Last updated on 2026-08-02 12:51:37 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.7.2 | 25.97 | 274.23 | 300.20 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.7.2 | 21.37 | 195.78 | 217.15 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 0.7.2 | 50.00 | 416.19 | 466.19 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 0.7.2 | 22.00 | 187.49 | 209.49 | OK | |
| r-devel-windows-x86_64 | 0.7.2 | 31.00 | 368.00 | 399.00 | OK | |
| r-patched-linux-x86_64 | 0.7.2 | 29.40 | 255.82 | 285.22 | OK | |
| r-release-linux-x86_64 | 0.7.2 | 30.01 | 258.71 | 288.72 | OK | |
| r-release-macos-arm64 | 0.7.2 | 8.00 | 105.00 | 113.00 | OK | |
| r-release-macos-x86_64 | 0.7.2 | 21.00 | 515.00 | 536.00 | OK | |
| r-release-windows-x86_64 | 0.7.2 | 31.00 | 365.00 | 396.00 | OK | |
| r-oldrel-macos-arm64 | 0.7.2 | 7.00 | 106.00 | 113.00 | OK | |
| r-oldrel-macos-x86_64 | 0.7.2 | 20.00 | 342.00 | 362.00 | ERROR | |
| r-oldrel-windows-x86_64 | 0.7.2 | 47.00 | 482.00 | 529.00 | OK |
Version: 0.7.2
Check: for new files in some other directories
Result: NOTE
Found the following files/directories:
‘~/tmp/scratch/Rtmp0G4zWU’ ‘~/tmp/scratch/Rtmp0ZcpPy’
‘~/tmp/scratch/Rtmp0dyoPS’ ‘~/tmp/scratch/Rtmp0lCyGg’
‘~/tmp/scratch/Rtmp0s1WcO’ ‘~/tmp/scratch/Rtmp0zCd1K’
‘~/tmp/scratch/Rtmp13yrcA’ ‘~/tmp/scratch/Rtmp1qMYnd’
‘~/tmp/scratch/Rtmp1vMlGe’ ‘~/tmp/scratch/Rtmp20WH3g’
‘~/tmp/scratch/Rtmp26Fk1v’ ‘~/tmp/scratch/Rtmp34LLPO’
‘~/tmp/scratch/Rtmp3grBIT’ ‘~/tmp/scratch/Rtmp411PyG’
‘~/tmp/scratch/Rtmp47GSz0’ ‘~/tmp/scratch/Rtmp52IjTY’
‘~/tmp/scratch/Rtmp5br76S’ ‘~/tmp/scratch/Rtmp5dk6Ha’
‘~/tmp/scratch/Rtmp5hpE2i’ ‘~/tmp/scratch/Rtmp6auv6p’
‘~/tmp/scratch/Rtmp6mBTfP’ ‘~/tmp/scratch/Rtmp6qbQcM’
‘~/tmp/scratch/Rtmp6uqej6’ ‘~/tmp/scratch/Rtmp76qR23’
‘~/tmp/scratch/Rtmp7crJbr’ ‘~/tmp/scratch/Rtmp7nlc0Z’
‘~/tmp/scratch/Rtmp85Yztv’ ‘~/tmp/scratch/Rtmp92tbl6’
‘~/tmp/scratch/Rtmp930hgc’ ‘~/tmp/scratch/Rtmp9B8r5Z’
‘~/tmp/scratch/Rtmp9W6cUp’ ‘~/tmp/scratch/Rtmp9aFnbp’
‘~/tmp/scratch/RtmpAP3Vd7’ ‘~/tmp/scratch/RtmpARo834’
‘~/tmp/scratch/RtmpAbyQD9’ ‘~/tmp/scratch/RtmpAxQl7o’
‘~/tmp/scratch/RtmpB5DBcc’ ‘~/tmp/scratch/RtmpBeVq6a’
‘~/tmp/scratch/RtmpCiWehO’ ‘~/tmp/scratch/RtmpD2VfYx’
‘~/tmp/scratch/RtmpDNKNp7’ ‘~/tmp/scratch/RtmpDieLP8’
‘~/tmp/scratch/RtmpEUSHRW’ ‘~/tmp/scratch/RtmpEtmOu2’
‘~/tmp/scratch/RtmpFLqarV’ ‘~/tmp/scratch/RtmpFgefdV’
‘~/tmp/scratch/RtmpFj9kJY’ ‘~/tmp/scratch/RtmpGa9DGR’
‘~/tmp/scratch/RtmpGcE4xZ’ ‘~/tmp/scratch/RtmpGow7kZ’
‘~/tmp/scratch/RtmpHFC9lr’ ‘~/tmp/scratch/RtmpHmwLOZ’
‘~/tmp/scratch/RtmpI0oRYS’ ‘~/tmp/scratch/RtmpIAvV9F’
‘~/tmp/scratch/RtmpICUVQr’ ‘~/tmp/scratch/RtmpIiHYKe’
‘~/tmp/scratch/RtmpJULCX9’ ‘~/tmp/scratch/RtmpJy1SP0’
‘~/tmp/scratch/RtmpKE1jAh’ ‘~/tmp/scratch/RtmpKVMDwa’
‘~/tmp/scratch/RtmpKVgJgg’ ‘~/tmp/scratch/RtmpKjZpIs’
‘~/tmp/scratch/RtmpLo66zd’ ‘~/tmp/scratch/RtmpLryo1q’
‘~/tmp/scratch/RtmpM5Oper’ ‘~/tmp/scratch/RtmpMqKHnG’
‘~/tmp/scratch/RtmpNGVr4g’ ‘~/tmp/scratch/RtmpNhEpMH’
‘~/tmp/scratch/RtmpNvhwxE’ ‘~/tmp/scratch/RtmpNzUTJF’
‘~/tmp/scratch/RtmpOZCt2G’ ‘~/tmp/scratch/RtmpOykOZm’
‘~/tmp/scratch/RtmpP0ZUsQ’ ‘~/tmp/scratch/RtmpPOfpX1’
‘~/tmp/scratch/RtmpQ6VE5N’ ‘~/tmp/scratch/RtmpQJVCVr’
‘~/tmp/scratch/RtmpQaVY6Q’ ‘~/tmp/scratch/RtmpQoRlf6’
‘~/tmp/scratch/RtmpS5cFhA’ ‘~/tmp/scratch/RtmpSlcdP8’
‘~/tmp/scratch/RtmpSyKfv5’ ‘~/tmp/scratch/RtmpTDqDXf’
‘~/tmp/scratch/RtmpTJTFC4’ ‘~/tmp/scratch/RtmpTfFDRB’
‘~/tmp/scratch/RtmpTvK6QP’ ‘~/tmp/scratch/RtmpU4H8ba’
‘~/tmp/scratch/RtmpUCf3ok’ ‘~/tmp/scratch/RtmpUMNVZe’
‘~/tmp/scratch/RtmpUSr9AX’ ‘~/tmp/scratch/RtmpVXKKcI’
‘~/tmp/scratch/RtmpVeazNV’ ‘~/tmp/scratch/RtmpVfcTBQ’
‘~/tmp/scratch/RtmpVzcBl0’ ‘~/tmp/scratch/RtmpWFLnBH’
‘~/tmp/scratch/RtmpWs8LM2’ ‘~/tmp/scratch/RtmpWx9Z91’
‘~/tmp/scratch/RtmpZ5cf2d’ ‘~/tmp/scratch/RtmpZM62id’
‘~/tmp/scratch/Rtmpa0Z44M’ ‘~/tmp/scratch/Rtmpa9RhwT’
‘~/tmp/scratch/RtmpaMG7zq’ ‘~/tmp/scratch/RtmpaQ5fTb’
‘~/tmp/scratch/RtmpaZvOeC’ ‘~/tmp/scratch/Rtmpank41H’
‘~/tmp/scratch/RtmpcDbvZi’ ‘~/tmp/scratch/RtmpcyfKZk’
‘~/tmp/scratch/RtmpdObZY1’ ‘~/tmp/scratch/Rtmpdfy11X’
‘~/tmp/scratch/Rtmpdhtnqk’ ‘~/tmp/scratch/Rtmpe7okJB’
‘~/tmp/scratch/RtmpeDm1v2’ ‘~/tmp/scratch/RtmpeoMBET’
‘~/tmp/scratch/RtmpfJB0CF’ ‘~/tmp/scratch/RtmpfcalIy’
‘~/tmp/scratch/Rtmpfuszg3’ ‘~/tmp/scratch/RtmpgEyHVP’
‘~/tmp/scratch/RtmpgJuwqx’ ‘~/tmp/scratch/RtmpgKku9W’
‘~/tmp/scratch/RtmpgOwuqa’ ‘~/tmp/scratch/Rtmpgg0LrJ’
‘~/tmp/scratch/Rtmph6Rsxn’ ‘~/tmp/scratch/RtmphBEag7’
‘~/tmp/scratch/RtmpheF7DZ’ ‘~/tmp/scratch/RtmpiEWsIb’
‘~/tmp/scratch/RtmpjK9K3Z’ ‘~/tmp/scratch/RtmpjQe8hk’
‘~/tmp/scratch/RtmpkFaoW2’ ‘~/tmp/scratch/RtmpkISg2w’
‘~/tmp/scratch/RtmpkJ6lrx’ ‘~/tmp/scratch/RtmpkkcWiN’
‘~/tmp/scratch/RtmplELvdr’ ‘~/tmp/scratch/RtmplEpTzW’
‘~/tmp/scratch/RtmplMhlLE’ ‘~/tmp/scratch/RtmplVcVLS’
‘~/tmp/scratch/Rtmple31Cg’ ‘~/tmp/scratch/Rtmpm3YCF2’
