Last updated on 2025-12-20 07:49:25 CET.
| Package | ERROR | OK |
|---|---|---|
| behavr | 3 | 10 |
| damr | 13 | |
| ggetho | 3 | 10 |
| scopr | 3 | 10 |
| sleepr | 3 | 10 |
| zeitgebr | 3 | 10 |
Current CRAN status: ERROR: 3, OK: 10
Version: 0.3.3
Check: examples
Result: ERROR
Running examples in ‘behavr-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bin_apply
> ### Title: Bin a variable (typically time) and compute an aggregate for
> ### each bin
> ### Aliases: bin_apply bin_apply_all
>
> ### ** Examples
>
> metadata <- data.frame(id = paste0("toy_experiment|",1:5))
> dt <- toy_activity_data(metadata, duration = days(2))
>
> # average by 30min time bins, default
> dt_binned <- bin_apply_all(dt, moving)
> # equivalent to
> dt_binned <- dt[, bin_apply(.SD, moving), by = "id"]
>
> # if we want the opposite of moving:
> dt_binned <- bin_apply_all(dt, !moving)
>
> # More advanced usage
> dt <- toy_dam_data(metadata, duration = days(2))
Error in `[.data.table`(out, , `:=`(activity, abs(c(0, diff(sign(0.5 - :
attempt access index 5/5 in VECTOR_ELT
Calls: toy_dam_data -> [ -> [.behavr -> NextMethod -> [.data.table
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.3.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [5s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(behavr)
Loading required package: data.table
Attaching package: 'data.table'
The following object is masked from 'package:base':
%notin%
>
> test_check("behavr")
Saving _problems/test-behavr-157.R
==== METADATA ====
Key: <id>
id condition sex
<int> <char> <char>
1: 1 a M
2: 2 b M
3: 3 c M
4: 4 d F
5: 5 e F
====== DATA ======
Key: <id>
id t x y eating
<int> <int> <num> <num> <lgcl>
1: 1 1 -0.6264538 -0.62036668 TRUE
2: 1 2 0.1836433 0.04211587 FALSE
3: 1 3 -0.8356286 -0.91092165 TRUE
4: 1 4 1.5952808 0.15802877 TRUE
5: 1 5 0.3295078 -0.65458464 TRUE
---
496: 5 96 -2.0908461 -0.30824994 TRUE
497: 5 97 1.6973939 0.01551524 FALSE
498: 5 98 1.0638812 -0.44231772 TRUE
499: 5 99 -0.7666166 -1.63800773 FALSE
500: 5 100 0.3820076 -0.64140116 FALSE
behavr table with:
5 individuals
2 metavariables
4 variables
5e+02 measurements
1 key (id)
Summary of each individual (one per row):
Key: <id>
id condition sex data_points time_range
<int> <char> <char> <int> <char>
1: 1 a M 100 [1 -> 100 (99)]
2: 2 b M 100 [1 -> 100 (99)]
3: 3 c M 100 [1 -> 100 (99)]
4: 4 d F 100 [1 -> 100 (99)]
5: 5 e F 100 [1 -> 100 (99)]
behavr table with:
5 individuals
2 metavariables
4 variables
5e+02 measurements
1 key (id)
Saving _problems/test-stitch_on-23.R
Saving _problems/test-stitch_on-74.R
Saving _problems/test-toy-data-13.R
[ FAIL 4 | WARN 0 | SKIP 2 | PASS 74 ]
══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• empty test (2): 'test-print_summary.R:3:1', 'test-print_summary.R:12:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-behavr.R:157:3'): metadata columns can be extracted without id ──
Error in ``[.data.table`(out, , `:=`(activity, abs(c(0, diff(sign(0.5 - x))))), by = "id")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─behavr::toy_dam_data(metadata = met, duration = hours(1)) at test-behavr.R:157:3
2. ├─out[, `:=`(activity, abs(c(0, diff(sign(0.5 - x))))), by = "id"]
3. ├─behavr:::`[.behavr`(...)
4. ├─base::NextMethod()
5. └─data.table:::`[.data.table`(...)
── Error ('test-stitch_on.R:23:3'): stitch works ───────────────────────────────
Error in ``[.data.table`(md, , `:=`(lag, as.numeric(as.Date(time_ref__) - as.Date(min(time_ref__)), units = "secs")), by = on)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─behavr::stitch_on(d, on = "uid") at test-stitch_on.R:23:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Failure ('test-stitch_on.R:74:3'): stitch fails when overlap ────────────────
`stitch_on(d, on = "uid")` threw an error with unexpected message.
Expected match: "overlap"
Actual message: "attempt access index 5/5 in VECTOR_ELT"
Backtrace:
▆
1. ├─testthat::expect_error(stitch_on(d, on = "uid"), "overlap") at test-stitch_on.R:74:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─behavr::stitch_on(d, on = "uid")
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-toy-data.R:13:3'): toy data returns behavr object ──────────────
Error in ``[.data.table`(out, , `:=`(activity, abs(c(0, diff(sign(0.5 - x))))), by = "id")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─behavr::toy_dam_data() at test-toy-data.R:13:3
2. ├─out[, `:=`(activity, abs(c(0, diff(sign(0.5 - x))))), by = "id"]
3. ├─behavr:::`[.behavr`(...)
4. ├─base::NextMethod()
5. └─data.table:::`[.data.table`(...)
