Last updated on 2026-08-04 02:50:59 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.4.0 | 7.34 | 73.20 | 80.54 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.4.0 | 6.26 | 56.67 | 62.93 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 0.4.0 | 13.00 | 111.23 | 124.23 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 0.4.0 | 6.00 | 51.61 | 57.61 | OK | |
| r-devel-windows-x86_64 | 0.4.0 | 10.00 | 84.00 | 94.00 | OK | |
| r-patched-linux-x86_64 | 0.4.0 | 8.01 | 67.93 | 75.94 | OK | |
| r-release-linux-x86_64 | 0.4.0 | 8.07 | 67.37 | 75.44 | 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 | 23.00 | 25.00 | ERROR | |
| r-oldrel-macos-x86_64 | 0.4.0 | 6.00 | 122.00 | 128.00 | ERROR | |
| r-oldrel-windows-x86_64 | 0.4.0 | 14.00 | 100.00 | 114.00 | ERROR |
Version: 0.4.0
Check: for new files in some other directories
Result: NOTE
Found the following files/directories:
‘~/tmp/scratch/Rtmp0UbWEx’ ‘~/tmp/scratch/Rtmp131Nxj’
‘~/tmp/scratch/Rtmp1of3vM’ ‘~/tmp/scratch/Rtmp240IDQ’
‘~/tmp/scratch/Rtmp2ZasVX’ ‘~/tmp/scratch/Rtmp2wfCdQ’
‘~/tmp/scratch/Rtmp3eTrYv’ ‘~/tmp/scratch/Rtmp3od68f’
‘~/tmp/scratch/Rtmp4ENm8S’ ‘~/tmp/scratch/Rtmp4gqqpy’
‘~/tmp/scratch/Rtmp4vNZEW’ ‘~/tmp/scratch/Rtmp5hRt8D’
‘~/tmp/scratch/Rtmp6BKQGf’ ‘~/tmp/scratch/Rtmp6OdHtc’
‘~/tmp/scratch/Rtmp6lJuQ1’ ‘~/tmp/scratch/Rtmp7Lv7Nn’
‘~/tmp/scratch/Rtmp7VtHxr’ ‘~/tmp/scratch/Rtmp7YsdZC’
‘~/tmp/scratch/Rtmp8XCdbM’ ‘~/tmp/scratch/Rtmp9NqAIS’
‘~/tmp/scratch/Rtmp9ozunJ’ ‘~/tmp/scratch/RtmpAmeMN0’
‘~/tmp/scratch/RtmpB3IEJY’ ‘~/tmp/scratch/RtmpBwGstr’
‘~/tmp/scratch/RtmpCCVr4y’ ‘~/tmp/scratch/RtmpCSxZnD’
‘~/tmp/scratch/RtmpD1neRI’ ‘~/tmp/scratch/RtmpD7KGYU’
‘~/tmp/scratch/RtmpDHh5yd’ ‘~/tmp/scratch/RtmpDX4ZsU’
‘~/tmp/scratch/RtmpDmmdpm’ ‘~/tmp/scratch/RtmpECTo3a’
‘~/tmp/scratch/RtmpEFtN06’ ‘~/tmp/scratch/RtmpEUxgIO’
‘~/tmp/scratch/RtmpEaehRm’ ‘~/tmp/scratch/RtmpFPUzKN’
‘~/tmp/scratch/RtmpG398zP’ ‘~/tmp/scratch/RtmpGBt56E’
‘~/tmp/scratch/RtmpGGTITl’ ‘~/tmp/scratch/RtmpGIjph8’
‘~/tmp/scratch/RtmpI5xwyQ’ ‘~/tmp/scratch/RtmpI8HFi1’
‘~/tmp/scratch/RtmpJG7fZr’ ‘~/tmp/scratch/RtmpKDIISR’
‘~/tmp/scratch/RtmpKa4LdK’ ‘~/tmp/scratch/RtmpL7LON9’
‘~/tmp/scratch/RtmpLEXYZP’ ‘~/tmp/scratch/RtmpLG9fTD’
‘~/tmp/scratch/RtmpLpMi8m’ ‘~/tmp/scratch/RtmpMl0bc6’
‘~/tmp/scratch/RtmpMwaFQn’ ‘~/tmp/scratch/RtmpNSh5pH’
