Closed Swarchal closed 4 years ago
Removed due to failing on esteemed Prof's computer, but cannot be replicated elsewhere...
ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(platetools) > > test_check("platetools") ----------- FAILURE REPORT -------------- --- failure: the condition has length > 1 --- --- srcref --- : --- package (from environment) --- platetools --- call from context --- fill_plate(df_missing, df_missing$wells) --- call from argument --- if (well %in% colnames(df) == FALSE) { stop(paste(well, "is not a column in", substitute(df)), call. = FALSE) } --- R stacktrace --- where 1: fill_plate(df_missing, df_missing$wells) where 2: eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) where 3: withCallingHandlers({ code NULL }, error = function(cnd) { if (can_entrace(cnd)) { cnd <- cnd_entrace(cnd) } return_from(env, cnd) }) where 4: .capture(act$val <- eval_bare(quo_get_expr(.quo), quo_get_env(.quo)), ...) where 5: quasi_capture(enquo(object), label, capture_error, entrace = TRUE) where 6 at testthat/test-fill_plate.R#11: expect_error(fill_plate(df_missing, df_missing$wells)) where 7: eval(code, test_env) where 8: eval(code, test_env) where 9: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() } }, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error) where 10: doTryCatch(return(expr), name, parentenv, handler) where 11: tryCatchOne(expr, names, parentenv, handlers[[1L]]) where 12: tryCatchList(expr, names[-nh], parentenv, handlers[-nh]) where 13: doTryCatch(return(expr), name, parentenv, handler) where 14: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]]) where 15: tryCatchList(expr, classes, parentenv, handlers) where 16: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() } }, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { }) where 17: test_code(desc, code, env = parent.frame()) where 18 at testthat/test-fill_plate.R#10: test_that("returns error when expected", { expect_error(fill_plate(df_missing, df_missing$wells)) expect_error(fill_plate("not_a_df", "string")) expect_error(fill_plate(df_missing, "wells", plate = 1)) expect_error(fill_plate(df_missing, "not_in")) }) where 19: eval(code, test_env) where 20: eval(code, test_env) where 21: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() } }, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error) where 22: doTryCatch(return(expr), name, parentenv, handler) where 23: tryCatchOne(expr, names, parentenv, handlers[[1L]]) where 24: tryCatchList(expr, names[-nh], parentenv, handlers[-nh]) where 25: doTryCatch(return(expr), name, parentenv, handler) where 26: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]]) where 27: tryCatchList(expr, classes, parentenv, handlers) where 28: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() } }, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { }) where 29: test_code(NULL, exprs, env) where 30: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap) where 31: force(code) where 32: doWithOneRestart(return(expr), restart) where 33: withOneRestart(expr, restarts[[1L]]) where 34: withRestarts(testthat_abort_reporter = function() NULL, force(code)) where 35: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter, { reporter$start_file(basename(path)) lister$start_file(basename(path)) source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap) reporter$.end_context() reporter$end_file() }) where 36: FUN(X[[i]], ...) where 37: lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap) where 38: force(code) where 39: doWithOneRestart(return(expr), restart) where 40: withOneRestart(expr, restarts[[1L]]) where 41: withRestarts(testthat_abort_reporter = function() NULL, force(code)) where 42: with_reporter(reporter = current_reporter, results <- lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)) where 43: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap) where 44: test_dir(path = test_path, reporter = reporter, env = env, filter = filter, ..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap) where 45: test_package_dir(package = package, test_path = test_path, filter = filter, reporter = reporter, ..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap) where 46: test_check("platetools") --- value of length: 86 type: logical --- [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE [16] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE [31] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE [46] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE [61] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE [76] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE --- function from context --- function (df, well, plate = 96) { if (!is.character(well)) { stop("'well' should be a string of the column name", call. = FALSE) } if (!is.data.frame(df)) { stop("'df' needs to be a dataframe", call. = FALSE) } accepted_plates <- c(96L, 384L, 1536L) if (plate %in% accepted_plates == FALSE) { stop("'plate' needs to be either 96, 384 or 1536", call. = FALSE) } if (well %in% colnames(df) == FALSE) { stop(paste(well, "is not a column in", substitute(df)), call. = FALSE) } well_col <- df[, well] complete_plate <- num_to_well(1:plate, plate = plate) missing_indices <- which(complete_plate %!in% well_col) missing_wells <- complete_plate[missing_indices] missing_df <- data.frame(missing_wells) names(missing_df) <- eval(substitute(well)) filled_df <- rbind_fill(df, missing_df) return(filled_df) } <bytecode: 0x68102b0> <environment: namespace:platetools> --- function search by body --- Function fill_plate in namespace platetools has this body. ----------- END OF FAILURE REPORT -------------- Fatal error: the condition has length > 1 * checking PDF version of manual ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR See ‘/data/blackswan/ripley/R/packages/tests/platetools.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 0:59.11, 50.97 + 5.11
Removed due to failing on esteemed Prof's computer, but cannot be replicated elsewhere...