Last updated on 2026-08-01 09:50:13 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 | 20.79 | 195.80 | 216.59 | 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 | 28.32 | 255.76 | 284.08 | 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 | 21.00 | 391.00 | 412.00 | 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/Rtmp0652tk’ ‘~/tmp/scratch/Rtmp0HHc7P’
‘~/tmp/scratch/Rtmp0zx7o8’ ‘~/tmp/scratch/Rtmp1ZznE3’
‘~/tmp/scratch/Rtmp22sXV9’ ‘~/tmp/scratch/Rtmp27lGZR’
‘~/tmp/scratch/Rtmp2He5fK’ ‘~/tmp/scratch/Rtmp2SXiYD’
‘~/tmp/scratch/Rtmp32PtX3’ ‘~/tmp/scratch/Rtmp371SQE’
‘~/tmp/scratch/Rtmp40042k’ ‘~/tmp/scratch/Rtmp42C3PS’
‘~/tmp/scratch/Rtmp50y0uT’ ‘~/tmp/scratch/Rtmp5Pjrqh’
‘~/tmp/scratch/Rtmp5e30tf’ ‘~/tmp/scratch/Rtmp6Va5rQ’
‘~/tmp/scratch/Rtmp6hvPhG’ ‘~/tmp/scratch/Rtmp6p51dq’
‘~/tmp/scratch/Rtmp73Mrew’ ‘~/tmp/scratch/Rtmp8KmfOr’
‘~/tmp/scratch/Rtmp8Utn9t’ ‘~/tmp/scratch/Rtmp8eI5Zh’
‘~/tmp/scratch/Rtmp8jndLD’ ‘~/tmp/scratch/Rtmp8so4ka’
‘~/tmp/scratch/Rtmp9EnKGy’ ‘~/tmp/scratch/Rtmp9LuwnZ’
‘~/tmp/scratch/Rtmp9PNWUb’ ‘~/tmp/scratch/Rtmp9SKaYN’
‘~/tmp/scratch/Rtmp9cQjGu’ ‘~/tmp/scratch/RtmpA9zfks’
‘~/tmp/scratch/RtmpB7YyIH’ ‘~/tmp/scratch/RtmpCGrRM9’
‘~/tmp/scratch/RtmpDbJtyz’ ‘~/tmp/scratch/RtmpDipMn4’
‘~/tmp/scratch/RtmpDtD2qJ’ ‘~/tmp/scratch/RtmpENxw3l’
‘~/tmp/scratch/RtmpFC3LRi’ ‘~/tmp/scratch/RtmpFqG0ST’
‘~/tmp/scratch/RtmpGDiIHQ’ ‘~/tmp/scratch/RtmpGhLGCq’
‘~/tmp/scratch/RtmpGs4RNZ’ ‘~/tmp/scratch/RtmpGurQ2N’
‘~/tmp/scratch/RtmpH7hwGq’ ‘~/tmp/scratch/RtmpHOPGEJ’
‘~/tmp/scratch/RtmpHdliNN’ ‘~/tmp/scratch/RtmpHnG8uw’
‘~/tmp/scratch/RtmpI4SGbt’ ‘~/tmp/scratch/RtmpII6UR9’
‘~/tmp/scratch/RtmpIu9ntH’ ‘~/tmp/scratch/RtmpIzJxGo’
‘~/tmp/scratch/RtmpJ4BlDZ’ ‘~/tmp/scratch/RtmpJ8QKi6’
‘~/tmp/scratch/RtmpJWm6EK’ ‘~/tmp/scratch/RtmpJzXN3x’
‘~/tmp/scratch/RtmpKw1wel’ ‘~/tmp/scratch/RtmpL8KZuR’
‘~/tmp/scratch/RtmpLBEFPk’ ‘~/tmp/scratch/RtmpLnKtFZ’
‘~/tmp/scratch/RtmpM2RTXS’ ‘~/tmp/scratch/RtmpM7VxX9’
‘~/tmp/scratch/RtmpMaptPq’ ‘~/tmp/scratch/RtmpN5Z1kz’
