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Last updated on 2026-07-04 17:51:40 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.4.0 | 8.72 | 74.22 | 82.94 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.4.0 | 6.87 | 56.61 | 63.48 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.4.0 | 13.00 | 111.36 | 124.36 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 0.4.0 | 13.00 | 107.67 | 120.67 | OK | |
| r-devel-windows-x86_64 | 0.4.0 | 11.00 | 87.00 | 98.00 | OK | |
| r-patched-linux-x86_64 | 0.4.0 | 8.40 | 67.84 | 76.24 | OK | |
| r-release-linux-x86_64 | 0.4.0 | OK | ||||
| r-release-macos-arm64 | 0.4.0 | 2.00 | 26.00 | 28.00 | OK | |
| r-release-macos-x86_64 | 0.4.0 | 7.00 | 67.00 | 74.00 | OK | |
| r-release-windows-x86_64 | 0.4.0 | 12.00 | 81.00 | 93.00 | OK | |
| r-oldrel-macos-arm64 | 0.4.0 | 2.00 | 24.00 | 26.00 | ERROR | |
| r-oldrel-macos-x86_64 | 0.4.0 | 7.00 | 69.00 | 76.00 | ERROR | |
| r-oldrel-windows-x86_64 | 0.4.0 | 14.00 | 100.00 | 114.00 | ERROR |
Version: 0.4.0
Check: R code for possible problems
Result: NOTE
listPOsets: no visible global function definition for ‘%notin%’
Undefined global functions or variables:
%notin%
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Version: 0.4.0
Check: examples
Result: ERROR
Running examples in ‘pedbuildr-Ex.R’ failed
The error most likely occurred in:
> ### Name: buildPeds
> ### Title: Build a list of pedigrees
> ### Aliases: buildPeds
>
> ### ** Examples
>
> # Two individuals + 1 extra
> plist = buildPeds(1:2, extra = 1, age = "1>2")
Pedigree parameters:
ID labels: 1, 2
Sex: 1, 1
Extra: 1
Age info: 1>2
Known PO: -
Known non-PO: -
No children: -
Connected only: TRUE
Symmetry filter: TRUE
Max inbreeding: 0.0625
Linear inbreeding: FALSE
Building pedigree list:
All 2 + 0 extra: 1 solutions | 2 candidates (0.00018 secs)
All 2 + 1 extra: 2 solutions | 2 candidates | 2 duplicates removed (0.000673 secs)
Total solutions: 3
Converting to ped
Excessive inbreeding: 0
Time used: 0.00193 secs
> plot(plist)
>
> # Allow disconnected
> plist2 = buildPeds(1:2, extra = 1, age = "1>2", connected = FALSE)
Pedigree parameters:
ID labels: 1, 2
Sex: 1, 1
Extra: 1
Age info: 1>2
Known PO: -
Known non-PO: -
No children: -
Connected only: FALSE
Symmetry filter: TRUE
Max inbreeding: 0.0625
Linear inbreeding: FALSE
Building pedigree list:
All 2 + 0 extra: 2 solutions | 2 candidates (0.00016 secs)
All 2 + 1 extra: 2 solutions | 2 candidates | 2 duplicates removed (0.00058 secs)
Total solutions: 4
Converting to ped
Excessive inbreeding: 0
Time used: 0.0014 secs
> plot(plist2, frames = TRUE)
>
> # Note that full sibs require 2 extras
> plist3 = buildPeds(1:2, extra = 2, age = "1>2")
Pedigree parameters:
ID labels: 1, 2
Sex: 1, 1
Extra: 2
Age info: 1>2
Known PO: -
Known non-PO: -
No children: -
Connected only: TRUE
Symmetry filter: TRUE
Max inbreeding: 0.0625
Linear inbreeding: FALSE
Building pedigree list:
All 2 + 0 extra: 1 solutions | 2 candidates (0.00017 secs)
All 2 + 1 extra: 2 solutions | 12 candidates | 11 duplicates removed (0.00096 secs)
All 2 + 2 extra: 6 solutions | 6 candidates | 11 duplicates removed (0.00441 secs)
