Last updated on 2026-08-04 07:50:23 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 | 22.84 | 196.30 | 219.14 | 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 | 32.00 | 365.00 | 397.00 | 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 | 461.00 | 481.00 | ERROR | |
| r-oldrel-windows-x86_64 | 0.7.2 | 43.00 | 495.00 | 538.00 | OK |
Version: 0.7.2
Check: for new files in some other directories
Result: NOTE
Found the following files/directories:
‘~/tmp/scratch/Rtmp04rdh6’ ‘~/tmp/scratch/Rtmp17LLQN’
‘~/tmp/scratch/Rtmp1QuEdY’ ‘~/tmp/scratch/Rtmp1qWke6’
‘~/tmp/scratch/Rtmp2AZMNI’ ‘~/tmp/scratch/Rtmp2E89B5’
‘~/tmp/scratch/Rtmp2jZtuL’ ‘~/tmp/scratch/Rtmp2ml2tE’
‘~/tmp/scratch/Rtmp38iIOU’ ‘~/tmp/scratch/Rtmp3NJE2K’
‘~/tmp/scratch/Rtmp3yb1XF’ ‘~/tmp/scratch/Rtmp4Nu5jM’
‘~/tmp/scratch/Rtmp4n4hWp’ ‘~/tmp/scratch/Rtmp4ntDPg’
‘~/tmp/scratch/Rtmp4ulY2Z’ ‘~/tmp/scratch/Rtmp55hlqI’
‘~/tmp/scratch/Rtmp5EA3Jb’ ‘~/tmp/scratch/Rtmp5Hm0xp’
‘~/tmp/scratch/Rtmp5s482F’ ‘~/tmp/scratch/Rtmp7EkKlT’
‘~/tmp/scratch/Rtmp7Ltp7g’ ‘~/tmp/scratch/Rtmp80DhcV’
‘~/tmp/scratch/Rtmp82ElQE’ ‘~/tmp/scratch/Rtmp8AC5P4’
‘~/tmp/scratch/Rtmp8WYo4T’ ‘~/tmp/scratch/Rtmp8iFmqz’
‘~/tmp/scratch/RtmpAZZxUv’ ‘~/tmp/scratch/RtmpAjMpoB’
‘~/tmp/scratch/RtmpAz03wm’ ‘~/tmp/scratch/RtmpBujzqV’
‘~/tmp/scratch/RtmpDRqLd2’ ‘~/tmp/scratch/RtmpDSOLd8’
‘~/tmp/scratch/RtmpEAs1EQ’ ‘~/tmp/scratch/RtmpEFrNGO’
‘~/tmp/scratch/RtmpEZGxfS’ ‘~/tmp/scratch/RtmpF04BSp’
‘~/tmp/scratch/RtmpFjn4Dc’ ‘~/tmp/scratch/RtmpGnK4mU’
‘~/tmp/scratch/RtmpH1rbLU’ ‘~/tmp/scratch/RtmpIEEslW’
‘~/tmp/scratch/RtmpIEdeSU’ ‘~/tmp/scratch/RtmpIJKaQx’
‘~/tmp/scratch/RtmpITNHKM’ ‘~/tmp/scratch/RtmpIsVq3i’
‘~/tmp/scratch/RtmpItrPaT’ ‘~/tmp/scratch/RtmpJvSnYD’
‘~/tmp/scratch/RtmpKer2u8’ ‘~/tmp/scratch/RtmpKett89’
‘~/tmp/scratch/RtmpKmJ3ZT’ ‘~/tmp/scratch/RtmpKwWIYk’
‘~/tmp/scratch/RtmpLcEdiu’ ‘~/tmp/scratch/RtmpLdlGZZ’
‘~/tmp/scratch/RtmpLgeA3x’ ‘~/tmp/scratch/RtmpLjEEwf’
‘~/tmp/scratch/RtmpMK0ckQ’ ‘~/tmp/scratch/RtmpMe0Q6I’
‘~/tmp/scratch/RtmpMwXRQK’ ‘~/tmp/scratch/RtmpNGFnK1’
‘~/tmp/scratch/RtmpNJ7QKW’ ‘~/tmp/scratch/RtmpNNjw4C’
‘~/tmp/scratch/RtmpNjBGFY’ ‘~/tmp/scratch/RtmpNwXFal’
‘~/tmp/scratch/RtmpO9fTOR’ ‘~/tmp/scratch/RtmpONcZU5’
‘~/tmp/scratch/RtmpOcrRjj’ ‘~/tmp/scratch/RtmpOfpE2U’
‘~/tmp/scratch/RtmpPWNfST’ ‘~/tmp/scratch/RtmpPmnKux’
‘~/tmp/scratch/RtmpQ2uM9T’ ‘~/tmp/scratch/RtmpQAyuzs’
‘~/tmp/scratch/RtmpQOWvSh’ ‘~/tmp/scratch/RtmpR1hXNN’
‘~/tmp/scratch/RtmpR6FZIu’ ‘~/tmp/scratch/RtmpRDKGUk’
‘~/tmp/scratch/RtmpRKQzEX’ ‘~/tmp/scratch/RtmpSNTGH0’
‘~/tmp/scratch/RtmpSOxu0R’ ‘~/tmp/scratch/RtmpSRGff3’
‘~/tmp/scratch/RtmpSSEK32’ ‘~/tmp/scratch/RtmpSl9pzz’
‘~/tmp/scratch/RtmpTFWhxU’ ‘~/tmp/scratch/RtmpTPT6Af’
‘~/tmp/scratch/RtmpTiKSAx’ ‘~/tmp/scratch/RtmpTv3w1a’
‘~/tmp/scratch/RtmpU1uAgl’ ‘~/tmp/scratch/RtmpU3nBqA’
‘~/tmp/scratch/RtmpUSb5YS’ ‘~/tmp/scratch/RtmpUmeElL’
‘~/tmp/scratch/RtmpV444NZ’ ‘~/tmp/scratch/RtmpV7bdRP’
‘~/tmp/scratch/RtmpVR7IQQ’ ‘~/tmp/scratch/RtmpVsLmNG’
‘~/tmp/scratch/RtmpWp0Wcl’ ‘~/tmp/scratch/RtmpWxBf8p’
‘~/tmp/scratch/RtmpWxUq5x’ ‘~/tmp/scratch/RtmpWyBZ6s’
‘~/tmp/scratch/RtmpXYTr8u’ ‘~/tmp/scratch/RtmpYLE5R5’
‘~/tmp/scratch/RtmpYUTJLV’ ‘~/tmp/scratch/RtmpYfZGuA’
‘~/tmp/scratch/RtmpYy5oTX’ ‘~/tmp/scratch/RtmpZGtRDy’
‘~/tmp/scratch/RtmpZYFXcz’ ‘~/tmp/scratch/Rtmpa0bDSp’
‘~/tmp/scratch/RtmpaSrEef’ ‘~/tmp/scratch/RtmpaqqWBW’
‘~/tmp/scratch/RtmpavHEa2’ ‘~/tmp/scratch/RtmpcE8L2a’
‘~/tmp/scratch/RtmpcdAZwB’ ‘~/tmp/scratch/RtmpcqVSLj’
‘~/tmp/scratch/Rtmpd0eZDb’ ‘~/tmp/scratch/RtmpdFa33R’
‘~/tmp/scratch/RtmpdOOS18’ ‘~/tmp/scratch/Rtmpdfo0Nw’
‘~/tmp/scratch/RtmpeMhYMx’ ‘~/tmp/scratch/RtmpeaEE2S’
‘~/tmp/scratch/RtmpeeltAT’ ‘~/tmp/scratch/RtmpfDiDsz’
‘~/tmp/scratch/RtmpfLHUqk’ ‘~/tmp/scratch/RtmpfyAng0’
‘~/tmp/scratch/RtmphcF6R2’ ‘~/tmp/scratch/RtmphcNwRV’
‘~/tmp/scratch/RtmphwsoNx’ ‘~/tmp/scratch/Rtmpi50cTg’
‘~/tmp/scratch/RtmpiSiBGN’ ‘~/tmp/scratch/RtmpjDfuU6’
‘~/tmp/scratch/Rtmpjxscsk’ ‘~/tmp/scratch/Rtmpl4Z7Cx’
‘~/tmp/scratch/Rtmpl8SsVv’ ‘~/tmp/scratch/RtmplANkib’
‘~/tmp/scratch/RtmplBhwM3’ ‘~/tmp/scratch/RtmplbShJK’
‘~/tmp/scratch/Rtmplpc3B3’ ‘~/tmp/scratch/Rtmpm45ZtT’
