• using R version 4.5.1 (2025-06-13)
• 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 ‘0.5.5’
• 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 ... [17s/25s] 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 ... [5s/9s] OK
• checking whether the package can be loaded with stated dependencies ... [5s/9s] OK
• checking whether the package can be unloaded cleanly ... [5s/8s] OK
• checking whether the namespace can be loaded with stated dependencies ... [5s/7s] OK
• checking whether the namespace can be unloaded cleanly ... [5s/9s] OK
• checking loading without being on the library search path ... [5s/8s] 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 ... [13s/20s] 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 ... [11s/25s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [16s/41s] ERROR   Running ‘testthat.R’ [16s/41s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > library(testthat)   > library(BIGr)   >   > test_check("BIGr")   The Ref_0001 sequence had to be added for: 0 tags   The Alt_0002 sequence had to be added for: 1 tags   Tags discarded due to lack of Ref_0001 sequence: 0 tags   Tags discarded due to lack of Alt_0002 sequence: 0 tags   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 1 | WARN 0 | SKIP 0 | PASS 58 ]      ══ 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)      [ FAIL 1 | WARN 0 | SKIP 0 | PASS 58 ]   Error: Test failures   In addition: Warning messages:   1: In match.arg(method) : closing unused connection 6 (<-localhost:11249)   2: In match.arg(method) : closing unused connection 5 (<-localhost:11249)   Execution halted
• checking PDF version of manual ... [6s/8s] OK
• DONE Status: 1 ERROR
• using check arguments '--no-clean-on-error '