- using R version 4.5.2 Patched (2026-01-31 r89382)
- using platform: x86_64-apple-darwin20
- R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
- running under: macOS Ventura 13.3.1
- using session charset: UTF-8
- checking for file ‘BIGr/DESCRIPTION’ ... OK
- this is package ‘BIGr’ version ‘0.7.2’
- package encoding: UTF-8
- checking package namespace information ... OK
- checking package dependencies ... OK
- checking if this is a source package ... OK
- checking if there is a namespace ... OK
- checking for executable files ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... OK
- checking whether package ‘BIGr’ can be installed ... [21s/27s] OK
See the install log for details.
- checking installed package size ... OK
- checking package directory ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking for left-over files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking code files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... [6s/7s] OK
- checking whether the package can be loaded with stated dependencies ... [5s/6s] OK
- checking whether the package can be unloaded cleanly ... [5s/6s] OK
- checking whether the namespace can be loaded with stated dependencies ... [5s/6s] OK
- checking whether the namespace can be unloaded cleanly ... [6s/7s] OK
- checking loading without being on the library search path ... [6s/7s] OK
- checking dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... [18s/32s] OK
- checking Rd files ... [0s/0s] OK
- checking Rd metadata ... OK
- checking Rd cross-references ... OK
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... OK
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- checking for unstated dependencies in examples ... OK
- checking examples ... [13s/16s] OK
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [29s/78s] ERROR
Running ‘testthat.R’ [29s/78s]
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:11861)
2: In for (pkg in package) { :
closing unused connection 7 (<-localhost:11861)
3: In for (pkg in package) { :
closing unused connection 6 (<-localhost:11861)
4: In for (pkg in package) { :
closing unused connection 5 (<-localhost:11861)
Execution halted
- checking PDF version of manual ... [9s/11s] OK
- DONE
Status: 1 ERROR
- using check arguments '--no-clean-on-error '