‘~/tmp/scratch/RtmpmS4hkL’ ‘~/tmp/scratch/RtmpmYAD2I’
‘~/tmp/scratch/Rtmpmr2v0E’ ‘~/tmp/scratch/Rtmpn88Lsk’
‘~/tmp/scratch/RtmpnM4qyo’ ‘~/tmp/scratch/RtmpnbmBlt’
‘~/tmp/scratch/RtmpnmIwUp’ ‘~/tmp/scratch/Rtmpo0NxRF’
‘~/tmp/scratch/RtmpohdZr4’ ‘~/tmp/scratch/RtmpolSVxl’
‘~/tmp/scratch/RtmppKyTVz’ ‘~/tmp/scratch/RtmppbSQ9n’
‘~/tmp/scratch/RtmpqLJfx7’ ‘~/tmp/scratch/Rtmpql0F7m’
‘~/tmp/scratch/RtmpqpHgk6’ ‘~/tmp/scratch/RtmpqtFXgw’
‘~/tmp/scratch/RtmprIHxyO’ ‘~/tmp/scratch/RtmprUWL1g’
‘~/tmp/scratch/Rtmprzzb29’ ‘~/tmp/scratch/RtmpspdKjc’
‘~/tmp/scratch/RtmpswKsud’ ‘~/tmp/scratch/Rtmpu0Nppd’
‘~/tmp/scratch/RtmpujWK6R’ ‘~/tmp/scratch/RtmpuuVycF’
‘~/tmp/scratch/RtmpuziKp4’ ‘~/tmp/scratch/RtmpvG00fm’
‘~/tmp/scratch/RtmpvPNHnU’ ‘~/tmp/scratch/RtmpvQi2Vp’
‘~/tmp/scratch/RtmpwKgBpC’ ‘~/tmp/scratch/RtmpxHnkYP’
‘~/tmp/scratch/RtmpxPWDvO’ ‘~/tmp/scratch/Rtmpy92aME’
‘~/tmp/scratch/RtmpyEy3Hp’ ‘~/tmp/scratch/RtmpyqKKsS’
‘~/tmp/scratch/Rtmpyw1CJc’ ‘~/tmp/scratch/RtmpywQ1xT’
‘~/tmp/scratch/RtmpzDIz8D’ ‘~/tmp/scratch/RtmpzDTJBC’
‘~/tmp/scratch/RtmpzZ36Ly’ ‘~/tmp/scratch/Rtmpzjzxyf’
‘~/tmp/scratch/ccLHUPdN.s’ ‘~/tmp/scratch/xvfb-run.1l1KoW’
‘~/tmp/scratch/xvfb-run.2Rhi4z’ ‘~/tmp/scratch/xvfb-run.4RDxBK’
‘~/tmp/scratch/xvfb-run.4ppqC5’ ‘~/tmp/scratch/xvfb-run.4ueAJn’
‘~/tmp/scratch/xvfb-run.6kvoof’ ‘~/tmp/scratch/xvfb-run.6xD7A9’
‘~/tmp/scratch/xvfb-run.7t0ACX’ ‘~/tmp/scratch/xvfb-run.8AVgcN’
‘~/tmp/scratch/xvfb-run.8iO970’ ‘~/tmp/scratch/xvfb-run.8iU8Oj’
‘~/tmp/scratch/xvfb-run.9sZIeg’ ‘~/tmp/scratch/xvfb-run.A7noz6’
‘~/tmp/scratch/xvfb-run.Av458c’ ‘~/tmp/scratch/xvfb-run.BH9axs’
‘~/tmp/scratch/xvfb-run.ByV6oK’ ‘~/tmp/scratch/xvfb-run.Ej8RH3’
‘~/tmp/scratch/xvfb-run.FrT6eT’ ‘~/tmp/scratch/xvfb-run.Fzzbip’
‘~/tmp/scratch/xvfb-run.GrU3Cx’ ‘~/tmp/scratch/xvfb-run.IbuLsy’
‘~/tmp/scratch/xvfb-run.IlbVxW’ ‘~/tmp/scratch/xvfb-run.KkrEhD’
‘~/tmp/scratch/xvfb-run.MWs6WC’ ‘~/tmp/scratch/xvfb-run.Mwc8Mi’
‘~/tmp/scratch/xvfb-run.NAsbmR’ ‘~/tmp/scratch/xvfb-run.O6gQWg’
‘~/tmp/scratch/xvfb-run.POjB7x’ ‘~/tmp/scratch/xvfb-run.PQ7c9i’
‘~/tmp/scratch/xvfb-run.QKpiuZ’ ‘~/tmp/scratch/xvfb-run.QSt58L’
‘~/tmp/scratch/xvfb-run.Ql6QzQ’ ‘~/tmp/scratch/xvfb-run.TVP7Jx’
‘~/tmp/scratch/xvfb-run.Tq71RG’ ‘~/tmp/scratch/xvfb-run.TtBGXX’
‘~/tmp/scratch/xvfb-run.UaGyob’ ‘~/tmp/scratch/xvfb-run.VGPCBM’
‘~/tmp/scratch/xvfb-run.Wo8mgR’ ‘~/tmp/scratch/xvfb-run.ZFocwV’
‘~/tmp/scratch/xvfb-run.Zrk9ML’ ‘~/tmp/scratch/xvfb-run.b0CqnW’
‘~/tmp/scratch/xvfb-run.bqmoiK’ ‘~/tmp/scratch/xvfb-run.bwxyRI’
‘~/tmp/scratch/xvfb-run.cBTjRG’ ‘~/tmp/scratch/xvfb-run.dzOCYY’
‘~/tmp/scratch/xvfb-run.ekQ6t9’ ‘~/tmp/scratch/xvfb-run.esBmB0’
‘~/tmp/scratch/xvfb-run.fL2kbL’ ‘~/tmp/scratch/xvfb-run.foA9dC’
‘~/tmp/scratch/xvfb-run.gD9v5O’ ‘~/tmp/scratch/xvfb-run.gStfQP’
‘~/tmp/scratch/xvfb-run.hFLQv7’ ‘~/tmp/scratch/xvfb-run.hoYZjG’
‘~/tmp/scratch/xvfb-run.iVua4j’ ‘~/tmp/scratch/xvfb-run.iuCZBH’
‘~/tmp/scratch/xvfb-run.jklinj’ ‘~/tmp/scratch/xvfb-run.jlI877’
‘~/tmp/scratch/xvfb-run.lhRXcl’ ‘~/tmp/scratch/xvfb-run.mVLk4k’
‘~/tmp/scratch/xvfb-run.mhwrBp’ ‘~/tmp/scratch/xvfb-run.nLEsN2’
‘~/tmp/scratch/xvfb-run.nb0GkQ’ ‘~/tmp/scratch/xvfb-run.ndAaht’
‘~/tmp/scratch/xvfb-run.oI3q2E’ ‘~/tmp/scratch/xvfb-run.oIgyTf’
‘~/tmp/scratch/xvfb-run.oY2DdD’ ‘~/tmp/scratch/xvfb-run.odNQ14’
‘~/tmp/scratch/xvfb-run.ois016’ ‘~/tmp/scratch/xvfb-run.ozyKMT’
‘~/tmp/scratch/xvfb-run.qBiXAc’ ‘~/tmp/scratch/xvfb-run.qMSIwI’
‘~/tmp/scratch/xvfb-run.r9YJhp’ ‘~/tmp/scratch/xvfb-run.s9Fei2’
‘~/tmp/scratch/xvfb-run.tIzL3a’ ‘~/tmp/scratch/xvfb-run.tikteT’
‘~/tmp/scratch/xvfb-run.uEnf1A’ ‘~/tmp/scratch/xvfb-run.vDBMW6’
‘~/tmp/scratch/xvfb-run.vZWwn6’ ‘~/tmp/scratch/xvfb-run.wjs8ji’
‘~/tmp/scratch/xvfb-run.xBU4Uo’ ‘~/tmp/scratch/xvfb-run.ykz6WF’
‘~/tmp/scratch/xvfb-run.yvaUED’ ‘~/tmp/scratch/xvfb-run.zr5ZIZ’
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.7.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [27s/94s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(BIGr)
>
> test_check("BIGr")
--- Parentage Assignment Summary ---
Total progeny evaluated: 1
LOW_MARKERS : 1 (100.0%)
Min markers threshold : 10
Error threshold : 5 %
--- Parentage Assignment Results ---
Progeny Male_Parent Female_Parent Mendelian_Error_Pct Markers_Tested
<char> <char> <char> <char> <int>
1: child1 S1 D1 0.00 5
Assignment_Status
<char>
1: LOW_MARKERS
ID Concordance
1 ID1 91.67%
2 ID10 95.45%
3 ID11 90%
4 ID12 94.74%
5 ID13 100%
6 ID14 100%
7 ID15 100%
8 ID16 100%
9 ID17 100%
10 ID18 89.47%
11 ID19 93.75%
12 ID2 95.45%
13 ID20 100%
14 ID3 100%
15 ID4 100%
16 ID5 100%
17 ID6 73.68%
18 ID7 81.82%
19 ID8 100%
20 ID9 100%
Saving _problems/test-madc2vcf_all-25.R
Saving _problems/test-madc2vcf_all-80.R
Saving _problems/test-madc2vcf_all-112.R
Scanning file to determine attributes.