Total solutions: 9
Converting to ped
Excessive inbreeding: 2
Time used: 0.00616 secs
> plot(plist3)
>
> # With 2 extras, allowing any inbreeding
> plist4 = buildPeds(1:2, extra = 2, age = "1>2", maxInbreeding = 1)
Pedigree parameters:
ID labels: 1, 2
Sex: 1, 1
Extra: 2
Age info: 1>2
Known PO: -
Known non-PO: -
No children: -
Connected only: TRUE
Symmetry filter: TRUE
Max inbreeding: 1
Linear inbreeding: FALSE
Building pedigree list:
All 2 + 0 extra: 1 solutions | 2 candidates (0.000202 secs)
All 2 + 1 extra: 2 solutions | 12 candidates | 11 duplicates removed (0.00106 secs)
All 2 + 2 extra: 6 solutions | 6 candidates | 11 duplicates removed (0.00434 secs)
Total solutions: 9
Converting to ped
Time used: 0.00464 secs
> plot(plist4)
>
> # Full sibs are also included when `extra = "parents"`
> plist5 = buildPeds(1:2, extra = "parents", age = "1>2")
Pedigree parameters:
ID labels: 1, 2
Sex: 1, 1
Extra: parents
Age info: 1>2
Known PO: -
Known non-PO: -
No children: -
Connected only: TRUE
Symmetry filter: TRUE
Max inbreeding: 0.0625
Linear inbreeding: FALSE
Building pedigree list:
Error in allPOchar %notin% c(knownPOchar, notPOchar) :
could not find function "%notin%"
Calls: buildPeds -> buildPedsParents -> listPOsets
Execution halted
Flavor: r-oldrel-macos-arm64
Version: 0.4.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(pedbuildr)
Loading required package: pedtools
>
> test_check("pedbuildr")
Saving _problems/test-buildPeds-9.R
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 10 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-buildPeds.R:8:3'): buildPeds cathces errors ──────────────────
`bp(1:3, sex = 1:3, verb = F)` threw an error with unexpected message.
Expected match: "Illegal elements found in `sex`"
Actual message: "could not find function \"%notin%\""
Backtrace:
▆
1. ├─testthat::expect_error(bp(1:3, sex = 1:3, verb = F), "Illegal elements found in `sex`") at test-buildPeds.R:8:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─pedbuildr (local) bp(1:3, sex = 1:3, verb = F)
7. └─pedbuildr::buildPeds(ids, sex, verbose = verb, ...) at test-buildPeds.R:2:3
8. └─pedbuildr:::buildPedsParents(...)
9. └─pedbuildr:::listPOsets(...)
── Error ('test-buildPeds.R:17:3'): buildPeds() parses age correctly ───────────
Error in `allPOchar %notin% c(knownPOchar, notPOchar)`: could not find function "%notin%"
Backtrace:
▆
1. ├─testthat::expect_output(bp(1:3, age = c(1, 1, 1)), "Age info: -") at test-buildPeds.R:17:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─testthat::capture_output_lines(code, print, width = width)
5. │ │ └─testthat:::eval_with_output(code, print = print, width = width)
6. │ │ ├─withr::with_output_sink(path, withVisible(code))
7. │ │ │ └─base::force(code)
8. │ │ └─base::withVisible(code)
9. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
10. └─pedbuildr (local) bp(1:3, age = c(1, 1, 1))
11. └─pedbuildr::buildPeds(ids, sex, verbose = verb, ...) at test-buildPeds.R:2:3
12. └─pedbuildr:::buildPedsParents(...)
13. └─pedbuildr:::listPOsets(...)
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 10 ]
Error:
! Test failures.
