CRAN Package Check Results for Package mccount

Last updated on 2025-12-21 03:49:40 CET.

Flavor	Version	T_install	T_check	T_total	Status
r-devel-linux-x86_64-debian-clang	0.1.1	6.88	129.91	136.79	ERROR
r-devel-linux-x86_64-debian-gcc	0.1.1	3.76	83.57	87.33	ERROR
r-devel-linux-x86_64-fedora-clang	0.1.1	11.00	192.21	203.21	ERROR
r-devel-linux-x86_64-fedora-gcc	0.1.1	10.00	179.74	189.74	ERROR
r-devel-windows-x86_64	0.1.1	9.00	143.00	152.00	OK
r-patched-linux-x86_64	0.1.1	6.05	131.14	137.19	OK
r-release-linux-x86_64	0.1.1	5.52	131.94	137.46	OK
r-release-macos-arm64	0.1.1				OK
r-release-macos-x86_64	0.1.1	5.00	169.00	174.00	OK
r-release-windows-x86_64	0.1.1	10.00	146.00	156.00	OK
r-oldrel-macos-arm64	0.1.1				OK
r-oldrel-macos-x86_64	0.1.1	5.00	170.00	175.00	OK
r-oldrel-windows-x86_64	0.1.1	13.00	180.00	193.00	OK

Check Details

Version: 0.1.1
Check: examples
Result: ERROR Running examples in ‘mccount-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: as.data.frame.mcc > ### Title: Convert 'mcc' object to data.frame > ### Aliases: as.data.frame.mcc > > ### ** Examples > > # Create sample data > library(dplyr) Attaching package: ‘dplyr’ The following objects are masked from ‘package:stats’: filter, lag The following objects are masked from ‘package:base’: intersect, setdiff, setequal, union > df <- data.frame( + id = c(1, 2, 3, 4, 4, 4, 4, 5, 5), + time = c(8, 1, 5, 2, 6, 7, 8, 3, 3), + cause = c(0, 0, 2, 1, 1, 1, 0, 1, 2) + ) |> + arrange(id, time) > > # Calculate MCC > mcc_result <- mcc(df, "id", "time", "cause") Error in `[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, : attempt access index 5/5 in VECTOR_ELT Calls: mcc ... mcc_equation -> handle_simultaneous_events -> [ -> [.data.table Execution halted Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 0.1.1
Check: tests
Result: ERROR Running ‘spelling.R’ [0s/0s] Running ‘testthat.R’ [54s/43s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(mccount) Loading required package: ggplot2 > > test_check("mccount") Saving _problems/test-calculation_helpers-25.R Saving _problems/test-mcc-31.R Saving _problems/test-mcc-79.R Saving _problems/test-mcc-188.R Saving _problems/test-mcc-360.R Saving _problems/test-mcc-471.R Saving _problems/test-mcc-492.R Saving _problems/test-mcc-646.R Saving _problems/test-mcc-758.R Saving _problems/test-mcc-790.R Saving _problems/test-mcc-793.R i Converting numeric grouping variable "by_var" to <factor> i Found 2 unique groups: 10 and 20 Saving _problems/test-mcc-1021.R Saving _problems/test-mcc-1023.R Saving _problems/test-mcc-1048.R Saving _problems/test-mcc-1050.R Saving _problems/test-mcc-1072.R Saving _problems/test-mcc-1205.R Saving _problems/test-mcc-1406.R Saving _problems/test-mcc-1458.R Saving _problems/test-mcc_equation-49.R Saving _problems/test-mcc_equation-173.R Saving _problems/test-mcc_equation-315.R Saving _problems/test-mcc_equation-389.R Saving _problems/test-mcc_equation-451.R Saving _problems/test-mcc_equation-783.R Saving _problems/test-mcc_equation-798.R Saving _problems/test-mcc_equation-956.R Saving _problems/test-mcc_sci-15.R Saving _problems/test-mcc_sci-57.R Saving _problems/test-mcc_sci-97.R Saving _problems/test-mcc_sci-148.R Saving _problems/test-mcc_sci-180.R Saving _problems/test-mcc_sci-206.R Saving _problems/test-mcc_sci-233.R Saving _problems/test-mcc_sci-261.R Saving _problems/test-mcc_sci-347.R Saving _problems/test-mcc_sci-365.R Saving _problems/test-mcc_sci-403.R Saving _problems/test-mcc_sci-468.R Saving _problems/test-mcc_sci-537.R Saving _problems/test-mcc_sci-569.R Saving _problems/test-mcc_sci-621.R Saving _problems/test-mcc_sci-652.R Saving _problems/test-mcc_sci-672.R Saving _problems/test-mcc_sci-701.R Saving _problems/test-mcc_sci-724.R Saving _problems/test-plot-52.R Saving _problems/test-plot-90.R Saving _problems/test-plot-129.R Saving _problems/test-plot-150.R i MCC never reaches 2 in the observed follow-up period i No reference lines added Saving _problems/test-plot-372.R Saving _problems/test-plot-400.R Saving _problems/test-plot-436.R Saving _problems/test-plot-471.R Saving _problems/test-plot-495.R Saving _problems/test-s3_classes-10.R Saving _problems/test-s3_classes-39.R Saving _problems/test-s3_classes-60.R -- Mean Cumulative Count Results ----------------------------------------------- i Method: Dong-Yasui Equation Method -- MCC Estimates -- # A tibble: 4 x 2 time mcc <dbl> <dbl> 1 0 0 2 2 0.333 3 6 0.667 4 7 1 -- Call -- mcc(data = df, id_var = "id", time_var = "time", cause_var = "cause") -- Summary of Mean Cumulative Count Results ------------------------------------ i Method: Dong-Yasui Equation Method i Total participants: 4 -- Summary Statistics -- Observation period: [0, 8] Time to MCC = 1.0: 7 Time to maximum MCC: 7 MCC at end of follow-up: 1 -- Event Count Composition Events of interest: 3 Competing risk events: 1 Censoring events: 3 Saving _problems/test-s3_classes-115.R Saving _problems/test-s3_classes-136.R Saving _problems/test-s3_classes-182.R Saving _problems/test-s3_classes-206.R Saving _problems/test-s3_classes-292.R Saving _problems/test-s3_classes-457.R Saving _problems/test-s3_classes-489.R -- Mean Cumulative Count Results ----------------------------------------------- i Method: Dong-Yasui Equation Method -- MCC Estimates -- -- Call -- mcc(data = df_minimal, id_var = "id", time_var = "time", cause_var = "cause") Saving _problems/test-s3_classes-560.R Saving _problems/test-s3_classes-743.R Saving _problems/test-s3_classes-768.R [ FAIL 68 | WARN 0 | SKIP 24 | PASS 442 ] ══ Skipped tests (24 • On CRAN (24): 'test-calculation_helpers.R:482:1', 'test-calculation_helpers.R:529:1', 'test-calculation_helpers.R:611:1', 'test-mcc.R:94:1', 'test-mcc.R:191:1', 'test-mcc.R:669:1', 'test-mcc.R:851:1', 'test-mcc.R:1167:1', 'test-mcc.R:1253:1', 'test-mcc_equation.R:203:1', 'test-mcc_equation.R:477:1', 'test-mcc_equation.R:652:1', 'test-mcc_sci.R:583:1', 'test-s3_classes.R:80:1', 'test-s3_classes.R:509:1', 'test-validation_helpers.R:1:1', 'test-validation_helpers.R:44:1', 'test-validation_helpers.R:49:1', 'test-validation_helpers.R:57:1', 'test-validation_helpers.R:69:1', 'test-validation_helpers.R:101:1', 'test-validation_helpers.R:113:1', 'test-validation_helpers.R:142:1', 'test-validation_helpers.R:181:1' ══ Failed tests ════ ── Error ('test-calculation_helpers.R:21:3'): handle_simultaneous_events() works ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 4/4 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::handle_simultaneous_events(...) 2. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 3. └─data.table:::`[.data.table`(...) ── Error ('test-mcc.R:25:3'): mcc() dispatches to the correct implementation based on method ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(...) at test-mcc.R:25:3 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc.R:71:3'): mcc() validates the method argument correctly ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(...) 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc.R:179:3'): mcc() validates tstart_var compatibility with method ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(...) 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc.R:354:3'): mcc() handles method parameter with partial matching ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(...) at test-mcc.R:354:3 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc.R:459:3'): mcc() end-to-end functionality through snapshots ── Error: object 'result_sci' not found Backtrace: ▆ 1. └─base::print(result_sci$mcc_final) ── Error ('test-mcc.R:492:3'): mcc() produces equivalent results from both methods ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df1, id_var = "id", time_var = "time", cause_var = "cause") at test-mcc.R:492:3 2. └─mccount:::mcc_equation(...) 3. └─mccount:::handle_simultaneous_events(...) 4. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 5. └─data.table:::`[.data.table`(...) ── Error ('test-mcc.R:639:3'): mcc() correctly passes include_details parameter to implementation functions ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(...) at test-mcc.R:639:3 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Failure ('test-mcc.R:758:7'): mcc() with include_details=FALSE is suitable for bootstrapping ── Bootstrap failed: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─base::tryCatch(...) at test-mcc.R:744:3 2. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 3. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 4. └─value[[3L]](cond) ── Failure ('test-mcc.R:773:3'): mcc() documentation example works with include_details=FALSE ── Expected `{ ... }` not to throw any errors. Actually got a <simpleError> with message: attempt access index 5/5 in VECTOR_ELT ── Error ('test-mcc.R:793:3'): mcc() documentation example works with include_details=FALSE ── Error in `eval(code, test_env)`: object 'mcc_eq' not found Backtrace: ▆ 1. └─testthat::expect_named(...) at test-mcc.R:793:3 2. └─testthat::quasi_label(enquo(object), label) 3. └─rlang::eval_bare(expr, quo_get_env(quo)) ── Failure ('test-mcc.R:1012:3'): mcc() with by argument works with both methods ── Expected `... <- NULL` not to throw any errors. Actually got a <simpleError> with message: attempt access index 7/7 in VECTOR_ELT ── Error ('test-mcc.R:1023:3'): mcc() with by argument works with both methods ── Error in `eval(code, test_env)`: object 'result_sci' not found Backtrace: ▆ 1. ├─testthat::expect_true("sci_table" %in% names(result_sci)) at test-mcc.R:1023:3 2. │ └─testthat::quasi_label(enquo(object), label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─"sci_table" %in% names(result_sci) ── Failure ('test-mcc.R:1038:3'): mcc() with by argument and tstart_var works ── Expected `... <- NULL` not to throw any errors. Actually got a <simpleError> with message: attempt access index 7/7 in VECTOR_ELT ── Error ('test-mcc.R:1050:3'): mcc() with by argument and tstart_var works ── Error in `eval(code, test_env)`: object 'result_sci_tstart' not found Backtrace: ▆ 1. ├─testthat::expect_true("sci_table" %in% names(result_sci_tstart)) at test-mcc.R:1050:3 2. │ └─testthat::quasi_label(enquo(object), label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─"sci_table" %in% names(result_sci_tstart) ── Error ('test-mcc.R:1064:3'): mcc() with by argument preserves group information in all components ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(...) at test-mcc.R:1064:3 2. └─mccount:::mcc_by_group(...) 3. └─mccount:::mcc_sci(...) 4. ├─dt[, `:=`(first, seq_len(.N)), by = id] 5. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc.R:1197:3'): mcc() with by argument preserves group information in all components ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(...) at test-mcc.R:1197:3 2. └─mccount:::mcc_by_group(...) 3. └─mccount:::mcc_sci(...) 4. ├─dt[, `:=`(first, seq_len(.N)), by = id] 5. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc.R:1398:3'): mcc() converts numeric grouping variables to factors ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df_numeric_groups, "id", "time", "cause", by = "group_numeric") 2. └─mccount:::mcc_by_group(...) 3. └─mccount:::mcc_equation(...) 4. └─mccount:::handle_simultaneous_events(...) 5. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 6. └─data.table:::`[.data.table`(...) ── Error ('test-mcc.R:1456:3'): plotting works correctly with converted numeric groups ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df_plot_test, "id", "time", "cause", by = "treatment") 2. └─mccount:::mcc_by_group(...) 3. └─mccount:::mcc_equation(...) 4. └─mccount:::handle_simultaneous_events(...) 5. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 6. └─data.table:::`[.data.table`(...) ── Error ('test-mcc_equation.R:43:3'): mcc_equation() handles simultaneous events correctly ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_equation(...) at test-mcc_equation.R:43:3 2. └─mccount:::handle_simultaneous_events(...) 3. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 4. └─data.table:::`[.data.table`(...) ── Error ('test-mcc_equation.R:167:3'): mcc_equation() properly uses time_precision parameter ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_equation(...) at test-mcc_equation.R:167:3 2. └─mccount:::handle_simultaneous_events(...) 3. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 4. └─data.table:::`[.data.table`(...) ── Error ('test-mcc_equation.R:309:3'): mcc_equation() with include_details=FALSE works with various scenarios ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_equation(...) at test-mcc_equation.R:309:3 2. └─mccount:::handle_simultaneous_events(...) 3. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 4. └─data.table:::`[.data.table`(...) ── Error ('test-mcc_equation.R:384:3'): mcc_equation() with include_details=FALSE does not include adjusted_data ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_equation(...) at test-mcc_equation.R:384:3 2. └─mccount:::handle_simultaneous_events(...) 3. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 4. └─data.table:::`[.data.table`(...) ── Error ('test-mcc_equation.R:445:5'): mcc_equation() with include_details=FALSE provides sufficient data for bootstrapping ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_equation(...) at test-mcc_equation.R:445:5 2. └─mccount:::handle_simultaneous_events(...) 3. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 4. └─data.table:::`[.data.table`(...) ── Failure ('test-mcc_equation.R:774:3'): weighted MCC handles simultaneous events correctly ── Expected `... <- NULL` not to throw any errors. Actually got a <simpleError> with message: attempt access index 6/6 in VECTOR_ELT ── Error ('test-mcc_equation.R:798:3'): weighted MCC handles simultaneous events correctly ── Error in `eval(code, test_env)`: object 'result1' not found Backtrace: ▆ 1. └─testthat::expect_true(result1$weighted) at test-mcc_equation.R:798:3 2. └─testthat::quasi_label(enquo(object), label) 3. └─rlang::eval_bare(expr, quo_get_env(quo)) ── Error ('test-mcc_equation.R:948:3'): weighted MCC parameter combinations work correctly ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 6/6 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(...) at test-mcc_equation.R:948:3 2. └─mccount:::mcc_equation(...) 3. └─mccount:::handle_simultaneous_events(...) 4. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 5. └─data.table:::`[.data.table`(...) ── Error ('test-mcc_sci.R:10:3'): mcc_sci() correctly calculates MCC with basic data ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:10:3 2. ├─dt[, `:=`(first, seq_len(.N)), by = id] 3. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc_sci.R:51:3'): mcc_sci() handles tstart_var correctly ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:51:3 2. ├─dt[, `:=`(first, seq_len(.N)), by = id] 3. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc_sci.R:91:3'): mcc_sci() correctly handles left-truncated data ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:91:3 2. ├─dt[, `:=`(first, seq_len(.N)), by = id] 3. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc_sci.R:142:3'): mcc_sci() correctly handles simultaneous events ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:142:3 2. └─mccount:::handle_simultaneous_events(...) 3. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 4. └─data.table:::`[.data.table`(...) ── Error ('test-mcc_sci.R:175:3'): mcc_sci() generates correct CI columns ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:175:3 2. ├─dt[, `:=`(first, seq_len(.N)), by = id] 3. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc_sci.R:201:3'): mcc_sci() processes multiple recurrent events correctly ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:201:3 2. ├─dt[, `:=`(first, seq_len(.N)), by = id] 3. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc_sci.R:228:3'): mcc_sci() handles recurrent events with competing risks ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:228:3 2. ├─dt[, `:=`(first, seq_len(.N)), by = id] 3. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc_sci.R:255:3'): mcc_sci() uses time_precision parameter correctly ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:255:3 2. └─mccount:::handle_simultaneous_events(...) 3. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 4. └─data.table:::`[.data.table`(...) ── Error ('test-mcc_sci.R:330:3'): mcc_sci() works with snapshot testing for complex cases ── Error: object 'result' not found Backtrace: ▆ 1. └─base::print(length(result$all_cis)) ── Error ('test-mcc_sci.R:360:3'): mcc_sci() respects include_details=FALSE parameter ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:360:3 2. ├─dt[, `:=`(first, seq_len(.N)), by = id] 3. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc_sci.R:397:3'): mcc_sci() with include_details=FALSE works with all key scenarios ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:397:3 2. └─mccount:::handle_simultaneous_events(...) 3. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 4. └─data.table:::`[.data.table`(...) ── Error ('test-mcc_sci.R:462:3'): mcc_sci() with include_details=FALSE provides sufficient data for bootstrapping ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:462:3 2. ├─dt[, `:=`(first, seq_len(.N)), by = id] 3. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc_sci.R:532:3'): mcc_sci cleans up time precision adjustments in output ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:532:3 2. ├─dt[, `:=`(first, seq_len(.N)), by = id] 3. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc_sci.R:564:3'): mcc_sci only calculates CI for event numbers with actual events ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:564:3 2. ├─dt[, `:=`(first, seq_len(.N)), by = id] 3. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc_sci.R:614:3'): grouped mcc fills missing CI columns with 0, not NA ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(...) at test-mcc_sci.R:614:3 2. └─mccount:::mcc_by_group(...) 3. └─mccount:::mcc_sci(...) 4. ├─dt[, `:=`(first, seq_len(.N)), by = id] 5. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc_sci.R:646:3'): mcc_sci uses time_precision parameter consistently ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:646:3 2. ├─dt[, `:=`(first, seq_len(.N)), by = id] 3. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc_sci.R:667:3'): mcc_sci handles mixed events at time 0 correctly ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:667:3 2. ├─dt[, `:=`(first, seq_len(.N)), by = id] 3. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc_sci.R:695:3'): both methods show consistent time values for events at time 0 ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(...) at test-mcc_sci.R:695:3 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc_sci.R:717:3'): CI column names are consistent across groups with different max events ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(...) at test-mcc_sci.R:717:3 2. └─mccount:::mcc_by_group(...) 3. └─mccount:::mcc_sci(...) 4. ├─dt[, `:=`(first, seq_len(.N)), by = id] 5. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-plot.R:45:3'): plot.mcc error handling works correctly ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", method = "sci", include_details = FALSE) at test-plot.R:45:3 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-plot.R:90:3'): plot.mcc throws error when type='components' with equation method ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", method = "equation") at test-plot.R:90:3 2. └─mccount:::mcc_equation(...) 3. └─mccount:::handle_simultaneous_events(...) 4. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 5. └─data.table:::`[.data.table`(...) ── Error ('test-plot.R:129:3'): plot.mcc works correctly with type='components' for SCI method ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", method = "sci") at test-plot.R:129:3 2. └─mccount:::mcc_sci(...) 3. └─mccount:::handle_simultaneous_events(...) 4. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 5. └─data.table:::`[.data.table`(...) ── Error ('test-plot.R:150:3'): plot.mcc type argument matching works correctly ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", method = "equation") at test-plot.R:150:3 2. └─mccount:::mcc_equation(...) 3. └─mccount:::handle_simultaneous_events(...) 4. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 5. └─data.table:::`[.data.table`(...) ── Error ('test-plot.R:372:3'): geom_line_mcc works with different methods (equation vs sci) ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", method = "sci") at test-plot.R:372:3 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-plot.R:400:3'): plot.mcc uses correct data table for each method ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", method = "sci") at test-plot.R:400:3 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-plot.R:429:3'): plot.mcc handles grouped data correctly with both methods ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", by = "group", method = "sci") at test-plot.R:429:3 2. └─mccount:::mcc_by_group(...) 3. └─mccount:::mcc_sci(...) 4. ├─dt[, `:=`(first, seq_len(.N)), by = id] 5. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-plot.R:471:3'): plot.mcc handles group filtering correctly ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", by = "group") at test-plot.R:471:3 2. └─mccount:::mcc_by_group(...) 3. └─mccount:::mcc_equation(...) 4. └─mccount:::handle_simultaneous_events(...) 5. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 6. └─data.table:::`[.data.table`(...) ── Error ('test-plot.R:495:3'): plot.mcc color customization works ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause") at test-plot.R:495:3 2. └─mccount:::mcc_equation(...) 3. └─mccount:::handle_simultaneous_events(...) 4. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 5. └─data.table:::`[.data.table`(...) ── Error ('test-s3_classes.R:10:3'): S3 object creation works correctly ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", method = "equation") at test-s3_classes.R:10:3 2. └─mccount:::mcc_equation(...) 3. └─mccount:::handle_simultaneous_events(...) 4. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 5. └─data.table:::`[.data.table`(...) ── Error ('test-s3_classes.R:39:3'): Grouped S3 objects work correctly ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", by = "group") at test-s3_classes.R:39:3 2. └─mccount:::mcc_by_group(...) 3. └─mccount:::mcc_equation(...) 4. └─mccount:::handle_simultaneous_events(...) 5. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 6. └─data.table:::`[.data.table`(...) ── Error ('test-s3_classes.R:60:3'): Weighted S3 objects work correctly ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 6/6 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", weights = "weights") at test-s3_classes.R:60:3 2. └─mccount:::mcc_equation(...) 3. └─mccount:::handle_simultaneous_events(...) 4. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 5. └─data.table:::`[.data.table`(...) ── Error ('test-s3_classes.R:115:3'): Print methods work for grouped objects ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", by = "group") at test-s3_classes.R:115:3 2. └─mccount:::mcc_by_group(...) 3. └─mccount:::mcc_equation(...) 4. └─mccount:::handle_simultaneous_events(...) 5. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 6. └─data.table:::`[.data.table`(...) ── Error ('test-s3_classes.R:136:3'): Print methods work for weighted objects ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 6/6 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", weights = "weights") at test-s3_classes.R:136:3 2. └─mccount:::mcc_equation(...) 3. └─mccount:::handle_simultaneous_events(...) 4. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 5. └─data.table:::`[.data.table`(...) ── Error ('test-s3_classes.R:182:3'): Grouped utility functions work correctly ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", by = "group") at test-s3_classes.R:182:3 2. └─mccount:::mcc_by_group(...) 3. └─mccount:::mcc_equation(...) 4. └─mccount:::handle_simultaneous_events(...) 5. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 6. └─data.table:::`[.data.table`(...) ── Error ('test-s3_classes.R:206:3'): MCC comparison print works correctly ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", method = "sci") at test-s3_classes.R:206:3 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-s3_classes.R:292:3'): S3 classes are assigned correctly for all combinations ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", method = "sci") at test-s3_classes.R:292:3 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-s3_classes.R:457:3'): filter_mcc works correctly ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", by = "group") at test-s3_classes.R:457:3 2. └─mccount:::mcc_by_group(...) 3. └─mccount:::mcc_equation(...) 4. └─mccount:::handle_simultaneous_events(...) 5. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 6. └─data.table:::`[.data.table`(...) ── Error ('test-s3_classes.R:489:3'): compare_mcc works correctly ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", method = "sci") at test-s3_classes.R:489:3 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-s3_classes.R:560:3'): S3 method dispatch works correctly ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", method = "sci") at test-s3_classes.R:560:3 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-s3_classes.R:743:3'): mcc_details correctly dispatches based on class ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", method = "sci") at test-s3_classes.R:743:3 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-s3_classes.R:768:3'): create_subtitle function works correctly ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", method = "sci") at test-s3_classes.R:768:3 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) [ FAIL 68 | WARN 0 | SKIP 24 | PASS 442 ] Error: ! Test failures. Execution halted Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.1.1
