Last updated on 2026-05-18 05:52:07 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.6.2 | 25.45 | 254.12 | 279.57 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.6.2 | 21.51 | 178.30 | 199.81 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.6.2 | 48.00 | 386.72 | 434.72 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 0.6.2 | 46.00 | 383.30 | 429.30 | OK | |
| r-devel-windows-x86_64 | 0.6.2 | 28.00 | 310.00 | 338.00 | OK | |
| r-patched-linux-x86_64 | 0.6.2 | 25.49 | 234.64 | 260.13 | OK | |
| r-release-linux-x86_64 | 0.6.2 | 23.65 | 236.78 | 260.43 | 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 | 34.00 | 390.00 | 424.00 | OK | |
| r-oldrel-macos-arm64 | 0.7.2 | 7.00 | 82.00 | 89.00 | OK | |
| r-oldrel-macos-x86_64 | 0.7.2 | 21.00 | 287.00 | 308.00 | ERROR | |
| r-oldrel-windows-x86_64 | 0.6.2 | 41.00 | 428.00 | 469.00 | OK |
Version: 0.7.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [27s/85s]
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:11241)
2: In for (nme in names(lhs)) { :
closing unused connection 7 (<-localhost:11241)
3: In for (nme in names(lhs)) { :
closing unused connection 6 (<-localhost:11241)
4: In for (nme in names(lhs)) { :
closing unused connection 5 (<-localhost:11241)
Execution halted
Flavor: r-oldrel-macos-x86_64