‘~/tmp/scratch/RtmpNIic1A’ ‘~/tmp/scratch/RtmpNNZVFj’
‘~/tmp/scratch/RtmpNZuzSU’ ‘~/tmp/scratch/RtmpNleQcC’
‘~/tmp/scratch/RtmpOgrpgy’ ‘~/tmp/scratch/RtmpOm71Fs’
‘~/tmp/scratch/RtmpP7f0VG’ ‘~/tmp/scratch/RtmpPOkDfX’
‘~/tmp/scratch/RtmpPPRH1p’ ‘~/tmp/scratch/RtmpPjULnK’
‘~/tmp/scratch/RtmpQ68WCN’ ‘~/tmp/scratch/RtmpQDOS7u’
‘~/tmp/scratch/RtmpQGHH7K’ ‘~/tmp/scratch/RtmpQYbMkE’
‘~/tmp/scratch/RtmpQdBicm’ ‘~/tmp/scratch/RtmpRQFesQ’
‘~/tmp/scratch/RtmpSX2TJY’ ‘~/tmp/scratch/RtmpSuL00e’
‘~/tmp/scratch/RtmpSzOSet’ ‘~/tmp/scratch/RtmpTpg3uC’
‘~/tmp/scratch/RtmpTuVlNV’ ‘~/tmp/scratch/RtmpU3nYXB’
‘~/tmp/scratch/RtmpUPBbPh’ ‘~/tmp/scratch/RtmpUQGnO8’
‘~/tmp/scratch/RtmpUbn9Q1’ ‘~/tmp/scratch/RtmpUcA8yK’
‘~/tmp/scratch/RtmpUcpIAq’ ‘~/tmp/scratch/RtmpVDpWob’
‘~/tmp/scratch/RtmpVFKT9u’ ‘~/tmp/scratch/RtmpVm4T0G’
‘~/tmp/scratch/RtmpW4QN8e’ ‘~/tmp/scratch/RtmpW8RUYl’
‘~/tmp/scratch/RtmpWGrteT’ ‘~/tmp/scratch/RtmpWK3Jej’
‘~/tmp/scratch/RtmpXDdtBO’ ‘~/tmp/scratch/RtmpXlNj1n’
‘~/tmp/scratch/RtmpY5lXN0’ ‘~/tmp/scratch/RtmpYIBdXq’
‘~/tmp/scratch/RtmpYYbkQq’ ‘~/tmp/scratch/RtmpZH1C0v’
‘~/tmp/scratch/Rtmpa2b8ER’ ‘~/tmp/scratch/RtmpaKBast’
‘~/tmp/scratch/RtmpaPgsze’ ‘~/tmp/scratch/RtmpayKOo9’
‘~/tmp/scratch/RtmpbLqpcq’ ‘~/tmp/scratch/RtmpbbMuv7’
‘~/tmp/scratch/RtmpbgfFSS’ ‘~/tmp/scratch/RtmpbuDo6A’
‘~/tmp/scratch/Rtmpc8Dzrp’ ‘~/tmp/scratch/Rtmpc8jRVS’
‘~/tmp/scratch/Rtmpd5alcY’ ‘~/tmp/scratch/Rtmpd9F9Sf’
‘~/tmp/scratch/RtmpdALHif’ ‘~/tmp/scratch/RtmpdKqfWy’
‘~/tmp/scratch/RtmpdYF3S1’ ‘~/tmp/scratch/Rtmpdukobp’
‘~/tmp/scratch/RtmpeLguYO’ ‘~/tmp/scratch/RtmpeRNIak’
‘~/tmp/scratch/RtmpeqJtZY’ ‘~/tmp/scratch/RtmperUH9B’
‘~/tmp/scratch/Rtmpf5QRCJ’ ‘~/tmp/scratch/RtmpfBbFsa’
‘~/tmp/scratch/RtmpfXBkt5’ ‘~/tmp/scratch/RtmpfiPtgn’
‘~/tmp/scratch/Rtmpfr0KPO’ ‘~/tmp/scratch/RtmpfsbegQ’
‘~/tmp/scratch/RtmpgNrbgZ’ ‘~/tmp/scratch/RtmpgU0Hie’
‘~/tmp/scratch/RtmpgUeLLi’ ‘~/tmp/scratch/RtmpgnpLXy’
‘~/tmp/scratch/RtmpgvW9YJ’ ‘~/tmp/scratch/RtmphaNwJ6’
‘~/tmp/scratch/RtmpiEk5wh’ ‘~/tmp/scratch/RtmpitfLgx’
‘~/tmp/scratch/RtmpizIdKL’ ‘~/tmp/scratch/Rtmpj6tavF’