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘choosing-between-methods.Rmd’ using rmarkdown Quitting from choosing-between-methods.Rmd:50-73 [dong-example] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `[.data.table`: ! attempt access index 5/5 in VECTOR_ELT --- Backtrace: ▆ 1. └─mccount::mcc(...) 2. └─mccount:::mcc_equation(...) 3. └─mccount:::handle_simultaneous_events(...) 4. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 5. └─data.table:::`[.data.table`(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'choosing-between-methods.Rmd' failed with diagnostics: attempt access index 5/5 in VECTOR_ELT --- failed re-building ‘choosing-between-methods.Rmd’ --- re-building ‘estimating-mcc-after-matching-or-weighting.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘estimating-mcc-after-matching-or-weighting.Rmd’ SUMMARY: processing the following file failed: ‘choosing-between-methods.Rmd’ Error: Vignette re-building failed. Execution halted Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 0.1.1
Check: tests
Result: ERROR Running ‘spelling.R’ [0s/0s] Running ‘testthat.R’ [28s/33s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(mccount) Loading required package: ggplot2 > > test_check("mccount") Saving _problems/test-calculation_helpers-25.R Saving _problems/test-mcc-31.R Saving _problems/test-mcc-79.R Saving _problems/test-mcc-188.R Saving _problems/test-mcc-360.R Saving _problems/test-mcc-471.R Saving _problems/test-mcc-492.R Saving _problems/test-mcc-646.R Saving _problems/test-mcc-758.R Saving _problems/test-mcc-790.R Saving _problems/test-mcc-793.R i Converting numeric grouping variable "by_var" to <factor> i Found 2 unique groups: 10 and 20 Saving _problems/test-mcc-1021.R Saving _problems/test-mcc-1023.R Saving _problems/test-mcc-1048.R Saving _problems/test-mcc-1050.R Saving _problems/test-mcc-1072.R Saving _problems/test-mcc-1205.R Saving _problems/test-mcc-1406.R Saving _problems/test-mcc-1458.R Saving _problems/test-mcc_equation-49.R Saving _problems/test-mcc_equation-173.R Saving _problems/test-mcc_equation-315.R Saving _problems/test-mcc_equation-389.R Saving _problems/test-mcc_equation-451.R Saving _problems/test-mcc_equation-783.R Saving _problems/test-mcc_equation-798.R Saving _problems/test-mcc_equation-956.R Saving _problems/test-mcc_sci-15.R Saving _problems/test-mcc_sci-57.R Saving _problems/test-mcc_sci-97.R Saving _problems/test-mcc_sci-148.R Saving _problems/test-mcc_sci-180.R Saving _problems/test-mcc_sci-206.R Saving _problems/test-mcc_sci-233.R Saving _problems/test-mcc_sci-261.R Saving _problems/test-mcc_sci-347.R Saving _problems/test-mcc_sci-365.R Saving _problems/test-mcc_sci-403.R Saving _problems/test-mcc_sci-468.R Saving _problems/test-mcc_sci-537.R Saving _problems/test-mcc_sci-569.R Saving _problems/test-mcc_sci-621.R Saving _problems/test-mcc_sci-652.R Saving _problems/test-mcc_sci-672.R Saving _problems/test-mcc_sci-701.R Saving _problems/test-mcc_sci-724.R Saving _problems/test-plot-52.R Saving _problems/test-plot-90.R Saving _problems/test-plot-129.R Saving _problems/test-plot-150.R i MCC never reaches 2 in the observed follow-up period i No reference lines added Saving _problems/test-plot-372.R Saving _problems/test-plot-400.R Saving _problems/test-plot-436.R Saving _problems/test-plot-471.R Saving _problems/test-plot-495.R Saving _problems/test-s3_classes-10.R Saving _problems/test-s3_classes-39.R Saving _problems/test-s3_classes-60.R -- Mean Cumulative Count Results ----------------------------------------------- i Method: Dong-Yasui Equation Method -- MCC Estimates -- # A tibble: 4 x 2 time mcc <dbl> <dbl> 1 0 0 2 2 0.333 3 6 0.667 4 7 1 -- Call -- mcc(data = df, id_var = "id", time_var = "time", cause_var = "cause") -- Summary of Mean Cumulative Count Results ------------------------------------ i Method: Dong-Yasui Equation Method i Total participants: 4 -- Summary Statistics -- Observation period: [0, 8] Time to MCC = 1.0: 7 Time to maximum MCC: 7 MCC at end of follow-up: 1 -- Event Count Composition Events of interest: 3 Competing risk events: 1 Censoring events: 3 Saving _problems/test-s3_classes-115.R Saving _problems/test-s3_classes-136.R Saving _problems/test-s3_classes-182.R Saving _problems/test-s3_classes-206.R Saving _problems/test-s3_classes-292.R Saving _problems/test-s3_classes-457.R Saving _problems/test-s3_classes-489.R -- Mean Cumulative Count Results ----------------------------------------------- i Method: Dong-Yasui Equation Method -- MCC Estimates -- -- Call -- mcc(data = df_minimal, id_var = "id", time_var = "time", cause_var = "cause") Saving _problems/test-s3_classes-560.R Saving _problems/test-s3_classes-743.R Saving _problems/test-s3_classes-768.R [ FAIL 68 | WARN 0 | SKIP 24 | PASS 442 ] ══ Skipped tests (24 • On CRAN (24): 'test-calculation_helpers.R:482:1', 'test-calculation_helpers.R:529:1', 'test-calculation_helpers.R:611:1', 'test-mcc.R:94:1', 'test-mcc.R:191:1', 'test-mcc.R:669:1', 'test-mcc.R:851:1', 'test-mcc.R:1167:1', 'test-mcc.R:1253:1', 'test-mcc_equation.R:203:1', 'test-mcc_equation.R:477:1', 'test-mcc_equation.R:652:1', 'test-mcc_sci.R:583:1', 'test-s3_classes.R:80:1', 'test-s3_classes.R:509:1', 'test-validation_helpers.R:1:1', 'test-validation_helpers.R:44:1', 'test-validation_helpers.R:49:1', 'test-validation_helpers.R:57:1', 'test-validation_helpers.R:69:1', 'test-validation_helpers.R:101:1', 'test-validation_helpers.R:113:1', 'test-validation_helpers.R:142:1', 'test-validation_helpers.R:181:1' ══ Failed tests ════ ── Error ('test-calculation_helpers.R:21:3'): handle_simultaneous_events() works ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 4/4 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::handle_simultaneous_events(...) 2. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 3. └─data.table:::`[.data.table`(...) ── Error ('test-mcc.R:25:3'): mcc() dispatches to the correct implementation based on method ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(...) at test-mcc.R:25:3 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc.R:71:3'): mcc() validates the method argument correctly ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(...) 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc.R:179:3'): mcc() validates tstart_var compatibility with method ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(...) 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc.R:354:3'): mcc() handles method parameter with partial matching ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(...) at test-mcc.R:354:3 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc.R:459:3'): mcc() end-to-end functionality through snapshots ── Error: object 'result_sci' not found Backtrace: ▆ 1. └─base::print(result_sci$mcc_final) ── Error ('test-mcc.R:492:3'): mcc() produces equivalent results from both methods ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df1, id_var = "id", time_var = "time", cause_var = "cause") at test-mcc.R:492:3 2. └─mccount:::mcc_equation(...) 3. └─mccount:::handle_simultaneous_events(...) 4. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 5. └─data.table:::`[.data.table`(...) ── Error ('test-mcc.R:639:3'): mcc() correctly passes include_details parameter to implementation functions ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(...) at test-mcc.R:639:3 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Failure ('test-mcc.R:758:7'): mcc() with include_details=FALSE is suitable for bootstrapping ── Bootstrap failed: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─base::tryCatch(...) at test-mcc.R:744:3 2. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 3. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 4. └─value[[3L]](cond) ── Failure ('test-mcc.R:773:3'): mcc() documentation example works with include_details=FALSE ── Expected `{ ... }` not to throw any errors. Actually got a <simpleError> with message: attempt access index 5/5 in VECTOR_ELT ── Error ('test-mcc.R:793:3'): mcc() documentation example works with include_details=FALSE ── Error in `eval(code, test_env)`: object 'mcc_eq' not found Backtrace: ▆ 1. └─testthat::expect_named(...) at test-mcc.R:793:3 2. └─testthat::quasi_label(enquo(object), label) 3. └─rlang::eval_bare(expr, quo_get_env(quo)) ── Failure ('test-mcc.R:1012:3'): mcc() with by argument works with both methods ── Expected `... <- NULL` not to throw any errors. Actually got a <simpleError> with message: attempt access index 7/7 in VECTOR_ELT ── Error ('test-mcc.R:1023:3'): mcc() with by argument works with both methods ── Error in `eval(code, test_env)`: object 'result_sci' not found Backtrace: ▆ 1. ├─testthat::expect_true("sci_table" %in% names(result_sci)) at test-mcc.R:1023:3 2. │ └─testthat::quasi_label(enquo(object), label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─"sci_table" %in% names(result_sci) ── Failure ('test-mcc.R:1038:3'): mcc() with by argument and tstart_var works ── Expected `... <- NULL` not to throw any errors. Actually got a <simpleError> with message: attempt access index 7/7 in VECTOR_ELT ── Error ('test-mcc.R:1050:3'): mcc() with by argument and tstart_var works ── Error in `eval(code, test_env)`: object 'result_sci_tstart' not found Backtrace: ▆ 1. ├─testthat::expect_true("sci_table" %in% names(result_sci_tstart)) at test-mcc.R:1050:3 2. │ └─testthat::quasi_label(enquo(object), label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─"sci_table" %in% names(result_sci_tstart) ── Error ('test-mcc.R:1064:3'): mcc() with by argument preserves group information in all components ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(...) at test-mcc.R:1064:3 2. └─mccount:::mcc_by_group(...) 3. └─mccount:::mcc_sci(...) 4. ├─dt[, `:=`(first, seq_len(.N)), by = id] 5. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc.R:1197:3'): mcc() with by argument preserves group information in all components ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(...) at test-mcc.R:1197:3 2. └─mccount:::mcc_by_group(...) 3. └─mccount:::mcc_sci(...) 4. ├─dt[, `:=`(first, seq_len(.N)), by = id] 5. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc.R:1398:3'): mcc() converts numeric grouping variables to factors ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df_numeric_groups, "id", "time", "cause", by = "group_numeric") 2. └─mccount:::mcc_by_group(...) 3. └─mccount:::mcc_equation(...) 4. └─mccount:::handle_simultaneous_events(...) 5. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 6. └─data.table:::`[.data.table`(...) ── Error ('test-mcc.R:1456:3'): plotting works correctly with converted numeric groups ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df_plot_test, "id", "time", "cause", by = "treatment") 2. └─mccount:::mcc_by_group(...) 3. └─mccount:::mcc_equation(...) 4. └─mccount:::handle_simultaneous_events(...) 5. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 6. └─data.table:::`[.data.table`(...) ── Error ('test-mcc_equation.R:43:3'): mcc_equation() handles simultaneous events correctly ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_equation(...) at test-mcc_equation.R:43:3 2. └─mccount:::handle_simultaneous_events(...) 3. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 4. └─data.table:::`[.data.table`(...) ── Error ('test-mcc_equation.R:167:3'): mcc_equation() properly uses time_precision parameter ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_equation(...) at test-mcc_equation.R:167:3 2. └─mccount:::handle_simultaneous_events(...) 3. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 4. └─data.table:::`[.data.table`(...) ── Error ('test-mcc_equation.R:309:3'): mcc_equation() with include_details=FALSE works with various scenarios ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_equation(...) at test-mcc_equation.R:309:3 2. └─mccount:::handle_simultaneous_events(...) 3. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 4. └─data.table:::`[.data.table`(...) ── Error ('test-mcc_equation.R:384:3'): mcc_equation() with include_details=FALSE does not include adjusted_data ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_equation(...) at test-mcc_equation.R:384:3 2. └─mccount:::handle_simultaneous_events(...) 3. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 4. └─data.table:::`[.data.table`(...) ── Error ('test-mcc_equation.R:445:5'): mcc_equation() with include_details=FALSE provides sufficient data for bootstrapping ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_equation(...) at test-mcc_equation.R:445:5 2. └─mccount:::handle_simultaneous_events(...) 3. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 4. └─data.table:::`[.data.table`(...) ── Failure ('test-mcc_equation.R:774:3'): weighted MCC handles simultaneous events correctly ── Expected `... <- NULL` not to throw any errors. Actually got a <simpleError> with message: attempt access index 6/6 in VECTOR_ELT ── Error ('test-mcc_equation.R:798:3'): weighted MCC handles simultaneous events correctly ── Error in `eval(code, test_env)`: object 'result1' not found Backtrace: ▆ 1. └─testthat::expect_true(result1$weighted) at test-mcc_equation.R:798:3 2. └─testthat::quasi_label(enquo(object), label) 3. └─rlang::eval_bare(expr, quo_get_env(quo)) ── Error ('test-mcc_equation.R:948:3'): weighted MCC parameter combinations work correctly ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 6/6 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(...) at test-mcc_equation.R:948:3 2. └─mccount:::mcc_equation(...) 3. └─mccount:::handle_simultaneous_events(...) 4. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 5. └─data.table:::`[.data.table`(...) ── Error ('test-mcc_sci.R:10:3'): mcc_sci() correctly calculates MCC with basic data ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:10:3 2. ├─dt[, `:=`(first, seq_len(.N)), by = id] 3. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc_sci.R:51:3'): mcc_sci() handles tstart_var correctly ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:51:3 2. ├─dt[, `:=`(first, seq_len(.N)), by = id] 3. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc_sci.R:91:3'): mcc_sci() correctly handles left-truncated data ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:91:3 2. ├─dt[, `:=`(first, seq_len(.N)), by = id] 3. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc_sci.R:142:3'): mcc_sci() correctly handles simultaneous events ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:142:3 2. └─mccount:::handle_simultaneous_events(...) 3. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 4. └─data.table:::`[.data.table`(...) ── Error ('test-mcc_sci.R:175:3'): mcc_sci() generates correct CI columns ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:175:3 2. ├─dt[, `:=`(first, seq_len(.N)), by = id] 3. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc_sci.R:201:3'): mcc_sci() processes multiple recurrent events correctly ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:201:3 2. ├─dt[, `:=`(first, seq_len(.N)), by = id] 3. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc_sci.R:228:3'): mcc_sci() handles recurrent events with competing risks ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:228:3 2. ├─dt[, `:=`(first, seq_len(.N)), by = id] 3. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc_sci.R:255:3'): mcc_sci() uses time_precision parameter correctly ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:255:3 2. └─mccount:::handle_simultaneous_events(...) 3. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 4. └─data.table:::`[.data.table`(...) ── Error ('test-mcc_sci.R:330:3'): mcc_sci() works with snapshot testing for complex cases ── Error: object 'result' not found Backtrace: ▆ 1. └─base::print(length(result$all_cis)) ── Error ('test-mcc_sci.R:360:3'): mcc_sci() respects include_details=FALSE parameter ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:360:3 2. ├─dt[, `:=`(first, seq_len(.N)), by = id] 3. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc_sci.R:397:3'): mcc_sci() with include_details=FALSE works with all key scenarios ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:397:3 2. └─mccount:::handle_simultaneous_events(...) 3. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 4. └─data.table:::`[.data.table`(...) ── Error ('test-mcc_sci.R:462:3'): mcc_sci() with include_details=FALSE provides sufficient data for bootstrapping ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:462:3 2. ├─dt[, `:=`(first, seq_len(.N)), by = id] 3. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc_sci.R:532:3'): mcc_sci cleans up time precision adjustments in output ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:532:3 2. ├─dt[, `:=`(first, seq_len(.N)), by = id] 3. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc_sci.R:564:3'): mcc_sci only calculates CI for event numbers with actual events ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:564:3 2. ├─dt[, `:=`(first, seq_len(.N)), by = id] 3. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc_sci.R:614:3'): grouped mcc fills missing CI columns with 0, not NA ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(...) at test-mcc_sci.R:614:3 2. └─mccount:::mcc_by_group(...) 3. └─mccount:::mcc_sci(...) 4. ├─dt[, `:=`(first, seq_len(.N)), by = id] 5. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc_sci.R:646:3'): mcc_sci uses time_precision parameter consistently ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:646:3 2. ├─dt[, `:=`(first, seq_len(.N)), by = id] 3. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc_sci.R:667:3'): mcc_sci handles mixed events at time 0 correctly ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:667:3 2. ├─dt[, `:=`(first, seq_len(.N)), by = id] 3. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc_sci.R:695:3'): both methods show consistent time values for events at time 0 ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(...) at test-mcc_sci.R:695:3 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc_sci.R:717:3'): CI column names are consistent across groups with different max events ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(...) at test-mcc_sci.R:717:3 2. └─mccount:::mcc_by_group(...) 3. └─mccount:::mcc_sci(...) 4. ├─dt[, `:=`(first, seq_len(.N)), by = id] 5. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-plot.R:45:3'): plot.mcc error handling works correctly ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", method = "sci", include_details = FALSE) at test-plot.R:45:3 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-plot.R:90:3'): plot.mcc throws error when type='components' with equation method ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", method = "equation") at test-plot.R:90:3 2. └─mccount:::mcc_equation(...) 3. └─mccount:::handle_simultaneous_events(...) 4. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 5. └─data.table:::`[.data.table`(...) ── Error ('test-plot.R:129:3'): plot.mcc works correctly with type='components' for SCI method ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", method = "sci") at test-plot.R:129:3 2. └─mccount:::mcc_sci(...) 3. └─mccount:::handle_simultaneous_events(...) 4. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 5. └─data.table:::`[.data.table`(...) ── Error ('test-plot.R:150:3'): plot.mcc type argument matching works correctly ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", method = "equation") at test-plot.R:150:3 2. └─mccount:::mcc_equation(...) 3. └─mccount:::handle_simultaneous_events(...) 4. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 5. └─data.table:::`[.data.table`(...) ── Error ('test-plot.R:372:3'): geom_line_mcc works with different methods (equation vs sci) ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", method = "sci") at test-plot.R:372:3 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-plot.R:400:3'): plot.mcc uses correct data table for each method ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", method = "sci") at test-plot.R:400:3 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-plot.R:429:3'): plot.mcc handles grouped data correctly with both methods ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", by = "group", method = "sci") at test-plot.R:429:3 2. └─mccount:::mcc_by_group(...) 3. └─mccount:::mcc_sci(...) 4. ├─dt[, `:=`(first, seq_len(.N)), by = id] 5. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-plot.R:471:3'): plot.mcc handles group filtering correctly ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", by = "group") at test-plot.R:471:3 2. └─mccount:::mcc_by_group(...) 3. └─mccount:::mcc_equation(...) 4. └─mccount:::handle_simultaneous_events(...) 5. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 6. └─data.table:::`[.data.table`(...) ── Error ('test-plot.R:495:3'): plot.mcc color customization works ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause") at test-plot.R:495:3 2. └─mccount:::mcc_equation(...) 3. └─mccount:::handle_simultaneous_events(...) 4. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 5. └─data.table:::`[.data.table`(...) ── Error ('test-s3_classes.R:10:3'): S3 object creation works correctly ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", method = "equation") at test-s3_classes.R:10:3 2. └─mccount:::mcc_equation(...) 3. └─mccount:::handle_simultaneous_events(...) 4. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 5. └─data.table:::`[.data.table`(...) ── Error ('test-s3_classes.R:39:3'): Grouped S3 objects work correctly ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", by = "group") at test-s3_classes.R:39:3 2. └─mccount:::mcc_by_group(...) 3. └─mccount:::mcc_equation(...) 4. └─mccount:::handle_simultaneous_events(...) 5. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 6. └─data.table:::`[.data.table`(...) ── Error ('test-s3_classes.R:60:3'): Weighted S3 objects work correctly ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 6/6 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", weights = "weights") at test-s3_classes.R:60:3 2. └─mccount:::mcc_equation(...) 3. └─mccount:::handle_simultaneous_events(...) 4. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 5. └─data.table:::`[.data.table`(...) ── Error ('test-s3_classes.R:115:3'): Print methods work for grouped objects ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", by = "group") at test-s3_classes.R:115:3 2. └─mccount:::mcc_by_group(...) 3. └─mccount:::mcc_equation(...) 4. └─mccount:::handle_simultaneous_events(...) 5. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 6. └─data.table:::`[.data.table`(...) ── Error ('test-s3_classes.R:136:3'): Print methods work for weighted objects ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 6/6 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", weights = "weights") at test-s3_classes.R:136:3 2. └─mccount:::mcc_equation(...) 3. └─mccount:::handle_simultaneous_events(...) 4. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 5. └─data.table:::`[.data.table`(...) ── Error ('test-s3_classes.R:182:3'): Grouped utility functions work correctly ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", by = "group") at test-s3_classes.R:182:3 2. └─mccount:::mcc_by_group(...) 3. └─mccount:::mcc_equation(...) 4. └─mccount:::handle_simultaneous_events(...) 5. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 6. └─data.table:::`[.data.table`(...) ── Error ('test-s3_classes.R:206:3'): MCC comparison print works correctly ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", method = "sci") at test-s3_classes.R:206:3 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-s3_classes.R:292:3'): S3 classes are assigned correctly for all combinations ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", method = "sci") at test-s3_classes.R:292:3 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-s3_classes.R:457:3'): filter_mcc works correctly ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", by = "group") at test-s3_classes.R:457:3 2. └─mccount:::mcc_by_group(...) 3. └─mccount:::mcc_equation(...) 4. └─mccount:::handle_simultaneous_events(...) 5. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 6. └─data.table:::`[.data.table`(...) ── Error ('test-s3_classes.R:489:3'): compare_mcc works correctly ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", method = "sci") at test-s3_classes.R:489:3 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-s3_classes.R:560:3'): S3 method dispatch works correctly ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", method = "sci") at test-s3_classes.R:560:3 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-s3_classes.R:743:3'): mcc_details correctly dispatches based on class ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", method = "sci") at test-s3_classes.R:743:3 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-s3_classes.R:768:3'): create_subtitle function works correctly ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", method = "sci") at test-s3_classes.R:768:3 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) [ FAIL 68 | WARN 0 | SKIP 24 | PASS 442 ] Error: ! Test failures. Execution halted Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.1.1