Execution halted
Flavor: r-oldrel-macos-arm64
Version: 0.4.0
Check: examples
Result: ERROR
Running examples in ‘pedbuildr-Ex.R’ failed
The error most likely occurred in:
> ### Name: buildPeds
> ### Title: Build a list of pedigrees
> ### Aliases: buildPeds
>
> ### ** Examples
>
> # Two individuals + 1 extra
> plist = buildPeds(1:2, extra = 1, age = "1>2")
Pedigree parameters:
ID labels: 1, 2
Sex: 1, 1
Extra: 1
Age info: 1>2
Known PO: -
Known non-PO: -
No children: -
Connected only: TRUE
Symmetry filter: TRUE
Max inbreeding: 0.0625
Linear inbreeding: FALSE
Building pedigree list:
All 2 + 0 extra: 1 solutions | 2 candidates (0.000467 secs)
All 2 + 1 extra: 2 solutions | 2 candidates | 2 duplicates removed (0.0021 secs)
Total solutions: 3
Converting to ped
Excessive inbreeding: 0
Time used: 0.00601 secs
> plot(plist)
>
> # Allow disconnected
> plist2 = buildPeds(1:2, extra = 1, age = "1>2", connected = FALSE)
Pedigree parameters:
ID labels: 1, 2
Sex: 1, 1
Extra: 1
Age info: 1>2
Known PO: -
Known non-PO: -
No children: -
Connected only: FALSE
Symmetry filter: TRUE
Max inbreeding: 0.0625
Linear inbreeding: FALSE
Building pedigree list:
All 2 + 0 extra: 2 solutions | 2 candidates (0.000418 secs)
All 2 + 1 extra: 2 solutions | 2 candidates | 2 duplicates removed (0.00173 secs)
Total solutions: 4
Converting to ped
Excessive inbreeding: 0
Time used: 0.00427 secs
> plot(plist2, frames = TRUE)
>
> # Note that full sibs require 2 extras
> plist3 = buildPeds(1:2, extra = 2, age = "1>2")
Pedigree parameters:
ID labels: 1, 2
Sex: 1, 1
Extra: 2
Age info: 1>2
Known PO: -
Known non-PO: -
No children: -
Connected only: TRUE
Symmetry filter: TRUE
Max inbreeding: 0.0625
Linear inbreeding: FALSE
Building pedigree list:
All 2 + 0 extra: 1 solutions | 2 candidates (0.000502 secs)
All 2 + 1 extra: 2 solutions | 12 candidates | 11 duplicates removed (0.00461 secs)
All 2 + 2 extra: 6 solutions | 6 candidates | 11 duplicates removed (0.0181 secs)
Total solutions: 9
Converting to ped
Excessive inbreeding: 2
Time used: 0.025 secs
> plot(plist3)
>
> # With 2 extras, allowing any inbreeding
> plist4 = buildPeds(1:2, extra = 2, age = "1>2", maxInbreeding = 1)
Pedigree parameters:
ID labels: 1, 2
Sex: 1, 1
Extra: 2
Age info: 1>2
Known PO: -
Known non-PO: -
No children: -
Connected only: TRUE
Symmetry filter: TRUE
Max inbreeding: 1
Linear inbreeding: FALSE
Building pedigree list:
All 2 + 0 extra: 1 solutions | 2 candidates (0.000467 secs)
All 2 + 1 extra: 2 solutions | 12 candidates | 11 duplicates removed (0.00337 secs)
All 2 + 2 extra: 6 solutions | 6 candidates | 11 duplicates removed (0.0148 secs)
Total solutions: 9
Converting to ped
Time used: 0.0159 secs
> plot(plist4)
>
> # Full sibs are also included when `extra = "parents"`
> plist5 = buildPeds(1:2, extra = "parents", age = "1>2")
Pedigree parameters:
ID labels: 1, 2
Sex: 1, 1
Extra: parents
Age info: 1>2
Known PO: -
Known non-PO: -
No children: -
Connected only: TRUE
Symmetry filter: TRUE
Max inbreeding: 0.0625
Linear inbreeding: FALSE
Building pedigree list:
Error in allPOchar %notin% c(knownPOchar, notPOchar) :
could not find function "%notin%"
Calls: buildPeds -> buildPedsParents -> listPOsets
Execution halted
Flavor: r-oldrel-macos-x86_64
Version: 0.4.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(pedbuildr)
Loading required package: pedtools
>
> test_check("pedbuildr")
Saving _problems/test-buildPeds-9.R
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 10 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-buildPeds.R:8:3'): buildPeds cathces errors ──────────────────
`bp(1:3, sex = 1:3, verb = F)` threw an error with unexpected message.
