Last updated on 2026-08-03 19:49:59 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 | 22.01 | 193.47 | 215.48 | 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 | 21.00 | 474.00 | 495.00 | 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/Rtmp00NYyP’ ‘~/tmp/scratch/Rtmp0FmzAo’
‘~/tmp/scratch/Rtmp0juL3N’ ‘~/tmp/scratch/Rtmp0uUhKJ’
‘~/tmp/scratch/Rtmp0x0D0x’ ‘~/tmp/scratch/Rtmp1mozuJ’
‘~/tmp/scratch/Rtmp1wLWN8’ ‘~/tmp/scratch/Rtmp35Vv5Y’
‘~/tmp/scratch/Rtmp3XQrHe’ ‘~/tmp/scratch/Rtmp4CjjmR’
‘~/tmp/scratch/Rtmp4H2RUZ’ ‘~/tmp/scratch/Rtmp5evoBo’
‘~/tmp/scratch/Rtmp5xNy5N’ ‘~/tmp/scratch/Rtmp669vlS’
‘~/tmp/scratch/Rtmp7Lg0Jl’ ‘~/tmp/scratch/Rtmp7QYfjA’
‘~/tmp/scratch/Rtmp7mHgHY’ ‘~/tmp/scratch/Rtmp7oq1ht’
‘~/tmp/scratch/Rtmp7paytr’ ‘~/tmp/scratch/Rtmp7sQZzJ’
‘~/tmp/scratch/Rtmp8IzNbl’ ‘~/tmp/scratch/Rtmp8LcRhZ’
‘~/tmp/scratch/Rtmp8aheC8’ ‘~/tmp/scratch/Rtmp8iSDdp’
‘~/tmp/scratch/RtmpA0obad’ ‘~/tmp/scratch/RtmpAn7xzO’
‘~/tmp/scratch/RtmpBRaPq5’ ‘~/tmp/scratch/RtmpBo28Dy’
‘~/tmp/scratch/RtmpC6vVa3’ ‘~/tmp/scratch/RtmpCFSbIw’
‘~/tmp/scratch/RtmpCIUvDX’ ‘~/tmp/scratch/RtmpCOdops’
‘~/tmp/scratch/RtmpD5uXOE’ ‘~/tmp/scratch/RtmpDBLMqY’
‘~/tmp/scratch/RtmpDiCZMB’ ‘~/tmp/scratch/RtmpEUBB9c’
‘~/tmp/scratch/RtmpEYkWT0’ ‘~/tmp/scratch/RtmpEaDffG’
‘~/tmp/scratch/RtmpEh02QI’ ‘~/tmp/scratch/RtmpErqK0e’
‘~/tmp/scratch/RtmpFMQesq’ ‘~/tmp/scratch/RtmpFdIEOl’
‘~/tmp/scratch/RtmpGE9MzE’ ‘~/tmp/scratch/RtmpGpkTsG’
‘~/tmp/scratch/RtmpHARQxC’ ‘~/tmp/scratch/RtmpHBZTvU’
‘~/tmp/scratch/RtmpHItnGv’ ‘~/tmp/scratch/RtmpHVDxaT’
‘~/tmp/scratch/RtmpHW6VXg’ ‘~/tmp/scratch/RtmpHdhEIL’
‘~/tmp/scratch/RtmpI2u6MK’ ‘~/tmp/scratch/RtmpIE2EKN’
‘~/tmp/scratch/RtmpIE85Vs’ ‘~/tmp/scratch/RtmpIGPY78’
‘~/tmp/scratch/RtmpIHXFdw’ ‘~/tmp/scratch/RtmpIMeZVM’
‘~/tmp/scratch/RtmpIaOGMz’ ‘~/tmp/scratch/RtmpIjHld9’
‘~/tmp/scratch/RtmpIzyI2H’ ‘~/tmp/scratch/RtmpJ4QazY’
‘~/tmp/scratch/RtmpJ7sZjX’ ‘~/tmp/scratch/RtmpJYMp7F’
‘~/tmp/scratch/RtmpJgQMBQ’ ‘~/tmp/scratch/RtmpJtOxM0’