Check: examples
Result: ERROR Running examples in ‘mccount-Ex.R’ failed The error most likely occurred in: > ### Name: as.data.frame.mcc > ### Title: Convert 'mcc' object to data.frame > ### Aliases: as.data.frame.mcc > > ### ** Examples > > # Create sample data > library(dplyr) Attaching package: ‘dplyr’ The following objects are masked from ‘package:stats’: filter, lag The following objects are masked from ‘package:base’: intersect, setdiff, setequal, union > df <- data.frame( + id = c(1, 2, 3, 4, 4, 4, 4, 5, 5), + time = c(8, 1, 5, 2, 6, 7, 8, 3, 3), + cause = c(0, 0, 2, 1, 1, 1, 0, 1, 2) + ) |> + arrange(id, time) > > # Calculate MCC > mcc_result <- mcc(df, "id", "time", "cause") Error in `[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, : attempt access index 5/5 in VECTOR_ELT Calls: mcc ... mcc_equation -> handle_simultaneous_events -> [ -> [.data.table Execution halted Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 0.1.1
Check: tests
Result: ERROR Running ‘spelling.R’ Running ‘testthat.R’ [68s/98s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(mccount) Loading required package: ggplot2 > > test_check("mccount") Saving _problems/test-calculation_helpers-25.R Saving _problems/test-mcc-31.R Saving _problems/test-mcc-79.R Saving _problems/test-mcc-188.R Saving _problems/test-mcc-360.R Saving _problems/test-mcc-471.R Saving _problems/test-mcc-492.R Saving _problems/test-mcc-646.R Saving _problems/test-mcc-758.R Saving _problems/test-mcc-790.R Saving _problems/test-mcc-793.R i Converting numeric grouping variable "by_var" to <factor> i Found 2 unique groups: 10 and 20 Saving _problems/test-mcc-1021.R Saving _problems/test-mcc-1023.R Saving _problems/test-mcc-1048.R Saving _problems/test-mcc-1050.R Saving _problems/test-mcc-1072.R Saving _problems/test-mcc-1205.R Saving _problems/test-mcc-1406.R Saving _problems/test-mcc-1458.R Saving _problems/test-mcc_equation-49.R Saving _problems/test-mcc_equation-173.R Saving _problems/test-mcc_equation-315.R Saving _problems/test-mcc_equation-389.R Saving _problems/test-mcc_equation-451.R Saving _problems/test-mcc_equation-783.R Saving _problems/test-mcc_equation-798.R Saving _problems/test-mcc_equation-956.R Saving _problems/test-mcc_sci-15.R Saving _problems/test-mcc_sci-57.R Saving _problems/test-mcc_sci-97.R Saving _problems/test-mcc_sci-148.R Saving _problems/test-mcc_sci-180.R Saving _problems/test-mcc_sci-206.R Saving _problems/test-mcc_sci-233.R Saving _problems/test-mcc_sci-261.R Saving _problems/test-mcc_sci-347.R Saving _problems/test-mcc_sci-365.R Saving _problems/test-mcc_sci-403.R Saving _problems/test-mcc_sci-468.R Saving _problems/test-mcc_sci-537.R Saving _problems/test-mcc_sci-569.R Saving _problems/test-mcc_sci-621.R Saving _problems/test-mcc_sci-652.R Saving _problems/test-mcc_sci-672.R Saving _problems/test-mcc_sci-701.R Saving _problems/test-mcc_sci-724.R Saving _problems/test-plot-52.R Saving _problems/test-plot-90.R Saving _problems/test-plot-129.R Saving _problems/test-plot-150.R i MCC never reaches 2 in the observed follow-up period i No reference lines added Saving _problems/test-plot-372.R Saving _problems/test-plot-400.R Saving _problems/test-plot-436.R Saving _problems/test-plot-471.R Saving _problems/test-plot-495.R Saving _problems/test-s3_classes-10.R Saving _problems/test-s3_classes-39.R Saving _problems/test-s3_classes-60.R -- Mean Cumulative Count Results ----------------------------------------------- i Method: Dong-Yasui Equation Method -- MCC Estimates -- # A tibble: 4 x 2 time mcc <dbl> <dbl> 1 0 0 2 2 0.333 3 6 0.667 4 7 1 -- Call -- mcc(data = df, id_var = "id", time_var = "time", cause_var = "cause") -- Summary of Mean Cumulative Count Results ------------------------------------ i Method: Dong-Yasui Equation Method i Total participants: 4 -- Summary Statistics -- Observation period: [0, 8] Time to MCC = 1.0: 7 Time to maximum MCC: 7 MCC at end of follow-up: 1 -- Event Count Composition Events of interest: 3 Competing risk events: 1 Censoring events: 3 Saving _problems/test-s3_classes-115.R Saving _problems/test-s3_classes-136.R Saving _problems/test-s3_classes-182.R Saving _problems/test-s3_classes-206.R Saving _problems/test-s3_classes-292.R Saving _problems/test-s3_classes-457.R Saving _problems/test-s3_classes-489.R -- Mean Cumulative Count Results ----------------------------------------------- i Method: Dong-Yasui Equation Method -- MCC Estimates -- -- Call -- mcc(data = df_minimal, id_var = "id", time_var = "time", cause_var = "cause") Saving _problems/test-s3_classes-560.R Saving _problems/test-s3_classes-743.R Saving _problems/test-s3_classes-768.R [ FAIL 68 | WARN 0 | SKIP 24 | PASS 442 ] ══ Skipped tests (24 • On CRAN (24): 'test-calculation_helpers.R:482:1', 'test-calculation_helpers.R:529:1', 'test-calculation_helpers.R:611:1', 'test-mcc.R:94:1', 'test-mcc.R:191:1', 'test-mcc.R:669:1', 'test-mcc.R:851:1', 'test-mcc.R:1167:1', 'test-mcc.R:1253:1', 'test-mcc_equation.R:203:1', 'test-mcc_equation.R:477:1', 'test-mcc_equation.R:652:1', 'test-mcc_sci.R:583:1', 'test-s3_classes.R:80:1', 'test-s3_classes.R:509:1', 'test-validation_helpers.R:1:1', 'test-validation_helpers.R:44:1', 'test-validation_helpers.R:49:1', 'test-validation_helpers.R:57:1', 'test-validation_helpers.R:69:1', 'test-validation_helpers.R:101:1', 'test-validation_helpers.R:113:1', 'test-validation_helpers.R:142:1', 'test-validation_helpers.R:181:1' ══ Failed tests ════ ── Error ('test-calculation_helpers.R:21:3'): handle_simultaneous_events() works ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 4/4 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::handle_simultaneous_events(...) 2. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 3. └─data.table:::`[.data.table`(...) ── Error ('test-mcc.R:25:3'): mcc() dispatches to the correct implementation based on method ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(...) at test-mcc.R:25:3 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc.R:71:3'): mcc() validates the method argument correctly ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(...) 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc.R:179:3'): mcc() validates tstart_var compatibility with method ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(...) 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc.R:354:3'): mcc() handles method parameter with partial matching ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(...) at test-mcc.R:354:3 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc.R:459:3'): mcc() end-to-end functionality through snapshots ── Error: object 'result_sci' not found Backtrace: ▆ 1. └─base::print(result_sci$mcc_final) ── Error ('test-mcc.R:492:3'): mcc() produces equivalent results from both methods ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df1, id_var = "id", time_var = "time", cause_var = "cause") at test-mcc.R:492:3 2. └─mccount:::mcc_equation(...) 3. └─mccount:::handle_simultaneous_events(...) 4. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 5. └─data.table:::`[.data.table`(...) ── Error ('test-mcc.R:639:3'): mcc() correctly passes include_details parameter to implementation functions ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(...) at test-mcc.R:639:3 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Failure ('test-mcc.R:758:7'): mcc() with include_details=FALSE is suitable for bootstrapping ── Bootstrap failed: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─base::tryCatch(...) at test-mcc.R:744:3 2. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 3. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 4. └─value[[3L]](cond) ── Failure ('test-mcc.R:773:3'): mcc() documentation example works with include_details=FALSE ── Expected `{ ... }` not to throw any errors. Actually got a <simpleError> with message: attempt access index 5/5 in VECTOR_ELT ── Error ('test-mcc.R:793:3'): mcc() documentation example works with include_details=FALSE ── Error in `eval(code, test_env)`: object 'mcc_eq' not found Backtrace: ▆ 1. └─testthat::expect_named(...) at test-mcc.R:793:3 2. └─testthat::quasi_label(enquo(object), label) 3. └─rlang::eval_bare(expr, quo_get_env(quo)) ── Failure ('test-mcc.R:1012:3'): mcc() with by argument works with both methods ── Expected `... <- NULL` not to throw any errors. Actually got a <simpleError> with message: attempt access index 7/7 in VECTOR_ELT ── Error ('test-mcc.R:1023:3'): mcc() with by argument works with both methods ── Error in `eval(code, test_env)`: object 'result_sci' not found Backtrace: ▆ 1. ├─testthat::expect_true("sci_table" %in% names(result_sci)) at test-mcc.R:1023:3 2. │ └─testthat::quasi_label(enquo(object), label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─"sci_table" %in% names(result_sci) ── Failure ('test-mcc.R:1038:3'): mcc() with by argument and tstart_var works ── Expected `... <- NULL` not to throw any errors. Actually got a <simpleError> with message: attempt access index 7/7 in VECTOR_ELT ── Error ('test-mcc.R:1050:3'): mcc() with by argument and tstart_var works ── Error in `eval(code, test_env)`: object 'result_sci_tstart' not found Backtrace: ▆ 1. ├─testthat::expect_true("sci_table" %in% names(result_sci_tstart)) at test-mcc.R:1050:3 2. │ └─testthat::quasi_label(enquo(object), label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─"sci_table" %in% names(result_sci_tstart) ── Error ('test-mcc.R:1064:3'): mcc() with by argument preserves group information in all components ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(...) at test-mcc.R:1064:3 2. └─mccount:::mcc_by_group(...) 3. └─mccount:::mcc_sci(...) 4. ├─dt[, `:=`(first, seq_len(.N)), by = id] 5. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc.R:1197:3'): mcc() with by argument preserves group information in all components ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(...) at test-mcc.R:1197:3 2. └─mccount:::mcc_by_group(...) 3. └─mccount:::mcc_sci(...) 4. ├─dt[, `:=`(first, seq_len(.N)), by = id] 5. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc.R:1398:3'): mcc() converts numeric grouping variables to factors ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df_numeric_groups, "id", "time", "cause", by = "group_numeric") 2. └─mccount:::mcc_by_group(...) 3. └─mccount:::mcc_equation(...) 4. └─mccount:::handle_simultaneous_events(...) 5. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 6. └─data.table:::`[.data.table`(...) ── Error ('test-mcc.R:1456:3'): plotting works correctly with converted numeric groups ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df_plot_test, "id", "time", "cause", by = "treatment") 2. └─mccount:::mcc_by_group(...) 3. └─mccount:::mcc_equation(...) 4. └─mccount:::handle_simultaneous_events(...) 5. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 6. └─data.table:::`[.data.table`(...) ── Error ('test-mcc_equation.R:43:3'): mcc_equation() handles simultaneous events correctly ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_equation(...) at test-mcc_equation.R:43:3 2. └─mccount:::handle_simultaneous_events(...) 3. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 4. └─data.table:::`[.data.table`(...) ── Error ('test-mcc_equation.R:167:3'): mcc_equation() properly uses time_precision parameter ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_equation(...) at test-mcc_equation.R:167:3 2. └─mccount:::handle_simultaneous_events(...) 3. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 4. └─data.table:::`[.data.table`(...) ── Error ('test-mcc_equation.R:309:3'): mcc_equation() with include_details=FALSE works with various scenarios ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_equation(...) at test-mcc_equation.R:309:3 2. └─mccount:::handle_simultaneous_events(...) 3. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 4. └─data.table:::`[.data.table`(...) ── Error ('test-mcc_equation.R:384:3'): mcc_equation() with include_details=FALSE does not include adjusted_data ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_equation(...) at test-mcc_equation.R:384:3 2. └─mccount:::handle_simultaneous_events(...) 3. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 4. └─data.table:::`[.data.table`(...) ── Error ('test-mcc_equation.R:445:5'): mcc_equation() with include_details=FALSE provides sufficient data for bootstrapping ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_equation(...) at test-mcc_equation.R:445:5 2. └─mccount:::handle_simultaneous_events(...) 3. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 4. └─data.table:::`[.data.table`(...) ── Failure ('test-mcc_equation.R:774:3'): weighted MCC handles simultaneous events correctly ── Expected `... <- NULL` not to throw any errors. Actually got a <simpleError> with message: attempt access index 6/6 in VECTOR_ELT ── Error ('test-mcc_equation.R:798:3'): weighted MCC handles simultaneous events correctly ── Error in `eval(code, test_env)`: object 'result1' not found Backtrace: ▆ 1. └─testthat::expect_true(result1$weighted) at test-mcc_equation.R:798:3 2. └─testthat::quasi_label(enquo(object), label) 3. └─rlang::eval_bare(expr, quo_get_env(quo)) ── Error ('test-mcc_equation.R:948:3'): weighted MCC parameter combinations work correctly ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 6/6 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(...) at test-mcc_equation.R:948:3 2. └─mccount:::mcc_equation(...) 3. └─mccount:::handle_simultaneous_events(...) 4. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 5. └─data.table:::`[.data.table`(...) ── Error ('test-mcc_sci.R:10:3'): mcc_sci() correctly calculates MCC with basic data ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:10:3 2. ├─dt[, `:=`(first, seq_len(.N)), by = id] 3. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc_sci.R:51:3'): mcc_sci() handles tstart_var correctly ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:51:3 2. ├─dt[, `:=`(first, seq_len(.N)), by = id] 3. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc_sci.R:91:3'): mcc_sci() correctly handles left-truncated data ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:91:3 2. ├─dt[, `:=`(first, seq_len(.N)), by = id] 3. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc_sci.R:142:3'): mcc_sci() correctly handles simultaneous events ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:142:3 2. └─mccount:::handle_simultaneous_events(...) 3. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 4. └─data.table:::`[.data.table`(...) ── Error ('test-mcc_sci.R:175:3'): mcc_sci() generates correct CI columns ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:175:3 2. ├─dt[, `:=`(first, seq_len(.N)), by = id] 3. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc_sci.R:201:3'): mcc_sci() processes multiple recurrent events correctly ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:201:3 2. ├─dt[, `:=`(first, seq_len(.N)), by = id] 3. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc_sci.R:228:3'): mcc_sci() handles recurrent events with competing risks ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:228:3 2. ├─dt[, `:=`(first, seq_len(.N)), by = id] 3. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc_sci.R:255:3'): mcc_sci() uses time_precision parameter correctly ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:255:3 2. └─mccount:::handle_simultaneous_events(...) 3. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 4. └─data.table:::`[.data.table`(...) ── Error ('test-mcc_sci.R:330:3'): mcc_sci() works with snapshot testing for complex cases ── Error: object 'result' not found Backtrace: ▆ 1. └─base::print(length(result$all_cis)) ── Error ('test-mcc_sci.R:360:3'): mcc_sci() respects include_details=FALSE parameter ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:360:3 2. ├─dt[, `:=`(first, seq_len(.N)), by = id] 3. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc_sci.R:397:3'): mcc_sci() with include_details=FALSE works with all key scenarios ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:397:3 2. └─mccount:::handle_simultaneous_events(...) 3. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 4. └─data.table:::`[.data.table`(...) ── Error ('test-mcc_sci.R:462:3'): mcc_sci() with include_details=FALSE provides sufficient data for bootstrapping ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:462:3 2. ├─dt[, `:=`(first, seq_len(.N)), by = id] 3. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc_sci.R:532:3'): mcc_sci cleans up time precision adjustments in output ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:532:3 2. ├─dt[, `:=`(first, seq_len(.N)), by = id] 3. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc_sci.R:564:3'): mcc_sci only calculates CI for event numbers with actual events ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:564:3 2. ├─dt[, `:=`(first, seq_len(.N)), by = id] 3. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc_sci.R:614:3'): grouped mcc fills missing CI columns with 0, not NA ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(...) at test-mcc_sci.R:614:3 2. └─mccount:::mcc_by_group(...) 3. └─mccount:::mcc_sci(...) 4. ├─dt[, `:=`(first, seq_len(.N)), by = id] 5. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc_sci.R:646:3'): mcc_sci uses time_precision parameter consistently ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:646:3 2. ├─dt[, `:=`(first, seq_len(.N)), by = id] 3. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc_sci.R:667:3'): mcc_sci handles mixed events at time 0 correctly ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:667:3 2. ├─dt[, `:=`(first, seq_len(.N)), by = id] 3. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc_sci.R:695:3'): both methods show consistent time values for events at time 0 ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(...) at test-mcc_sci.R:695:3 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc_sci.R:717:3'): CI column names are consistent across groups with different max events ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(...) at test-mcc_sci.R:717:3 2. └─mccount:::mcc_by_group(...) 3. └─mccount:::mcc_sci(...) 4. ├─dt[, `:=`(first, seq_len(.N)), by = id] 5. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-plot.R:45:3'): plot.mcc error handling works correctly ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", method = "sci", include_details = FALSE) at test-plot.R:45:3 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-plot.R:90:3'): plot.mcc throws error when type='components' with equation method ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", method = "equation") at test-plot.R:90:3 2. └─mccount:::mcc_equation(...) 3. └─mccount:::handle_simultaneous_events(...) 4. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 5. └─data.table:::`[.data.table`(...) ── Error ('test-plot.R:129:3'): plot.mcc works correctly with type='components' for SCI method ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", method = "sci") at test-plot.R:129:3 2. └─mccount:::mcc_sci(...) 3. └─mccount:::handle_simultaneous_events(...) 4. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 5. └─data.table:::`[.data.table`(...) ── Error ('test-plot.R:150:3'): plot.mcc type argument matching works correctly ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", method = "equation") at test-plot.R:150:3 2. └─mccount:::mcc_equation(...) 3. └─mccount:::handle_simultaneous_events(...) 4. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 5. └─data.table:::`[.data.table`(...) ── Error ('test-plot.R:372:3'): geom_line_mcc works with different methods (equation vs sci) ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", method = "sci") at test-plot.R:372:3 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-plot.R:400:3'): plot.mcc uses correct data table for each method ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", method = "sci") at test-plot.R:400:3 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-plot.R:429:3'): plot.mcc handles grouped data correctly with both methods ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", by = "group", method = "sci") at test-plot.R:429:3 2. └─mccount:::mcc_by_group(...) 3. └─mccount:::mcc_sci(...) 4. ├─dt[, `:=`(first, seq_len(.N)), by = id] 5. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-plot.R:471:3'): plot.mcc handles group filtering correctly ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", by = "group") at test-plot.R:471:3 2. └─mccount:::mcc_by_group(...) 3. └─mccount:::mcc_equation(...) 4. └─mccount:::handle_simultaneous_events(...) 5. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 6. └─data.table:::`[.data.table`(...) ── Error ('test-plot.R:495:3'): plot.mcc color customization works ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause") at test-plot.R:495:3 2. └─mccount:::mcc_equation(...) 3. └─mccount:::handle_simultaneous_events(...) 4. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 5. └─data.table:::`[.data.table`(...) ── Error ('test-s3_classes.R:10:3'): S3 object creation works correctly ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", method = "equation") at test-s3_classes.R:10:3 2. └─mccount:::mcc_equation(...) 3. └─mccount:::handle_simultaneous_events(...) 4. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 5. └─data.table:::`[.data.table`(...) ── Error ('test-s3_classes.R:39:3'): Grouped S3 objects work correctly ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", by = "group") at test-s3_classes.R:39:3 2. └─mccount:::mcc_by_group(...) 3. └─mccount:::mcc_equation(...) 4. └─mccount:::handle_simultaneous_events(...) 5. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 6. └─data.table:::`[.data.table`(...) ── Error ('test-s3_classes.R:60:3'): Weighted S3 objects work correctly ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 6/6 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", weights = "weights") at test-s3_classes.R:60:3 2. └─mccount:::mcc_equation(...) 3. └─mccount:::handle_simultaneous_events(...) 4. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 5. └─data.table:::`[.data.table`(...) ── Error ('test-s3_classes.R:115:3'): Print methods work for grouped objects ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", by = "group") at test-s3_classes.R:115:3 2. └─mccount:::mcc_by_group(...) 3. └─mccount:::mcc_equation(...) 4. └─mccount:::handle_simultaneous_events(...) 5. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 6. └─data.table:::`[.data.table`(...) ── Error ('test-s3_classes.R:136:3'): Print methods work for weighted objects ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 6/6 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", weights = "weights") at test-s3_classes.R:136:3 2. └─mccount:::mcc_equation(...) 3. └─mccount:::handle_simultaneous_events(...) 4. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 5. └─data.table:::`[.data.table`(...) ── Error ('test-s3_classes.R:182:3'): Grouped utility functions work correctly ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", by = "group") at test-s3_classes.R:182:3 2. └─mccount:::mcc_by_group(...) 3. └─mccount:::mcc_equation(...) 4. └─mccount:::handle_simultaneous_events(...) 5. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 6. └─data.table:::`[.data.table`(...) ── Error ('test-s3_classes.R:206:3'): MCC comparison print works correctly ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", method = "sci") at test-s3_classes.R:206:3 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-s3_classes.R:292:3'): S3 classes are assigned correctly for all combinations ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", method = "sci") at test-s3_classes.R:292:3 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-s3_classes.R:457:3'): filter_mcc works correctly ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", by = "group") at test-s3_classes.R:457:3 2. └─mccount:::mcc_by_group(...) 3. └─mccount:::mcc_equation(...) 4. └─mccount:::handle_simultaneous_events(...) 5. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 6. └─data.table:::`[.data.table`(...) ── Error ('test-s3_classes.R:489:3'): compare_mcc works correctly ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", method = "sci") at test-s3_classes.R:489:3 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-s3_classes.R:560:3'): S3 method dispatch works correctly ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", method = "sci") at test-s3_classes.R:560:3 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-s3_classes.R:743:3'): mcc_details correctly dispatches based on class ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", method = "sci") at test-s3_classes.R:743:3 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-s3_classes.R:768:3'): create_subtitle function works correctly ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", method = "sci") at test-s3_classes.R:768:3 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) [ FAIL 68 | WARN 0 | SKIP 24 | PASS 442 ] Error: ! Test failures. Execution halted Flavor: r-devel-linux-x86_64-fedora-clang

Version: 0.1.1
