From 8e931f880addd17a1645413615bb7130cfcf30b7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?G=C3=A1bor=20Cs=C3=A1rdi?= <csardi.gabor@gmail.com>
Date: Tue, 21 Nov 2023 15:55:40 +0100
Subject: [PATCH] Do not import via NAMESPACE

To make embedding easier into pak.
Run-time dependencies and base packages are OK.
---
 NAMESPACE                                   | 11 -----
 R/archive.R                                 | 12 ++---
 R/async-http.R                              |  5 +--
 R/metadata-cache.R                          | 49 ++++++++++-----------
 R/onload.R                                  |  2 +-
 R/package-cache.R                           | 12 ++---
 R/progress-bar.R                            | 20 +++------
 tests/testthat/_snaps/1-metadata-cache-3.md |  2 +-
 tests/testthat/test-1-metadata-cache-1.R    |  6 +--
 tests/testthat/test-1-metadata-cache-3.R    |  2 +-
 10 files changed, 50 insertions(+), 71 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index 097688a3..dc0dded2 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -48,17 +48,6 @@ export(repo_status)
 export(with_repo)
 if (getRversion() >= "4.0.0") importFrom(tools, R_user_dir)
 importFrom(R6,R6Class)
-importFrom(cli,cli_alert_info)
-importFrom(cli,cli_process_done)
-importFrom(cli,cli_process_start)
-importFrom(cli,cli_status)
-importFrom(cli,cli_status_clear)
-importFrom(cli,cli_status_update)
-importFrom(cli,get_spinner)
-importFrom(cli,hash_obj_md5)
-importFrom(curl,parse_headers_list)
-importFrom(filelock,lock)
-importFrom(filelock,unlock)
 importFrom(tools,file_ext)
 importFrom(utils,URLencode)
 importFrom(utils,getSrcDirectory)
diff --git a/R/archive.R b/R/archive.R
index ed3792fe..0cbf4ad0 100644
--- a/R/archive.R
+++ b/R/archive.R
@@ -264,7 +264,7 @@ cac_cleanup <- function(self, private, force) {
   rep_etag <- paste0(rep_rds, "-etag")
   unlink(c(rep_rds, rep_etag), recursive = TRUE, force = TRUE)
   private$data <- NULL
-  cli_alert_info("Cleaning up archive cache in {.path {pri_rds}}.")
+  cli::cli_alert_info("Cleaning up archive cache in {.path {pri_rds}}.")
   unlink(c(pri_rds, pri_etag, pri_lock), recursive = TRUE, force = TRUE)
   invisible(self)
 }
@@ -331,9 +331,9 @@ cac__load_primary <- function(self, private, max_age) {
 
   pri_lock <- paste0(pri_file, "-lock")
   mkdirp(dirname(pri_lock))
-  l <- lock(pri_lock, exclusive = FALSE, private$lock_timeout)
+  l <- filelock::lock(pri_lock, exclusive = FALSE, private$lock_timeout)
   if (is.null(l)) stop("Cannot acquire lock to copy RDS")
-  on.exit(unlock(l), add = TRUE)
+  on.exit(filelock::unlock(l), add = TRUE)
 
   if (!file.exists(pri_file)) stop("No primary RDS file in cache")
   time <- file_get_time(pri_file)
@@ -345,7 +345,7 @@ cac__load_primary <- function(self, private, max_age) {
   rep_etag <- paste0(rep_file, "-etag")
   file_copy_with_time(pri_etag, rep_etag)
 
-  unlock(l)
+  filelock::unlock(l)
 
   private$data <- readRDS(rep_file)
   private$data_time <- time
@@ -422,9 +422,9 @@ cac__update_primary <- function(self, private, lock) {
   if (lock) {
     pri_lock <- paste0(pri_file, "-lock")
     mkdirp(dirname(pri_lock))
-    l <- lock(pri_lock, exclusive = FALSE, private$lock_timeout)
+    l <- filelock::lock(pri_lock, exclusive = FALSE, private$lock_timeout)
     if (is.null(l)) stop("Cannot acquire lock to copy RDS")
-    on.exit(unlock(l), add = TRUE)
+    on.exit(filelock::unlock(l), add = TRUE)
   }
 