Expected match: "Illegal elements found in `sex`"
Actual message: "could not find function \"%notin%\""
Backtrace:
▆
1. ├─testthat::expect_error(bp(1:3, sex = 1:3, verb = F), "Illegal elements found in `sex`") at test-buildPeds.R:8:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─pedbuildr (local) bp(1:3, sex = 1:3, verb = F)
7. └─pedbuildr::buildPeds(ids, sex, verbose = verb, ...) at test-buildPeds.R:2:3
8. └─pedbuildr:::buildPedsParents(...)
9. └─pedbuildr:::listPOsets(...)
── Error ('test-buildPeds.R:17:3'): buildPeds() parses age correctly ───────────
Error in `allPOchar %notin% c(knownPOchar, notPOchar)`: could not find function "%notin%"
Backtrace:
▆
1. ├─testthat::expect_output(bp(1:3, age = c(1, 1, 1)), "Age info: -") at test-buildPeds.R:17:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─testthat::capture_output_lines(code, print, width = width)
5. │ │ └─testthat:::eval_with_output(code, print = print, width = width)
6. │ │ ├─withr::with_output_sink(path, withVisible(code))
7. │ │ │ └─base::force(code)
8. │ │ └─base::withVisible(code)
9. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
10. └─pedbuildr (local) bp(1:3, age = c(1, 1, 1))
11. └─pedbuildr::buildPeds(ids, sex, verbose = verb, ...) at test-buildPeds.R:2:3
12. └─pedbuildr:::buildPedsParents(...)
13. └─pedbuildr:::listPOsets(...)
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 10 ]
Error:
! Test failures.
Execution halted
Flavor: r-oldrel-macos-x86_64
Version: 0.4.0
Check: examples
Result: ERROR
Running examples in 'pedbuildr-Ex.R' failed
The error most likely occurred in:
> ### Name: buildPeds
> ### Title: Build a list of pedigrees
> ### Aliases: buildPeds
>
> ### ** Examples
>
> # Two individuals + 1 extra
> plist = buildPeds(1:2, extra = 1, age = "1>2")
Pedigree parameters:
ID labels: 1, 2
Sex: 1, 1
Extra: 1
Age info: 1>2
Known PO: -
Known non-PO: -
No children: -
Connected only: TRUE
Symmetry filter: TRUE
Max inbreeding: 0.0625
Linear inbreeding: FALSE
Building pedigree list:
All 2 + 0 extra: 1 solutions | 2 candidates (0.000907 secs)
All 2 + 1 extra: 2 solutions | 2 candidates | 2 duplicates removed (0.00399 secs)
Total solutions: 3
Converting to ped
Excessive inbreeding: 0
Time used: 0.0107 secs
> plot(plist)
>
> # Allow disconnected
> plist2 = buildPeds(1:2, extra = 1, age = "1>2", connected = FALSE)
Pedigree parameters:
ID labels: 1, 2
Sex: 1, 1
Extra: 1
Age info: 1>2
Known PO: -
Known non-PO: -
No children: -
Connected only: FALSE
Symmetry filter: TRUE
Max inbreeding: 0.0625
Linear inbreeding: FALSE
Building pedigree list:
All 2 + 0 extra: 2 solutions | 2 candidates (0.000558 secs)
All 2 + 1 extra: 2 solutions | 2 candidates | 2 duplicates removed (0.00229 secs)
Total solutions: 4
Converting to ped
Excessive inbreeding: 0
Time used: 0.00593 secs
> plot(plist2, frames = TRUE)
>
> # Note that full sibs require 2 extras
> plist3 = buildPeds(1:2, extra = 2, age = "1>2")
Pedigree parameters:
ID labels: 1, 2
Sex: 1, 1
Extra: 2
Age info: 1>2
Known PO: -
Known non-PO: -
No children: -
Connected only: TRUE
Symmetry filter: TRUE
Max inbreeding: 0.0625
Linear inbreeding: FALSE
Building pedigree list:
All 2 + 0 extra: 1 solutions | 2 candidates (0.00105 secs)
All 2 + 1 extra: 2 solutions | 12 candidates | 11 duplicates removed (0.00638 secs)