‘~/tmp/scratch/RtmpK5Gwx8’ ‘~/tmp/scratch/RtmpKFBaqL’
‘~/tmp/scratch/RtmpKS63PC’ ‘~/tmp/scratch/RtmpKkJbOV’
‘~/tmp/scratch/RtmpLChJYG’ ‘~/tmp/scratch/RtmpLq17QD’
‘~/tmp/scratch/RtmpM4nczn’ ‘~/tmp/scratch/RtmpM9543b’
‘~/tmp/scratch/RtmpMCMXT9’ ‘~/tmp/scratch/RtmpMDqPlJ’
‘~/tmp/scratch/RtmpNFjZL5’ ‘~/tmp/scratch/RtmpO8NJQz’
‘~/tmp/scratch/RtmpO9zVxa’ ‘~/tmp/scratch/RtmpOaOZUJ’
‘~/tmp/scratch/RtmpOtj3vy’ ‘~/tmp/scratch/RtmpOyJQmt’
‘~/tmp/scratch/RtmpPHtZWb’ ‘~/tmp/scratch/RtmpPXFTjo’
‘~/tmp/scratch/RtmpPavilI’ ‘~/tmp/scratch/RtmpQ6CMMi’
‘~/tmp/scratch/RtmpQRaLtM’ ‘~/tmp/scratch/RtmpQddvnT’
‘~/tmp/scratch/RtmpQkVFJm’ ‘~/tmp/scratch/RtmpQv0Lsg’
‘~/tmp/scratch/RtmpR0MuHs’ ‘~/tmp/scratch/RtmpR1JCGx’
‘~/tmp/scratch/RtmpReAUr8’ ‘~/tmp/scratch/RtmpS09fhS’
‘~/tmp/scratch/RtmpSCMHH3’ ‘~/tmp/scratch/RtmpSGAjX1’
‘~/tmp/scratch/RtmpT5Ke2I’ ‘~/tmp/scratch/RtmpT7lWXV’
‘~/tmp/scratch/RtmpT9WGUa’ ‘~/tmp/scratch/RtmpTX4Atu’
‘~/tmp/scratch/RtmpTmt2cd’ ‘~/tmp/scratch/RtmpUTbsJH’
‘~/tmp/scratch/RtmpVI1SDq’ ‘~/tmp/scratch/RtmpX3uhRt’
‘~/tmp/scratch/RtmpXQXcw4’ ‘~/tmp/scratch/RtmpXYHmuu’
‘~/tmp/scratch/RtmpY09lDJ’ ‘~/tmp/scratch/RtmpY7narK’
‘~/tmp/scratch/RtmpYOOq6x’ ‘~/tmp/scratch/RtmpZW2IQP’
‘~/tmp/scratch/RtmpZs4g5k’ ‘~/tmp/scratch/Rtmpa4jHuQ’
‘~/tmp/scratch/RtmpaBHqGG’ ‘~/tmp/scratch/RtmpaCsH7P’
‘~/tmp/scratch/RtmpaMR41l’ ‘~/tmp/scratch/RtmpaWylIt’
‘~/tmp/scratch/RtmpaZ8xFs’ ‘~/tmp/scratch/Rtmpabe5iF’
‘~/tmp/scratch/RtmpaltxcQ’ ‘~/tmp/scratch/Rtmpb2isM1’
‘~/tmp/scratch/RtmpbLtHn0’ ‘~/tmp/scratch/RtmpbW8uUG’
‘~/tmp/scratch/RtmpbwQMzu’ ‘~/tmp/scratch/RtmpcKfcVh’
‘~/tmp/scratch/RtmpcoM5ic’ ‘~/tmp/scratch/RtmpcrlbLc’
‘~/tmp/scratch/RtmpdieU3A’ ‘~/tmp/scratch/RtmpdnTUPn’
‘~/tmp/scratch/RtmpexiFJu’ ‘~/tmp/scratch/RtmpfKmT07’
‘~/tmp/scratch/Rtmpfm4idN’ ‘~/tmp/scratch/RtmpghebFL’
‘~/tmp/scratch/RtmpgsLAUt’ ‘~/tmp/scratch/RtmpgyqWW0’
‘~/tmp/scratch/Rtmph4PlLC’ ‘~/tmp/scratch/RtmphcfmHd’
‘~/tmp/scratch/Rtmphdpks4’ ‘~/tmp/scratch/RtmphlPTVI’
‘~/tmp/scratch/Rtmpi03wCg’ ‘~/tmp/scratch/RtmpiZmbbj’
