Running 'testthat.R' [112s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # Work-around for bug (https://github.com/hadley/testthat/issues/144)
  > Sys.setenv("R_TESTS" = "")
  > 
  > # library 
  > library(testthat)
  > library(HTSSIP)
  > 
  > # test check
  > test_check('HTSSIP')
  Sparsity threshold: 0.25 
  Density window: 1.71-1.75 
  -- 1. Error: DESeq2_l2fc runs with default params (@test-DESeq2_l2fc.R#2)  -----
  failed to coerce 'list(value)' to a DESeqResults object of length 1
  Backtrace:
    1. HTSSIP::DESeq2_l2fc(...)
    2. DESeq2::results(dds, independentFiltering = FALSE)
    3. DESeq2:::pvalueAdjustment(...)
    5. S4Vectors:::`$<-`(...)
    7. S4Vectors:::`[[<-`(...)
   11. S4Vectors:::.nextMethod(x, i, value = value)
   13. S4Vectors::setListElement(x, i, value)
   14. S4Vectors:::.append_list_element(x, value, name)
   15. S4Vectors:::.wrap_in_length_one_list_like_object(...)
  
  Sparsity threshold: 0.25 
  Density window: 1.71-1.75 
  -- 2. Error: DESeq2_l2fc runs with sparsity_apply=heavy (@test-DESeq2_l2fc.R#15)
  failed to coerce 'list(value)' to a DESeqResults object of length 1
  Backtrace:
    1. HTSSIP::DESeq2_l2fc(...)
    2. DESeq2::results(dds, independentFiltering = FALSE)
    3. DESeq2:::pvalueAdjustment(...)
    5. S4Vectors:::`$<-`(...)
    7. S4Vectors:::`[[<-`(...)
   11. S4Vectors:::.nextMethod(x, i, value = value)
   13. S4Vectors::setListElement(x, i, value)
   14. S4Vectors:::.append_list_element(x, value, name)
   15. S4Vectors:::.wrap_in_length_one_list_like_object(...)
  
  Sparsity threshold: 0 
  Density window: 1.7-1.75 
  -- 3. Error: HRSIP runs with default (@test-HRSIP.R#3)  ------------------------
  failed to coerce 'list(value)' to a DESeqResults object of length 1
  Backtrace:
    1. HTSSIP::HRSIP(...)
    2. plyr::mdply(...)
    3. plyr::adply(...)
    4. plyr::ldply(...)
    5. plyr::llply(...)
    8. plyr:::.fun(piece, ...)
   11. DESeq2::results(dds, independentFiltering = FALSE)
   12. DESeq2:::pvalueAdjustment(...)
   14. S4Vectors:::`$<-`(...)
   16. S4Vectors:::`[[<-`(...)
   20. S4Vectors:::.nextMethod(x, i, value = value)
   22. S4Vectors::setListElement(x, i, value)
   23. S4Vectors:::.append_list_element(x, value, name)
   24. S4Vectors:::.wrap_in_length_one_list_like_object(...)
  
  == testthat results  ===========================================================
  [ OK: 102 | SKIPPED: 18 | WARNINGS: 3 | FAILED: 3 ]
  1. Error: DESeq2_l2fc runs with default params (@test-DESeq2_l2fc.R#2) 
  2. Error: DESeq2_l2fc runs with sparsity_apply=heavy (@test-DESeq2_l2fc.R#15) 
  3. Error: HRSIP runs with default (@test-HRSIP.R#3) 
  
  Error: testthat unit tests failed
  Execution halted