Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tidygenomics)
  > 
  > test_check("tidygenomics")
  # A tibble: 4 x 6
       id bla   chromosome start   end cluster_id
    <int> <chr> <chr>      <dbl> <dbl>      <dbl>
  1     1 a     chr1         100   150          0
  2     2 b     chr1         120   250          0
  3     3 c     chr2         300   350          2
  4     4 d     chr1         260   450          1
  -- 1. Error: Calculating the complement of a sequence works (@test_complement.R#
  .onLoad failed in loadNamespace() for 'S4Vectors', details:
    call: validObject(.Object)
    error: invalid class "LLint" object: superclass "integer_OR_LLint" not defined in the environment of the object's class
  Backtrace:
    1. tidygenomics::genome_complement(...)
   10. tidygenomics::genome_subtract(., x, by = by)
   11. tidygenomics:::f(d1, d2)
   12. purrr::map2_df(joined$data.x, joined$data.y, find_subtractions)
   13. purrr::map2(.x, .y, .f, ...)
   14. tidygenomics:::.f(.x[[i]], .y[[i]], ...)
   15. IRanges::IRanges
   16. base::getExportedValue(pkg, name)
   17. base::asNamespace(ns)
   18. base::getNamespace(ns)
   19. base::loadNamespace(name)
   21. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   22. base:::runHook(".onLoad", env, package.lib, package)
  
  -- 2. Error: Intersection (both) of 2 data frames works as expected (@test_inter
  .onLoad failed in loadNamespace() for 'S4Vectors', details:
    call: validObject(.Object)
    error: invalid class "LLint" object: superclass "integer_OR_LLint" not defined in the environment of the object's class
  Backtrace:
    1. tidygenomics::genome_intersect(...)
    2. tidygenomics:::index_match_fun(d1, d2)
    3. purrr::map2_df(joined$data.x, joined$data.y, find_overlaps)
    4. purrr::map2(.x, .y, .f, ...)
    5. tidygenomics:::.f(.x[[i]], .y[[i]], ...)
    6. IRanges::IRanges
    7. base::getExportedValue(pkg, name)
    8. base::asNamespace(ns)
    9. base::getNamespace(ns)
   10. base::loadNamespace(name)
   12. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   13. base:::runHook(".onLoad", env, package.lib, package)
  
  -- 3. Error: Intersection of 2 data frames works for multi-overlap ranges (@test
  .onLoad failed in loadNamespace() for 'S4Vectors', details:
    call: validObject(.Object)
    error: invalid class "LLint" object: superclass "integer_OR_LLint" not defined in the environment of the object's class
  Backtrace:
    1. tidygenomics::genome_intersect(...)
    2. tidygenomics:::index_match_fun(d1, d2)
    3. purrr::map2_df(joined$data.x, joined$data.y, find_overlaps)
    4. purrr::map2(.x, .y, .f, ...)
    5. tidygenomics:::.f(.x[[1L]], .y[[1L]], ...)
    6. IRanges::IRanges
    7. base::getExportedValue(pkg, name)
    8. base::asNamespace(ns)
    9. base::getNamespace(ns)
   10. base::loadNamespace(name)
   12. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   13. base:::runHook(".onLoad", env, package.lib, package)
  
  -- 4. Error: Intersection of 2 data frames works for multi-overlap ranges the ot
  .onLoad failed in loadNamespace() for 'S4Vectors', details:
    call: validObject(.Object)
    error: invalid class "LLint" object: superclass "integer_OR_LLint" not defined in the environment of the object's class
  Backtrace:
    1. tidygenomics::genome_intersect(...)
    2. tidygenomics:::index_match_fun(d1, d2)
    3. purrr::map2_df(joined$data.x, joined$data.y, find_overlaps)
    4. purrr::map2(.x, .y, .f, ...)
    5. tidygenomics:::.f(.x[[1L]], .y[[1L]], ...)
    6. IRanges::IRanges
    7. base::getExportedValue(pkg, name)
    8. base::asNamespace(ns)
    9. base::getNamespace(ns)
   10. base::loadNamespace(name)
   12. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   13. base:::runHook(".onLoad", env, package.lib, package)
  
  -- 5. Error: Intersect and findOverlap always match (@test_intersect.R#58)  ----
  .onLoad failed in loadNamespace() for 'S4Vectors', details:
    call: validObject(.Object)
    error: invalid class "LLint" object: superclass "integer_OR_LLint" not defined in the environment of the object's class
  Backtrace:
   1. IRanges::IRanges
   2. base::getExportedValue(pkg, name)
   3. base::asNamespace(ns)
   4. base::getNamespace(ns)
   5. base::loadNamespace(name)
   7. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   8. base:::runHook(".onLoad", env, package.lib, package)
  
  -- 6. Error: Joining with closest works as expected (@test_join_closest.R#17)  -
  genome_join_closest requires the IRanges package: https://bioconductor.org/packages/release/bioc/html/IRanges.html
  Backtrace:
   1. tidygenomics::genome_join_closest(...)
  
  -- 7. Error: Subtraction of 2 data frames works as expected (@test_subtract.R#18
  .onLoad failed in loadNamespace() for 'S4Vectors', details:
    call: validObject(.Object)
    error: invalid class "LLint" object: superclass "integer_OR_LLint" not defined in the environment of the object's class
  Backtrace:
    1. tidygenomics::genome_subtract(...)
    2. tidygenomics:::f(d1, d2)
    3. purrr::map2_df(joined$data.x, joined$data.y, find_subtractions)
    4. purrr::map2(.x, .y, .f, ...)
    5. tidygenomics:::.f(.x[[i]], .y[[i]], ...)
    6. IRanges::IRanges
    7. base::getExportedValue(pkg, name)
    8. base::asNamespace(ns)
    9. base::getNamespace(ns)
   10. base::loadNamespace(name)
   12. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   13. base:::runHook(".onLoad", env, package.lib, package)
  
  -- 8. Error: Edge cases of subtraction of 2 data frames works as expected (@test
  .onLoad failed in loadNamespace() for 'S4Vectors', details:
    call: validObject(.Object)
    error: invalid class "LLint" object: superclass "integer_OR_LLint" not defined in the environment of the object's class
  Backtrace:
    1. tidygenomics::genome_subtract(...)
    2. tidygenomics:::f(d1, d2)
    3. purrr::map2_df(joined$data.x, joined$data.y, find_subtractions)
    4. purrr::map2(.x, .y, .f, ...)
    5. tidygenomics:::.f(.x[[1L]], .y[[1L]], ...)
    6. IRanges::IRanges
    7. base::getExportedValue(pkg, name)
    8. base::asNamespace(ns)
    9. base::getNamespace(ns)
   10. base::loadNamespace(name)
   12. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   13. base:::runHook(".onLoad", env, package.lib, package)
  
  -- 9. Error: during subtraction the intervals are not unified (@test_subtract.R#
  .onLoad failed in loadNamespace() for 'S4Vectors', details:
    call: validObject(.Object)
    error: invalid class "LLint" object: superclass "integer_OR_LLint" not defined in the environment of the object's class
  Backtrace:
    1. tidygenomics::genome_subtract(...)
    2. tidygenomics:::f(d1, d2)
    3. purrr::map2_df(joined$data.x, joined$data.y, find_subtractions)
    4. purrr::map2(.x, .y, .f, ...)
    5. tidygenomics:::.f(.x[[1L]], .y[[1L]], ...)
    6. IRanges::IRanges
    7. base::getExportedValue(pkg, name)
    8. base::asNamespace(ns)
    9. base::getNamespace(ns)
   10. base::loadNamespace(name)
   12. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   13. base:::runHook(".onLoad", env, package.lib, package)
  
  == testthat results  ===========================================================
  [ OK: 7 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 9 ]
  1. Error: Calculating the complement of a sequence works (@test_complement.R#12) 
  2. Error: Intersection (both) of 2 data frames works as expected (@test_intersect.R#17) 
  3. Error: Intersection of 2 data frames works for multi-overlap ranges (@test_intersect.R#29) 
  4. Error: Intersection of 2 data frames works for multi-overlap ranges the other way around (@test_intersect.R#46) 
  5. Error: Intersect and findOverlap always match (@test_intersect.R#58) 
  6. Error: Joining with closest works as expected (@test_join_closest.R#17) 
  7. Error: Subtraction of 2 data frames works as expected (@test_subtract.R#18) 
  8. Error: Edge cases of subtraction of 2 data frames works as expected (@test_subtract.R#38) 
  9. Error: during subtraction the intervals are not unified (@test_subtract.R#57) 
  
  Error: testthat unit tests failed
  Execution halted