‘~/tmp/scratch/RtmpNfaOTK’ ‘~/tmp/scratch/RtmpO6qNHU’
‘~/tmp/scratch/RtmpOH32l6’ ‘~/tmp/scratch/RtmpOaHHdV’
‘~/tmp/scratch/RtmpPLRViD’ ‘~/tmp/scratch/RtmpPi8gby’
‘~/tmp/scratch/RtmpPkw5Vt’ ‘~/tmp/scratch/RtmpQREF2O’
‘~/tmp/scratch/RtmpQePvhN’ ‘~/tmp/scratch/RtmpQsKjXE’
‘~/tmp/scratch/RtmpR9MoLI’ ‘~/tmp/scratch/RtmpRBuHD6’
‘~/tmp/scratch/RtmpRLAKN8’ ‘~/tmp/scratch/RtmpRTKXoA’
‘~/tmp/scratch/RtmpSSxPtm’ ‘~/tmp/scratch/RtmpSzWlkr’
‘~/tmp/scratch/RtmpTOTKGw’ ‘~/tmp/scratch/RtmpTW2O8e’
‘~/tmp/scratch/RtmpTnDMOj’ ‘~/tmp/scratch/RtmpUEEndj’
‘~/tmp/scratch/RtmpUoGUcE’ ‘~/tmp/scratch/RtmpVH2lh4’
‘~/tmp/scratch/RtmpVYASJ1’ ‘~/tmp/scratch/RtmpVfQpYx’
‘~/tmp/scratch/RtmpVrPdKI’ ‘~/tmp/scratch/RtmpWPGWA7’
‘~/tmp/scratch/RtmpXQV9SI’ ‘~/tmp/scratch/RtmpYzRrlv’
‘~/tmp/scratch/RtmpZIpSKE’ ‘~/tmp/scratch/RtmpZh5bUr’
‘~/tmp/scratch/Rtmpa2bMb4’ ‘~/tmp/scratch/RtmpaZF4SL’
‘~/tmp/scratch/RtmpbYXPXg’ ‘~/tmp/scratch/RtmpczYDYr’
‘~/tmp/scratch/RtmpdmNcLX’ ‘~/tmp/scratch/RtmpeeLvBm’
‘~/tmp/scratch/Rtmpf8tAPU’ ‘~/tmp/scratch/Rtmpf9EQqX’
‘~/tmp/scratch/RtmpfKtAEG’ ‘~/tmp/scratch/Rtmpfv3dLD’
‘~/tmp/scratch/RtmpguiMGb’ ‘~/tmp/scratch/RtmphJSkel’
‘~/tmp/scratch/RtmpignoBi’ ‘~/tmp/scratch/Rtmpjv6Oli’
‘~/tmp/scratch/RtmpkZMDwj’ ‘~/tmp/scratch/Rtmpkkwx7u’
‘~/tmp/scratch/Rtmpl6dV1r’ ‘~/tmp/scratch/RtmplmRaRN’
‘~/tmp/scratch/RtmplmvQPO’ ‘~/tmp/scratch/RtmplrVHp8’
‘~/tmp/scratch/RtmpmEH65r’ ‘~/tmp/scratch/RtmpmWK5Zl’
‘~/tmp/scratch/RtmpmrXvMg’ ‘~/tmp/scratch/RtmpnHHK40’
‘~/tmp/scratch/Rtmpo2KuMO’ ‘~/tmp/scratch/RtmpoFNrLn’
‘~/tmp/scratch/RtmpowX4E4’ ‘~/tmp/scratch/RtmppAD5CJ’
‘~/tmp/scratch/RtmppejrGR’ ‘~/tmp/scratch/Rtmpq4AluV’
‘~/tmp/scratch/Rtmpqfh4AC’ ‘~/tmp/scratch/RtmpqvyqEi’
‘~/tmp/scratch/RtmprvWYZP’ ‘~/tmp/scratch/RtmpsKdcA9’
‘~/tmp/scratch/RtmpsVsECJ’ ‘~/tmp/scratch/RtmpsXG3xB’
‘~/tmp/scratch/RtmpseCUul’ ‘~/tmp/scratch/Rtmpt2Ymx3’
‘~/tmp/scratch/Rtmpu9WYzC’ ‘~/tmp/scratch/RtmpupGZ05’
‘~/tmp/scratch/RtmpvPrIDV’ ‘~/tmp/scratch/RtmpvYq5zD’
‘~/tmp/scratch/Rtmpvi8NHm’ ‘~/tmp/scratch/Rtmpw5RlQP’
‘~/tmp/scratch/Rtmpwm1zmm’ ‘~/tmp/scratch/RtmpxJaWwA’
‘~/tmp/scratch/Rtmpxa2BVB’ ‘~/tmp/scratch/Rtmpy30pPU’
‘~/tmp/scratch/xvfb-run.0gx0G9’ ‘~/tmp/scratch/xvfb-run.0qi9fR’
‘~/tmp/scratch/xvfb-run.1vWZpo’ ‘~/tmp/scratch/xvfb-run.23qUgr’
‘~/tmp/scratch/xvfb-run.2Ga0Tp’ ‘~/tmp/scratch/xvfb-run.3Kgi3B’
‘~/tmp/scratch/xvfb-run.5rlFx1’ ‘~/tmp/scratch/xvfb-run.6dgSB7’