All 2 + 2 extra: 6 solutions | 6 candidates | 11 duplicates removed (0.0294 secs)
Total solutions: 9
Converting to ped
Excessive inbreeding: 2
Time used: 0.0416 secs
> plot(plist3)
>
> # With 2 extras, allowing any inbreeding
> plist4 = buildPeds(1:2, extra = 2, age = "1>2", maxInbreeding = 1)
Pedigree parameters:
ID labels: 1, 2
Sex: 1, 1
Extra: 2
Age info: 1>2
Known PO: -
Known non-PO: -
No children: -
Connected only: TRUE
Symmetry filter: TRUE
Max inbreeding: 1
Linear inbreeding: FALSE
Building pedigree list:
All 2 + 0 extra: 1 solutions | 2 candidates (0.000934 secs)
All 2 + 1 extra: 2 solutions | 12 candidates | 11 duplicates removed (0.00659 secs)
All 2 + 2 extra: 6 solutions | 6 candidates | 11 duplicates removed (0.0298 secs)
Total solutions: 9
Converting to ped
Time used: 0.0318 secs
> plot(plist4)
>
> # Full sibs are also included when `extra = "parents"`
> plist5 = buildPeds(1:2, extra = "parents", age = "1>2")
Pedigree parameters:
ID labels: 1, 2
Sex: 1, 1
Extra: parents
Age info: 1>2
Known PO: -
Known non-PO: -
No children: -
Connected only: TRUE
Symmetry filter: TRUE
Max inbreeding: 0.0625
Linear inbreeding: FALSE
Building pedigree list:
Error in allPOchar %notin% c(knownPOchar, notPOchar) :
could not find function "%notin%"
Calls: buildPeds -> buildPedsParents -> listPOsets
Execution halted
Flavor: r-oldrel-windows-x86_64
Version: 0.4.0
Check: tests
Result: ERROR
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(pedbuildr)
Loading required package: pedtools
>
> test_check("pedbuildr")
Saving _problems/test-buildPeds-9.R
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 10 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-buildPeds.R:8:3'): buildPeds cathces errors ──────────────────
`bp(1:3, sex = 1:3, verb = F)` threw an error with unexpected message.
Expected match: "Illegal elements found in `sex`"
Actual message: "could not find function \"%notin%\""
Backtrace:
▆
1. ├─testthat::expect_error(bp(1:3, sex = 1:3, verb = F), "Illegal elements found in `sex`") at test-buildPeds.R:8:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─pedbuildr (local) bp(1:3, sex = 1:3, verb = F)
7. └─pedbuildr::buildPeds(ids, sex, verbose = verb, ...) at test-buildPeds.R:2:3
8. └─pedbuildr:::buildPedsParents(...)
9. └─pedbuildr:::listPOsets(...)
── Error ('test-buildPeds.R:17:3'): buildPeds() parses age correctly ───────────
Error in `allPOchar %notin% c(knownPOchar, notPOchar)`: could not find function "%notin%"
Backtrace:
▆
1. ├─testthat::expect_output(bp(1:3, age = c(1, 1, 1)), "Age info: -") at test-buildPeds.R:17:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─testthat::capture_output_lines(code, print, width = width)
5. │ │ └─testthat:::eval_with_output(code, print = print, width = width)
6. │ │ ├─withr::with_output_sink(path, withVisible(code))
7. │ │ │ └─base::force(code)
8. │ │ └─base::withVisible(code)
9. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
10. └─pedbuildr (local) bp(1:3, age = c(1, 1, 1))
11. └─pedbuildr::buildPeds(ids, sex, verbose = verb, ...) at test-buildPeds.R:2:3
12. └─pedbuildr:::buildPedsParents(...)
13. └─pedbuildr:::listPOsets(...)
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 10 ]
Error:
! Test failures.
Execution halted
Flavor: r-oldrel-windows-x86_64
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