Last updated on 2026-08-01 05:55:58 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 | 5.22 | 54.92 | 60.14 | 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 | 8.19 | 67.70 | 75.89 | 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 | 11.00 | 81.00 | 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 | 113.00 | 120.00 | ERROR | |
| r-oldrel-windows-x86_64 | 0.4.0 | 14.00 | 104.00 | 118.00 | ERROR |
Version: 0.4.0
Check: for new files in some other directories
Result: NOTE
Found the following files/directories:
‘~/tmp/scratch/Rtmp0m6O32’ ‘~/tmp/scratch/Rtmp0rbBRb’
‘~/tmp/scratch/Rtmp0tT8rz’ ‘~/tmp/scratch/Rtmp159K4k’
‘~/tmp/scratch/Rtmp1BWSju’ ‘~/tmp/scratch/Rtmp1DwKDA’
‘~/tmp/scratch/Rtmp1gmj5s’ ‘~/tmp/scratch/Rtmp2IVDpn’
‘~/tmp/scratch/Rtmp2LcqOL’ ‘~/tmp/scratch/Rtmp31cEiI’
‘~/tmp/scratch/Rtmp3NhI0W’ ‘~/tmp/scratch/Rtmp3PQO6h’
‘~/tmp/scratch/Rtmp4ZMzwG’ ‘~/tmp/scratch/Rtmp4yREvu’
‘~/tmp/scratch/Rtmp5JNnBC’ ‘~/tmp/scratch/Rtmp5aLUH5’
‘~/tmp/scratch/Rtmp5foE9K’ ‘~/tmp/scratch/Rtmp63piWt’
‘~/tmp/scratch/Rtmp6oWY7n’ ‘~/tmp/scratch/Rtmp70VoIi’
‘~/tmp/scratch/Rtmp8dRX9S’ ‘~/tmp/scratch/Rtmp8fLfPC’
‘~/tmp/scratch/RtmpAd8c2u’ ‘~/tmp/scratch/RtmpBr2u6I’
‘~/tmp/scratch/RtmpCzfJsy’ ‘~/tmp/scratch/RtmpDbUCr1’
‘~/tmp/scratch/RtmpDkWnD6’ ‘~/tmp/scratch/RtmpDl7R70’
‘~/tmp/scratch/RtmpEgPrPT’ ‘~/tmp/scratch/RtmpFC89n5’
‘~/tmp/scratch/RtmpGmDjj7’ ‘~/tmp/scratch/RtmpH11Qq7’
‘~/tmp/scratch/RtmpHPXhlH’ ‘~/tmp/scratch/RtmpHStNqQ’
‘~/tmp/scratch/RtmpHTrRYk’ ‘~/tmp/scratch/RtmpHYGBjA’
‘~/tmp/scratch/RtmpHYiyuv’ ‘~/tmp/scratch/RtmpHnug8r’
‘~/tmp/scratch/RtmpI0twPh’ ‘~/tmp/scratch/RtmpI4sbor’
‘~/tmp/scratch/RtmpJi71jH’ ‘~/tmp/scratch/RtmpJm06ts’
‘~/tmp/scratch/RtmpJsoI4O’ ‘~/tmp/scratch/RtmpKCb1SC’
‘~/tmp/scratch/RtmpL2O5lb’ ‘~/tmp/scratch/RtmpMqEGNJ’
‘~/tmp/scratch/RtmpMvUvV4’ ‘~/tmp/scratch/RtmpNsmmiU’
‘~/tmp/scratch/RtmpOPHbo4’ ‘~/tmp/scratch/RtmpOTUFFB’
‘~/tmp/scratch/RtmpOkcSWg’ ‘~/tmp/scratch/RtmpP11NE9’
‘~/tmp/scratch/RtmpPNvPC8’ ‘~/tmp/scratch/RtmpPb1viR’
‘~/tmp/scratch/RtmpPiLeAc’ ‘~/tmp/scratch/RtmpPrkUFp’
‘~/tmp/scratch/RtmpRGEqdR’ ‘~/tmp/scratch/RtmpRLF7iE’
‘~/tmp/scratch/RtmpRcsZBn’ ‘~/tmp/scratch/RtmpT09UZi’
‘~/tmp/scratch/RtmpThsMfv’ ‘~/tmp/scratch/RtmpUuQkwB’
‘~/tmp/scratch/RtmpZoLwWa’ ‘~/tmp/scratch/RtmpbLVyJa’
‘~/tmp/scratch/Rtmpc2D8Xv’ ‘~/tmp/scratch/RtmpcdtR7i’
‘~/tmp/scratch/RtmpcstfFB’ ‘~/tmp/scratch/RtmpetpyO4’
‘~/tmp/scratch/RtmpgWD1PC’ ‘~/tmp/scratch/RtmpgcIuzy’
‘~/tmp/scratch/RtmpgzastJ’ ‘~/tmp/scratch/RtmphkWnqz’
‘~/tmp/scratch/RtmpjHDaNG’ ‘~/tmp/scratch/Rtmpjjllul’
‘~/tmp/scratch/Rtmpjlyeee’ ‘~/tmp/scratch/RtmpkBuB8i’
‘~/tmp/scratch/RtmpkPdK2O’ ‘~/tmp/scratch/Rtmpl2lTQM’
‘~/tmp/scratch/RtmploFnTe’ ‘~/tmp/scratch/RtmpltoXBi’
‘~/tmp/scratch/Rtmpm3VuPk’ ‘~/tmp/scratch/RtmpmIEZoQ’
‘~/tmp/scratch/RtmpmVCAKm’ ‘~/tmp/scratch/RtmpmaHKHz’
‘~/tmp/scratch/RtmpmboGoD’ ‘~/tmp/scratch/Rtmpng7iEz’
‘~/tmp/scratch/RtmpnybCli’ ‘~/tmp/scratch/RtmpoGfXwd’
‘~/tmp/scratch/RtmpoKZJ20’ ‘~/tmp/scratch/RtmpomnfPg’
‘~/tmp/scratch/Rtmpovbiaf’ ‘~/tmp/scratch/RtmppAY8cr’
‘~/tmp/scratch/RtmppBow6r’ ‘~/tmp/scratch/RtmpqUurbM’
‘~/tmp/scratch/RtmpqtUCiD’ ‘~/tmp/scratch/Rtmpqvhscq’
‘~/tmp/scratch/Rtmpr15Tax’ ‘~/tmp/scratch/RtmprasTCO’
‘~/tmp/scratch/RtmprlSq1F’ ‘~/tmp/scratch/Rtmps3H4Bd’
‘~/tmp/scratch/RtmpsHjIsv’ ‘~/tmp/scratch/RtmpsiiGHo’
‘~/tmp/scratch/RtmpsppD1B’ ‘~/tmp/scratch/Rtmpt5Rm8C’
‘~/tmp/scratch/RtmptHJpHm’ ‘~/tmp/scratch/RtmptQdMjD’
‘~/tmp/scratch/Rtmptxu6JC’ ‘~/tmp/scratch/RtmpuNAhMQ’
‘~/tmp/scratch/Rtmpv7jX9C’ ‘~/tmp/scratch/RtmpvYfO2M’
‘~/tmp/scratch/RtmpvbaDZp’ ‘~/tmp/scratch/Rtmpvq5YGX’
‘~/tmp/scratch/RtmpwTkfu9’ ‘~/tmp/scratch/RtmpxcMBYh’
‘~/tmp/scratch/RtmpxgnNCt’ ‘~/tmp/scratch/RtmpxpED2g’
‘~/tmp/scratch/RtmpxwHLNG’ ‘~/tmp/scratch/Rtmpy3mNIZ’
‘~/tmp/scratch/RtmpyGJ0i3’ ‘~/tmp/scratch/RtmpyYNQ1D’
‘~/tmp/scratch/RtmpyiOtVK’ ‘~/tmp/scratch/xvfb-run.1VKI24’
‘~/tmp/scratch/xvfb-run.3ffO3A’ ‘~/tmp/scratch/xvfb-run.40PLAQ’
‘~/tmp/scratch/xvfb-run.5ffa9g’ ‘~/tmp/scratch/xvfb-run.6JIGIl’
‘~/tmp/scratch/xvfb-run.72QtBg’ ‘~/tmp/scratch/xvfb-run.7m1pEs’
‘~/tmp/scratch/xvfb-run.9gnkWQ’ ‘~/tmp/scratch/xvfb-run.BTBczy’
‘~/tmp/scratch/xvfb-run.BiUPF9’ ‘~/tmp/scratch/xvfb-run.CX2lH0’
‘~/tmp/scratch/xvfb-run.IT3Eam’ ‘~/tmp/scratch/xvfb-run.KYgvIT’
‘~/tmp/scratch/xvfb-run.Luvl0S’ ‘~/tmp/scratch/xvfb-run.MQsQcE’
‘~/tmp/scratch/xvfb-run.NRGLag’ ‘~/tmp/scratch/xvfb-run.QTq6Tk’
‘~/tmp/scratch/xvfb-run.SsD3eH’ ‘~/tmp/scratch/xvfb-run.UQEcmC’
‘~/tmp/scratch/xvfb-run.V2YXl5’ ‘~/tmp/scratch/xvfb-run.Vm6L1w’
‘~/tmp/scratch/xvfb-run.VvsSky’ ‘~/tmp/scratch/xvfb-run.X5XHBF’
‘~/tmp/scratch/xvfb-run.cBdHQu’ ‘~/tmp/scratch/xvfb-run.cHJnbn’
‘~/tmp/scratch/xvfb-run.ce7ku8’ ‘~/tmp/scratch/xvfb-run.fd5Kqc’
‘~/tmp/scratch/xvfb-run.gJOCzb’ ‘~/tmp/scratch/xvfb-run.il9MNn’
‘~/tmp/scratch/xvfb-run.lfOzcP’ ‘~/tmp/scratch/xvfb-run.mrrs8C’
‘~/tmp/scratch/xvfb-run.qC2iVh’ ‘~/tmp/scratch/xvfb-run.qhOaO6’
‘~/tmp/scratch/xvfb-run.smA6yg’ ‘~/tmp/scratch/xvfb-run.tGPgSH’
‘~/tmp/scratch/xvfb-run.unqaur’ ‘~/tmp/scratch/xvfb-run.vcZ8zo’
‘~/tmp/scratch/xvfb-run.vy4EXM’ ‘~/tmp/scratch/xvfb-run.xNXWjh’
‘~/tmp/scratch/xvfb-run.xU6QZw’ ‘~/tmp/scratch/xvfb-run.xsvKjL’
‘~/tmp/scratch/xvfb-run.yHdkLO’ ‘~/tmp/scratch/xvfb-run.zl5sdJ’
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 (0.000204 secs)
All 2 + 1 extra: 2 solutions | 2 candidates | 2 duplicates removed (0.000715 secs)
Total solutions: 3
Converting to ped
Excessive inbreeding: 0
Time used: 0.00202 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 (0.000154 secs)
All 2 + 1 extra: 2 solutions | 2 candidates | 2 duplicates removed (0.000578 secs)
Total solutions: 4
Converting to ped
Excessive inbreeding: 0
Time used: 0.00144 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 (0.000165 secs)
All 2 + 1 extra: 2 solutions | 12 candidates | 11 duplicates removed (0.000976 secs)
All 2 + 2 extra: 6 solutions | 6 candidates | 11 duplicates removed (0.00447 secs)
Total solutions: 9
Converting to ped
Excessive inbreeding: 2
Time used: 0.00628 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 (0.000187 secs)
All 2 + 1 extra: 2 solutions | 12 candidates | 11 duplicates removed (0.00101 secs)
All 2 + 2 extra: 6 solutions | 6 candidates | 11 duplicates removed (0.00432 secs)
Total solutions: 9
Converting to ped
Time used: 0.00462 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 (0.0114 secs)
All 2 + 1 extra: 2 solutions | 2 candidates | 2 duplicates removed (0.013 secs)
Total solutions: 3
Converting to ped
Excessive inbreeding: 0
Time used: 0.0184 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 (0.000476 secs)
All 2 + 1 extra: 2 solutions | 2 candidates | 2 duplicates removed (0.00189 secs)
Total solutions: 4
Converting to ped
Excessive inbreeding: 0
Time used: 0.0206 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 (0.000486 secs)
All 2 + 1 extra: 2 solutions | 12 candidates | 11 duplicates removed (0.00306 secs)
All 2 + 2 extra: 6 solutions | 6 candidates | 11 duplicates removed (0.0249 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 (0.000506 secs)
All 2 + 1 extra: 2 solutions | 12 candidates | 11 duplicates removed (0.0031 secs)
All 2 + 2 extra: 6 solutions | 6 candidates | 11 duplicates removed (0.0265 secs)
Total solutions: 9
Converting to ped
Time used: 0.0382 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 (0.000892 secs)
All 2 + 1 extra: 2 solutions | 2 candidates | 2 duplicates removed (0.0038 secs)
Total solutions: 3
Converting to ped
Excessive inbreeding: 0
Time used: 0.0105 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 (0.000997 secs)
All 2 + 1 extra: 2 solutions | 2 candidates | 2 duplicates removed (0.00427 secs)
Total solutions: 4
Converting to ped
Excessive inbreeding: 0
Time used: 0.0104 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 (0.000963 secs)
All 2 + 1 extra: 2 solutions | 12 candidates | 11 duplicates removed (0.00641 secs)
All 2 + 2 extra: 6 solutions | 6 candidates | 11 duplicates removed (0.0265 secs)
Total solutions: 9
Converting to ped
Excessive inbreeding: 2
Time used: 0.0342 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 (0.000927 secs)
All 2 + 1 extra: 2 solutions | 12 candidates | 11 duplicates removed (0.00648 secs)
All 2 + 2 extra: 6 solutions | 6 candidates | 11 duplicates removed (0.0298 secs)
Total solutions: 9
Converting to ped
Time used: 0.0319 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