‘~/tmp/scratch/xvfb-run.6esOet’ ‘~/tmp/scratch/xvfb-run.7WJyV3’
‘~/tmp/scratch/xvfb-run.7bfqdW’ ‘~/tmp/scratch/xvfb-run.8RP7wL’
‘~/tmp/scratch/xvfb-run.9UHH9z’ ‘~/tmp/scratch/xvfb-run.9mJSNI’
‘~/tmp/scratch/xvfb-run.FS5L5t’ ‘~/tmp/scratch/xvfb-run.Ft0lEh’
‘~/tmp/scratch/xvfb-run.GZJ1OA’ ‘~/tmp/scratch/xvfb-run.HvBtR7’
‘~/tmp/scratch/xvfb-run.ICnqUG’ ‘~/tmp/scratch/xvfb-run.JLAU3w’
‘~/tmp/scratch/xvfb-run.JdwLQe’ ‘~/tmp/scratch/xvfb-run.Jy3A7h’
‘~/tmp/scratch/xvfb-run.KycoKS’ ‘~/tmp/scratch/xvfb-run.M0bhP4’
‘~/tmp/scratch/xvfb-run.MRLYtX’ ‘~/tmp/scratch/xvfb-run.MSFhyn’
‘~/tmp/scratch/xvfb-run.OwTi0p’ ‘~/tmp/scratch/xvfb-run.PDXv4y’
‘~/tmp/scratch/xvfb-run.PoRTxv’ ‘~/tmp/scratch/xvfb-run.Sqf70L’
‘~/tmp/scratch/xvfb-run.StzY6W’ ‘~/tmp/scratch/xvfb-run.TtopKs’
‘~/tmp/scratch/xvfb-run.UBqHn5’ ‘~/tmp/scratch/xvfb-run.Uz5Ja5’
‘~/tmp/scratch/xvfb-run.V84L0W’ ‘~/tmp/scratch/xvfb-run.VV6nRn’
‘~/tmp/scratch/xvfb-run.VqZQLY’ ‘~/tmp/scratch/xvfb-run.XY3zmm’
‘~/tmp/scratch/xvfb-run.YtBVpB’ ‘~/tmp/scratch/xvfb-run.Zhj1Wv’
‘~/tmp/scratch/xvfb-run.a0ioNz’ ‘~/tmp/scratch/xvfb-run.cllJRo’
‘~/tmp/scratch/xvfb-run.eVqyH9’ ‘~/tmp/scratch/xvfb-run.hRTvO0’
‘~/tmp/scratch/xvfb-run.jjRHwL’ ‘~/tmp/scratch/xvfb-run.kk4biW’
‘~/tmp/scratch/xvfb-run.llyz0m’ ‘~/tmp/scratch/xvfb-run.oRtp9X’
‘~/tmp/scratch/xvfb-run.pxMVMY’ ‘~/tmp/scratch/xvfb-run.rVovAz’
‘~/tmp/scratch/xvfb-run.tmUYOI’ ‘~/tmp/scratch/xvfb-run.wTUgVI’
Flavor: r-devel-linux-x86_64-debian-gcc
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 (0.000206 secs)
All 2 + 1 extra: 2 solutions | 2 candidates | 2 duplicates removed (0.000735 secs)
Total solutions: 3
Converting to ped
Excessive inbreeding: 0
Time used: 0.00223 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 (0.000168 secs)
All 2 + 1 extra: 2 solutions | 2 candidates | 2 duplicates removed (0.000623 secs)
Total solutions: 4
Converting to ped
Excessive inbreeding: 0
Time used: 0.00147 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 (0.000171 secs)
All 2 + 1 extra: 2 solutions | 12 candidates | 11 duplicates removed (0.000987 secs)
All 2 + 2 extra: 6 solutions | 6 candidates | 11 duplicates removed (0.00454 secs)
Total solutions: 9
Converting to ped
Excessive inbreeding: 2
Time used: 0.00646 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 (0.000177 secs)
