CRAN Package Check Results for Package tidygenomics

Last updated on 2020-04-03 04:47:40 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.1.2 22.14 58.36 80.50 OK
r-devel-linux-x86_64-debian-gcc 0.1.2 13.89 44.20 58.09 OK
r-devel-linux-x86_64-fedora-clang 0.1.2 105.67 OK
r-devel-linux-x86_64-fedora-gcc 0.1.2 94.23 OK
r-devel-windows-ix86+x86_64 0.1.2 39.00 81.00 120.00 ERROR
r-devel-windows-ix86+x86_64-gcc8 0.1.2 45.00 80.00 125.00 ERROR
r-patched-linux-x86_64 0.1.2 14.79 54.75 69.54 OK
r-patched-solaris-x86 0.1.2 117.70 OK
r-release-linux-x86_64 0.1.2 14.99 49.90 64.89 OK
r-release-windows-ix86+x86_64 0.1.2 45.00 96.00 141.00 OK
r-release-osx-x86_64 0.1.2 OK
r-oldrel-windows-ix86+x86_64 0.1.2 34.00 99.00 133.00 OK
r-oldrel-osx-x86_64 0.1.2 OK

Check Details

Version: 0.1.2
Check: running examples for arch ‘i386’
Result: ERROR
    Running examples in 'tidygenomics-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: genome_complement
    > ### Title: Calculates the complement to the intervals covered by the
    > ### intervals in a data frame. It can optionally take a 'chromosome_size'
    > ### data frame that contains 2 or 3 columns, the first the names of
    > ### chromosome and in case there are 2 columns the size or first the
    > ### start index and lastly the end index on the chromosome.
    > ### Aliases: genome_complement
    >
    > ### ** Examples
    >
    >
    > library(dplyr)
    
    Attaching package: 'dplyr'
    
    The following objects are masked from 'package:stats':
    
     filter, lag
    
    The following objects are masked from 'package:base':
    
     intersect, setdiff, setequal, union
    
    >
    > x1 <- data.frame(id = 1:4, bla=letters[1:4],
    + chromosome = c("chr1", "chr1", "chr2", "chr1"),
    + start = c(100, 200, 300, 400),
    + end = c(150, 250, 350, 450))
    >
    > genome_complement(x1, by=c("chromosome", "start", "end"))
    Error: .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
    Execution halted
Flavors: r-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8

Version: 0.1.2
Check: running examples for arch ‘x64’
Result: ERROR
    Running examples in 'tidygenomics-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: genome_complement
    > ### Title: Calculates the complement to the intervals covered by the
    > ### intervals in a data frame. It can optionally take a 'chromosome_size'
    > ### data frame that contains 2 or 3 columns, the first the names of
    > ### chromosome and in case there are 2 columns the size or first the
    > ### start index and lastly the end index on the chromosome.
    > ### Aliases: genome_complement
    >
    > ### ** Examples
    >
    >
    > library(dplyr)
    
    Attaching package: 'dplyr'
    
    The following objects are masked from 'package:stats':
    
     filter, lag
    
    The following objects are masked from 'package:base':
    
     intersect, setdiff, setequal, union
    
    >
    > x1 <- data.frame(id = 1:4, bla=letters[1:4],
    + chromosome = c("chr1", "chr1", "chr2", "chr1"),
    + start = c(100, 200, 300, 400),
    + end = c(150, 250, 350, 450))
    >
    > genome_complement(x1, by=c("chromosome", "start", "end"))
    Error: .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
    Execution halted
Flavors: r-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8

Version: 0.1.2
Check: running tests for arch ‘i386’
Result: ERROR
     Running 'testthat.R' [3s]
    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
Flavor: r-devel-windows-ix86+x86_64

Version: 0.1.2
Check: running tests for arch ‘x64’
Result: ERROR
     Running 'testthat.R' [4s]
    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
Flavor: r-devel-windows-ix86+x86_64

Version: 0.1.2
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building 'intro.Rmd' using rmarkdown
    
    Attaching package: 'dplyr'
    
    The following objects are masked from 'package:stats':
    
     filter, lag
    
    The following objects are masked from 'package:base':
    
     intersect, setdiff, setequal, union
    
    Quitting from lines 55-66 (intro.Rmd)
    Error: processing vignette 'intro.Rmd' failed with diagnostics:
    .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
    --- failed re-building 'intro.Rmd'
    
    SUMMARY: processing the following file failed:
     'intro.Rmd'
    
    Error: Vignette re-building failed.
    Execution halted
Flavors: r-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8

Version: 0.1.2
Check: running tests for arch ‘i386’
Result: ERROR
     Running 'testthat.R' [4s]
    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
Flavor: r-devel-windows-ix86+x86_64-gcc8

Version: 0.1.2
Check: running tests for arch ‘x64’
Result: ERROR
     Running 'testthat.R' [3s]
    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
Flavor: r-devel-windows-ix86+x86_64-gcc8