• using R version 4.5.0 (2025-04-11)
  • using platform: aarch64-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 13.4
  • 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 ... [11s/12s] 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 ... [3s/4s] OK
  • checking whether the package can be loaded with stated dependencies ... [3s/3s] OK
  • checking whether the package can be unloaded cleanly ... [3s/3s] OK
  • checking whether the namespace can be loaded with stated dependencies ... [3s/4s] OK
  • checking whether the namespace can be unloaded cleanly ... [3s/3s] OK
  • checking loading without being on the library search path ... [3s/4s] 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 ... [8s/8s] 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 ... [6s/7s] OK
  • checking for unstated dependencies in ‘tests’ ... OK
  • checking tests ... [9s/18s] ERROR   Running ‘testthat.R’ [9s/18s] 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 UseMethod("sort") : closing unused connection 6 (<-localhost:11738)   2: In UseMethod("sort") : closing unused connection 5 (<-localhost:11738)   Execution halted
  • checking PDF version of manual ... [4s/4s] OK
  • DONE Status: 1 ERROR
  • using check arguments '--no-clean-on-error '