   file_copy_with_time(rep_file, pri_file)
diff --git a/R/async-http.R b/R/async-http.R
index fda9422a..38ddb6ae 100644
--- a/R/async-http.R
+++ b/R/async-http.R
@@ -67,7 +67,6 @@ update_async_timeouts <- function(options) {
 #'   * `etag_file`: The file the ETag was written to, or `NULL` otherwise
 #'
 #' @family async HTTP tools
-#' @importFrom curl parse_headers_list
 #' @noRd
 #' @section Examples:
 #' ```
@@ -122,7 +121,7 @@ download_file <- function(url, destfile, etag_file = NULL,
     then(function(resp) {
       "!DEBUG downloaded `url`"
       file.rename(tmp_destfile, destfile)
-      etag <- parse_headers_list(resp$headers)[["etag"]] %||% NA_character_
+      etag <- curl::parse_headers_list(resp$headers)[["etag"]] %||% NA_character_
       if (!is.null(etag_file) && !is.na(etag[1])) {
         mkdirp(dirname(etag_file))
         writeLines(etag, etag_file)
@@ -245,7 +244,7 @@ download_if_newer <- function(url, destfile, etag_file = NULL,
       } else if (resp$status_code == 200 || resp$status_code == 0) {
         "!DEBUG downloaded `url`"
         file.rename(tmp_destfile, destfile)
-        etag <- parse_headers_list(resp$headers)[["etag"]] %||% NA_character_
+        etag <- curl::parse_headers_list(resp$headers)[["etag"]] %||% NA_character_
         if (!is.null(etag_file) && !is.na(etag[1])) {
           mkdirp(dirname(etag_file))
           writeLines(etag, etag_file)
diff --git a/R/metadata-cache.R b/R/metadata-cache.R
index 0bfe15e4..37ca9840 100644
--- a/R/metadata-cache.R
+++ b/R/metadata-cache.R
@@ -376,8 +376,6 @@ cmc_summary <- function(self, private) {
   )
 }
 
-#' @importFrom cli cli_alert_info
-
 cmc_cleanup <- function(self, private, force) {
   if (!force && !interactive()) {
     stop("Not cleaning up cache, please specify `force = TRUE`")
@@ -396,13 +394,16 @@ cmc_cleanup <- function(self, private, force) {
   unlink(local_cache_dir, recursive = TRUE, force = TRUE)
   private$data <- NULL
   private$data_messaged <- NULL
-  cli_alert_info("Cleaning up cache directory {.path {cache_dir}}.")
+  cli::cli_alert_info("Cleaning up cache directory {.path {cache_dir}}.")
   unlink(cache_dir, recursive = TRUE, force = TRUE)
 }
 
-#' @importFrom cli hash_obj_md5
 #' @importFrom utils URLencode
 
+hash_obj_md5 <- function(x, ...) {
+  cli::hash_obj_md5(x, ...)
+}
+
 repo_encode <- function(repos) {
   paste0(
     vcapply(repos$name, URLencode, reserved = TRUE), "-",
@@ -603,7 +604,6 @@ cmc__get_memory_cache  <- function(self, private, max_age) {
 #'   as current.
 #' @return The metadata.
 #' @keywords internal
-#' @importFrom cli cli_process_start cli_process_done
 
 cmc__load_replica_rds <- function(self, private, max_age) {
   "!!DEBUG Load replica RDS?"
@@ -613,13 +613,13 @@ cmc__load_replica_rds <- function(self, private, max_age) {
   time <- file_get_time(rds)
   if (Sys.time() - time > max_age) stop("Replica RDS cache file outdated")
 
-  sts <- cli_process_start("Loading metadata database")
+  sts <- cli::cli_process_start("Loading metadata database")
   private$data <- readRDS(rds)
   private$data_time <- time
   private$data_messaged <- NULL
   "!!DEBUG Loaded replica RDS!"
   private$update_memory_cache()
-  cli_process_done(sts)
+  cli::cli_process_done(sts)
 
   private$data
 }
@@ -632,7 +632,6 @@ cmc__load_replica_rds <- function(self, private, max_age) {
 #' @inheritParams cmc__load_replica_rds
 #' @return Metadata.
 #' @keywords internal
-#' @importFrom cli cli_process_start cli_process_done
 
 cmc__load_primary_rds <- function(self, private, max_age) {
   "!!DEBUG Load primary RDS?"
@@ -640,9 +639,9 @@ cmc__load_primary_rds <- function(self, private, max_age) {
   rep_files <- private$get_cache_files("replica")
 
   mkdirp(dirname(pri_files$lock))
-  l <- lock(pri_files$lock, exclusive = FALSE, private$lock_timeout)
+  l <- filelock::lock(pri_files$lock, exclusive = FALSE, private$lock_timeout)
   if (is.null(l)) stop("Cannot acquire lock to copy RDS")
-  on.exit(unlock(l), add = TRUE)
+  on.exit(filelock::unlock(l), add = TRUE)
 
   if (!file.exists(pri_files$rds)) stop("No primary RDS file in cache")
   time <- file_get_time(pri_files$rds)
@@ -655,16 +654,16 @@ cmc__load_primary_rds <- function(self, private, max_age) {
     stop("Primary PACKAGES missing or newer than replica RDS, removing")
   }
 
-  sts <- cli_process_start("Loading metadata database")
+  sts <- cli::cli_process_start("Loading metadata database")
   file_copy_with_time(pri_files$rds, rep_files$rds)
-  unlock(l)
+  filelock::unlock(l)
 
   private$data <- readRDS(rep_files$rds)
   private$data_time <- time
   private$data_messaged <- NULL
 
   private$update_memory_cache()
-  cli_process_done(sts)
+  cli::cli_process_done(sts)
 
   private$data
 }
@@ -681,7 +680,6 @@ cmc__load_primary_rds <- function(self, private, max_age) {
 #' @param max_age Max age to consider the files current.
 #' @return Metadata.
 #' @keywords internal
-#' @importFrom cli cli_process_start cli_process_done
 
 cmc__load_primary_pkgs <- function(self, private, max_age) {
   "!!DEBUG Load replica PACKAGES*?"
@@ -690,9 +688,9 @@ cmc__load_primary_pkgs <- function(self, private, max_age) {
 
   ## Lock
   mkdirp(dirname(pri_files$lock))
-  l <- lock(pri_files$lock, exclusive = FALSE, private$lock_timeout)
+  l <- filelock::lock(pri_files$lock, exclusive = FALSE, private$lock_timeout)
   if (is.null(l)) stop("Cannot acquire lock to copy PACKAGES files")
-  on.exit(unlock(l), add = TRUE)
+  on.exit(filelock::unlock(l), add = TRUE)
 
   ## Check if PACKAGES exist and current. It is OK if metadata is missing
   pkg_files <- pri_files$pkgs$path
@@ -705,7 +703,7 @@ cmc__load_primary_pkgs <- function(self, private, max_age) {
   }
 
   ## Copy to replica, if we cannot copy the etags, that's ok
-  sts <- cli_process_start("Loading metadata database")
+  sts <- cli::cli_process_start("Loading metadata database")
   private$copy_to_replica(rds = FALSE, pkgs = TRUE, etags = TRUE)
 
   ## Update RDS in replica, this also loads it
@@ -713,7 +711,7 @@ cmc__load_primary_pkgs <- function(self, private, max_age) {
 
   ## Update primary, but not the PACKAGES
   private$update_primary(rds = TRUE, packages = FALSE, lock = FALSE)
-  cli_process_done(sts)
+  cli::cli_process_done(sts)
 
   private$data
 }
@@ -785,7 +783,7 @@ missing_pkgs_note <- function(pkgs, result) {
   where <- vcapply(msgs, "[[", 2)
   for (wt in unique(what)) {
     wh <- unique(where[what == wt])
-    cli_alert_info("{wt} packages are missing from {wh}")
+    cli::cli_alert_info("{wt} packages are missing from {wh}")
   }
 }
 
@@ -797,11 +795,10 @@ missing_pkgs_note <- function(pkgs, result) {
 #' @param private private self
 #' @param alert whether to show message about the update
 #' @keywords internal
-#' @importFrom cli cli_process_start cli_process_done
 
 cmc__update_replica_rds <- function(self, private, alert) {
   "!!DEBUG Update replica RDS"
-  if (alert) sts <- cli_process_start("Updating metadata database")
+  if (alert) sts <- cli::cli_process_start("Updating metadata database")
   rep_files <- private$get_cache_files("replica")
 
   data_list <- lapply_rows(
@@ -827,7 +824,7 @@ cmc__update_replica_rds <- function(self, private, alert) {
 
   private$update_memory_cache()
 
-  if (alert) cli_process_done(sts)
+  if (alert) cli::cli_process_done(sts)
   private$data
 }
 
