Last updated on 2026-07-17 06:50:23 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.4.0 | 7.26 | 75.10 | 82.36 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.4.0 | 5.97 | 58.85 | 64.82 | 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 | 53.94 | OK | |||
| r-devel-windows-x86_64 | 0.4.0 | 10.00 | 81.00 | 91.00 | OK | |
| r-patched-linux-x86_64 | 0.4.0 | 8.77 | 68.79 | 77.56 | OK | |
| r-release-linux-x86_64 | 0.4.0 | 6.85 | 68.17 | 75.02 | 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 | 10.00 | 82.00 | 92.00 | 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 | 121.00 | 128.00 | ERROR | |
| r-oldrel-windows-x86_64 | 0.4.0 | 15.00 | 101.00 | 116.00 | 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 (0.000184 secs)
All 2 + 1 extra: 2 solutions | 2 candidates | 2 duplicates removed (0.000671 secs)
Total solutions: 3
Converting to ped
Excessive inbreeding: 0
Time used: 0.00197 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 (0.000157 secs)
All 2 + 1 extra: 2 solutions | 2 candidates | 2 duplicates removed (0.000597 secs)
Total solutions: 4
Converting to ped
Excessive inbreeding: 0
Time used: 0.00146 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 (0.000162 secs)
All 2 + 1 extra: 2 solutions | 12 candidates | 11 duplicates removed (0.000985 secs)
All 2 + 2 extra: 6 solutions | 6 candidates | 11 duplicates removed (0.00443 secs)
Total solutions: 9
Converting to ped
Excessive inbreeding: 2
Time used: 0.00615 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 (0.000173 secs)
All 2 + 1 extra: 2 solutions | 12 candidates | 11 duplicates removed (0.00102 secs)
All 2 + 2 extra: 6 solutions | 6 candidates | 11 duplicates removed (0.00426 secs)
Total solutions: 9
Converting to ped
Time used: 0.00455 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 (0.00057 secs)
All 2 + 1 extra: 2 solutions | 2 candidates | 2 duplicates removed (0.00238 secs)
Total solutions: 3
Converting to ped
Excessive inbreeding: 0
Time used: 0.00642 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 (0.000453 secs)
All 2 + 1 extra: 2 solutions | 2 candidates | 2 duplicates removed (0.0018 secs)
Total solutions: 4
Converting to ped
Excessive inbreeding: 0
Time used: 0.00464 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 (0.000487 secs)
All 2 + 1 extra: 2 solutions | 12 candidates | 11 duplicates removed (0.0138 secs)
All 2 + 2 extra: 6 solutions | 6 candidates | 11 duplicates removed (0.043 secs)
Total solutions: 9
Converting to ped
Excessive inbreeding: 2
Time used: 0.0491 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 (0.000491 secs)
All 2 + 1 extra: 2 solutions | 12 candidates | 11 duplicates removed (0.0205 secs)
All 2 + 2 extra: 6 solutions | 6 candidates | 11 duplicates removed (0.0532 secs)
Total solutions: 9
Converting to ped
Time used: 0.0542 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/5s]
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 (0.000973 secs)
All 2 + 1 extra: 2 solutions | 2 candidates | 2 duplicates removed (0.00422 secs)
Total solutions: 3
Converting to ped
Excessive inbreeding: 0
Time used: 0.0113 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 (0.000869 secs)
All 2 + 1 extra: 2 solutions | 2 candidates | 2 duplicates removed (0.00365 secs)
Total solutions: 4
Converting to ped
Excessive inbreeding: 0
Time used: 0.00903 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 (0.000922 secs)
All 2 + 1 extra: 2 solutions | 12 candidates | 11 duplicates removed (0.00625 secs)
All 2 + 2 extra: 6 solutions | 6 candidates | 11 duplicates removed (0.0296 secs)
Total solutions: 9
Converting to ped
Excessive inbreeding: 2
Time used: 0.0413 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 (0.00096 secs)
All 2 + 1 extra: 2 solutions | 12 candidates | 11 duplicates removed (0.00652 secs)
All 2 + 2 extra: 6 solutions | 6 candidates | 11 duplicates removed (0.0299 secs)
Total solutions: 9
Converting to ped
Time used: 0.032 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