Last updated on 2025-12-21 11:50:36 CET.
| Package | ERROR | OK |
|---|---|---|
| mccount | 4 | 9 |
| mmequiv | 13 |
Current CRAN status: ERROR: 4, OK: 9
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
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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
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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
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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
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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
Current CRAN status: OK: 13