[ FAIL 4 | WARN 0 | SKIP 2 | PASS 74 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.3.3
Check: examples
Result: ERROR
Running examples in ‘behavr-Ex.R’ failed
The error most likely occurred in:
> ### Name: bin_apply
> ### Title: Bin a variable (typically time) and compute an aggregate for
> ### each bin
> ### Aliases: bin_apply bin_apply_all
>
> ### ** Examples
>
> metadata <- data.frame(id = paste0("toy_experiment|",1:5))
> dt <- toy_activity_data(metadata, duration = days(2))
>
> # average by 30min time bins, default
> dt_binned <- bin_apply_all(dt, moving)
> # equivalent to
> dt_binned <- dt[, bin_apply(.SD, moving), by = "id"]
>
> # if we want the opposite of moving:
> dt_binned <- bin_apply_all(dt, !moving)
>
> # More advanced usage
> dt <- toy_dam_data(metadata, duration = days(2))
Error in `[.data.table`(out, , `:=`(activity, abs(c(0, diff(sign(0.5 - :
attempt access index 5/5 in VECTOR_ELT
Calls: toy_dam_data -> [ -> [.behavr -> NextMethod -> [.data.table
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.3.3
Check: tests
Result: ERROR
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(behavr)
Loading required package: data.table
Attaching package: 'data.table'
The following object is masked from 'package:base':
%notin%
>
> test_check("behavr")
Saving _problems/test-behavr-157.R
==== METADATA ====
Key: <id>
id condition sex
<int> <char> <char>
1: 1 a M
2: 2 b M
3: 3 c M
4: 4 d F
5: 5 e F
====== DATA ======
Key: <id>
id t x y eating
<int> <int> <num> <num> <lgcl>
1: 1 1 -0.6264538 -0.62036668 TRUE
2: 1 2 0.1836433 0.04211587 FALSE
3: 1 3 -0.8356286 -0.91092165 TRUE
4: 1 4 1.5952808 0.15802877 TRUE
5: 1 5 0.3295078 -0.65458464 TRUE
---
496: 5 96 -2.0908461 -0.30824994 TRUE
497: 5 97 1.6973939 0.01551524 FALSE
498: 5 98 1.0638812 -0.44231772 TRUE
499: 5 99 -0.7666166 -1.63800773 FALSE
500: 5 100 0.3820076 -0.64140116 FALSE
behavr table with:
5 individuals
2 metavariables
4 variables
5e+02 measurements
1 key (id)
Summary of each individual (one per row):
Key: <id>
id condition sex data_points time_range
<int> <char> <char> <int> <char>
1: 1 a M 100 [1 -> 100 (99)]
2: 2 b M 100 [1 -> 100 (99)]
3: 3 c M 100 [1 -> 100 (99)]
4: 4 d F 100 [1 -> 100 (99)]
5: 5 e F 100 [1 -> 100 (99)]
behavr table with:
5 individuals
2 metavariables
4 variables
5e+02 measurements
1 key (id)
Saving _problems/test-stitch_on-23.R
Saving _problems/test-stitch_on-74.R
Saving _problems/test-toy-data-13.R
[ FAIL 4 | WARN 0 | SKIP 2 | PASS 74 ]
══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• empty test (2): 'test-print_summary.R:3:1', 'test-print_summary.R:12:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-behavr.R:157:3'): metadata columns can be extracted without id ──
Error in ``[.data.table`(out, , `:=`(activity, abs(c(0, diff(sign(0.5 - x))))), by = "id")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─behavr::toy_dam_data(metadata = met, duration = hours(1)) at test-behavr.R:157:3
2. ├─out[, `:=`(activity, abs(c(0, diff(sign(0.5 - x))))), by = "id"]
3. ├─behavr:::`[.behavr`(...)
4. ├─base::NextMethod()
5. └─data.table:::`[.data.table`(...)
── Error ('test-stitch_on.R:23:3'): stitch works ───────────────────────────────
Error in ``[.data.table`(md, , `:=`(lag, as.numeric(as.Date(time_ref__) - as.Date(min(time_ref__)), units = "secs")), by = on)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─behavr::stitch_on(d, on = "uid") at test-stitch_on.R:23:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Failure ('test-stitch_on.R:74:3'): stitch fails when overlap ────────────────
`stitch_on(d, on = "uid")` threw an error with unexpected message.
Expected match: "overlap"
Actual message: "attempt access index 5/5 in VECTOR_ELT"
Backtrace:
▆
1. ├─testthat::expect_error(stitch_on(d, on = "uid"), "overlap") at test-stitch_on.R:74:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─behavr::stitch_on(d, on = "uid")
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-toy-data.R:13:3'): toy data returns behavr object ──────────────
Error in ``[.data.table`(out, , `:=`(activity, abs(c(0, diff(sign(0.5 - x))))), by = "id")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─behavr::toy_dam_data() at test-toy-data.R:13:3
2. ├─out[, `:=`(activity, abs(c(0, diff(sign(0.5 - x))))), by = "id"]
3. ├─behavr:::`[.behavr`(...)
4. ├─base::NextMethod()
5. └─data.table:::`[.data.table`(...)
[ FAIL 4 | WARN 0 | SKIP 2 | PASS 74 ]
Error:
! Test failures.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Current CRAN status: OK: 13
Current CRAN status: ERROR: 3, OK: 10
Version: 0.3.7
Check: tests
Result: ERROR
Running ‘testthat.R’ [53s/58s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(ggetho)
Loading required package: ggplot2
Loading required package: behavr
Loading required package: data.table
Attaching package: 'data.table'
The following object is masked from 'package:base':
%notin%
>
> test_check("ggetho")
Saving _problems/test-stat_tile-7.R
[ FAIL 1 | WARN 292 | SKIP 1 | PASS 41 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test-scales.R:47:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-stat_tile.R:7:3'): stat_bar_tile_works ─────────────────────────
Error in ``[.data.table`(out, , `:=`(activity, abs(c(0, diff(sign(0.5 - x))))), by = "id")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─behavr::toy_dam_data(metadata, duration = days(4)) at test-stat_tile.R:7:3
2. ├─out[, `:=`(activity, abs(c(0, diff(sign(0.5 - x))))), by = "id"]
3. ├─behavr:::`[.behavr`(...)
4. ├─base::NextMethod()
5. └─data.table:::`[.data.table`(...)
[ FAIL 1 | WARN 292 | SKIP 1 | PASS 41 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.3.7
Check: tests
Result: ERROR
Running ‘testthat.R’ [103s/145s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(ggetho)
Loading required package: ggplot2
Loading required package: behavr
Loading required package: data.table
Attaching package: 'data.table'
The following object is masked from 'package:base':
%notin%
>
> test_check("ggetho")
Saving _problems/test-stat_tile-7.R
[ FAIL 1 | WARN 292 | SKIP 1 | PASS 41 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test-scales.R:47:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-stat_tile.R:7:3'): stat_bar_tile_works ─────────────────────────
Error in ``[.data.table`(out, , `:=`(activity, abs(c(0, diff(sign(0.5 - x))))), by = "id")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─behavr::toy_dam_data(metadata, duration = days(4)) at test-stat_tile.R:7:3
2. ├─out[, `:=`(activity, abs(c(0, diff(sign(0.5 - x))))), by = "id"]
3. ├─behavr:::`[.behavr`(...)
4. ├─base::NextMethod()
5. └─data.table:::`[.data.table`(...)
[ FAIL 1 | WARN 292 | SKIP 1 | PASS 41 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.3.7
Check: tests
Result: ERROR
Running ‘testthat.R’ [95s/179s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(ggetho)
Loading required package: ggplot2
Loading required package: behavr
Loading required package: data.table
Attaching package: 'data.table'
The following object is masked from 'package:base':
%notin%
>
> test_check("ggetho")
Saving _problems/test-stat_tile-7.R
[ FAIL 1 | WARN 292 | SKIP 1 | PASS 41 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test-scales.R:47:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-stat_tile.R:7:3'): stat_bar_tile_works ─────────────────────────
Error in ``[.data.table`(out, , `:=`(activity, abs(c(0, diff(sign(0.5 - x))))), by = "id")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─behavr::toy_dam_data(metadata, duration = days(4)) at test-stat_tile.R:7:3
2. ├─out[, `:=`(activity, abs(c(0, diff(sign(0.5 - x))))), by = "id"]
3. ├─behavr:::`[.behavr`(...)
4. ├─base::NextMethod()
5. └─data.table:::`[.data.table`(...)
