Running ‘testthat.R’ [29s/84s]
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 (pkg in package) { :
    closing unused connection 8 (<-localhost:11043)
  2: In for (pkg in package) { :
    closing unused connection 7 (<-localhost:11043)
  3: In for (pkg in package) { :
    closing unused connection 6 (<-localhost:11043)
  4: In for (pkg in package) { :
    closing unused connection 5 (<-localhost:11043)
  Execution halted