File attributes:
meta lines: 14
header_line: 15
variant count: 499
column count: 159
Meta line 14 read in.
All meta lines processed.
gt matrix initialized.
Character matrix gt created.
Character matrix gt rows: 499
Character matrix gt cols: 159
skip: 0
nrows: 499
row_num: 0
Processed variant: 499
All variants processed
Scanning file to determine attributes.
File attributes:
meta lines: 14
header_line: 15
variant count: 499
column count: 159
Meta line 14 read in.
All meta lines processed.
gt matrix initialized.
Character matrix gt created.
Character matrix gt rows: 499
Character matrix gt cols: 159
skip: 0
nrows: 499
row_num: 0
Processed variant: 499
All variants processed
Scanning file to determine attributes.
File attributes:
meta lines: 14
header_line: 15
variant count: 499
column count: 159
Meta line 14 read in.
All meta lines processed.
gt matrix initialized.
Character matrix gt created.
Character matrix gt rows: 499
Character matrix gt cols: 159
skip: 0
nrows: 499
row_num: 0
Processed variant: 499
All variants processed
[ FAIL 3 | WARN 0 | SKIP 4 | PASS 250 ]
══ Skipped tests (4) ═══════════════════════════════════════════════════════════
• On CRAN (4): 'test-check_madc_sanity.R:2:3', 'test-madc2vcf_all.R:162:3',
'test-madc2vcf_multi.R:35:3', 'test-madc2vcf_targets.R:154:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-madc2vcf_all.R:16:3'): test madc offtargets ────────────────────
Error in `checkForRemoteErrors(val)`: 2 nodes produced errors; first error: 'recursive' must be a length-1 vector
Backtrace:
▆
1. └─BIGr::madc2vcf_all(...) at test-madc2vcf_all.R:16:3
2. └─BIGr:::loop_though_dartag_report(...)
3. └─parallel::parLapply(...)
4. ├─base::do.call(...)
5. └─parallel::clusterApply(...)
6. └─parallel:::staticClusterApply(cl, fun, length(x), argfun)
7. └─parallel:::checkForRemoteErrors(val)
── Error ('test-madc2vcf_all.R:75:3'): madc2vcf_all preserves comma-separated AD for biallelic targets ──
Error in `checkForRemoteErrors(val)`: one node produced an error: 'recursive' must be a length-1 vector
Backtrace:
▆
1. └─BIGr::madc2vcf_all(...) at test-madc2vcf_all.R:75:3
2. └─BIGr:::loop_though_dartag_report(...)
3. └─parallel::parLapply(...)
4. ├─base::do.call(...)
5. └─parallel::clusterApply(...)
6. └─parallel:::staticClusterApply(cl, fun, length(x), argfun)
7. └─parallel:::checkForRemoteErrors(val)
── Failure ('test-madc2vcf_all.R:104:3'): madc2vcf_all accepts BI_markerID matches when CloneID does not match ──
Expected `madc2vcf_all(...)` not to throw any errors.
Actually got a <simpleError> with message:
one node produced an error: 'recursive' must be a length-1 vector
[ FAIL 3 | WARN 0 | SKIP 4 | PASS 250 ]
Error:
! Test failures.
Warning messages:
1: In for (nme in names(lhs)) { :
closing unused connection 8 (<-localhost:11688)
2: In for (nme in names(lhs)) { :
closing unused connection 7 (<-localhost:11688)
3: In for (nme in names(lhs)) { :
closing unused connection 6 (<-localhost:11688)
4: In for (nme in names(lhs)) { :
closing unused connection 5 (<-localhost:11688)
Execution halted
Flavor: r-oldrel-macos-x86_64