‘~/tmp/scratch/RtmpjpxqDc’ ‘~/tmp/scratch/Rtmpjqj8PC’
‘~/tmp/scratch/Rtmpjv9SrE’ ‘~/tmp/scratch/RtmpjwYvZH’
‘~/tmp/scratch/Rtmpkzt4LY’ ‘~/tmp/scratch/Rtmpl8d4l5’
‘~/tmp/scratch/RtmplRaeyR’ ‘~/tmp/scratch/RtmplvRwo7’
‘~/tmp/scratch/RtmpnHkB5F’ ‘~/tmp/scratch/RtmpnSj3jh’
‘~/tmp/scratch/RtmpnyrNy3’ ‘~/tmp/scratch/Rtmpon7vdE’
‘~/tmp/scratch/Rtmpp3xjmq’ ‘~/tmp/scratch/RtmppA2FWz’
‘~/tmp/scratch/RtmppLB20l’ ‘~/tmp/scratch/RtmpqHMaUn’
‘~/tmp/scratch/Rtmprv4scX’ ‘~/tmp/scratch/Rtmps1n9JG’
‘~/tmp/scratch/RtmpsjgTHn’ ‘~/tmp/scratch/Rtmptb3XAK’
‘~/tmp/scratch/Rtmpu3jdbx’ ‘~/tmp/scratch/RtmpuI4bAZ’
‘~/tmp/scratch/RtmpusOBq8’ ‘~/tmp/scratch/RtmpvHgUSN’
‘~/tmp/scratch/RtmpvO1cch’ ‘~/tmp/scratch/RtmpvgHEwL’
‘~/tmp/scratch/RtmpvsKCvw’ ‘~/tmp/scratch/RtmpwTYm9V’
‘~/tmp/scratch/Rtmpxj5sFQ’ ‘~/tmp/scratch/Rtmpy32Zt1’
‘~/tmp/scratch/Rtmpz5VVXc’ ‘~/tmp/scratch/RtmpzH5aK5’
‘~/tmp/scratch/RtmpzeHO2e’ ‘~/tmp/scratch/RtmpzfyBPa’
‘~/tmp/scratch/RtmpzkbjnD’ ‘~/tmp/scratch/ccFDph4f.s’
‘~/tmp/scratch/xvfb-run.10PCgq’ ‘~/tmp/scratch/xvfb-run.1P9UeC’
‘~/tmp/scratch/xvfb-run.1PizkC’ ‘~/tmp/scratch/xvfb-run.2E51sI’
‘~/tmp/scratch/xvfb-run.41cgHi’ ‘~/tmp/scratch/xvfb-run.4TIa2r’
‘~/tmp/scratch/xvfb-run.67f1x5’ ‘~/tmp/scratch/xvfb-run.6TjOJU’
‘~/tmp/scratch/xvfb-run.7E4vZW’ ‘~/tmp/scratch/xvfb-run.8BRqkV’
‘~/tmp/scratch/xvfb-run.8W6p1T’ ‘~/tmp/scratch/xvfb-run.8mcTpU’
‘~/tmp/scratch/xvfb-run.945Lll’ ‘~/tmp/scratch/xvfb-run.9cXSES’
‘~/tmp/scratch/xvfb-run.AWxkP0’ ‘~/tmp/scratch/xvfb-run.Aw5BjW’
‘~/tmp/scratch/xvfb-run.BEuxV5’ ‘~/tmp/scratch/xvfb-run.BcMkwd’
‘~/tmp/scratch/xvfb-run.CCtQ47’ ‘~/tmp/scratch/xvfb-run.DS4CLQ’
‘~/tmp/scratch/xvfb-run.EeOU1p’ ‘~/tmp/scratch/xvfb-run.F7t6O8’
‘~/tmp/scratch/xvfb-run.FZzIfX’ ‘~/tmp/scratch/xvfb-run.FzttkH’
‘~/tmp/scratch/xvfb-run.GRbIzl’ ‘~/tmp/scratch/xvfb-run.Gvd6p1’
‘~/tmp/scratch/xvfb-run.HoSPQI’ ‘~/tmp/scratch/xvfb-run.IbVrHT’
‘~/tmp/scratch/xvfb-run.JCQCLw’ ‘~/tmp/scratch/xvfb-run.Jl1DqT’
‘~/tmp/scratch/xvfb-run.KyeE5b’ ‘~/tmp/scratch/xvfb-run.LKhMhF’