All 2 + 1 extra: 2 solutions | 12 candidates | 11 duplicates removed (0.000996 secs)
All 2 + 2 extra: 6 solutions | 6 candidates | 11 duplicates removed (0.00443 secs)
Total solutions: 9
Converting to ped
Time used: 0.00476 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 (0.000494 secs)
All 2 + 1 extra: 2 solutions | 2 candidates | 2 duplicates removed (0.00197 secs)
Total solutions: 3
Converting to ped
Excessive inbreeding: 0
Time used: 0.0185 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 (0.000464 secs)
All 2 + 1 extra: 2 solutions | 2 candidates | 2 duplicates removed (0.00214 secs)
Total solutions: 4
Converting to ped
Excessive inbreeding: 0
Time used: 0.00502 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 (0.000507 secs)
All 2 + 1 extra: 2 solutions | 12 candidates | 11 duplicates removed (0.00304 secs)
All 2 + 2 extra: 6 solutions | 6 candidates | 11 duplicates removed (0.0312 secs)
Total solutions: 9
Converting to ped
Excessive inbreeding: 2
Time used: 0.0518 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 (0.00049 secs)
All 2 + 1 extra: 2 solutions | 12 candidates | 11 duplicates removed (0.00312 secs)
All 2 + 2 extra: 6 solutions | 6 candidates | 11 duplicates removed (0.0371 secs)
Total solutions: 9
Converting to ped
Time used: 0.0381 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 (0.000982 secs)
All 2 + 1 extra: 2 solutions | 2 candidates | 2 duplicates removed (0.0042 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 (0.000553 secs)
All 2 + 1 extra: 2 solutions | 2 candidates | 2 duplicates removed (0.00301 secs)
Total solutions: 4
Converting to ped
Excessive inbreeding: 0
Time used: 0.00817 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 (0.000629 secs)
All 2 + 1 extra: 2 solutions | 12 candidates | 11 duplicates removed (0.00593 secs)
All 2 + 2 extra: 6 solutions | 6 candidates | 11 duplicates removed (0.0193 secs)
Total solutions: 9
Converting to ped
Excessive inbreeding: 2
Time used: 0.0263 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 (0.000636 secs)
All 2 + 1 extra: 2 solutions | 12 candidates | 11 duplicates removed (0.00385 secs)
All 2 + 2 extra: 6 solutions | 6 candidates | 11 duplicates removed (0.019 secs)
Total solutions: 9
Converting to ped
Time used: 0.0204 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