- using R Under development (unstable) (2025-12-18 r89199)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
Debian clang version 21.1.7 (1)
Debian flang version 21.1.7 (1)
- running under: Debian GNU/Linux forky/sid
- using session charset: UTF-8
- checking for file ‘psmineR/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘psmineR’ version ‘0.1.1’
- package encoding: UTF-8
- checking CRAN incoming feasibility ... [1s/1s] OK
- checking package namespace information ... OK
- checking package dependencies ... OK
- checking if this is a source package ... OK
- checking if there is a namespace ... OK
- checking for executable files ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... OK
- checking whether package ‘psmineR’ can be installed ... OK
See the install log for details.
- checking package directory ... OK
- checking for future file timestamps ... OK
- checking ‘build’ directory ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking for left-over files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking code files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... [3s/5s] OK
- checking whether the package can be loaded with stated dependencies ... [2s/3s] OK
- checking whether the package can be unloaded cleanly ... [3s/4s] OK
- checking whether the namespace can be loaded with stated dependencies ... [2s/3s] OK
- checking whether the namespace can be unloaded cleanly ... [3s/4s] OK
- checking loading without being on the library search path ... [3s/5s] OK
- checking use of S3 registration ... OK
- checking dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... [14s/19s] OK
- checking Rd files ... [0s/0s] OK
- checking Rd metadata ... OK
- checking Rd line widths ... OK
- checking Rd cross-references ... OK
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... OK
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- checking for unstated dependencies in examples ... OK
- checking installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [4s/5s] ERROR
Running examples in ‘psmineR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ps_aggregated
> ### Title: Aggregated Performance Spectrum
> ### Aliases: ps_aggregated ps_aggregated.log ps_aggregated.grouped_log
>
> ### ** Examples
>
> library(psmineR)
> library(eventdataR)
>
> sepsis %>%
+ ps_aggregated(segment_coverage = 0.2,
+ classification = "quartile",
+ grouping = "start",
+ bins = 15)
Error in `[.data.table`(dt, , `:=`((classification), fcase(delta <= quantile(delta, :
attempt access index 9/9 in VECTOR_ELT
Calls: %>% ... filter_segments -> build_classifier -> [ -> [.data.table
Execution halted
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [9s/9s] ERROR
Running ‘testthat.R’ [9s/9s]
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/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(psmineR)
>
> test_check("psmineR")
Saving _problems/test_ps_aggregated-13.R
Saving _problems/test_ps_aggregated-14.R
Saving _problems/test_ps_aggregated-160.R
Saving _problems/test_ps_aggregated-161.R
Saving _problems/test_ps_aggregated-174.R
Saving _problems/test_ps_aggregated-176.R
Saving _problems/test_ps_detailed-13.R
Saving _problems/test_ps_detailed-18.R
Saving _problems/test_ps_detailed-141.R
Saving _problems/test_ps_detailed-146.R
Saving _problems/test_ps_detailed-160.R
Saving _problems/test_ps_detailed-166.R
[ FAIL 12 | WARN 2 | SKIP 8 | PASS 6 ]
══ Skipped tests (8) ═══════════════════════════════════════════════════════════
• On CRAN (8): 'test_ps_aggregated.R:70:1', 'test_ps_aggregated.R:90:1',
'test_ps_aggregated.R:110:1', 'test_ps_aggregated.R:120:1',
'test_ps_detailed.R:46:1', 'test_ps_detailed.R:71:1',
'test_ps_detailed.R:91:1', 'test_ps_detailed.R:101:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_ps_aggregated.R:9:3'): test ps_aggregated on eventlog ────────
Expected `ps <- patients %>% ps_aggregated()` not to throw any errors.
Actually got a <simpleError> with message:
attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_error(ps <- patients %>% ps_aggregated(), NA) at test_ps_aggregated.R:9:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─patients %>% ps_aggregated()
8. ├─psmineR::ps_aggregated(.)
9. ├─psmineR:::ps_aggregated.log(.)
10. │ └─psmineR:::get_segments(...)
11. │ └─... %>% order_segments(log)
12. ├─psmineR:::order_segments(., log)
13. │ └─data.table::setorderv(dt, cols = "start_t")
14. │ └─base::is.data.frame(x)
15. ├─psmineR:::filter_segments(...)
16. └─psmineR:::build_classifier(., classification)
17. ├─...[]
18. └─data.table:::`[.data.table`(...)
── Error ('test_ps_aggregated.R:14:3'): test ps_aggregated on eventlog ─────────
Error in `eval(code, test_env)`: object 'ps' not found
Backtrace:
▆
1. └─testthat::expect_s3_class(ps, "ggplot") at test_ps_aggregated.R:14:3
2. └─testthat::quasi_label(enquo(object))
3. └─rlang::eval_bare(expr, quo_get_env(quo))
── Failure ('test_ps_aggregated.R:156:3'): test ps_aggregated on activitylog ───
Expected `ps <- patients_act %>% ps_aggregated()` not to throw any errors.