[ FAIL 1 | WARN 292 | SKIP 1 | PASS 41 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Current CRAN status: ERROR: 3, OK: 10
Version: 0.3.5
Check: examples
Result: ERROR
Running examples in ‘scopr-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: link_ethoscope_metadata_remote
> ### Title: Link ethoscope metadata to the matching result files
> ### Aliases: link_ethoscope_metadata_remote link_ethoscope_metadata
>
> ### ** Examples
>
> # Metadata with no region_id -> all regions will be loaded with the same metadata
> dir <- paste0(scopr_example_dir(), "/ethoscope_results/")
> data(no_region_id_metadata)
> metadata <- link_ethoscope_metadata(no_region_id_metadata, dir)
Error in `[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", :
attempt access index 6/6 in VECTOR_ELT
Calls: link_ethoscope_metadata -> build_query -> [ -> [.data.table
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.3.5
Check: tests
Result: ERROR
Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(scopr)
Loading required package: behavr
Loading required package: data.table
Attaching package: 'data.table'
The following object is masked from 'package:base':
%notin%
>
> test_check("scopr")
Saving _problems/test-build_query-12.R
Saving _problems/test-build_query-40.R
Saving _problems/test-build_query-53.R
Saving _problems/test-build_query-68.R
Saving _problems/test-build_query-83.R
machine_name date time test
1 E_014 2016-01-25 21:36:04 1
2 E_014 2016-02-17 <NA> 2
3 E_029 2016-01-25 <NA> 3
Saving _problems/test-build_query-110.R
Saving _problems/test-link_ethocope_metadata-6.R
Saving _problems/test-link_ethocope_metadata-24.R
Saving _problems/test-link_ethocope_metadata-39.R
Saving _problems/test-link_ethocope_metadata-60.R
Saving _problems/test-link_ethocope_metadata-73.R
Saving _problems/test-link_ethocope_metadata-94.R
Saving _problems/test-link_ethoscope_metadata_remote-18.R
Saving _problems/test-link_ethoscope_metadata_remote-55.R
Saving _problems/test-load_ethoscope-11.R
Saving _problems/test-load_ethoscope-23.R
Saving _problems/test-load_ethoscope-36.R
[ FAIL 17 | WARN 0 | SKIP 0 | PASS 17 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-build_query.R:12:3'): build query works when time is supplied ──
Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. └─scopr:::build_query(dir, query) at test-build_query.R:12:3
2. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]
3. └─data.table:::`[.data.table`(...)
── Error ('test-build_query.R:40:3'): build_query with date, machine name, and ROIs, and two experiments on the same date, but different times! ──
Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. └─scopr:::build_query(dir, query) at test-build_query.R:40:3
2. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]
3. └─data.table:::`[.data.table`(...)
── Error ('test-build_query.R:53:3'): build query works when only date supplied ──
Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-build_query.R:53:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─scopr:::build_query(dir, query)
7. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]
8. └─data.table:::`[.data.table`(...)
── Error ('test-build_query.R:68:3'): build query works when only date supplied and ROIs ──
Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-build_query.R:68:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─scopr:::build_query(dir, query)
7. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]
8. └─data.table:::`[.data.table`(...)
── Error ('test-build_query.R:83:3'): missing results! ─────────────────────────
Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-build_query.R:83:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─scopr:::build_query(dir, query)
7. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]
8. └─data.table:::`[.data.table`(...)
── Error ('test-build_query.R:110:3'): build query works datetime is a datetime, not a string (https://github.com/rethomics/scopr/issues/16) ──
Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. └─scopr:::build_query(dir, query) at test-build_query.R:110:3
2. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]
3. └─data.table:::`[.data.table`(...)
── Error ('test-link_ethocope_metadata.R:6:3'): link_ethoscope_metadata with single file ──
Error in ``[.data.table`(out, , `:=`(n, .N), keyby = key(out))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─scopr::link_ethoscope_metadata(test_file) at test-link_ethocope_metadata.R:6:3
2. ├─out[, `:=`(n, .N), keyby = key(out)]
3. └─data.table:::`[.data.table`(out, , `:=`(n, .N), keyby = key(out))
── Error ('test-link_ethocope_metadata.R:24:3'): link_ethoscope_metadata with date and machine name ──
Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. └─scopr::link_ethoscope_metadata(query, dir) at test-link_ethocope_metadata.R:24:3
2. └─scopr:::build_query(result_dir, query, index_file)
3. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]
4. └─data.table:::`[.data.table`(...)
── Error ('test-link_ethocope_metadata.R:39:3'): link_ethoscope_metadata with name of a text csv ──
Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. └─scopr::link_ethoscope_metadata(file, dir) at test-link_ethocope_metadata.R:39:3
2. └─scopr:::build_query(result_dir, query, index_file)
3. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]
4. └─data.table:::`[.data.table`(...)
── Error ('test-link_ethocope_metadata.R:60:3'): link_ethoscope_metadata with date, machine name, and ROIs ──
Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. └─scopr::link_ethoscope_metadata(query, dir) at test-link_ethocope_metadata.R:60:3
2. └─scopr:::build_query(result_dir, query, index_file)
3. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]
4. └─data.table:::`[.data.table`(...)
── Error ('test-link_ethocope_metadata.R:73:3'): link_ethoscope_metadata with path ──
Error in ``[.data.table`(out, , `:=`(n, .N), keyby = key(out))`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. └─scopr::link_ethoscope_metadata(query, dir) at test-link_ethocope_metadata.R:73:3
2. ├─out[, `:=`(n, .N), keyby = key(out)]
3. └─data.table:::`[.data.table`(out, , `:=`(n, .N), keyby = key(out))
── Error ('test-link_ethocope_metadata.R:94:3'): link_ethoscope_metadata detect duplicated rows ──
Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-link_ethocope_metadata.R:94:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─scopr:::link_ethoscope_metadata(query, dir)
7. └─scopr:::build_query(result_dir, query, index_file)
8. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]
9. └─data.table:::`[.data.table`(...)
── Error ('test-link_ethoscope_metadata_remote.R:14:3'): link_ethoscope_metadata_remote with date and machine name ──
Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. └─scopr:::link_ethoscope_metadata_remote(...) at test-link_ethoscope_metadata_remote.R:14:3
2. └─scopr:::build_query(result_dir = remote_dir, query = query, index_file = index_file)
3. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]
4. └─data.table:::`[.data.table`(...)
── Error ('test-link_ethoscope_metadata_remote.R:51:3'): parse_query with date, machine name, and ROIs ──
Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. └─scopr:::link_ethoscope_metadata_remote(...) at test-link_ethoscope_metadata_remote.R:51:3
2. └─scopr:::build_query(result_dir = remote_dir, query = query, index_file = index_file)
3. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]
4. └─data.table:::`[.data.table`(...)
── Error ('test-load_ethoscope.R:11:3'): query ethoscopes functions ────────────
Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. └─scopr::link_ethoscope_metadata(metadata, dir) at test-load_ethoscope.R:11:3
2. └─scopr:::build_query(result_dir, query, index_file)
3. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]
4. └─data.table:::`[.data.table`(...)
── Error ('test-load_ethoscope.R:23:3'): query ethoscopes works ────────────────
Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. └─scopr::link_ethoscope_metadata(metadata, dir) at test-load_ethoscope.R:23:3
2. └─scopr:::build_query(result_dir, query, index_file)
3. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]
4. └─data.table:::`[.data.table`(...)
