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
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