Running 'testthat.R' [7s]
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')
  -- 1. Error: Beta diversity from a list of phyloseq objects (@test-BD_ordination
  .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. HTSSIP::physeq_list_betaDiv(physeq_S2D2_l)
    3. phyloseq::distance
    4. base::getExportedValue(pkg, name)
    5. base::asNamespace(ns)
    6. base::getNamespace(ns)
    7. base::loadNamespace(name)
   10. base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   12. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   13. base:::runHook(".onLoad", env, package.lib, package)
  
  -- 2. Error: DESeq2_l2fc runs with default params (@test-DESeq2_l2fc.R#2)  -----
  .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. HTSSIP::DESeq2_l2fc(...)
    2. phyloseq::sample_data
    3. base::getExportedValue(pkg, name)
    4. base::asNamespace(ns)
    5. base::getNamespace(ns)
    6. base::loadNamespace(name)
    9. base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   11. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   12. base:::runHook(".onLoad", env, package.lib, package)
  
  -- 3. Error: DESeq2_l2fc runs with sparsity_apply=heavy (@test-DESeq2_l2fc.R#15)
  .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. HTSSIP::DESeq2_l2fc(...)
    2. phyloseq::sample_data
    3. base::getExportedValue(pkg, name)
    4. base::asNamespace(ns)
    5. base::getNamespace(ns)
    6. base::loadNamespace(name)
    9. base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   11. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   12. base:::runHook(".onLoad", env, package.lib, package)
  
  -- 4. Error: HRSIP runs with default (@test-HRSIP.R#3)  ------------------------
  .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. HTSSIP::HRSIP(...)
    2. plyr::mdply(...)
    3. plyr::adply(...)
    4. plyr::ldply(...)
    5. plyr::llply(...)
    8. plyr:::.fun(piece, ...)
   11. phyloseq::sample_data
   12. base::getExportedValue(pkg, name)
   13. base::asNamespace(ns)
   14. base::getNamespace(ns)
   15. base::loadNamespace(name)
   18. base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   20. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   21. base:::runHook(".onLoad", env, package.lib, package)
  
  -- 5. Error: phyloseq sim (@test-HTSSIP_sim.R#57)  -----------------------------
  .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. HTSSIP::HTSSIP_sim(L$locs, L$params)
    2. phyloseq::phyloseq
    3. base::getExportedValue(pkg, name)
    4. base::asNamespace(ns)
    5. base::getNamespace(ns)
    6. base::loadNamespace(name)
    9. base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   11. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   12. base:::runHook(".onLoad", env, package.lib, package)
  
  -- 6. Error: phyloseq sim w/ metadata (@test-HTSSIP_sim.R#73)  -----------------
  .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. HTSSIP::HTSSIP_sim(L$locs, L$params, meta = meta)
    2. phyloseq::phyloseq
    3. base::getExportedValue(pkg, name)
    4. base::asNamespace(ns)
    5. base::getNamespace(ns)
    6. base::loadNamespace(name)
    9. base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   11. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   12. base:::runHook(".onLoad", env, package.lib, package)
  
  -- 7. Error: phyloseq sample_data can be converted to dataframe (@test-Util.R#9)
  .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. HTSSIP::phyloseq2df(physeq_S2D2, phyloseq::sample_data)
    2. phyloseq::sample_data
    3. base::getExportedValue(pkg, name)
    4. base::asNamespace(ns)
    5. base::getNamespace(ns)
    6. base::loadNamespace(name)
    9. base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   11. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   12. base:::runHook(".onLoad", env, package.lib, package)
  
  -- 8. Error: phyloseq tax_table can be converted to dataframe (@test-Util.R#17) 
  .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. HTSSIP::phyloseq2df(physeq_S2D2, phyloseq::tax_table)
    2. phyloseq::tax_table
    3. base::getExportedValue(pkg, name)
    4. base::asNamespace(ns)
    5. base::getNamespace(ns)
    6. base::loadNamespace(name)
    9. base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   11. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   12. base:::runHook(".onLoad", env, package.lib, package)
  
  -- 9. Error: phyloseq otu_table can be converted to dataframe (@test-Util.R#24) 
  .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. HTSSIP::phyloseq2df(physeq_S2D2, phyloseq::otu_table)
    2. phyloseq::otu_table
    3. base::getExportedValue(pkg, name)
    4. base::asNamespace(ns)
    5. base::getNamespace(ns)
    6. base::loadNamespace(name)
    9. base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   11. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   12. base:::runHook(".onLoad", env, package.lib, package)
  