── Error ('test-load_ethoscope.R:36:3'): query ethoscopes works with multiple cores ──
Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. └─scopr::link_ethoscope_metadata(query, dir) at test-load_ethoscope.R:36:3
2. └─scopr:::build_query(result_dir, query, index_file)
3. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]
4. └─data.table:::`[.data.table`(...)
[ FAIL 17 | WARN 0 | SKIP 0 | PASS 17 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.3.5
Check: examples
Result: ERROR
Running examples in ‘scopr-Ex.R’ failed
The error most likely occurred in:
> ### Name: link_ethoscope_metadata_remote
> ### Title: Link ethoscope metadata to the matching result files
> ### Aliases: link_ethoscope_metadata_remote link_ethoscope_metadata
>
> ### ** Examples
>
> # Metadata with no region_id -> all regions will be loaded with the same metadata
> dir <- paste0(scopr_example_dir(), "/ethoscope_results/")
> data(no_region_id_metadata)
> metadata <- link_ethoscope_metadata(no_region_id_metadata, dir)
Error in `[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", :
attempt access index 6/6 in VECTOR_ELT
Calls: link_ethoscope_metadata -> build_query -> [ -> [.data.table
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.3.5
Check: tests
Result: ERROR
Running ‘testthat.R’ [8s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(scopr)
Loading required package: behavr
Loading required package: data.table
Attaching package: 'data.table'
The following object is masked from 'package:base':
%notin%
>
> test_check("scopr")
Saving _problems/test-build_query-12.R
Saving _problems/test-build_query-40.R
Saving _problems/test-build_query-53.R
Saving _problems/test-build_query-68.R
Saving _problems/test-build_query-83.R
machine_name date time test
1 E_014 2016-01-25 21:36:04 1
2 E_014 2016-02-17 <NA> 2
3 E_029 2016-01-25 <NA> 3
Saving _problems/test-build_query-110.R
Saving _problems/test-link_ethocope_metadata-6.R
Saving _problems/test-link_ethocope_metadata-24.R
Saving _problems/test-link_ethocope_metadata-39.R
Saving _problems/test-link_ethocope_metadata-60.R
Saving _problems/test-link_ethocope_metadata-73.R
Saving _problems/test-link_ethocope_metadata-94.R
Saving _problems/test-link_ethoscope_metadata_remote-18.R
Saving _problems/test-link_ethoscope_metadata_remote-55.R
Saving _problems/test-load_ethoscope-11.R
Saving _problems/test-load_ethoscope-23.R
Saving _problems/test-load_ethoscope-36.R
[ FAIL 17 | WARN 0 | SKIP 0 | PASS 17 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-build_query.R:12:3'): build query works when time is supplied ──
Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. └─scopr:::build_query(dir, query) at test-build_query.R:12:3
2. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]
3. └─data.table:::`[.data.table`(...)
── Error ('test-build_query.R:40:3'): build_query with date, machine name, and ROIs, and two experiments on the same date, but different times! ──
Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. └─scopr:::build_query(dir, query) at test-build_query.R:40:3
2. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]
3. └─data.table:::`[.data.table`(...)
── Error ('test-build_query.R:53:3'): build query works when only date supplied ──
Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-build_query.R:53:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─scopr:::build_query(dir, query)
7. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]
8. └─data.table:::`[.data.table`(...)
── Error ('test-build_query.R:68:3'): build query works when only date supplied and ROIs ──
Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-build_query.R:68:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─scopr:::build_query(dir, query)
7. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]
8. └─data.table:::`[.data.table`(...)
── Error ('test-build_query.R:83:3'): missing results! ─────────────────────────
Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-build_query.R:83:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─scopr:::build_query(dir, query)
7. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]
8. └─data.table:::`[.data.table`(...)
── Error ('test-build_query.R:110:3'): build query works datetime is a datetime, not a string (https://github.com/rethomics/scopr/issues/16) ──
Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. └─scopr:::build_query(dir, query) at test-build_query.R:110:3
2. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]
3. └─data.table:::`[.data.table`(...)
── Error ('test-link_ethocope_metadata.R:6:3'): link_ethoscope_metadata with single file ──
Error in ``[.data.table`(out, , `:=`(n, .N), keyby = key(out))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─scopr::link_ethoscope_metadata(test_file) at test-link_ethocope_metadata.R:6:3
2. ├─out[, `:=`(n, .N), keyby = key(out)]
3. └─data.table:::`[.data.table`(out, , `:=`(n, .N), keyby = key(out))
── Error ('test-link_ethocope_metadata.R:24:3'): link_ethoscope_metadata with date and machine name ──
Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. └─scopr::link_ethoscope_metadata(query, dir) at test-link_ethocope_metadata.R:24:3
2. └─scopr:::build_query(result_dir, query, index_file)
3. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]
4. └─data.table:::`[.data.table`(...)
── Error ('test-link_ethocope_metadata.R:39:3'): link_ethoscope_metadata with name of a text csv ──
Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. └─scopr::link_ethoscope_metadata(file, dir) at test-link_ethocope_metadata.R:39:3
2. └─scopr:::build_query(result_dir, query, index_file)
3. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]
4. └─data.table:::`[.data.table`(...)
── Error ('test-link_ethocope_metadata.R:60:3'): link_ethoscope_metadata with date, machine name, and ROIs ──
Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. └─scopr::link_ethoscope_metadata(query, dir) at test-link_ethocope_metadata.R:60:3
2. └─scopr:::build_query(result_dir, query, index_file)
3. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]
4. └─data.table:::`[.data.table`(...)
── Error ('test-link_ethocope_metadata.R:73:3'): link_ethoscope_metadata with path ──
Error in ``[.data.table`(out, , `:=`(n, .N), keyby = key(out))`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. └─scopr::link_ethoscope_metadata(query, dir) at test-link_ethocope_metadata.R:73:3
2. ├─out[, `:=`(n, .N), keyby = key(out)]
3. └─data.table:::`[.data.table`(out, , `:=`(n, .N), keyby = key(out))
── Error ('test-link_ethocope_metadata.R:94:3'): link_ethoscope_metadata detect duplicated rows ──
Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-link_ethocope_metadata.R:94:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─scopr:::link_ethoscope_metadata(query, dir)
7. └─scopr:::build_query(result_dir, query, index_file)
8. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]
9. └─data.table:::`[.data.table`(...)
── Error ('test-link_ethoscope_metadata_remote.R:14:3'): link_ethoscope_metadata_remote with date and machine name ──
Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. └─scopr:::link_ethoscope_metadata_remote(...) at test-link_ethoscope_metadata_remote.R:14:3
2. └─scopr:::build_query(result_dir = remote_dir, query = query, index_file = index_file)
3. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]
4. └─data.table:::`[.data.table`(...)
── Error ('test-link_ethoscope_metadata_remote.R:51:3'): parse_query with date, machine name, and ROIs ──
Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. └─scopr:::link_ethoscope_metadata_remote(...) at test-link_ethoscope_metadata_remote.R:51:3
2. └─scopr:::build_query(result_dir = remote_dir, query = query, index_file = index_file)
3. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]
4. └─data.table:::`[.data.table`(...)
