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Last updated on 2026-08-02 11:52:26 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 | 6.27 | 54.93 | 61.20 | 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 | 11.00 | 81.00 | 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 | 112.00 | 118.00 | 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/Rtmp0Spig2’ ‘~/tmp/scratch/Rtmp0zi4QY’
‘~/tmp/scratch/Rtmp12kCdR’ ‘~/tmp/scratch/Rtmp2CuiNC’
‘~/tmp/scratch/Rtmp2EplCw’ ‘~/tmp/scratch/Rtmp2c33AU’
‘~/tmp/scratch/Rtmp2w1sff’ ‘~/tmp/scratch/Rtmp3nIdHp’
‘~/tmp/scratch/Rtmp4UVfTt’ ‘~/tmp/scratch/Rtmp4pvsJu’
‘~/tmp/scratch/Rtmp4wRvHP’ ‘~/tmp/scratch/Rtmp57fJ9F’
‘~/tmp/scratch/Rtmp5M8ACp’ ‘~/tmp/scratch/Rtmp5Q1miQ’
‘~/tmp/scratch/Rtmp5ZqgjE’ ‘~/tmp/scratch/Rtmp6swiBa’
‘~/tmp/scratch/Rtmp71ffhE’ ‘~/tmp/scratch/Rtmp8CYQ3j’
‘~/tmp/scratch/Rtmp8YexSN’ ‘~/tmp/scratch/Rtmp8dMaWR’
‘~/tmp/scratch/RtmpAD4onV’ ‘~/tmp/scratch/RtmpADmkr1’
‘~/tmp/scratch/RtmpASiHtY’ ‘~/tmp/scratch/RtmpAeRRuE’
‘~/tmp/scratch/RtmpAg4nbI’ ‘~/tmp/scratch/RtmpB2ywTd’
‘~/tmp/scratch/RtmpBBwA6c’ ‘~/tmp/scratch/RtmpBJl355’
‘~/tmp/scratch/RtmpCHES3l’ ‘~/tmp/scratch/RtmpDu1oxw’
‘~/tmp/scratch/RtmpEEhjVj’ ‘~/tmp/scratch/RtmpFHtjA7’
‘~/tmp/scratch/RtmpGqAiK0’ ‘~/tmp/scratch/RtmpGrE6Z5’
‘~/tmp/scratch/RtmpIFzhGQ’ ‘~/tmp/scratch/RtmpIKDTjM’
‘~/tmp/scratch/RtmpJLMe4J’ ‘~/tmp/scratch/RtmpJNHQ4b’
‘~/tmp/scratch/RtmpKRsLGs’ ‘~/tmp/scratch/RtmpKYskpe’
‘~/tmp/scratch/RtmpLOndXe’ ‘~/tmp/scratch/RtmpLwhPF3’
‘~/tmp/scratch/RtmpN6ytQ6’ ‘~/tmp/scratch/RtmpNHAObB’
‘~/tmp/scratch/RtmpNqduJm’ ‘~/tmp/scratch/RtmpOObAo0’
‘~/tmp/scratch/RtmpOQfacK’ ‘~/tmp/scratch/RtmpOTliqp’
‘~/tmp/scratch/RtmpOlgC60’ ‘~/tmp/scratch/RtmpQ0kM59’
‘~/tmp/scratch/RtmpQ6947s’ ‘~/tmp/scratch/RtmpQZgjEr’
‘~/tmp/scratch/RtmpR8yadN’ ‘~/tmp/scratch/RtmpRApDTV’
‘~/tmp/scratch/RtmpRYagtp’ ‘~/tmp/scratch/RtmpS9LUMY’
‘~/tmp/scratch/RtmpST9hLD’ ‘~/tmp/scratch/RtmpT61HBI’
‘~/tmp/scratch/RtmpT64tBp’ ‘~/tmp/scratch/RtmpTvxuzo’
‘~/tmp/scratch/RtmpUHskL9’ ‘~/tmp/scratch/RtmpUK7R1J’
‘~/tmp/scratch/RtmpWPV9lt’ ‘~/tmp/scratch/RtmpXUiete’
‘~/tmp/scratch/RtmpXaKilc’ ‘~/tmp/scratch/RtmpYUiZwB’
‘~/tmp/scratch/RtmpZD08da’ ‘~/tmp/scratch/RtmpZHYXQX’
‘~/tmp/scratch/RtmpZNLpTB’ ‘~/tmp/scratch/RtmpZdHult’
‘~/tmp/scratch/RtmpZfF7nG’ ‘~/tmp/scratch/RtmpaIKDxf’
‘~/tmp/scratch/RtmpaloJEY’ ‘~/tmp/scratch/RtmpaqCrGz’
‘~/tmp/scratch/Rtmparhk3Z’ ‘~/tmp/scratch/Rtmpavnod5’
‘~/tmp/scratch/Rtmpc99tWw’ ‘~/tmp/scratch/RtmpcjiXsq’
‘~/tmp/scratch/Rtmpck2pao’ ‘~/tmp/scratch/RtmpckglzI’
‘~/tmp/scratch/RtmpdFRL33’ ‘~/tmp/scratch/Rtmped84NF’
‘~/tmp/scratch/RtmpekAb7G’ ‘~/tmp/scratch/Rtmpf5PNby’
‘~/tmp/scratch/RtmpgVXKCA’ ‘~/tmp/scratch/RtmpgZkD2U’
‘~/tmp/scratch/RtmphAgOQG’ ‘~/tmp/scratch/RtmphYqSKg’
‘~/tmp/scratch/RtmpiSIo7v’ ‘~/tmp/scratch/RtmpivBlNj’
‘~/tmp/scratch/RtmpjZOl1W’ ‘~/tmp/scratch/RtmplKV9KJ’
‘~/tmp/scratch/RtmpmCh2dJ’ ‘~/tmp/scratch/RtmpmDVNFC’
‘~/tmp/scratch/Rtmpn3FZGF’ ‘~/tmp/scratch/Rtmpn3UTbv’
‘~/tmp/scratch/RtmpnH7nA2’ ‘~/tmp/scratch/Rtmpo275mJ’
‘~/tmp/scratch/RtmpoESf9s’ ‘~/tmp/scratch/RtmpoGYXMx’
‘~/tmp/scratch/RtmpoRJgt7’ ‘~/tmp/scratch/RtmpokrX4i’
‘~/tmp/scratch/RtmpomiIoH’ ‘~/tmp/scratch/RtmpovwsIL’
‘~/tmp/scratch/RtmpqP7iCu’ ‘~/tmp/scratch/RtmprEmygX’
‘~/tmp/scratch/RtmprTxtH4’ ‘~/tmp/scratch/RtmprV6e7C’
‘~/tmp/scratch/RtmpsfwFWH’ ‘~/tmp/scratch/Rtmpt0Sk8O’
‘~/tmp/scratch/RtmptDNDg4’ ‘~/tmp/scratch/Rtmpts3vIx’
‘~/tmp/scratch/RtmpvCw98Q’ ‘~/tmp/scratch/RtmpvVhkgC’
‘~/tmp/scratch/RtmpvoGn0X’ ‘~/tmp/scratch/RtmpwdKSnK’
‘~/tmp/scratch/RtmpwzIXed’ ‘~/tmp/scratch/RtmpxEQpdM’
‘~/tmp/scratch/Rtmpxb10BP’ ‘~/tmp/scratch/RtmpxbCxtW’
‘~/tmp/scratch/RtmpyENwox’ ‘~/tmp/scratch/RtmpybJuip’
‘~/tmp/scratch/RtmpzI8SoP’ ‘~/tmp/scratch/Rtmpzl8U2i’
‘~/tmp/scratch/RtmpzlX14c’ ‘~/tmp/scratch/xvfb-run.1eUMUe’
‘~/tmp/scratch/xvfb-run.2yKNMn’ ‘~/tmp/scratch/xvfb-run.5r273y’
‘~/tmp/scratch/xvfb-run.723cgL’ ‘~/tmp/scratch/xvfb-run.8SbxYU’
‘~/tmp/scratch/xvfb-run.94PZqX’ ‘~/tmp/scratch/xvfb-run.A8yzBH’
‘~/tmp/scratch/xvfb-run.AM1yfG’ ‘~/tmp/scratch/xvfb-run.Aydrx4’
‘~/tmp/scratch/xvfb-run.BlJLpY’ ‘~/tmp/scratch/xvfb-run.BmO1sd’
‘~/tmp/scratch/xvfb-run.CrlYl2’ ‘~/tmp/scratch/xvfb-run.DCCNDU’
‘~/tmp/scratch/xvfb-run.DHaQT7’ ‘~/tmp/scratch/xvfb-run.Dprusz’
‘~/tmp/scratch/xvfb-run.FNus4l’ ‘~/tmp/scratch/xvfb-run.FUENV9’
‘~/tmp/scratch/xvfb-run.GeeLBh’ ‘~/tmp/scratch/xvfb-run.Ht1DkE’
‘~/tmp/scratch/xvfb-run.JcLVsh’ ‘~/tmp/scratch/xvfb-run.Kmq3Iw’
‘~/tmp/scratch/xvfb-run.NABeLv’ ‘~/tmp/scratch/xvfb-run.NGlV2K’
‘~/tmp/scratch/xvfb-run.RQCId7’ ‘~/tmp/scratch/xvfb-run.Roy0b3’
‘~/tmp/scratch/xvfb-run.SbmXUW’ ‘~/tmp/scratch/xvfb-run.Uz1O3f’
‘~/tmp/scratch/xvfb-run.VPmpYD’ ‘~/tmp/scratch/xvfb-run.WvhAwv’
‘~/tmp/scratch/xvfb-run.XKlOGX’ ‘~/tmp/scratch/xvfb-run.Yj7HX0’
‘~/tmp/scratch/xvfb-run.YzwzVw’ ‘~/tmp/scratch/xvfb-run.ZCgr8n’
‘~/tmp/scratch/xvfb-run.aJEAfb’ ‘~/tmp/scratch/xvfb-run.bykia7’
‘~/tmp/scratch/xvfb-run.cJxYH4’ ‘~/tmp/scratch/xvfb-run.dPocec’
‘~/tmp/scratch/xvfb-run.e9M9VH’ ‘~/tmp/scratch/xvfb-run.eoGsT8’
‘~/tmp/scratch/xvfb-run.f56jhK’ ‘~/tmp/scratch/xvfb-run.fyNLdW’
‘~/tmp/scratch/xvfb-run.gSqQIq’ ‘~/tmp/scratch/xvfb-run.hSRqA7’
‘~/tmp/scratch/xvfb-run.iOG8Ui’ ‘~/tmp/scratch/xvfb-run.k6Tt81’