Actually got a <simpleError> with message:
attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_error(...) at test_ps_aggregated.R:156:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─patients_act %>% ps_aggregated()
8. ├─psmineR::ps_aggregated(.)
9. ├─psmineR:::ps_aggregated.log(.)
10. │ └─psmineR:::get_segments(...)
11. │ └─... %>% order_segments(log)
12. ├─psmineR:::order_segments(., log)
13. │ └─data.table::setorderv(dt, cols = "start_t")
14. │ └─base::is.data.frame(x)
15. ├─psmineR:::filter_segments(...)
16. └─psmineR:::build_classifier(., classification)
17. ├─...[]
18. └─data.table:::`[.data.table`(...)
── Error ('test_ps_aggregated.R:161:3'): test ps_aggregated on activitylog ─────
Error in `eval(code, test_env)`: object 'ps' not found
Backtrace:
▆
1. └─testthat::expect_s3_class(ps, "ggplot") at test_ps_aggregated.R:161:3
2. └─testthat::quasi_label(enquo(object))
3. └─rlang::eval_bare(expr, quo_get_env(quo))
── Failure ('test_ps_aggregated.R:169:3'): test ps_aggregated on grouped_activitylog ──
Expected `ps <- patients_act %>% group_by_resource() %>% ps_aggregated()` not to throw any errors.
Actually got a <simpleError> with message:
attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_error(...) at test_ps_aggregated.R:169:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─patients_act %>% group_by_resource() %>% ps_aggregated()
8. ├─psmineR::ps_aggregated(.)
9. ├─psmineR:::ps_aggregated.grouped_log(.)
10. │ └─psmineR:::ps_aggregated.log(...)
11. │ └─psmineR:::get_segments(...)
12. │ └─... %>% order_segments(log)
13. ├─psmineR:::order_segments(., log)
14. │ └─data.table::setorderv(dt, cols = "start_t")
15. │ └─base::is.data.frame(x)
16. ├─psmineR:::filter_segments(...)
17. ├─psmineR:::build_classifier(., classification)
18. └─psmineR:::construct_segments(., classification)
19. └─psmineR:::construct_segments.activitylog(...)
20. ├─...[]
21. └─data.table:::`[.data.table`(...)
── Error ('test_ps_aggregated.R:176:3'): test ps_aggregated on grouped_activitylog ──
Error in `eval(code, test_env)`: object 'ps' not found
Backtrace:
▆
1. └─testthat::expect_s3_class(ps, "ggplot") at test_ps_aggregated.R:176:3
2. └─testthat::quasi_label(enquo(object))
3. └─rlang::eval_bare(expr, quo_get_env(quo))
── Failure ('test_ps_detailed.R:9:3'): test ps_detailed on eventlog ────────────
Expected `ps <- patients %>% ps_detailed()` not to throw any errors.
Actually got a <simpleError> with message:
attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_error(ps <- patients %>% ps_detailed(), NA) at test_ps_detailed.R:9:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─patients %>% ps_detailed()
8. ├─psmineR::ps_detailed(.)
9. ├─psmineR:::ps_detailed.log(.)
10. │ └─psmineR:::get_segments(...)
11. │ └─... %>% order_segments(log)
12. ├─psmineR:::order_segments(., log)
13. │ └─data.table::setorderv(dt, cols = "start_t")
14. │ └─base::is.data.frame(x)
15. ├─psmineR:::filter_segments(...)
16. └─psmineR:::build_classifier(., classification)
17. ├─...[]
18. └─data.table:::`[.data.table`(...)
── Error ('test_ps_detailed.R:14:3'): test ps_detailed on eventlog ─────────────
Error in ``[.data.table`(dt, , `:=`((classification), fcase(delta <= quantile(delta, 0.25), 1L, delta <= quantile(delta, 0.5), 2L, delta <= quantile(delta, 0.75), 3L, default = 4L)), by = "segment")`: attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_warning(ps <- patients %>% ps_detailed(), NA) at test_ps_detailed.R:14:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─patients %>% ps_detailed()
8. ├─psmineR::ps_detailed(.)
9. ├─psmineR:::ps_detailed.log(.)
10. │ └─psmineR:::get_segments(...)
11. │ └─... %>% order_segments(log)
12. ├─psmineR:::order_segments(., log)
13. │ └─data.table::setorderv(dt, cols = "start_t")
14. │ └─base::is.data.frame(x)
15. ├─psmineR:::filter_segments(...)
16. └─psmineR:::build_classifier(., classification)
17. ├─...[]
18. └─data.table:::`[.data.table`(...)
── Failure ('test_ps_detailed.R:137:3'): test ps_detailed on activitylog ───────
Expected `ps <- patients_act %>% ps_detailed()` not to throw any errors.
Actually got a <simpleError> with message:
attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_error(...) at test_ps_detailed.R:137:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─patients_act %>% ps_detailed()
8. ├─psmineR::ps_detailed(.)
9. ├─psmineR:::ps_detailed.log(.)
10. │ └─psmineR:::get_segments(...)
11. │ └─... %>% order_segments(log)
12. ├─psmineR:::order_segments(., log)
13. │ └─data.table::setorderv(dt, cols = "start_t")
14. │ └─base::is.data.frame(x)
15. ├─psmineR:::filter_segments(...)
16. └─psmineR:::build_classifier(., classification)
17. ├─...[]
18. └─data.table:::`[.data.table`(...)
── Error ('test_ps_detailed.R:142:3'): test ps_detailed on activitylog ─────────
Error in ``[.data.table`(dt, , `:=`((classification), fcase(delta <= quantile(delta, 0.25), 1L, delta <= quantile(delta, 0.5), 2L, delta <= quantile(delta, 0.75), 3L, default = 4L)), by = "segment")`: attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test_ps_detailed.R:142:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─patients_act %>% ps_detailed()
8. ├─psmineR::ps_detailed(.)
9. ├─psmineR:::ps_detailed.log(.)
10. │ └─psmineR:::get_segments(...)
11. │ └─... %>% order_segments(log)
12. ├─psmineR:::order_segments(., log)
13. │ └─data.table::setorderv(dt, cols = "start_t")
14. │ └─base::is.data.frame(x)
15. ├─psmineR:::filter_segments(...)
16. └─psmineR:::build_classifier(., classification)
17. ├─...[]
18. └─data.table:::`[.data.table`(...)
── Failure ('test_ps_detailed.R:155:3'): test ps_detailed on grouped_activitylog ──
Expected `ps <- patients_act %>% group_by_resource() %>% ps_detailed()` not to throw any errors.
Actually got a <simpleError> with message:
attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_error(...) at test_ps_detailed.R:155:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─patients_act %>% group_by_resource() %>% ps_detailed()
8. ├─psmineR::ps_detailed(.)
9. ├─psmineR:::ps_detailed.grouped_log(.)
10. │ └─psmineR:::ps_detailed.log(...)
11. │ └─psmineR:::get_segments(...)
12. │ └─... %>% order_segments(log)
13. ├─psmineR:::order_segments(., log)
14. │ └─data.table::setorderv(dt, cols = "start_t")
15. │ └─base::is.data.frame(x)
16. ├─psmineR:::filter_segments(...)
17. ├─psmineR:::build_classifier(., classification)
18. └─psmineR:::construct_segments(., classification)
19. └─psmineR:::construct_segments.activitylog(...)
20. ├─...[]
21. └─data.table:::`[.data.table`(...)
── Error ('test_ps_detailed.R:161:3'): test ps_detailed on grouped_activitylog ──
Error in ``[.data.table`(dt, , `:=`(start_t = do.call(pmin, c(na.rm = TRUE, .SD)), end_t = do.call(pmax, c(na.rm = TRUE, .SD))), .SDcols = TIMESTAMP_CLASSIFIERS, by = c(case_id(log), activity_id(log), "ACTIVITY_INSTANCE", classification))`: attempt access index 8/8 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test_ps_detailed.R:161:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─patients_act %>% group_by_resource() %>% ps_detailed()
8. ├─psmineR::ps_detailed(.)
9. ├─psmineR:::ps_detailed.grouped_log(.)
10. │ └─psmineR:::ps_detailed.log(...)
11. │ └─psmineR:::get_segments(...)
12. │ └─... %>% order_segments(log)
13. ├─psmineR:::order_segments(., log)
14. │ └─data.table::setorderv(dt, cols = "start_t")
15. │ └─base::is.data.frame(x)
16. ├─psmineR:::filter_segments(...)
17. ├─psmineR:::build_classifier(., classification)
18. └─psmineR:::construct_segments(., classification)
19. └─psmineR:::construct_segments.activitylog(...)
20. ├─...[]
21. └─data.table:::`[.data.table`(...)
[ FAIL 12 | WARN 2 | SKIP 8 | PASS 6 ]
Error:
! Test failures.
Execution halted
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [6s/6s] ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘introduction_to_psmineR.Rmd’ using rmarkdown
Quitting from introduction_to_psmineR.Rmd:30-33 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 9/9 in VECTOR_ELT
---
Backtrace:
▆
1. ├─traffic_fines %>% ps_detailed()
2. ├─psmineR::ps_detailed(.)
3. ├─psmineR:::ps_detailed.log(.)
4. │ └─psmineR:::get_segments(...)
5. │ └─... %>% order_segments(log)
6. ├─psmineR:::order_segments(., log)
7. │ └─data.table::setorderv(dt, cols = "start_t")
8. │ └─base::is.data.frame(x)
9. ├─psmineR:::filter_segments(...)
10. └─psmineR:::build_classifier(., classification)
11. ├─...[]
12. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'introduction_to_psmineR.Rmd' failed with diagnostics:
attempt access index 9/9 in VECTOR_ELT
--- failed re-building ‘introduction_to_psmineR.Rmd’
SUMMARY: processing the following file failed:
‘introduction_to_psmineR.Rmd’
Error: Vignette re-building failed.
Execution halted
- checking PDF version of manual ... [4s/6s] OK
- checking HTML version of manual ... [1s/1s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 3 ERRORs