Warning on saveRDS of qenv object #194
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Perhaps this is because you need the class definition to deserialize on object? |
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When googling for this topic I encountered this issue with linked PR. In there, the problem was about saveRDS of list with functions which inherits from attached environment (that is in the middle of search path - don't know if it's relevant). I came up with the following warning-free snippet: library(teal.code)
q <- qenv()
parent.env(q@env) <- baseenv()
saveRDS(q, tempfile())Created on 2024-01-23 with reprex v2.1.0 I'm not suggesting this to be a solution (don't know this yet) - I think this is related. Will dig more into this tomorrow. |
Utterly unacceptable. |
averissimo
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Apr 22, 2024
# Pull Request <!--- Replace `#nnn` with your issue link for reference. --> Part of #712 #### Changes description - Adds tests that iterate on each documentation file and runs the examples apps by mocking `interactive` and `shinyApp` functions. - Checks if there are no errors nor validation errors (with exceptions) - Implements insightsengineering/teal.modules.clinical#983 on this repository #### Changes from insightsengineering/teal.modules.clinical#983 - Adds: - Regex rules define "accepted" validation errors - Fixes: - Reverts to use `library` instead of `pkgload::load_all` due to problems with `system.file` call that cannot find package files. ```diff diff -u teal.modules.clinical/tests/testthat/test-examples.R teal.modules.general/tests/testthat/test-examples.R --- teal.modules.clinical/tests/testthat/test-examples.R 2024-04-12 10:32:33.100707738 +0200 +++ teal.modules.general/tests/testthat/test-examples.R 2024-04-12 10:26:27.645642183 +0200 @@ -38,12 +38,7 @@ with_mocked_app_bindings <- function(code) { # change to `print(shiny__shinyApp(...))` and remove allow warning once fixed mocked_shinyApp <- function(ui, server, ...) { # nolint object_name_linter. functionBody(server) <- bquote({ - pkgload::load_all( - .(normalizePath(file.path(testthat::test_path(), "..", ".."))), - export_all = FALSE, - attach_testthat = FALSE, - warn_conflicts = FALSE - ) + library(.(testthat::testing_package()), character.only = TRUE) .(functionBody(server)) }) print(do.call(shiny__shinyApp, append(x = list(ui = ui, server = server), list(...)))) @@ -56,16 +51,34 @@ with_mocked_app_bindings <- function(code) { app_driver <- shinytest2::AppDriver$new( x, shiny_args = args, + timeout = 20 * 1000, + load_timeout = 30 * 1000, check_names = FALSE, # explicit check below options = options() # rstudio/shinytest2#377 ) on.exit(app_driver$stop(), add = TRUE) - app_driver$wait_for_idle(timeout = 20000) + app_driver$wait_for_idle() # Simple testing ## warning in the app does not invoke a warning in the test ## rstudio/shinytest2#378 app_logs <- subset(app_driver$get_logs(), location == "shiny")[["message"]] + + # Check if the teal app has content (indicator of a Shiny App fatal error) + if (identical(trimws(app_driver$get_text("#teal-main_ui_container")), "")) { + tryCatch( + app_driver$wait_for_idle(duration = 2000), # wait 2 seconds for session to disconnect + error = function(err) { + stop( + sprintf( + "Teal Application is empty. An Error may have occured:\n%s", + paste0(subset(app_driver$get_logs(), location == "shiny")[["message"]], collapse = "\n") + ) + ) + } + ) + } + # allow `Warning in file(con, "r")` warning coming from pkgload::load_all() if (any(grepl("Warning in.*", app_logs) & !grepl("Warning in file\\(con, \"r\"\\)", app_logs))) { warning( @@ -79,9 +92,17 @@ with_mocked_app_bindings <- function(code) { ## Throw an error instead of a warning (default `AppDriver$new(..., check_names = TRUE)` throws a warning) app_driver$expect_unique_names() + err_el <- Filter( + function(x) { + allowed_errors <- getOption("test_examples.discard_error_regex", "") + identical(allowed_errors, "") || !grepl(allowed_errors, x) + }, + app_driver$get_html(".shiny-output-error") + ) + ## shinytest2 captures app crash but teal continues on error inside the module ## we need to use a different way to check if there are errors - if (!is.null(err_el <- app_driver$get_html(".shiny-output-error"))) { + if (!is.null(err_el) && length(err_el) > 0) { stop(sprintf("Module error is observed:\n%s", err_el)) } @@ -110,11 +131,14 @@ with_mocked_app_bindings <- function(code) { strict_exceptions <- c( # r-lib/gtable#94 - "tm_g_barchart_simple.Rd", - "tm_g_ci.Rd", - "tm_g_ipp.Rd", - "tm_g_pp_adverse_events.Rd", - "tm_g_pp_vitals.Rd" + "tm_outliers.Rd", + "tm_g_response.Rd", + "tm_a_pca.Rd" +) + +discard_validation_regex <- list( + "tm_file_viewer.Rd" = "Please select a file\\.", + "tm_g_distribution.Rd" = "Please select a test" ) for (i in rd_files()) { @@ -122,11 +146,18 @@ for (i in rd_files()) { paste0("example-", basename(i)), { testthat::skip_on_cran() + skip_if_too_deep(5) if (basename(i) %in% strict_exceptions) { op <- options() withr::local_options(opts_partial_match_old) withr::defer(options(op)) } + # Allow for specific validation errors for individual examples + withr::local_options( + list( + "test_examples.discard_error_regex" = discard_validation_regex[[basename(i)]] + ) + ) with_mocked_app_bindings( # suppress warnings coming from saving qenv insightsengineering/teal.code#194 suppress_warnings(``` --------- Signed-off-by: André Veríssimo <211358+averissimo@users.noreply.github.com> Co-authored-by: kartikeya kirar <kirar.kartikeya1@gmail.com> Co-authored-by: Vedha Viyash <49812166+vedhav@users.noreply.github.com>
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I was having issues with shinytest2 and I narrowed this to the following reprex:
Created on 2024-01-23 with reprex v2.1.0
Not digging into why one might want to call
saveRDS()(in my case it's out of my control) - is there a way to avoid this warning?The text was updated successfully, but these errors were encountered: