Fix random download of source tarball instead of binary (#47)

# Pull Request

- Closes #44 

Part of insightsengineering/coredev-tasks#546

Upstream bug: r-lib/pkgdepends#367

#### Changes description:

- Removes sources links that include "src/contrib/Archive"
- When `{pkgdepends}` attempts to download the tarball, it will try all
sources and archive-based sources are only source-code
- Re-downloads tarball using mirror.
  - Last attempt to explicitly use `ppm` snapshot mirror

#### Testing

1. Install or load this branch
-
`renv::install("insightsengineering/verdepcheck@fix-random-download%40main")`
3. Clone
[`{tmc}`](https://github.com/insightsengineering/teal.modules.clinical)
    - checkout `546-fix-verdepcheck@main` branch
5. Run all strategies:
    - `verdepcheck::min_cohort_deps_check("/path/to/tmc")`
    - `verdepcheck::min_isolated_deps_check("/path/to/tmc")`
    - `verdepcheck::release_deps_check("/path/to/tmc")`
    - `verdepcheck::max_deps_check("/path/to/tmc")`

R/check.R

@@ -105,9 +105,59 @@ execute_ip <- function(ip, path, build_args, check_args, ...) {
 #'
 #' @export
 download_ip <- function(ip) {
+  res <- ip$get_resolution()
+
+  # Prevent downloads of non-binary files by removing source that has "Archive" in the URL
+  # Track issue: https://github.com/r-lib/pkgdepends/issues/367
+  ix <- res$platform == pkgdepends::current_r_platform()
+  new_sources <- lapply(
+    res$sources[ix],
+    function(x) {
+      if (length(x) > 1 && any(grepl("src/contrib/Archive", x))) {
+        x[!grepl("src/contrib/Archive", x)]
+      } else {
+        x
+      }
+    }
+  )
+  ip$.__enclos_env__$private$plan$.__enclos_env__$private$resolution$result$sources[ix] <- new_sources
+
   ip$download()
   ip$stop_for_download_error()
 
+  # Safety fallback that will try to download the binary again.
+  #
+  # note: that binary must be downloaded with relevant user agent with supported
+  # platform and R version.
+  for (ix_el in which(ix)) {
+    withr::with_tempdir(
+      code = {
+        tar_file <- file.path(ip$get_config()$get("cache_dir"), res$target[ix_el])
+
+        # Only do this for files that actually exist
+        if (!file.exists(tar_file)) next
+        utils::untar(tarfile = tar_file, exdir = "./")
+        tryCatch(
+          {
+            asNamespace("pkgdepends")$verify_extracted_package(res$package[ix_el], "./")
+          },
+          error = function(error) {
+            cli::cli_warn("{res$package[ix_el]} binary is not valid, trying to re-download.")
+            # Attempts to download again using {pkgcache} / {pkgdepends} http methods
+            async_fun <- asNamespace("pkgcache")$async(function() {
+              asNamespace("pkgcache")$download_file(
+                # Builds URL manually from mirror
+                url = file.path(res$mirror[ix_el], "src/contrib", basename(tar_file)),
+                destfile = tar_file
+              )
+            })
+            asNamespace("pkgcache")$synchronise(async_fun())
+          }
+        )
+      }
+    )
+  }
+
   return(invisible(ip))
 }
 

R/get_ref.R

@@ -451,9 +451,9 @@ get_release_date.remote_ref_cran <- function(remote_ref) {
         package_version(remote_ref$version, strict = FALSE)
       )
     )
-    as.Date(tail(rel_data[idx, "mtime"], 1))
+    as.Date(utils::tail(rel_data[idx, "mtime"], 1))
   } else {
-    as.Date(tail(rel_data$mtime, 1))
+    as.Date(utils::tail(rel_data$mtime, 1))
   }
 }
 

R/utils.R

@@ -15,7 +15,7 @@ default_config <- function() {
   )
 }
 append_config <- function(x1, x2) {
-  modifyList(x1, x2)
+  utils::modifyList(x1, x2)
 }
 
 #' @importFrom utils installed.packages

README.md

@@ -35,7 +35,7 @@ The main functions are:
 - `new_<strategy>_deps_installation_proposal` for creating `installation_proposal` objects
 - `<strategy>_deps_check` that creates and executes `installation_proposal` and then run `"R CMD CHECK"`
 
-This package is heavily based on [`pkgdepends`](https://r-lib.github.io/pkgdepends/) for dependency resolution and [`rcmdcheck`](https://r-lib.github.io/rcmdcheck/) for executing `"R CMD CHECK"`.
+This package is heavily based on [`pkgdepends`](https://r-lib.github.io/pkgdepends/) for dependency resolution and [`rcmdcheck`](https://rcmdcheck.r-lib.org/) for executing `"R CMD CHECK"`.
 
 ## Install