  -- 10. Error: phyloseq_re sample_data can be converted to dataframe (@test-Util.
  .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. HTSSIP::phyloseq2df(physeq_rep3, phyloseq::sample_data)
    2. phyloseq::sample_data
    3. base::getExportedValue(pkg, name)
    4. base::asNamespace(ns)
    5. base::getNamespace(ns)
    6. base::loadNamespace(name)
    9. base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   11. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   12. base:::runHook(".onLoad", env, package.lib, package)
  
  -- 11. Error: phyloseq otu_table can be converted to dataframe (@test-Util.R#47)
  .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. HTSSIP::phyloseq2df(physeq_rep3, phyloseq::otu_table)
    2. phyloseq::otu_table
    3. base::getExportedValue(pkg, name)
    4. base::asNamespace(ns)
    5. base::getNamespace(ns)
    6. base::loadNamespace(name)
    9. base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   11. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   12. base:::runHook(".onLoad", env, package.lib, package)
  
  -- 12. Error: physeq_format runs (@test-chk.R#3)  ------------------------------
  .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. HTSSIP::physeq_format(physeq_S2D2)
    2. phyloseq::sample_data
    3. base::getExportedValue(pkg, name)
    4. base::asNamespace(ns)
    5. base::getNamespace(ns)
    6. base::loadNamespace(name)
    9. base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   11. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   12. base:::runHook(".onLoad", env, package.lib, package)
  
  -- 13. Error: delta BD on rep3 dataset (@test-delta_BD.R#29)  ------------------
  .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. HTSSIP::delta_BD(physeq_rep3, control_expr = "Treatment==\"12C-Con\"")
    2. HTSSIP:::qSIP_atom_excess_format(physeq, control_expr, treatment_rep = NULL)
    3. HTSSIP::phyloseq2table(...)
    4. phyloseq::otu_table
    5. base::getExportedValue(pkg, name)
    6. base::asNamespace(ns)
    7. base::getNamespace(ns)
    8. base::loadNamespace(name)
   11. base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   13. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   14. base:::runHook(".onLoad", env, package.lib, package)
  
  -- 14. Error: heavy-SIP runs on replicated dataset with default settings (@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. HTSSIP::heavy_SIP(physeq_rep3, ex = "Treatment=='12C-Con'")
    2. phyloseq::filter_taxa
    3. base::getExportedValue(pkg, name)
    4. base::asNamespace(ns)
    5. base::getNamespace(ns)
    6. base::loadNamespace(name)
    9. base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   11. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   12. base:::runHook(".onLoad", env, package.lib, package)
  
  -- 15. Error: heavy-SIP runs on non-rep dataset with default settings (@test-hea
  .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. HTSSIP::heavy_SIP(physeq_S2D2_l[[1]], ex = "Substrate=='12C-Con'")
    2. phyloseq::filter_taxa
    3. base::getExportedValue(pkg, name)
    4. base::asNamespace(ns)
    5. base::getNamespace(ns)
    6. base::loadNamespace(name)
    9. base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   11. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   12. base:::runHook(".onLoad", env, package.lib, package)
  
  -- 16. Error: heavy-SIP runs on replicated dataset with t-test (@test-heavy_SIP.
  .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. HTSSIP::heavy_SIP(...)
    2. phyloseq::filter_taxa
    3. base::getExportedValue(pkg, name)
    4. base::asNamespace(ns)
    5. base::getNamespace(ns)
    6. base::loadNamespace(name)
    9. base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   11. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   12. base:::runHook(".onLoad", env, package.lib, package)
  
  -- 17. Error: heavy-SIP runs on replicated dataset with wilcox (@test-heavy_SIP.
  .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. HTSSIP::heavy_SIP(...)
    2. phyloseq::filter_taxa
    3. base::getExportedValue(pkg, name)
    4. base::asNamespace(ns)
    5. base::getNamespace(ns)
    6. base::loadNamespace(name)
    9. base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   11. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   12. base:::runHook(".onLoad", env, package.lib, package)
  