── Error ('test-load_ethoscope.R:11:3'): query ethoscopes functions ────────────
Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. └─scopr::link_ethoscope_metadata(metadata, dir) at test-load_ethoscope.R:11:3
2. └─scopr:::build_query(result_dir, query, index_file)
3. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]
4. └─data.table:::`[.data.table`(...)
── Error ('test-load_ethoscope.R:23:3'): query ethoscopes works ────────────────
Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. └─scopr::link_ethoscope_metadata(metadata, dir) at test-load_ethoscope.R:23:3
2. └─scopr:::build_query(result_dir, query, index_file)
3. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]
4. └─data.table:::`[.data.table`(...)
── Error ('test-load_ethoscope.R:36:3'): query ethoscopes works with multiple cores ──
Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. └─scopr::link_ethoscope_metadata(query, dir) at test-load_ethoscope.R:36:3
2. └─scopr:::build_query(result_dir, query, index_file)
3. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]
4. └─data.table:::`[.data.table`(...)
[ FAIL 17 | WARN 0 | SKIP 0 | PASS 17 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.3.5
Check: tests
Result: ERROR
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(scopr)
Loading required package: behavr
Loading required package: data.table
Attaching package: 'data.table'
The following object is masked from 'package:base':
%notin%
>
> test_check("scopr")
Saving _problems/test-build_query-12.R
Saving _problems/test-build_query-40.R
Saving _problems/test-build_query-53.R
Saving _problems/test-build_query-68.R
Saving _problems/test-build_query-83.R
machine_name date time test
1 E_014 2016-01-25 21:36:04 1
2 E_014 2016-02-17 <NA> 2
3 E_029 2016-01-25 <NA> 3
Saving _problems/test-build_query-110.R
Saving _problems/test-link_ethocope_metadata-6.R
Saving _problems/test-link_ethocope_metadata-24.R
Saving _problems/test-link_ethocope_metadata-39.R
Saving _problems/test-link_ethocope_metadata-60.R
Saving _problems/test-link_ethocope_metadata-73.R
Saving _problems/test-link_ethocope_metadata-94.R
Saving _problems/test-link_ethoscope_metadata_remote-18.R
Saving _problems/test-link_ethoscope_metadata_remote-55.R
Saving _problems/test-load_ethoscope-11.R
Saving _problems/test-load_ethoscope-23.R
Saving _problems/test-load_ethoscope-36.R
[ FAIL 17 | WARN 0 | SKIP 0 | PASS 17 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-build_query.R:12:3'): build query works when time is supplied ──
Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. └─scopr:::build_query(dir, query) at test-build_query.R:12:3
2. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]
3. └─data.table:::`[.data.table`(...)
── Error ('test-build_query.R:40:3'): build_query with date, machine name, and ROIs, and two experiments on the same date, but different times! ──
Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. └─scopr:::build_query(dir, query) at test-build_query.R:40:3
2. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]
3. └─data.table:::`[.data.table`(...)
── Error ('test-build_query.R:53:3'): build query works when only date supplied ──
Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-build_query.R:53:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─scopr:::build_query(dir, query)
7. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]
8. └─data.table:::`[.data.table`(...)
── Error ('test-build_query.R:68:3'): build query works when only date supplied and ROIs ──
Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-build_query.R:68:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─scopr:::build_query(dir, query)
7. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]
8. └─data.table:::`[.data.table`(...)
── Error ('test-build_query.R:83:3'): missing results! ─────────────────────────
Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-build_query.R:83:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─scopr:::build_query(dir, query)
7. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]
8. └─data.table:::`[.data.table`(...)
── Error ('test-build_query.R:110:3'): build query works datetime is a datetime, not a string (https://github.com/rethomics/scopr/issues/16) ──
Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. └─scopr:::build_query(dir, query) at test-build_query.R:110:3
2. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]
3. └─data.table:::`[.data.table`(...)
── Error ('test-link_ethocope_metadata.R:6:3'): link_ethoscope_metadata with single file ──
Error in ``[.data.table`(out, , `:=`(n, .N), keyby = key(out))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─scopr::link_ethoscope_metadata(test_file) at test-link_ethocope_metadata.R:6:3
2. ├─out[, `:=`(n, .N), keyby = key(out)]
3. └─data.table:::`[.data.table`(out, , `:=`(n, .N), keyby = key(out))
── Error ('test-link_ethocope_metadata.R:24:3'): link_ethoscope_metadata with date and machine name ──
Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. └─scopr::link_ethoscope_metadata(query, dir) at test-link_ethocope_metadata.R:24:3
2. └─scopr:::build_query(result_dir, query, index_file)
3. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]
4. └─data.table:::`[.data.table`(...)
── Error ('test-link_ethocope_metadata.R:39:3'): link_ethoscope_metadata with name of a text csv ──
Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. └─scopr::link_ethoscope_metadata(file, dir) at test-link_ethocope_metadata.R:39:3
2. └─scopr:::build_query(result_dir, query, index_file)
3. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]
4. └─data.table:::`[.data.table`(...)
── Error ('test-link_ethocope_metadata.R:60:3'): link_ethoscope_metadata with date, machine name, and ROIs ──
Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. └─scopr::link_ethoscope_metadata(query, dir) at test-link_ethocope_metadata.R:60:3
2. └─scopr:::build_query(result_dir, query, index_file)
3. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]
4. └─data.table:::`[.data.table`(...)
── Error ('test-link_ethocope_metadata.R:73:3'): link_ethoscope_metadata with path ──
Error in ``[.data.table`(out, , `:=`(n, .N), keyby = key(out))`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. └─scopr::link_ethoscope_metadata(query, dir) at test-link_ethocope_metadata.R:73:3
2. ├─out[, `:=`(n, .N), keyby = key(out)]
3. └─data.table:::`[.data.table`(out, , `:=`(n, .N), keyby = key(out))
── Error ('test-link_ethocope_metadata.R:94:3'): link_ethoscope_metadata detect duplicated rows ──
Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-link_ethocope_metadata.R:94:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─scopr:::link_ethoscope_metadata(query, dir)
7. └─scopr:::build_query(result_dir, query, index_file)
8. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]
9. └─data.table:::`[.data.table`(...)
── Error ('test-link_ethoscope_metadata_remote.R:14:3'): link_ethoscope_metadata_remote with date and machine name ──
Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. └─scopr:::link_ethoscope_metadata_remote(...) at test-link_ethoscope_metadata_remote.R:14:3
2. └─scopr:::build_query(result_dir = remote_dir, query = query, index_file = index_file)
3. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]
4. └─data.table:::`[.data.table`(...)
── Error ('test-link_ethoscope_metadata_remote.R:51:3'): parse_query with date, machine name, and ROIs ──
Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. └─scopr:::link_ethoscope_metadata_remote(...) at test-link_ethoscope_metadata_remote.R:51:3
2. └─scopr:::build_query(result_dir = remote_dir, query = query, index_file = index_file)
3. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]
4. └─data.table:::`[.data.table`(...)
── Error ('test-load_ethoscope.R:11:3'): query ethoscopes functions ────────────
Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. └─scopr::link_ethoscope_metadata(metadata, dir) at test-load_ethoscope.R:11:3
2. └─scopr:::build_query(result_dir, query, index_file)
3. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]
4. └─data.table:::`[.data.table`(...)