‘~/tmp/scratch/xvfb-run.mfVdjS’ ‘~/tmp/scratch/xvfb-run.o2MmuS’
‘~/tmp/scratch/xvfb-run.p4ZgID’ ‘~/tmp/scratch/xvfb-run.pvjEsz’
‘~/tmp/scratch/xvfb-run.r0QUF6’ ‘~/tmp/scratch/xvfb-run.rgPzgF’
‘~/tmp/scratch/xvfb-run.xArxcy’ ‘~/tmp/scratch/xvfb-run.zhdz5T’
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 (0.000191 secs)
All 2 + 1 extra: 2 solutions | 2 candidates | 2 duplicates removed (0.000703 secs)
Total solutions: 3
Converting to ped
Excessive inbreeding: 0
Time used: 0.00198 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 (0.000167 secs)
All 2 + 1 extra: 2 solutions | 2 candidates | 2 duplicates removed (0.000631 secs)
Total solutions: 4
Converting to ped
Excessive inbreeding: 0
Time used: 0.00159 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 (0.000189 secs)
All 2 + 1 extra: 2 solutions | 12 candidates | 11 duplicates removed (0.00107 secs)
All 2 + 2 extra: 6 solutions | 6 candidates | 11 duplicates removed (0.0046 secs)
Total solutions: 9
Converting to ped
Excessive inbreeding: 2
Time used: 0.00645 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 (0.000154 secs)
All 2 + 1 extra: 2 solutions | 12 candidates | 11 duplicates removed (0.000861 secs)
All 2 + 2 extra: 6 solutions | 6 candidates | 11 duplicates removed (0.00368 secs)
Total solutions: 9
Converting to ped
Time used: 0.00394 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 (0.000529 secs)
All 2 + 1 extra: 2 solutions | 2 candidates | 2 duplicates removed (0.00214 secs)
Total solutions: 3
Converting to ped
Excessive inbreeding: 0
Time used: 0.0124 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 (0.000505 secs)
All 2 + 1 extra: 2 solutions | 2 candidates | 2 duplicates removed (0.00202 secs)
Total solutions: 4
Converting to ped
Excessive inbreeding: 0
Time used: 0.00511 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 (0.00048 secs)
All 2 + 1 extra: 2 solutions | 12 candidates | 11 duplicates removed (0.00329 secs)
All 2 + 2 extra: 6 solutions | 6 candidates | 11 duplicates removed (0.0247 secs)
Total solutions: 9
Converting to ped
Excessive inbreeding: 2
Time used: 0.0426 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 (0.000477 secs)
All 2 + 1 extra: 2 solutions | 12 candidates | 11 duplicates removed (0.00302 secs)
All 2 + 2 extra: 6 solutions | 6 candidates | 11 duplicates removed (0.0281 secs)
Total solutions: 9
Converting to ped
Time used: 0.0292 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/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-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
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