‘~/tmp/scratch/RtmpixKcsx’ ‘~/tmp/scratch/Rtmpjc284W’
‘~/tmp/scratch/Rtmpk3iSsw’ ‘~/tmp/scratch/RtmpkM8seu’
‘~/tmp/scratch/RtmplQVUYp’ ‘~/tmp/scratch/Rtmplx3Idk’
‘~/tmp/scratch/RtmpnpLRml’ ‘~/tmp/scratch/RtmpoBZsbE’
‘~/tmp/scratch/RtmpozKGEs’ ‘~/tmp/scratch/RtmppOdg6k’
‘~/tmp/scratch/Rtmppd3rWx’ ‘~/tmp/scratch/Rtmpq0xvIS’
‘~/tmp/scratch/RtmpqILQHy’ ‘~/tmp/scratch/RtmpqpCVUs’
‘~/tmp/scratch/Rtmpr6hPjS’ ‘~/tmp/scratch/RtmprcNFqR’
‘~/tmp/scratch/RtmpryVXjC’ ‘~/tmp/scratch/RtmpsqjCWh’
‘~/tmp/scratch/Rtmpuq5gx5’ ‘~/tmp/scratch/Rtmpv7hWg9’
‘~/tmp/scratch/Rtmpv9j39z’ ‘~/tmp/scratch/RtmpvTRId9’
‘~/tmp/scratch/Rtmpw37oYD’ ‘~/tmp/scratch/Rtmpwr4Ivv’
‘~/tmp/scratch/RtmpwrZmMI’ ‘~/tmp/scratch/Rtmpx5fn9N’
‘~/tmp/scratch/Rtmpy1lpE0’ ‘~/tmp/scratch/RtmpyRRqkP’
‘~/tmp/scratch/RtmpysOkpG’ ‘~/tmp/scratch/RtmpyyVnBx’
‘~/tmp/scratch/RtmpzpL4Wm’ ‘~/tmp/scratch/ccZmMPqr.s’
‘~/tmp/scratch/ccdfbw4c.s’ ‘~/tmp/scratch/xvfb-run.0161pR’
‘~/tmp/scratch/xvfb-run.11JBIN’ ‘~/tmp/scratch/xvfb-run.26Qpkp’
‘~/tmp/scratch/xvfb-run.4ldFRv’ ‘~/tmp/scratch/xvfb-run.5A6PCe’
‘~/tmp/scratch/xvfb-run.6OoJ0E’ ‘~/tmp/scratch/xvfb-run.6UnnN2’
‘~/tmp/scratch/xvfb-run.6wgzU6’ ‘~/tmp/scratch/xvfb-run.9eVRsj’
‘~/tmp/scratch/xvfb-run.AuDZa0’ ‘~/tmp/scratch/xvfb-run.CFnYae’
‘~/tmp/scratch/xvfb-run.CO5Fm4’ ‘~/tmp/scratch/xvfb-run.CZu9xc’
‘~/tmp/scratch/xvfb-run.CuwIIj’ ‘~/tmp/scratch/xvfb-run.Cv8JMD’
‘~/tmp/scratch/xvfb-run.DntMur’ ‘~/tmp/scratch/xvfb-run.EdigNL’
‘~/tmp/scratch/xvfb-run.GVZrbX’ ‘~/tmp/scratch/xvfb-run.GmMLd7’
‘~/tmp/scratch/xvfb-run.HKI5Tf’ ‘~/tmp/scratch/xvfb-run.I6eTBF’
‘~/tmp/scratch/xvfb-run.KGWdaU’ ‘~/tmp/scratch/xvfb-run.LKEpFD’
‘~/tmp/scratch/xvfb-run.OBd2Fs’ ‘~/tmp/scratch/xvfb-run.OTYByw’
‘~/tmp/scratch/xvfb-run.OhWuiz’ ‘~/tmp/scratch/xvfb-run.OtHxa4’
‘~/tmp/scratch/xvfb-run.Ow8xqr’ ‘~/tmp/scratch/xvfb-run.PCSNSj’
‘~/tmp/scratch/xvfb-run.Q28vrw’ ‘~/tmp/scratch/xvfb-run.QIdYnh’
‘~/tmp/scratch/xvfb-run.QPljzG’ ‘~/tmp/scratch/xvfb-run.QcYrL0’
‘~/tmp/scratch/xvfb-run.QkBNsP’ ‘~/tmp/scratch/xvfb-run.R1Qqla’
‘~/tmp/scratch/xvfb-run.SnMP59’ ‘~/tmp/scratch/xvfb-run.T34OBZ’
‘~/tmp/scratch/xvfb-run.THzBt9’ ‘~/tmp/scratch/xvfb-run.TpzFpP’
‘~/tmp/scratch/xvfb-run.UChLSs’ ‘~/tmp/scratch/xvfb-run.VS8pW9’
‘~/tmp/scratch/xvfb-run.YdJBsv’ ‘~/tmp/scratch/xvfb-run.YpPz3o’
‘~/tmp/scratch/xvfb-run.ZAxKWZ’ ‘~/tmp/scratch/xvfb-run.ZmgJ0Q’
‘~/tmp/scratch/xvfb-run.ZmofPI’ ‘~/tmp/scratch/xvfb-run.bCuUBj’
‘~/tmp/scratch/xvfb-run.c74RQo’ ‘~/tmp/scratch/xvfb-run.d8P8t6’
‘~/tmp/scratch/xvfb-run.dJcyml’ ‘~/tmp/scratch/xvfb-run.e9X9us’
‘~/tmp/scratch/xvfb-run.fzBtnp’ ‘~/tmp/scratch/xvfb-run.g7UDKS’
‘~/tmp/scratch/xvfb-run.gFRbNK’ ‘~/tmp/scratch/xvfb-run.hSc82j’
‘~/tmp/scratch/xvfb-run.ix3qep’ ‘~/tmp/scratch/xvfb-run.jUptnP’
‘~/tmp/scratch/xvfb-run.jvl98G’ ‘~/tmp/scratch/xvfb-run.k60o5R’
‘~/tmp/scratch/xvfb-run.kq9rwu’ ‘~/tmp/scratch/xvfb-run.l329S1’
‘~/tmp/scratch/xvfb-run.nKfX2v’ ‘~/tmp/scratch/xvfb-run.nrx4Ca’
‘~/tmp/scratch/xvfb-run.o46eOh’ ‘~/tmp/scratch/xvfb-run.oJ5Xx6’
‘~/tmp/scratch/xvfb-run.p5BExV’ ‘~/tmp/scratch/xvfb-run.p64xGJ’
‘~/tmp/scratch/xvfb-run.pR1zyx’ ‘~/tmp/scratch/xvfb-run.qPyjmf’
‘~/tmp/scratch/xvfb-run.qRuwtM’ ‘~/tmp/scratch/xvfb-run.sUlQ0E’
‘~/tmp/scratch/xvfb-run.tEUU6k’ ‘~/tmp/scratch/xvfb-run.tUhJvV’
‘~/tmp/scratch/xvfb-run.tbFy0A’ ‘~/tmp/scratch/xvfb-run.trdX2X’
‘~/tmp/scratch/xvfb-run.v9l5ym’ ‘~/tmp/scratch/xvfb-run.vKxR2m’
‘~/tmp/scratch/xvfb-run.vtSwOE’ ‘~/tmp/scratch/xvfb-run.wi7zci’
‘~/tmp/scratch/xvfb-run.y9Empo’ ‘~/tmp/scratch/xvfb-run.yB8GWw’
‘~/tmp/scratch/xvfb-run.zCRiwK’
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.7.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [30s/158s]
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:11900)
2: In for (nme in names(lhs)) { :
closing unused connection 7 (<-localhost:11900)
3: In for (nme in names(lhs)) { :
closing unused connection 6 (<-localhost:11900)
4: In for (nme in names(lhs)) { :
closing unused connection 5 (<-localhost:11900)
Execution halted
Flavor: r-oldrel-macos-x86_64