  -- 18. Error: Getting params for subsetting (@test-phyloseq_subset.R#3)  -------
  .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. HTSSIP::get_treatment_params(physeq_S2D2, X)
    3. phyloseq::sample_data
    4. base::getExportedValue(pkg, name)
    5. base::asNamespace(ns)
    6. base::getNamespace(ns)
    7. base::loadNamespace(name)
   10. base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   12. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   13. base:::runHook(".onLoad", env, package.lib, package)
  
  -- 19. Error: Subsetting phyloseq object (@test-phyloseq_subset.R#43)  ---------
  .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. HTSSIP::get_treatment_params(physeq_S2D2, c("Substrate", "Day"))
    3. phyloseq::sample_data
    4. base::getExportedValue(pkg, name)
    5. base::asNamespace(ns)
    6. base::getNamespace(ns)
    7. base::loadNamespace(name)
   10. base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   12. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   13. base:::runHook(".onLoad", env, package.lib, package)
  
  -- 20. Error: Subsetting phyloseq object (@test-phyloseq_subset.R#60)  ---------
  .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. HTSSIP::get_treatment_params(physeq_rep3, c("Treatment", "Replicate"))
    3. phyloseq::sample_data
    4. base::getExportedValue(pkg, name)
    5. base::asNamespace(ns)
    6. base::getNamespace(ns)
    7. base::loadNamespace(name)
   10. base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   12. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   13. base:::runHook(".onLoad", env, package.lib, package)
  
  -- 21. Error: Naming phyloseq object (@test-phyloseq_subset.R#77)  -------------
  .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. HTSSIP::get_treatment_params(physeq_S2D2, c("Substrate", "Day"))
    3. phyloseq::sample_data
    4. base::getExportedValue(pkg, name)
    5. base::asNamespace(ns)
    6. base::getNamespace(ns)
    7. base::loadNamespace(name)
   10. base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   12. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   13. base:::runHook(".onLoad", env, package.lib, package)
  
  -- 22. Error: qPCR simulation warnings (@test-qPCR.R#101)  ---------------------
  .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. testthat::expect_warning(...)
    6. HTSSIP::qPCR_sim(...)
    8. phyloseq::sample_data
    9. base::getExportedValue(pkg, name)
   10. base::asNamespace(ns)
   11. base::getNamespace(ns)
   12. base::loadNamespace(name)
   15. base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   17. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   18. base:::runHook(".onLoad", env, package.lib, package)
  
  -- 23. Error: bootstrap iteration is working (@test-qSIP_atom_excess.R#33)  ----
  .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. HTSSIP::OTU_qPCR_trans(physeq_rep3, physeq_rep3_qPCR)
    4. phyloseq::otu_table
    5. base::getExportedValue(pkg, name)
    6. base::asNamespace(ns)
    7. base::getNamespace(ns)
    8. base::loadNamespace(name)
   11. base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   13. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   14. base:::runHook(".onLoad", env, package.lib, package)
  
  -- 24. Error: qPCR OTU table transformation (@test-qSIP_trans.R#38)  -----------
  .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. HTSSIP::OTU_qPCR_trans(physeq_rep3, physeq_rep3_qPCR)
    4. phyloseq::otu_table
    5. base::getExportedValue(pkg, name)
    6. base::asNamespace(ns)
    7. base::getNamespace(ns)
    8. base::loadNamespace(name)
   11. base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   13. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   14. base:::runHook(".onLoad", env, package.lib, package)
  
  == testthat results  ===========================================================
  [ OK: 28 | SKIPPED: 17 | WARNINGS: 1 | FAILED: 24 ]
  1. Error: Beta diversity from a list of phyloseq objects (@test-BD_ordinations.R#2) 
  2. Error: DESeq2_l2fc runs with default params (@test-DESeq2_l2fc.R#2) 
  3. Error: DESeq2_l2fc runs with sparsity_apply=heavy (@test-DESeq2_l2fc.R#15) 
  4. Error: HRSIP runs with default (@test-HRSIP.R#3) 
  5. Error: phyloseq sim (@test-HTSSIP_sim.R#57) 
  6. Error: phyloseq sim w/ metadata (@test-HTSSIP_sim.R#73) 
  7. Error: phyloseq sample_data can be converted to dataframe (@test-Util.R#9) 
  8. Error: phyloseq tax_table can be converted to dataframe (@test-Util.R#17) 
  9. Error: phyloseq otu_table can be converted to dataframe (@test-Util.R#24) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted