- 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 ‘enviPathR/DESCRIPTION’ ... OK
- this is package ‘enviPathR’ version ‘1.0.0’
- 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 ‘enviPathR’ can be installed ... [3s/6s] OK
See the install log for details.
- checking installed package size ... OK
- checking package directory ... OK
- checking ‘build’ 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 ... [1s/1s] OK
- checking whether the package can be loaded with stated dependencies ... [0s/1s] OK
- checking whether the package can be unloaded cleanly ... [0s/1s] OK
- checking whether the namespace can be loaded with stated dependencies ... [0s/1s] OK
- checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
- checking loading without being on the library search path ... [1s/1s] OK
- checking whether startup messages can be suppressed ... [1s/1s] 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 ... [2s/4s] 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 installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [1s/2s] OK
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [2s/6s] ERROR
Running ‘testthat.R’ [2s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(enviPathR)
>
> test_check("enviPathR")
objc[59380]: +[NSNumber initialize] may have been in progress in another thread when fork() was called.
objc[59380]: +[NSNumber initialize] may have been in progress in another thread when fork() was called. We cannot safely call it or ignore it in the fork() child process. Crashing instead. Set a breakpoint on objc_initializeAfterForkError to debug.
Saving _problems/test-get-18.R
objc[59404]: +[NSNumber initialize] may have been in progress in another thread when fork() was called.
objc[59404]: +[NSNumber initialize] may have been in progress in another thread when fork() was called. We cannot safely call it or ignore it in the fork() child process. Crashing instead. Set a breakpoint on objc_initializeAfterForkError to debug.
Saving _problems/test-link-19.R
[ FAIL 2 | WARN 2 | SKIP 0 | PASS 20 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-get.R:14:9'): get ──────────────────────────────────────────────
Error in `reducer$value.cache[[as.character(idx)]] <- values`: wrong args for environment subassignment
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-get.R:14:9
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─enviPathR::epGet("reaction", "wrong")
8. ├─BiocParallel::bpmapply(...)
9. └─BiocParallel::bpmapply(...)
10. ├─BiocParallel::bplapply(...)
11. └─BiocParallel::bplapply(...)
12. └─BiocParallel:::.bpinit(...)
13. ├─BiocParallel::bploop(...)
14. └─BiocParallel:::bploop.lapply(...)
15. └─BiocParallel:::.bploop_impl(...)
16. └─BiocParallel:::.collect_result(manager, reducer, progress, BPPARAM)
17. ├─BiocParallel:::.reducer_add(reducer, njob, value)
18. └─BiocParallel:::.reducer_add(reducer, njob, value)
── Error ('test-link.R:15:9'): link ────────────────────────────────────────────
Error in `reducer$value.cache[[as.character(idx)]] <- values`: wrong args for environment subassignment
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-link.R:15:9
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─enviPathR::epLink(types[1], types[2], "wrong")
8. ├─BiocParallel::bplapply(...)
9. └─BiocParallel::bplapply(...)
10. └─BiocParallel:::.bpinit(...)
11. ├─BiocParallel::bploop(...)
12. └─BiocParallel:::bploop.lapply(...)
13. └─BiocParallel:::.bploop_impl(...)
14. └─BiocParallel:::.collect_result(manager, reducer, progress, BPPARAM)
15. ├─BiocParallel:::.reducer_add(reducer, njob, value)
16. └─BiocParallel:::.reducer_add(reducer, njob, value)
[ FAIL 2 | WARN 2 | SKIP 0 | PASS 20 ]
Error:
! Test failures.
Execution halted
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [25s/58s] OK
- checking PDF version of manual ... [6s/9s] OK
- DONE
Status: 1 ERROR