Owner avatar OceanOmics-classifier-comparison trial run.R

gistfile1.txt

- Project '~/tmp/OceanOmics-classifier-comparison' loaded. [renv 1.0.3]
> targets::tar_make()
> dispatched target all_results_files
o completed target all_results_files [0 seconds]
> dispatched branch all_results_ecfccd47
o completed branch all_results_ecfccd47 [0 seconds]
> dispatched branch all_results_eccc5a34
o completed branch all_results_eccc5a34 [0 seconds]
> dispatched branch all_results_05574669
o completed branch all_results_05574669 [0 seconds]
> dispatched branch all_results_68979051
o completed branch all_results_68979051 [0 seconds]
> dispatched branch all_results_3794a5bc
o completed branch all_results_3794a5bc [0 seconds]
> dispatched branch all_results_eb29f5b6
o completed branch all_results_eb29f5b6 [0 seconds]
> dispatched branch all_results_0df11726
o completed branch all_results_0df11726 [0 seconds]
> dispatched branch all_results_c18f63bd
o completed branch all_results_c18f63bd [0 seconds]
> dispatched branch all_results_213d2d72
o completed branch all_results_213d2d72 [0 seconds]
> dispatched branch all_results_f4773b3e
o completed branch all_results_f4773b3e [0 seconds]
> dispatched branch all_results_acafb43d
o completed branch all_results_acafb43d [0 seconds]
> dispatched branch all_results_0e9a9698
o completed branch all_results_0e9a9698 [0 seconds]
o completed pattern all_results
> dispatched target nbc_hits
> dispatched target classifier_complexity
o completed target classifier_complexity [3.117 seconds]
> dispatched target classifier_distances
> dispatched target truth_set
> dispatched target blast_hits
> dispatched target plot_report
> dispatched target merged_all_results
> dispatched target kraken_hits
> dispatched target plot_asvs_per_dataset
o completed target plot_asvs_per_dataset [0.583 seconds]
o completed target nbc_hits [0.771 seconds]
> dispatched target nbc_hits_data
o completed target blast_hits [0.001 seconds]
> dispatched target blast_hits_data
o completed target plot_report [0 seconds]
o completed target classifier_distances [0.794 seconds]
> dispatched target classifier_data
o completed target truth_set [0.747 seconds]
> dispatched target truth_set_data
o completed target truth_set_data [0.123 seconds]
o completed target nbc_hits_data [0.408 seconds]
> dispatched target thirty_subsampled_nbc_hits_data
o completed target kraken_hits [0.794 seconds]
> dispatched target kraken_hits_data
o completed target blast_hits_data [0.931 seconds]
> dispatched target subsampled_nbc_hits_data
o completed target classifier_data [0.754 seconds]
> dispatched target dendrogram
> dispatched target thirty_subsambled_blast_hits_data
> dispatched target subsambled_blast_hits_data
o completed target thirty_subsampled_nbc_hits_data [0.003 seconds]
o completed target dendrogram [0.027 seconds]
> dispatched target saved
o completed target subsampled_nbc_hits_data [0.011 seconds]
o completed target thirty_subsambled_blast_hits_data [0.002 seconds]
o completed target subsambled_blast_hits_data [0.005 seconds]
o completed target saved [0.267 seconds]
o completed target kraken_hits_data [0.811 seconds]
> dispatched target subsambled_kraken_hits_data
> dispatched target thirty_subsampled_kraken_hits_data
o completed target merged_all_results [3.462 seconds]
> dispatched target correctness_table
o completed target subsambled_kraken_hits_data [0.004 seconds]
> dispatched target final_outcomes_100
/
Quitting from lines 173-184 [unnamed-chunk-15] (100_species_final_checks.Rmd)
x errored target final_outcomes_100
x errored pipeline [25.818 seconds]
Error:
! Error running targets::tar_make()
Error messages: targets::tar_meta(fields = error, complete_only = TRUE)
Debugging guide: https://books.ropensci.org/targets/debugging.html
How to ask for help: https://books.ropensci.org/targets/help.html
Last error message:
    Problem while mapping stat to aesthetics.
ℹ Error occurred in the 1st layer.
Caused by error in `match.fun()`:
! 'scale$transformation$inverse' is not a function, character or symbol
Last error traceback:
    tarchetypes::tar_render_run(path = "/Users/283204f/tmp/OceanOmics-classi...
    do.call(rmarkdown::render, args)
    (function (input, output_format = NULL, output_file = NULL, output_dir =...
    knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
    process_file(text, output)
    handle_error(withCallingHandlers(if (tangle) process_tangle(group) else ...
    withCallingHandlers(expr, error = function(e) {     loc = paste0(current...
    withCallingHandlers(if (tangle) process_tangle(group) else process_group...
    process_group(group)
    process_group.block(group)
    call_block(x)
    block_exec(params)
    eng_r(options)
    in_input_dir(evaluate(code, envir = env, new_device = FALSE,      keep_w...
    in_dir(input_dir(), expr)
    evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.nu...
    evaluate::evaluate(...)
    evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,    ...
    handle(pv <- withCallingHandlers(withVisible(value_fun(ev$value,      ev...
    withCallingHandlers(withVisible(value_fun(ev$value, ev$visible)),      w...
    withVisible(value_fun(ev$value, ev$visible))
    value_fun(ev$value, ev$visible)
    fun(x, options = options)
    withVisible(knit_print(x, ...))
    knit_print(x, ...)
    knit_print.default(x, ...)
    normal_print(x)
    print(x)
    print.ggplot(x)
    ggplot_build(x)
    ggplot_build.ggplot(x)
    by_layer(function(l, d) l$map_statistic(d, plot), layers, data,      "ma...
    try_fetch(for (i in seq_along(data)) {     out[[i]] <- f(l = layers[[i]]...
    tryCatch(withCallingHandlers(expr, condition = function(cnd) {     {    ...
    tryCatchList(expr, classes, parentenv, handlers)
    tryCatchOne(expr, names, parentenv, handlers[[1L]])
    doTryCatch(return(expr), name, parentenv, handler)
    withCallingHandlers(expr, condition = function(cnd) {     {         .__h...
    f(l = layers[[i]], d = data[[i]])
    l$map_statistic(d, plot)
    map_statistic(..., self = self)
    plot$scales$backtransform_df(data)
    backtransform_df(..., self = self)
    unlist(lapply(scales, function(scale) {     aesthetics <- intersect(scal...
    lapply(scales, function(scale) {     aesthetics <- intersect(scale$aesth...
    FUN(X[[i]], ...)
    lapply(df[aesthetics], scale$transformation$inverse)
    match.fun(FUN)
    stop(gettextf("'%s' is not a function, character or symbol",      depars...
    .handleSimpleError(function (cnd)  {     {         .__handler_frame__. <...
    h(simpleError(msg, call))
    handlers[[1L]](cnd)
    cli::cli_abort(c("Problem while {step}.", i = "Error occurred in the {or...
    rlang::abort(message, ..., call = call, use_cli_format = TRUE,      .fra...
    signal_abort(cnd, .file)
    signalCondition(cnd)
    (function (condition)  {     state$error <- build_message(condition)    ...