@@ -851,9 +848,9 @@ cmc__update_primary <- function(self, private, rds, packages, lock) {
 
   if (lock) {
     mkdirp(dirname(pri_files$lock))
-    l <- lock(pri_files$lock, exclusive = TRUE, private$lock_timeout)
+    l <- filelock::lock(pri_files$lock, exclusive = TRUE, private$lock_timeout)
     if (is.null(l)) stop("Cannot acquire lock to update primary cache")
-    on.exit(unlock(l), add = TRUE)
+    on.exit(filelock::unlock(l), add = TRUE)
   }
 
   if (rds) {
@@ -884,9 +881,9 @@ cmc__copy_to_replica <- function(self, private, rds, pkgs, etags) {
   rep_files <- private$get_cache_files("replica")
 
   mkdirp(dirname(pri_files$lock))
-  l <- lock(pri_files$lock, exclusive = FALSE, private$lock_timeout)
+  l <- filelock::lock(pri_files$lock, exclusive = FALSE, private$lock_timeout)
   if (is.null(l)) stop("Cannot acquire lock to copy primary cache")
-  on.exit(unlock(l), add = TRUE)
+  on.exit(filelock::unlock(l), add = TRUE)
 
   if (rds) {
     file_copy_with_time(pri_files$rds, rep_files$rds)
diff --git a/R/onload.R b/R/onload.R
index 4f336611..8d8ea770 100644
--- a/R/onload.R
+++ b/R/onload.R
@@ -641,7 +641,7 @@ if (exists(".onLoad", inherits = FALSE)) {
 
 get_cranlike_metadata_cache <- function() {
   repos <- repo_get()
-  hash <- cli::hash_obj_md5(repos$url)
+  hash <- hash_obj_md5(repos$url)
   if (is.null(pkgenv$global_metadata_cache[[hash]])) {
     pkgenv$global_metadata_cache[[hash]] <- cranlike_metadata_cache$new()
   }
diff --git a/R/package-cache.R b/R/package-cache.R
index cdca92db..6d6f8399 100644
--- a/R/package-cache.R
+++ b/R/package-cache.R
@@ -121,7 +121,7 @@ package_cache <- R6Class(
 
     list = function() {
       l <- private$lock(exclusive = FALSE)
-      on.exit(unlock(l), add = TRUE)
+      on.exit(filelock::unlock(l), add = TRUE)
       dbfile <- get_db_file(private$path)
       readRDS(dbfile)
     },
@@ -132,7 +132,7 @@ package_cache <- R6Class(
 
     copy_to = function(target, ..., .list = NULL) {
       l <- private$lock(exclusive = FALSE)
-      on.exit(unlock(l), add = TRUE)
+      on.exit(filelock::unlock(l), add = TRUE)
       res <- private$find_locked(..., .list = .list)
       if (!is.null(target) && nrow(res) >= 1) {
         mkdirp(dirname(target))
@@ -146,7 +146,7 @@ package_cache <- R6Class(
       assert_that(is_existing_file(file))
 
       l <- private$lock(exclusive = TRUE)
-      on.exit(unlock(l), add = TRUE)
+      on.exit(filelock::unlock(l), add = TRUE)
       dbfile <- get_db_file(private$path)
       db <- readRDS(dbfile)
 
@@ -294,7 +294,7 @@ package_cache <- R6Class(
 
     delete = function(..., .list = NULL) {
       l <- private$lock(exclusive = TRUE)
-      on.exit(unlock(l), add = TRUE)
+      on.exit(filelock::unlock(l), add = TRUE)
       dbfile <- get_db_file(private$path)
 
       ex <- private$find_locked(..., .list = .list)
@@ -345,8 +345,8 @@ create_empty_db_file_if_needed <- function(path) {
 
   df <- make_empty_db_data_frame()
 
-  l <- lock(lockfile)
-  on.exit(unlock(l))
+  l <- filelock::lock(lockfile)
+  on.exit(filelock::unlock(l))
   save_rds(df, dbfile)
 }
 
diff --git a/R/progress-bar.R b/R/progress-bar.R
index 51eedc17..134ecda1 100644
--- a/R/progress-bar.R
+++ b/R/progress-bar.R
@@ -1,19 +1,17 @@
 
-#' @importFrom cli get_spinner cli_status
-
 create_progress_bar <- function(data) {
   bar <- new.env(parent = emptyenv())
 
   if (isTRUE(getOption("pkg.show_progress", FALSE))) {
-    bar$status <- cli_status(
+    bar$status <- cli::cli_status(
       "Checking for {nrow(data)} new metadata file{?s}",
       .auto_close = FALSE
     )
   } else {
-    bar$status <- cli_status(character(), .auto_close = FALSE)
+    bar$status <- cli::cli_status(character(), .auto_close = FALSE)
   }
 
-  bar$spinner <- get_spinner()
+  bar$spinner <- cli::get_spinner()
   bar$spinner_state <- 1L
 
   bar$data <- data
@@ -52,8 +50,6 @@ update_progress_bar_done  <- function(bar, url) {
     file.size(bar$data$path[[wh]])
 }
 
-#' @importFrom cli cli_status_update
-
 show_progress_bar <- function(bar) {
   if (is.null(bar$status) ||
     !isTRUE(getOption("pkg.show_progress", FALSE))) {
@@ -76,18 +72,16 @@ show_progress_bar <- function(bar) {
     bar$spinner_state <- 1L
   }
 
-  cli_status_update(
+  cli::cli_status_update(
     bar$status,
     c("{spinner} Updating metadata database [{uptodate}/{numfiles}] | ",
       "Downloading {downloads}")
   )
 }
 
-#' @importFrom cli cli_status_clear
-
 finish_progress_bar <- function(ok, bar) {
   if (!ok) {
-    cli_status_clear(
+    cli::cli_status_clear(
       bar$status,
       result = "failed",
       msg_failed = "{.alert-danger Metadata update failed}"
@@ -97,14 +91,14 @@ finish_progress_bar <- function(ok, bar) {
     dl <- vlapply(bar$data$uptodate, identical, FALSE)
     files <- sum(dl)
     bytes <- format_bytes$pretty_bytes(sum(bar$data$size[dl], na.rm = TRUE))
-    cli_status_clear(
+    cli::cli_status_clear(
       bar$status,
       result = "done",
       msg_done = "{.alert-success Updated metadata database: {bytes} in {files} file{?s}.}"
     )
 
   } else {
-    cli_status_clear(bar$status)
+    cli::cli_status_clear(bar$status)
   }
 
   bar$status <- NULL
diff --git a/tests/testthat/_snaps/1-metadata-cache-3.md b/tests/testthat/_snaps/1-metadata-cache-3.md
index a8c282a6..d54db923 100644
--- a/tests/testthat/_snaps/1-metadata-cache-3.md
+++ b/tests/testthat/_snaps/1-metadata-cache-3.md
@@ -3,6 +3,6 @@
     Code
       suppressMessages(cmc$list())
     Condition
-      Error in `lock()`:
+      Error in `filelock::lock()`:
       ! Cannot open lock file: Not a directory
 
diff --git a/tests/testthat/test-1-metadata-cache-1.R b/tests/testthat/test-1-metadata-cache-1.R
index 41fedc4b..be26aaec 100644
--- a/tests/testthat/test-1-metadata-cache-1.R
+++ b/tests/testthat/test-1-metadata-cache-1.R
@@ -133,12 +133,12 @@ test_that("locking failures", {
 
   cmc <- cranlike_metadata_cache$new(pri, rep, "source", bioc = FALSE)
 
-  mockery::stub(cmc__load_primary_rds, "lock", function(...) NULL)
+  mockery::stub(cmc__load_primary_rds, "filelock::lock", function(...) NULL)
   expect_error(
     cmc__load_primary_rds(cmc, get_private(cmc), oneday()),
     "Cannot acquire lock to copy RDS")
 
-  mockery::stub(cmc__load_primary_pkgs, "lock", function(...) NULL)
+  mockery::stub(cmc__load_primary_pkgs, "filelock::lock", function(...) NULL)
   expect_error(
     cmc__load_primary_pkgs(cmc, get_private(cmc), oneday()),
     "Cannot acquire lock to copy PACKAGES")
@@ -291,7 +291,7 @@ test_that("update_primary 2", {
   cmc <- cranlike_metadata_cache$new(pri, rep, c("macos", "source"),
                                      bioc = FALSE)
 
-  mockery::stub(cmc__update_primary, "lock", function(...) NULL)
+  mockery::stub(cmc__update_primary, "filelock::lock", function(...) NULL)
   expect_error(
     cmc__update_primary(cmc, get_private(cmc), TRUE, TRUE, TRUE),
     "Cannot acquire lock to update primary cache")
diff --git a/tests/testthat/test-1-metadata-cache-3.R b/tests/testthat/test-1-metadata-cache-3.R
index 4fa62e3a..b71c17d5 100644
--- a/tests/testthat/test-1-metadata-cache-3.R
+++ b/tests/testthat/test-1-metadata-cache-3.R
@@ -106,7 +106,7 @@ test_that("update_memory_cache", {
   cmc <- cranlike_metadata_cache$new(pri, rep, c("macos", "source"),
                                      bioc = FALSE)
 
-  mockery::stub(cmc__copy_to_replica, "lock", function(...) NULL)
+  mockery::stub(cmc__copy_to_replica, "filelock::lock", function(...) NULL)
   expect_error(
     cmc__copy_to_replica(cmc, get_private(cmc), TRUE, TRUE, TRUE),
     "Cannot acquire lock to copy primary cache")