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building ‘choosing-between-methods.Rmd’ using rmarkdown Quitting from choosing-between-methods.Rmd:50-73 [dong-example] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `[.data.table`: ! attempt access index 5/5 in VECTOR_ELT --- Backtrace: ▆ 1. └─mccount::mcc(...) 2. └─mccount:::mcc_equation(...) 3. └─mccount:::handle_simultaneous_events(...) 4. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 5. └─data.table:::`[.data.table`(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'choosing-between-methods.Rmd' failed with diagnostics: attempt access index 5/5 in VECTOR_ELT --- failed re-building ‘choosing-between-methods.Rmd’ --- re-building ‘estimating-mcc-after-matching-or-weighting.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘estimating-mcc-after-matching-or-weighting.Rmd’ SUMMARY: processing the following file failed: ‘choosing-between-methods.Rmd’ Error: Vignette re-building failed. Execution halted Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 0.1.1
Check: tests
Result: ERROR Running ‘spelling.R’ Running ‘testthat.R’ [55s/87s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(mccount) Loading required package: ggplot2 > > test_check("mccount") Saving _problems/test-calculation_helpers-25.R Saving _problems/test-mcc-31.R Saving _problems/test-mcc-79.R Saving _problems/test-mcc-188.R Saving _problems/test-mcc-360.R Saving _problems/test-mcc-471.R Saving _problems/test-mcc-492.R Saving _problems/test-mcc-646.R Saving _problems/test-mcc-758.R Saving _problems/test-mcc-790.R Saving _problems/test-mcc-793.R i Converting numeric grouping variable "by_var" to <factor> i Found 2 unique groups: 10 and 20 Saving _problems/test-mcc-1021.R Saving _problems/test-mcc-1023.R Saving _problems/test-mcc-1048.R Saving _problems/test-mcc-1050.R Saving _problems/test-mcc-1072.R Saving _problems/test-mcc-1205.R Saving _problems/test-mcc-1406.R Saving _problems/test-mcc-1458.R Saving _problems/test-mcc_equation-49.R Saving _problems/test-mcc_equation-173.R Saving _problems/test-mcc_equation-315.R Saving _problems/test-mcc_equation-389.R Saving _problems/test-mcc_equation-451.R Saving _problems/test-mcc_equation-783.R Saving _problems/test-mcc_equation-798.R Saving _problems/test-mcc_equation-956.R Saving _problems/test-mcc_sci-15.R Saving _problems/test-mcc_sci-57.R Saving _problems/test-mcc_sci-97.R Saving _problems/test-mcc_sci-148.R Saving _problems/test-mcc_sci-180.R Saving _problems/test-mcc_sci-206.R Saving _problems/test-mcc_sci-233.R Saving _problems/test-mcc_sci-261.R Saving _problems/test-mcc_sci-347.R Saving _problems/test-mcc_sci-365.R Saving _problems/test-mcc_sci-403.R Saving _problems/test-mcc_sci-468.R Saving _problems/test-mcc_sci-537.R Saving _problems/test-mcc_sci-569.R Saving _problems/test-mcc_sci-621.R Saving _problems/test-mcc_sci-652.R Saving _problems/test-mcc_sci-672.R Saving _problems/test-mcc_sci-701.R Saving _problems/test-mcc_sci-724.R Saving _problems/test-plot-52.R Saving _problems/test-plot-90.R Saving _problems/test-plot-129.R Saving _problems/test-plot-150.R i MCC never reaches 2 in the observed follow-up period i No reference lines added Saving _problems/test-plot-372.R Saving _problems/test-plot-400.R Saving _problems/test-plot-436.R Saving _problems/test-plot-471.R Saving _problems/test-plot-495.R Saving _problems/test-s3_classes-10.R Saving _problems/test-s3_classes-39.R Saving _problems/test-s3_classes-60.R -- Mean Cumulative Count Results ----------------------------------------------- i Method: Dong-Yasui Equation Method -- MCC Estimates -- # A tibble: 4 x 2 time mcc <dbl> <dbl> 1 0 0 2 2 0.333 3 6 0.667 4 7 1 -- Call -- mcc(data = df, id_var = "id", time_var = "time", cause_var = "cause") -- Summary of Mean Cumulative Count Results ------------------------------------ i Method: Dong-Yasui Equation Method i Total participants: 4 -- Summary Statistics -- Observation period: [0, 8] Time to MCC = 1.0: 7 Time to maximum MCC: 7 MCC at end of follow-up: 1 -- Event Count Composition Events of interest: 3 Competing risk events: 1 Censoring events: 3 Saving _problems/test-s3_classes-115.R Saving _problems/test-s3_classes-136.R Saving _problems/test-s3_classes-182.R Saving _problems/test-s3_classes-206.R Saving _problems/test-s3_classes-292.R Saving _problems/test-s3_classes-457.R Saving _problems/test-s3_classes-489.R -- Mean Cumulative Count Results ----------------------------------------------- i Method: Dong-Yasui Equation Method -- MCC Estimates -- -- Call -- mcc(data = df_minimal, id_var = "id", time_var = "time", cause_var = "cause") Saving _problems/test-s3_classes-560.R Saving _problems/test-s3_classes-743.R Saving _problems/test-s3_classes-768.R [ FAIL 68 | WARN 0 | SKIP 24 | PASS 442 ] ══ Skipped tests (24 • On CRAN (24): 'test-calculation_helpers.R:482:1', 'test-calculation_helpers.R:529:1', 'test-calculation_helpers.R:611:1', 'test-mcc.R:94:1', 'test-mcc.R:191:1', 'test-mcc.R:669:1', 'test-mcc.R:851:1', 'test-mcc.R:1167:1', 'test-mcc.R:1253:1', 'test-mcc_equation.R:203:1', 'test-mcc_equation.R:477:1', 'test-mcc_equation.R:652:1', 'test-mcc_sci.R:583:1', 'test-s3_classes.R:80:1', 'test-s3_classes.R:509:1', 'test-validation_helpers.R:1:1', 'test-validation_helpers.R:44:1', 'test-validation_helpers.R:49:1', 'test-validation_helpers.R:57:1', 'test-validation_helpers.R:69:1', 'test-validation_helpers.R:101:1', 'test-validation_helpers.R:113:1', 'test-validation_helpers.R:142:1', 'test-validation_helpers.R:181:1' ══ Failed tests ════ ── Error ('test-calculation_helpers.R:21:3'): handle_simultaneous_events() works ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 4/4 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::handle_simultaneous_events(...) 2. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 3. └─data.table:::`[.data.table`(...) ── Error ('test-mcc.R:25:3'): mcc() dispatches to the correct implementation based on method ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(...) at test-mcc.R:25:3 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc.R:71:3'): mcc() validates the method argument correctly ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(...) 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc.R:179:3'): mcc() validates tstart_var compatibility with method ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(...) 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc.R:354:3'): mcc() handles method parameter with partial matching ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(...) at test-mcc.R:354:3 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc.R:459:3'): mcc() end-to-end functionality through snapshots ── Error: object 'result_sci' not found Backtrace: ▆ 1. └─base::print(result_sci$mcc_final) ── Error ('test-mcc.R:492:3'): mcc() produces equivalent results from both methods ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df1, id_var = "id", time_var = "time", cause_var = "cause") at test-mcc.R:492:3 2. └─mccount:::mcc_equation(...) 3. └─mccount:::handle_simultaneous_events(...) 4. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 5. └─data.table:::`[.data.table`(...) ── Error ('test-mcc.R:639:3'): mcc() correctly passes include_details parameter to implementation functions ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(...) at test-mcc.R:639:3 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Failure ('test-mcc.R:758:7'): mcc() with include_details=FALSE is suitable for bootstrapping ── Bootstrap failed: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─base::tryCatch(...) at test-mcc.R:744:3 2. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 3. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 4. └─value[[3L]](cond) ── Failure ('test-mcc.R:773:3'): mcc() documentation example works with include_details=FALSE ── Expected `{ ... }` not to throw any errors. Actually got a <simpleError> with message: attempt access index 5/5 in VECTOR_ELT ── Error ('test-mcc.R:793:3'): mcc() documentation example works with include_details=FALSE ── Error in `eval(code, test_env)`: object 'mcc_eq' not found Backtrace: ▆ 1. └─testthat::expect_named(...) at test-mcc.R:793:3 2. └─testthat::quasi_label(enquo(object), label) 3. └─rlang::eval_bare(expr, quo_get_env(quo)) ── Failure ('test-mcc.R:1012:3'): mcc() with by argument works with both methods ── Expected `... <- NULL` not to throw any errors. Actually got a <simpleError> with message: attempt access index 7/7 in VECTOR_ELT ── Error ('test-mcc.R:1023:3'): mcc() with by argument works with both methods ── Error in `eval(code, test_env)`: object 'result_sci' not found Backtrace: ▆ 1. ├─testthat::expect_true("sci_table" %in% names(result_sci)) at test-mcc.R:1023:3 2. │ └─testthat::quasi_label(enquo(object), label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─"sci_table" %in% names(result_sci) ── Failure ('test-mcc.R:1038:3'): mcc() with by argument and tstart_var works ── Expected `... <- NULL` not to throw any errors. Actually got a <simpleError> with message: attempt access index 7/7 in VECTOR_ELT ── Error ('test-mcc.R:1050:3'): mcc() with by argument and tstart_var works ── Error in `eval(code, test_env)`: object 'result_sci_tstart' not found Backtrace: ▆ 1. ├─testthat::expect_true("sci_table" %in% names(result_sci_tstart)) at test-mcc.R:1050:3 2. │ └─testthat::quasi_label(enquo(object), label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─"sci_table" %in% names(result_sci_tstart) ── Error ('test-mcc.R:1064:3'): mcc() with by argument preserves group information in all components ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(...) at test-mcc.R:1064:3 2. └─mccount:::mcc_by_group(...) 3. └─mccount:::mcc_sci(...) 4. ├─dt[, `:=`(first, seq_len(.N)), by = id] 5. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc.R:1197:3'): mcc() with by argument preserves group information in all components ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(...) at test-mcc.R:1197:3 2. └─mccount:::mcc_by_group(...) 3. └─mccount:::mcc_sci(...) 4. ├─dt[, `:=`(first, seq_len(.N)), by = id] 5. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc.R:1398:3'): mcc() converts numeric grouping variables to factors ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df_numeric_groups, "id", "time", "cause", by = "group_numeric") 2. └─mccount:::mcc_by_group(...) 3. └─mccount:::mcc_equation(...) 4. └─mccount:::handle_simultaneous_events(...) 5. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 6. └─data.table:::`[.data.table`(...) ── Error ('test-mcc.R:1456:3'): plotting works correctly with converted numeric groups ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df_plot_test, "id", "time", "cause", by = "treatment") 2. └─mccount:::mcc_by_group(...) 3. └─mccount:::mcc_equation(...) 4. └─mccount:::handle_simultaneous_events(...) 5. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 6. └─data.table:::`[.data.table`(...) ── Error ('test-mcc_equation.R:43:3'): mcc_equation() handles simultaneous events correctly ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_equation(...) at test-mcc_equation.R:43:3 2. └─mccount:::handle_simultaneous_events(...) 3. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 4. └─data.table:::`[.data.table`(...) ── Error ('test-mcc_equation.R:167:3'): mcc_equation() properly uses time_precision parameter ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_equation(...) at test-mcc_equation.R:167:3 2. └─mccount:::handle_simultaneous_events(...) 3. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 4. └─data.table:::`[.data.table`(...) ── Error ('test-mcc_equation.R:309:3'): mcc_equation() with include_details=FALSE works with various scenarios ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_equation(...) at test-mcc_equation.R:309:3 2. └─mccount:::handle_simultaneous_events(...) 3. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 4. └─data.table:::`[.data.table`(...) ── Error ('test-mcc_equation.R:384:3'): mcc_equation() with include_details=FALSE does not include adjusted_data ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_equation(...) at test-mcc_equation.R:384:3 2. └─mccount:::handle_simultaneous_events(...) 3. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 4. └─data.table:::`[.data.table`(...) ── Error ('test-mcc_equation.R:445:5'): mcc_equation() with include_details=FALSE provides sufficient data for bootstrapping ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_equation(...) at test-mcc_equation.R:445:5 2. └─mccount:::handle_simultaneous_events(...) 3. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 4. └─data.table:::`[.data.table`(...) ── Failure ('test-mcc_equation.R:774:3'): weighted MCC handles simultaneous events correctly ── Expected `... <- NULL` not to throw any errors. Actually got a <simpleError> with message: attempt access index 6/6 in VECTOR_ELT ── Error ('test-mcc_equation.R:798:3'): weighted MCC handles simultaneous events correctly ── Error in `eval(code, test_env)`: object 'result1' not found Backtrace: ▆ 1. └─testthat::expect_true(result1$weighted) at test-mcc_equation.R:798:3 2. └─testthat::quasi_label(enquo(object), label) 3. └─rlang::eval_bare(expr, quo_get_env(quo)) ── Error ('test-mcc_equation.R:948:3'): weighted MCC parameter combinations work correctly ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 6/6 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(...) at test-mcc_equation.R:948:3 2. └─mccount:::mcc_equation(...) 3. └─mccount:::handle_simultaneous_events(...) 4. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 5. └─data.table:::`[.data.table`(...) ── Error ('test-mcc_sci.R:10:3'): mcc_sci() correctly calculates MCC with basic data ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:10:3 2. ├─dt[, `:=`(first, seq_len(.N)), by = id] 3. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc_sci.R:51:3'): mcc_sci() handles tstart_var correctly ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:51:3 2. ├─dt[, `:=`(first, seq_len(.N)), by = id] 3. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc_sci.R:91:3'): mcc_sci() correctly handles left-truncated data ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:91:3 2. ├─dt[, `:=`(first, seq_len(.N)), by = id] 3. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc_sci.R:142:3'): mcc_sci() correctly handles simultaneous events ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:142:3 2. └─mccount:::handle_simultaneous_events(...) 3. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 4. └─data.table:::`[.data.table`(...) ── Error ('test-mcc_sci.R:175:3'): mcc_sci() generates correct CI columns ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:175:3 2. ├─dt[, `:=`(first, seq_len(.N)), by = id] 3. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc_sci.R:201:3'): mcc_sci() processes multiple recurrent events correctly ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:201:3 2. ├─dt[, `:=`(first, seq_len(.N)), by = id] 3. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc_sci.R:228:3'): mcc_sci() handles recurrent events with competing risks ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:228:3 2. ├─dt[, `:=`(first, seq_len(.N)), by = id] 3. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc_sci.R:255:3'): mcc_sci() uses time_precision parameter correctly ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:255:3 2. └─mccount:::handle_simultaneous_events(...) 3. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 4. └─data.table:::`[.data.table`(...) ── Error ('test-mcc_sci.R:330:3'): mcc_sci() works with snapshot testing for complex cases ── Error: object 'result' not found Backtrace: ▆ 1. └─base::print(length(result$all_cis)) ── Error ('test-mcc_sci.R:360:3'): mcc_sci() respects include_details=FALSE parameter ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:360:3 2. ├─dt[, `:=`(first, seq_len(.N)), by = id] 3. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc_sci.R:397:3'): mcc_sci() with include_details=FALSE works with all key scenarios ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:397:3 2. └─mccount:::handle_simultaneous_events(...) 3. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 4. └─data.table:::`[.data.table`(...) ── Error ('test-mcc_sci.R:462:3'): mcc_sci() with include_details=FALSE provides sufficient data for bootstrapping ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:462:3 2. ├─dt[, `:=`(first, seq_len(.N)), by = id] 3. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc_sci.R:532:3'): mcc_sci cleans up time precision adjustments in output ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:532:3 2. ├─dt[, `:=`(first, seq_len(.N)), by = id] 3. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc_sci.R:564:3'): mcc_sci only calculates CI for event numbers with actual events ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:564:3 2. ├─dt[, `:=`(first, seq_len(.N)), by = id] 3. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc_sci.R:614:3'): grouped mcc fills missing CI columns with 0, not NA ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(...) at test-mcc_sci.R:614:3 2. └─mccount:::mcc_by_group(...) 3. └─mccount:::mcc_sci(...) 4. ├─dt[, `:=`(first, seq_len(.N)), by = id] 5. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc_sci.R:646:3'): mcc_sci uses time_precision parameter consistently ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:646:3 2. ├─dt[, `:=`(first, seq_len(.N)), by = id] 3. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc_sci.R:667:3'): mcc_sci handles mixed events at time 0 correctly ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount:::mcc_sci(...) at test-mcc_sci.R:667:3 2. ├─dt[, `:=`(first, seq_len(.N)), by = id] 3. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc_sci.R:695:3'): both methods show consistent time values for events at time 0 ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(...) at test-mcc_sci.R:695:3 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-mcc_sci.R:717:3'): CI column names are consistent across groups with different max events ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(...) at test-mcc_sci.R:717:3 2. └─mccount:::mcc_by_group(...) 3. └─mccount:::mcc_sci(...) 4. ├─dt[, `:=`(first, seq_len(.N)), by = id] 5. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-plot.R:45:3'): plot.mcc error handling works correctly ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", method = "sci", include_details = FALSE) at test-plot.R:45:3 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-plot.R:90:3'): plot.mcc throws error when type='components' with equation method ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", method = "equation") at test-plot.R:90:3 2. └─mccount:::mcc_equation(...) 3. └─mccount:::handle_simultaneous_events(...) 4. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 5. └─data.table:::`[.data.table`(...) ── Error ('test-plot.R:129:3'): plot.mcc works correctly with type='components' for SCI method ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", method = "sci") at test-plot.R:129:3 2. └─mccount:::mcc_sci(...) 3. └─mccount:::handle_simultaneous_events(...) 4. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 5. └─data.table:::`[.data.table`(...) ── Error ('test-plot.R:150:3'): plot.mcc type argument matching works correctly ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", method = "equation") at test-plot.R:150:3 2. └─mccount:::mcc_equation(...) 3. └─mccount:::handle_simultaneous_events(...) 4. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 5. └─data.table:::`[.data.table`(...) ── Error ('test-plot.R:372:3'): geom_line_mcc works with different methods (equation vs sci) ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", method = "sci") at test-plot.R:372:3 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-plot.R:400:3'): plot.mcc uses correct data table for each method ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", method = "sci") at test-plot.R:400:3 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-plot.R:429:3'): plot.mcc handles grouped data correctly with both methods ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", by = "group", method = "sci") at test-plot.R:429:3 2. └─mccount:::mcc_by_group(...) 3. └─mccount:::mcc_sci(...) 4. ├─dt[, `:=`(first, seq_len(.N)), by = id] 5. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-plot.R:471:3'): plot.mcc handles group filtering correctly ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", by = "group") at test-plot.R:471:3 2. └─mccount:::mcc_by_group(...) 3. └─mccount:::mcc_equation(...) 4. └─mccount:::handle_simultaneous_events(...) 5. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 6. └─data.table:::`[.data.table`(...) ── Error ('test-plot.R:495:3'): plot.mcc color customization works ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause") at test-plot.R:495:3 2. └─mccount:::mcc_equation(...) 3. └─mccount:::handle_simultaneous_events(...) 4. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 5. └─data.table:::`[.data.table`(...) ── Error ('test-s3_classes.R:10:3'): S3 object creation works correctly ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", method = "equation") at test-s3_classes.R:10:3 2. └─mccount:::mcc_equation(...) 3. └─mccount:::handle_simultaneous_events(...) 4. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 5. └─data.table:::`[.data.table`(...) ── Error ('test-s3_classes.R:39:3'): Grouped S3 objects work correctly ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", by = "group") at test-s3_classes.R:39:3 2. └─mccount:::mcc_by_group(...) 3. └─mccount:::mcc_equation(...) 4. └─mccount:::handle_simultaneous_events(...) 5. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 6. └─data.table:::`[.data.table`(...) ── Error ('test-s3_classes.R:60:3'): Weighted S3 objects work correctly ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 6/6 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", weights = "weights") at test-s3_classes.R:60:3 2. └─mccount:::mcc_equation(...) 3. └─mccount:::handle_simultaneous_events(...) 4. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 5. └─data.table:::`[.data.table`(...) ── Error ('test-s3_classes.R:115:3'): Print methods work for grouped objects ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", by = "group") at test-s3_classes.R:115:3 2. └─mccount:::mcc_by_group(...) 3. └─mccount:::mcc_equation(...) 4. └─mccount:::handle_simultaneous_events(...) 5. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 6. └─data.table:::`[.data.table`(...) ── Error ('test-s3_classes.R:136:3'): Print methods work for weighted objects ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 6/6 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", weights = "weights") at test-s3_classes.R:136:3 2. └─mccount:::mcc_equation(...) 3. └─mccount:::handle_simultaneous_events(...) 4. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 5. └─data.table:::`[.data.table`(...) ── Error ('test-s3_classes.R:182:3'): Grouped utility functions work correctly ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", by = "group") at test-s3_classes.R:182:3 2. └─mccount:::mcc_by_group(...) 3. └─mccount:::mcc_equation(...) 4. └─mccount:::handle_simultaneous_events(...) 5. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 6. └─data.table:::`[.data.table`(...) ── Error ('test-s3_classes.R:206:3'): MCC comparison print works correctly ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", method = "sci") at test-s3_classes.R:206:3 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-s3_classes.R:292:3'): S3 classes are assigned correctly for all combinations ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", method = "sci") at test-s3_classes.R:292:3 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-s3_classes.R:457:3'): filter_mcc works correctly ── Error in ``[.data.table`(dt, , `:=`(row_within_time, seq_len(.N)), by = .(id, time))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", by = "group") at test-s3_classes.R:457:3 2. └─mccount:::mcc_by_group(...) 3. └─mccount:::mcc_equation(...) 4. └─mccount:::handle_simultaneous_events(...) 5. ├─dt[, `:=`(row_within_time, seq_len(.N)), by = .(id, time)] 6. └─data.table:::`[.data.table`(...) ── Error ('test-s3_classes.R:489:3'): compare_mcc works correctly ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", method = "sci") at test-s3_classes.R:489:3 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-s3_classes.R:560:3'): S3 method dispatch works correctly ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", method = "sci") at test-s3_classes.R:560:3 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-s3_classes.R:743:3'): mcc_details correctly dispatches based on class ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", method = "sci") at test-s3_classes.R:743:3 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) ── Error ('test-s3_classes.R:768:3'): create_subtitle function works correctly ── Error in ``[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─mccount::mcc(df, "id", "time", "cause", method = "sci") at test-s3_classes.R:768:3 2. └─mccount:::mcc_sci(...) 3. ├─dt[, `:=`(first, seq_len(.N)), by = id] 4. └─data.table:::`[.data.table`(dt, , `:=`(first, seq_len(.N)), by = id) [ FAIL 68 | WARN 0 | SKIP 24 | PASS 442 ] Error: ! Test failures. Execution halted Flavor: r-devel-linux-x86_64-fedora-gcc