── Error ('test-load_ethoscope.R:23:3'): query ethoscopes works ────────────────
Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. └─scopr::link_ethoscope_metadata(metadata, dir) at test-load_ethoscope.R:23:3
2. └─scopr:::build_query(result_dir, query, index_file)
3. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]
4. └─data.table:::`[.data.table`(...)
── Error ('test-load_ethoscope.R:36:3'): query ethoscopes works with multiple cores ──
Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. └─scopr::link_ethoscope_metadata(query, dir) at test-load_ethoscope.R:36:3
2. └─scopr:::build_query(result_dir, query, index_file)
3. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]
4. └─data.table:::`[.data.table`(...)
[ FAIL 17 | WARN 0 | SKIP 0 | PASS 17 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Current CRAN status: ERROR: 3, OK: 10
Version: 0.3.1
Check: examples
Result: ERROR
Running examples in ‘sleepr-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bout_analysis
> ### Title: Find "bouts" in categorical time series
> ### Aliases: bout_analysis
>
> ### ** Examples
>
> # Bout analysis on binary variable:
> dt <- toy_dam_data()
Error in `[.data.table`(out, , `:=`(activity, abs(c(0, diff(sign(0.5 - :
attempt access index 5/5 in VECTOR_ELT
Calls: toy_dam_data -> [ -> [.behavr -> NextMethod -> [.data.table
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.3.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [6s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(sleepr)
Loading required package: behavr
Loading required package: data.table
Attaching package: 'data.table'
The following object is masked from 'package:base':
%notin%
>
> test_check("sleepr")
Saving _problems/test-max_velocity_detector-10.R
Saving _problems/test-max_velocity_detector-22.R
Saving _problems/test-prepare_data_for_motion_detector-14.R
Saving _problems/test-sleep_annotation-6.R
Saving _problems/test-sleep_annotation-31.R
Saving _problems/test-virtual_beam_cross_detector-10.R
[ FAIL 6 | WARN 0 | SKIP 1 | PASS 25 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test-bout_analysis.R:3:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-max_velocity_detector.R:10:3'): max_velocity_detector works ────
Error in ``[.data.table`(data, , `:=`(n_points, .N), by = t_w)`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. └─sleepr::max_velocity_detector(data, 10) at test-max_velocity_detector.R:10:3
2. └─sleepr:::prepare_data_for_motion_detector(...)
3. └─sleepr:::curate_sparse_roi_data(d)
4. ├─data[, `:=`(n_points, .N), by = t_w]
5. └─data.table:::`[.data.table`(data, , `:=`(n_points, .N), by = t_w)
── Error ('test-max_velocity_detector.R:21:3'): max_velocity_detector wans when no interaction and masking ──
Error in ``[.data.table`(data, , `:=`(n_points, .N), by = t_w)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-max_velocity_detector.R:21:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─sleepr::max_velocity_detector(data, 10)
7. └─sleepr:::prepare_data_for_motion_detector(...)
8. └─sleepr:::curate_sparse_roi_data(d)
9. ├─data[, `:=`(n_points, .N), by = t_w]
10. └─data.table:::`[.data.table`(data, , `:=`(n_points, .N), by = t_w)
── Error ('test-prepare_data_for_motion_detector.R:11:3'): prepare_data_for_motion_detector works ──
Error in ``[.data.table`(data, , `:=`(n_points, .N), by = t_w)`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. └─sleepr:::prepare_data_for_motion_detector(...) at test-prepare_data_for_motion_detector.R:11:3
2. └─sleepr:::curate_sparse_roi_data(d)
3. ├─data[, `:=`(n_points, .N), by = t_w]
4. └─data.table:::`[.data.table`(data, , `:=`(n_points, .N), by = t_w)
── Error ('test-sleep_annotation.R:6:3'): sleep_annotation works return expected results ──
Error in ``[.data.table`(data, , `:=`(n_points, .N), by = t_w)`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. └─sleepr::sleep_annotation(data, motion_detector_FUN = virtual_beam_cross_detector) at test-sleep_annotation.R:6:3
2. └─sleepr (local) wrapped(data)
3. └─sleepr (local) motion_detector_FUN(d, time_window_length, ...)
4. └─sleepr:::prepare_data_for_motion_detector(...)
5. └─sleepr:::curate_sparse_roi_data(d)
6. ├─data[, `:=`(n_points, .N), by = t_w]
7. └─data.table:::`[.data.table`(data, , `:=`(n_points, .N), by = t_w)
── Error ('test-sleep_annotation.R:31:3'): sleep_annotation works for single or multiple animals ──
Error in ``[.data.table`(data, , `:=`(n_points, .N), by = t_w)`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. └─sleepr::sleep_annotation(data[id == 1][, -"id", with = F], motion_detector_FUN = virtual_beam_cross_detector) at test-sleep_annotation.R:31:3
2. └─sleepr (local) wrapped(data)
3. └─sleepr (local) motion_detector_FUN(d, time_window_length, ...)
4. └─sleepr:::prepare_data_for_motion_detector(...)
5. └─sleepr:::curate_sparse_roi_data(d)
6. ├─data[, `:=`(n_points, .N), by = t_w]
7. └─data.table:::`[.data.table`(data, , `:=`(n_points, .N), by = t_w)
── Error ('test-virtual_beam_cross_detector.R:10:3'): virtual_beam_cross_detector works ──
Error in ``[.data.table`(data, , `:=`(n_points, .N), by = t_w)`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. └─sleepr::virtual_beam_cross_detector(data, 10) at test-virtual_beam_cross_detector.R:10:3
2. └─sleepr:::prepare_data_for_motion_detector(...)
3. └─sleepr:::curate_sparse_roi_data(d)
4. ├─data[, `:=`(n_points, .N), by = t_w]
5. └─data.table:::`[.data.table`(data, , `:=`(n_points, .N), by = t_w)
[ FAIL 6 | WARN 0 | SKIP 1 | PASS 25 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.3.1
Check: examples
Result: ERROR
Running examples in ‘sleepr-Ex.R’ failed
The error most likely occurred in:
> ### Name: bout_analysis
> ### Title: Find "bouts" in categorical time series
> ### Aliases: bout_analysis
>
> ### ** Examples
>
> # Bout analysis on binary variable:
> dt <- toy_dam_data()
Error in `[.data.table`(out, , `:=`(activity, abs(c(0, diff(sign(0.5 - :
attempt access index 5/5 in VECTOR_ELT
Calls: toy_dam_data -> [ -> [.behavr -> NextMethod -> [.data.table
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.3.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [9s/11s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(sleepr)
Loading required package: behavr
Loading required package: data.table
Attaching package: 'data.table'
The following object is masked from 'package:base':
%notin%
>
> test_check("sleepr")
Saving _problems/test-max_velocity_detector-10.R
Saving _problems/test-max_velocity_detector-22.R
Saving _problems/test-prepare_data_for_motion_detector-14.R
Saving _problems/test-sleep_annotation-6.R
Saving _problems/test-sleep_annotation-31.R
Saving _problems/test-virtual_beam_cross_detector-10.R
[ FAIL 6 | WARN 0 | SKIP 1 | PASS 25 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test-bout_analysis.R:3:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-max_velocity_detector.R:10:3'): max_velocity_detector works ────
Error in ``[.data.table`(data, , `:=`(n_points, .N), by = t_w)`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. └─sleepr::max_velocity_detector(data, 10) at test-max_velocity_detector.R:10:3
2. └─sleepr:::prepare_data_for_motion_detector(...)