‘~/tmp/scratch/RtmpmGe6gL’ ‘~/tmp/scratch/RtmpmJUHrn’
‘~/tmp/scratch/RtmpnB1Ope’ ‘~/tmp/scratch/Rtmpnrw6mU’
‘~/tmp/scratch/RtmpobGqa3’ ‘~/tmp/scratch/RtmppNzqOz’
‘~/tmp/scratch/RtmppXkeIv’ ‘~/tmp/scratch/RtmppYQj2a’
‘~/tmp/scratch/Rtmpq9R8v0’ ‘~/tmp/scratch/RtmpqWTnj0’
‘~/tmp/scratch/Rtmpqa7Yar’ ‘~/tmp/scratch/RtmpqnAN9n’
‘~/tmp/scratch/RtmpqnkWPr’ ‘~/tmp/scratch/RtmpqohJ6Z’
‘~/tmp/scratch/Rtmpqy61ul’ ‘~/tmp/scratch/RtmprCxb2A’
‘~/tmp/scratch/RtmprvkhLb’ ‘~/tmp/scratch/RtmpsihOpR’
‘~/tmp/scratch/RtmpsrVu8j’ ‘~/tmp/scratch/RtmptSRO5L’
‘~/tmp/scratch/RtmptZ3whL’ ‘~/tmp/scratch/RtmptdnX4h’
‘~/tmp/scratch/RtmptizNpJ’ ‘~/tmp/scratch/RtmptqBYJN’
‘~/tmp/scratch/RtmpttOv58’ ‘~/tmp/scratch/RtmpuFOc5q’
‘~/tmp/scratch/RtmpuVOXCt’ ‘~/tmp/scratch/Rtmpuiwk6t’
‘~/tmp/scratch/RtmpuoBsro’ ‘~/tmp/scratch/RtmpvJgwit’
‘~/tmp/scratch/Rtmpw3MSS4’ ‘~/tmp/scratch/RtmpxBKogX’
‘~/tmp/scratch/RtmpxOL9ZI’ ‘~/tmp/scratch/Rtmpxhi1NV’
‘~/tmp/scratch/RtmpxjjzyH’ ‘~/tmp/scratch/Rtmpym1xeA’
‘~/tmp/scratch/Rtmpz63ZuS’ ‘~/tmp/scratch/RtmpzKMIQx’
‘~/tmp/scratch/ccdVF6Ks.s’ ‘~/tmp/scratch/xvfb-run.09RZHr’
‘~/tmp/scratch/xvfb-run.1VdHMO’ ‘~/tmp/scratch/xvfb-run.2SaQKX’
‘~/tmp/scratch/xvfb-run.33kHjo’ ‘~/tmp/scratch/xvfb-run.3EHB0O’
‘~/tmp/scratch/xvfb-run.3TGzow’ ‘~/tmp/scratch/xvfb-run.49FtTq’
‘~/tmp/scratch/xvfb-run.4OAwrz’ ‘~/tmp/scratch/xvfb-run.5RcMQ9’
‘~/tmp/scratch/xvfb-run.6Ro8OG’ ‘~/tmp/scratch/xvfb-run.6vJyOs’
‘~/tmp/scratch/xvfb-run.85AcBv’ ‘~/tmp/scratch/xvfb-run.9Hn303’
‘~/tmp/scratch/xvfb-run.9Vb4MC’ ‘~/tmp/scratch/xvfb-run.9lrQnj’
‘~/tmp/scratch/xvfb-run.9ttXD9’ ‘~/tmp/scratch/xvfb-run.B1Ryl3’
‘~/tmp/scratch/xvfb-run.BOxIYo’ ‘~/tmp/scratch/xvfb-run.ChgbAc’
‘~/tmp/scratch/xvfb-run.GuwkMF’ ‘~/tmp/scratch/xvfb-run.HVZ6ME’
‘~/tmp/scratch/xvfb-run.I13SqN’ ‘~/tmp/scratch/xvfb-run.KorNU6’
‘~/tmp/scratch/xvfb-run.KwsAQY’ ‘~/tmp/scratch/xvfb-run.Lgto7w’
‘~/tmp/scratch/xvfb-run.LzuSm8’ ‘~/tmp/scratch/xvfb-run.MiMeI5’
‘~/tmp/scratch/xvfb-run.Mjo2r6’ ‘~/tmp/scratch/xvfb-run.NORnPQ’
‘~/tmp/scratch/xvfb-run.OYJ8LW’ ‘~/tmp/scratch/xvfb-run.PYJNwj’
‘~/tmp/scratch/xvfb-run.QL8l80’ ‘~/tmp/scratch/xvfb-run.RZGSSq’
‘~/tmp/scratch/xvfb-run.Rdt4FC’ ‘~/tmp/scratch/xvfb-run.RsiErK’
‘~/tmp/scratch/xvfb-run.TGkkxC’ ‘~/tmp/scratch/xvfb-run.TtxZMf’
‘~/tmp/scratch/xvfb-run.UW4AaN’ ‘~/tmp/scratch/xvfb-run.VOAlfx’
‘~/tmp/scratch/xvfb-run.Vl4HXt’ ‘~/tmp/scratch/xvfb-run.YbVBwL’
‘~/tmp/scratch/xvfb-run.Ztjk2Q’ ‘~/tmp/scratch/xvfb-run.aO0qUG’
‘~/tmp/scratch/xvfb-run.btFcqJ’ ‘~/tmp/scratch/xvfb-run.bw0ZZr’
‘~/tmp/scratch/xvfb-run.dNIAyA’ ‘~/tmp/scratch/xvfb-run.e21HRW’
‘~/tmp/scratch/xvfb-run.eF2ayg’ ‘~/tmp/scratch/xvfb-run.eHVuq2’
‘~/tmp/scratch/xvfb-run.fNANyq’ ‘~/tmp/scratch/xvfb-run.fSg1Sj’
‘~/tmp/scratch/xvfb-run.fnd6So’ ‘~/tmp/scratch/xvfb-run.gMbynU’
‘~/tmp/scratch/xvfb-run.gZxhR3’ ‘~/tmp/scratch/xvfb-run.h4behY’
‘~/tmp/scratch/xvfb-run.hyXawV’ ‘~/tmp/scratch/xvfb-run.iFvP7R’
‘~/tmp/scratch/xvfb-run.jeHYFS’ ‘~/tmp/scratch/xvfb-run.nKL2Gu’
‘~/tmp/scratch/xvfb-run.nLnKRd’ ‘~/tmp/scratch/xvfb-run.nSna1q’
‘~/tmp/scratch/xvfb-run.ni2EnM’ ‘~/tmp/scratch/xvfb-run.nnRuC1’
‘~/tmp/scratch/xvfb-run.pVxWWO’ ‘~/tmp/scratch/xvfb-run.pd7Q6J’
‘~/tmp/scratch/xvfb-run.qbstiU’ ‘~/tmp/scratch/xvfb-run.qzBiFp’
‘~/tmp/scratch/xvfb-run.r88Ot7’ ‘~/tmp/scratch/xvfb-run.sF8yIy’
‘~/tmp/scratch/xvfb-run.t0Cyd9’ ‘~/tmp/scratch/xvfb-run.tXZ3cE’
‘~/tmp/scratch/xvfb-run.u5Mjl6’ ‘~/tmp/scratch/xvfb-run.vXJil6’
‘~/tmp/scratch/xvfb-run.wNL27I’ ‘~/tmp/scratch/xvfb-run.wP3nc9’
‘~/tmp/scratch/xvfb-run.xN0Zsn’ ‘~/tmp/scratch/xvfb-run.y5tPtS’
‘~/tmp/scratch/xvfb-run.yl4uK5’ ‘~/tmp/scratch/xvfb-run.zO0elv’
‘~/tmp/scratch/xvfb-run.zOZpLe’ ‘~/tmp/scratch/xvfb-run.zb3Y58’
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.7.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [30s/173s]
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:11549)
2: In for (nme in names(lhs)) { :
closing unused connection 7 (<-localhost:11549)
3: In for (nme in names(lhs)) { :
closing unused connection 6 (<-localhost:11549)
4: In for (nme in names(lhs)) { :
closing unused connection 5 (<-localhost:11549)
Execution halted
Flavor: r-oldrel-macos-x86_64