‘~/tmp/scratch/xvfb-run.LuJPOc’ ‘~/tmp/scratch/xvfb-run.M91JAb’
‘~/tmp/scratch/xvfb-run.NioxOl’ ‘~/tmp/scratch/xvfb-run.NlH5g5’
‘~/tmp/scratch/xvfb-run.ORFLEF’ ‘~/tmp/scratch/xvfb-run.QGHido’
‘~/tmp/scratch/xvfb-run.Qk1EuM’ ‘~/tmp/scratch/xvfb-run.QzOVir’
‘~/tmp/scratch/xvfb-run.RLBPa4’ ‘~/tmp/scratch/xvfb-run.RtaldY’
‘~/tmp/scratch/xvfb-run.RxNQKL’ ‘~/tmp/scratch/xvfb-run.To8iwd’
‘~/tmp/scratch/xvfb-run.VdDDdU’ ‘~/tmp/scratch/xvfb-run.WoSeRk’
‘~/tmp/scratch/xvfb-run.cJ4hai’ ‘~/tmp/scratch/xvfb-run.cKSLEZ’
‘~/tmp/scratch/xvfb-run.dw1b59’ ‘~/tmp/scratch/xvfb-run.fJA7yZ’
‘~/tmp/scratch/xvfb-run.g44bGd’ ‘~/tmp/scratch/xvfb-run.hZ4Tjj’
‘~/tmp/scratch/xvfb-run.hrMsxV’ ‘~/tmp/scratch/xvfb-run.hu1HVY’
‘~/tmp/scratch/xvfb-run.i1rJaz’ ‘~/tmp/scratch/xvfb-run.iHAcys’
‘~/tmp/scratch/xvfb-run.ivwbDj’ ‘~/tmp/scratch/xvfb-run.iwV8MH’
‘~/tmp/scratch/xvfb-run.j9iY0k’ ‘~/tmp/scratch/xvfb-run.jUOwfY’
‘~/tmp/scratch/xvfb-run.jVd1xn’ ‘~/tmp/scratch/xvfb-run.kab3vH’
‘~/tmp/scratch/xvfb-run.lLAD38’ ‘~/tmp/scratch/xvfb-run.mcwcT8’
‘~/tmp/scratch/xvfb-run.mxN53u’ ‘~/tmp/scratch/xvfb-run.nA2Jlj’
‘~/tmp/scratch/xvfb-run.oCgxTg’ ‘~/tmp/scratch/xvfb-run.oR7fvv’
‘~/tmp/scratch/xvfb-run.oS9hvH’ ‘~/tmp/scratch/xvfb-run.oegc70’
‘~/tmp/scratch/xvfb-run.qWyfBB’ ‘~/tmp/scratch/xvfb-run.sARSAr’
‘~/tmp/scratch/xvfb-run.ski2LL’ ‘~/tmp/scratch/xvfb-run.t11Z3g’
‘~/tmp/scratch/xvfb-run.takQ3k’ ‘~/tmp/scratch/xvfb-run.wsoYfd’
‘~/tmp/scratch/xvfb-run.x7ks6I’ ‘~/tmp/scratch/xvfb-run.xezGIq’
‘~/tmp/scratch/xvfb-run.y31lYP’ ‘~/tmp/scratch/xvfb-run.yXg7gr’
‘~/tmp/scratch/xvfb-run.yrj1q9’
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.7.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [29s/155s]
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:11499)
2: In for (nme in names(lhs)) { :
closing unused connection 7 (<-localhost:11499)
3: In for (nme in names(lhs)) { :
closing unused connection 6 (<-localhost:11499)
4: In for (nme in names(lhs)) { :
closing unused connection 5 (<-localhost:11499)
Execution halted
Flavor: r-oldrel-macos-x86_64