3. └─sleepr:::curate_sparse_roi_data(d)
4. ├─data[, `:=`(n_points, .N), by = t_w]
5. └─data.table:::`[.data.table`(data, , `:=`(n_points, .N), by = t_w)
── Error ('test-max_velocity_detector.R:21:3'): max_velocity_detector wans when no interaction and masking ──
Error in ``[.data.table`(data, , `:=`(n_points, .N), by = t_w)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-max_velocity_detector.R:21:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─sleepr::max_velocity_detector(data, 10)
7. └─sleepr:::prepare_data_for_motion_detector(...)
8. └─sleepr:::curate_sparse_roi_data(d)
9. ├─data[, `:=`(n_points, .N), by = t_w]
10. └─data.table:::`[.data.table`(data, , `:=`(n_points, .N), by = t_w)
── Error ('test-prepare_data_for_motion_detector.R:11:3'): prepare_data_for_motion_detector works ──
Error in ``[.data.table`(data, , `:=`(n_points, .N), by = t_w)`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. └─sleepr:::prepare_data_for_motion_detector(...) at test-prepare_data_for_motion_detector.R:11:3
2. └─sleepr:::curate_sparse_roi_data(d)
3. ├─data[, `:=`(n_points, .N), by = t_w]
4. └─data.table:::`[.data.table`(data, , `:=`(n_points, .N), by = t_w)
── Error ('test-sleep_annotation.R:6:3'): sleep_annotation works return expected results ──
Error in ``[.data.table`(data, , `:=`(n_points, .N), by = t_w)`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. └─sleepr::sleep_annotation(data, motion_detector_FUN = virtual_beam_cross_detector) at test-sleep_annotation.R:6:3
2. └─sleepr (local) wrapped(data)
3. └─sleepr (local) motion_detector_FUN(d, time_window_length, ...)
4. └─sleepr:::prepare_data_for_motion_detector(...)
5. └─sleepr:::curate_sparse_roi_data(d)
6. ├─data[, `:=`(n_points, .N), by = t_w]
7. └─data.table:::`[.data.table`(data, , `:=`(n_points, .N), by = t_w)
── Error ('test-sleep_annotation.R:31:3'): sleep_annotation works for single or multiple animals ──
Error in ``[.data.table`(data, , `:=`(n_points, .N), by = t_w)`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. └─sleepr::sleep_annotation(data[id == 1][, -"id", with = F], motion_detector_FUN = virtual_beam_cross_detector) at test-sleep_annotation.R:31:3
2. └─sleepr (local) wrapped(data)
3. └─sleepr (local) motion_detector_FUN(d, time_window_length, ...)
4. └─sleepr:::prepare_data_for_motion_detector(...)
5. └─sleepr:::curate_sparse_roi_data(d)
6. ├─data[, `:=`(n_points, .N), by = t_w]
7. └─data.table:::`[.data.table`(data, , `:=`(n_points, .N), by = t_w)
── Error ('test-virtual_beam_cross_detector.R:10:3'): virtual_beam_cross_detector works ──
Error in ``[.data.table`(data, , `:=`(n_points, .N), by = t_w)`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. └─sleepr::virtual_beam_cross_detector(data, 10) at test-virtual_beam_cross_detector.R:10:3
2. └─sleepr:::prepare_data_for_motion_detector(...)
3. └─sleepr:::curate_sparse_roi_data(d)
4. ├─data[, `:=`(n_points, .N), by = t_w]
5. └─data.table:::`[.data.table`(data, , `:=`(n_points, .N), by = t_w)
[ FAIL 6 | WARN 0 | SKIP 1 | PASS 25 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.3.1
Check: tests
Result: ERROR
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(sleepr)
Loading required package: behavr
Loading required package: data.table
Attaching package: 'data.table'
The following object is masked from 'package:base':
%notin%
>
> test_check("sleepr")
Saving _problems/test-max_velocity_detector-10.R
Saving _problems/test-max_velocity_detector-22.R
Saving _problems/test-prepare_data_for_motion_detector-14.R
Saving _problems/test-sleep_annotation-6.R
Saving _problems/test-sleep_annotation-31.R
Saving _problems/test-virtual_beam_cross_detector-10.R
[ FAIL 6 | WARN 0 | SKIP 1 | PASS 25 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test-bout_analysis.R:3:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-max_velocity_detector.R:10:3'): max_velocity_detector works ────
Error in ``[.data.table`(data, , `:=`(n_points, .N), by = t_w)`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. └─sleepr::max_velocity_detector(data, 10) at test-max_velocity_detector.R:10:3
2. └─sleepr:::prepare_data_for_motion_detector(...)
3. └─sleepr:::curate_sparse_roi_data(d)
4. ├─data[, `:=`(n_points, .N), by = t_w]
5. └─data.table:::`[.data.table`(data, , `:=`(n_points, .N), by = t_w)
── Error ('test-max_velocity_detector.R:21:3'): max_velocity_detector wans when no interaction and masking ──
Error in ``[.data.table`(data, , `:=`(n_points, .N), by = t_w)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-max_velocity_detector.R:21:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─sleepr::max_velocity_detector(data, 10)
7. └─sleepr:::prepare_data_for_motion_detector(...)
8. └─sleepr:::curate_sparse_roi_data(d)
9. ├─data[, `:=`(n_points, .N), by = t_w]
10. └─data.table:::`[.data.table`(data, , `:=`(n_points, .N), by = t_w)
── Error ('test-prepare_data_for_motion_detector.R:11:3'): prepare_data_for_motion_detector works ──
Error in ``[.data.table`(data, , `:=`(n_points, .N), by = t_w)`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. └─sleepr:::prepare_data_for_motion_detector(...) at test-prepare_data_for_motion_detector.R:11:3
2. └─sleepr:::curate_sparse_roi_data(d)
3. ├─data[, `:=`(n_points, .N), by = t_w]
4. └─data.table:::`[.data.table`(data, , `:=`(n_points, .N), by = t_w)
── Error ('test-sleep_annotation.R:6:3'): sleep_annotation works return expected results ──
Error in ``[.data.table`(data, , `:=`(n_points, .N), by = t_w)`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. └─sleepr::sleep_annotation(data, motion_detector_FUN = virtual_beam_cross_detector) at test-sleep_annotation.R:6:3
2. └─sleepr (local) wrapped(data)
3. └─sleepr (local) motion_detector_FUN(d, time_window_length, ...)
4. └─sleepr:::prepare_data_for_motion_detector(...)
