
+      s <- cff_validate(cff, verbose = FALSE)
+      df <- attr(s, "errors")
+      conn <- file(outmd, "a")
+      capture.output(knitr::kable(df, row.names = FALSE), file = conn)
+      close(conn)
+    }
+  }
+}