5. └─sleepr:::curate_sparse_roi_data(d)
6. ├─data[, `:=`(n_points, .N), by = t_w]
7. └─data.table:::`[.data.table`(data, , `:=`(n_points, .N), by = t_w)
── Error ('test-sleep_annotation.R:31:3'): sleep_annotation works for single or multiple animals ──
Error in ``[.data.table`(data, , `:=`(n_points, .N), by = t_w)`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. └─sleepr::sleep_annotation(data[id == 1][, -"id", with = F], motion_detector_FUN = virtual_beam_cross_detector) at test-sleep_annotation.R:31:3
2. └─sleepr (local) wrapped(data)
3. └─sleepr (local) motion_detector_FUN(d, time_window_length, ...)
4. └─sleepr:::prepare_data_for_motion_detector(...)
5. └─sleepr:::curate_sparse_roi_data(d)
6. ├─data[, `:=`(n_points, .N), by = t_w]
7. └─data.table:::`[.data.table`(data, , `:=`(n_points, .N), by = t_w)
── Error ('test-virtual_beam_cross_detector.R:10:3'): virtual_beam_cross_detector works ──
Error in ``[.data.table`(data, , `:=`(n_points, .N), by = t_w)`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. └─sleepr::virtual_beam_cross_detector(data, 10) at test-virtual_beam_cross_detector.R:10:3
2. └─sleepr:::prepare_data_for_motion_detector(...)
3. └─sleepr:::curate_sparse_roi_data(d)
4. ├─data[, `:=`(n_points, .N), by = t_w]
5. └─data.table:::`[.data.table`(data, , `:=`(n_points, .N), by = t_w)
[ FAIL 6 | WARN 0 | SKIP 1 | PASS 25 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Current CRAN status: ERROR: 3, OK: 10
Version: 0.3.6
Check: examples
Result: ERROR
Running examples in ‘zeitgebr-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: find_peaks
> ### Title: Find peaks in a periodogram
> ### Aliases: find_peaks
>
> ### ** Examples
>
> data(dams_sample)
> # only a half of the individuals for the sake of the example
> dt <- dams_sample[xmv(region_id) %in% (1:16 * 2)]
> per_dt_xs <- periodogram(activity, dt, FUN = chi_sq_periodogram)
> per_dt_xs_with_peaks <- find_peaks(per_dt_xs)
Error in `[.data.table`(out, , `:=`(peak, find_peaks_wapped(.SD, n_peaks = n_peaks)), :
attempt access index 5/5 in VECTOR_ELT
Calls: find_peaks -> [ -> [.behavr -> NextMethod -> [.data.table
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.3.6
Check: tests
Result: ERROR
Running ‘testthat.R’ [125s/54s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(zeitgebr)
Loading required package: behavr
Loading required package: data.table
Attaching package: 'data.table'
The following object is masked from 'package:base':
%notin%
>
> test_check("zeitgebr")
Saving _problems/test-find_peaks-6.R
[ FAIL 1 | WARN 0 | SKIP 4 | PASS 5 ]
══ Skipped tests (4) ═══════════════════════════════════════════════════════════
• empty test (4): 'test-chi_sq_periodogram.R:3:1',
'test-cwt_periodogram.R:3:1', 'test-ls_periodogram.R:3:1',
'test-periodogram.R:3:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-find_peaks.R:6:3'): find_peaks works in normal conditions ──────
Error in ``[.data.table`(out, , `:=`(peak, find_peaks_wapped(.SD, n_peaks = n_peaks)), by = c(data.table::key(out)))`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─zeitgebr::find_peaks(pdt) at test-find_peaks.R:6:3
2. ├─...[]
3. ├─behavr:::`[.behavr`(...)
4. ├─base::NextMethod()
5. └─data.table:::`[.data.table`(...)
[ FAIL 1 | WARN 0 | SKIP 4 | PASS 5 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.3.6
Check: examples
Result: ERROR
Running examples in ‘zeitgebr-Ex.R’ failed
The error most likely occurred in:
> ### Name: find_peaks
> ### Title: Find peaks in a periodogram
> ### Aliases: find_peaks
>
> ### ** Examples
>
> data(dams_sample)
> # only a half of the individuals for the sake of the example
> dt <- dams_sample[xmv(region_id) %in% (1:16 * 2)]
> per_dt_xs <- periodogram(activity, dt, FUN = chi_sq_periodogram)
> per_dt_xs_with_peaks <- find_peaks(per_dt_xs)
Error in `[.data.table`(out, , `:=`(peak, find_peaks_wapped(.SD, n_peaks = n_peaks)), :
attempt access index 5/5 in VECTOR_ELT
Calls: find_peaks -> [ -> [.behavr -> NextMethod -> [.data.table
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.3.6
Check: tests
Result: ERROR
Running ‘testthat.R’ [254s/181s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(zeitgebr)
Loading required package: behavr
Loading required package: data.table
Attaching package: 'data.table'
The following object is masked from 'package:base':
%notin%
>
> test_check("zeitgebr")
Saving _problems/test-find_peaks-6.R
[ FAIL 1 | WARN 0 | SKIP 4 | PASS 5 ]
══ Skipped tests (4) ═══════════════════════════════════════════════════════════
• empty test (4): 'test-chi_sq_periodogram.R:3:1',
'test-cwt_periodogram.R:3:1', 'test-ls_periodogram.R:3:1',
'test-periodogram.R:3:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-find_peaks.R:6:3'): find_peaks works in normal conditions ──────
Error in ``[.data.table`(out, , `:=`(peak, find_peaks_wapped(.SD, n_peaks = n_peaks)), by = c(data.table::key(out)))`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─zeitgebr::find_peaks(pdt) at test-find_peaks.R:6:3
2. ├─...[]
3. ├─behavr:::`[.behavr`(...)
4. ├─base::NextMethod()
5. └─data.table:::`[.data.table`(...)
[ FAIL 1 | WARN 0 | SKIP 4 | PASS 5 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.3.6
Check: tests
Result: ERROR
Running ‘testthat.R’ [333s/357s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(zeitgebr)
Loading required package: behavr
Loading required package: data.table
Attaching package: 'data.table'
The following object is masked from 'package:base':
%notin%
>
> test_check("zeitgebr")
Saving _problems/test-find_peaks-6.R
[ FAIL 1 | WARN 0 | SKIP 4 | PASS 5 ]
══ Skipped tests (4) ═══════════════════════════════════════════════════════════
• empty test (4): 'test-chi_sq_periodogram.R:3:1',
'test-cwt_periodogram.R:3:1', 'test-ls_periodogram.R:3:1',
'test-periodogram.R:3:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-find_peaks.R:6:3'): find_peaks works in normal conditions ──────
Error in ``[.data.table`(out, , `:=`(peak, find_peaks_wapped(.SD, n_peaks = n_peaks)), by = c(data.table::key(out)))`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─zeitgebr::find_peaks(pdt) at test-find_peaks.R:6:3
2. ├─...[]
3. ├─behavr:::`[.behavr`(...)
4. ├─base::NextMethod()
5. └─data.table:::`[.data.table`(...)
[ FAIL 1 | WARN 0 | SKIP 4 | PASS 5 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc