Running ‘testthat.R’ [222s/239s]
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 
  Sparsity threshold: 0.25 
  Density window: 1.71-1.75 
  Sparsity threshold: 0 
  Density window: 1.7-1.75 
  Sparsity threshold: 0.15 
  Density window: 1.7-1.75 
  Sparsity threshold: 0.3 
  Density window: 1.7-1.75 
  ── 1. Error: delta BD on rep3 dataset (@test-delta_BD.R#29)  ───────────────────
  `nest_()` is deprecated as of tidyr 1.0.0.
  Please use `nest()` instead.
  1: delta_BD(physeq_rep3, control_expr = "Treatment==\"12C-Con\"") at testthat/test-delta_BD.R:29
  2: df_OTU %>% dplyr::group_by_("IS_CONTROL", "OTU") %>% tidyr::nest_(key_col = "data", 
         nest_cols = nest_cols) %>% dplyr::mutate_(.dots = dots) %>% tidyr::unnest_(unnest_cols = "data") %>% 
         dplyr::group_by_("IS_CONTROL", "OTU") %>% dplyr::summarize_(center_of_mass = "stats::weighted.mean(x=Buoyant_density,\n                                                             w=Count_interp)") %>% 
         dplyr::group_by_("OTU") %>% dplyr::mutate_(IS_CONTROL = "ifelse(IS_CONTROL==TRUE, 'CM_control', 'CM_treatment')") %>% 
         tidyr::spread_("IS_CONTROL", "center_of_mass") %>% dplyr::mutate_(delta_BD = "CM_treatment - CM_control") %>% 
         dplyr::ungroup()
  3: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  4: eval(quote(`_fseq`(`_lhs`)), env, env)
  5: eval(quote(`_fseq`(`_lhs`)), env, env)
  6: `_fseq`(`_lhs`)
  7: freduce(value, `_function_list`)
  8: function_list[[i]](value)
  9: tidyr::nest_(., key_col = "data", nest_cols = nest_cols)
  10: lifecycle::deprecate_stop("1.0.0", "nest_()", "nest()")
  
  ── 2. Error: bootstrap iteration is working (@test-qSIP_atom_excess.R#41)  ─────
  `nest_()` is deprecated as of tidyr 1.0.0.
  Please use `nest()` instead.
  1: .qSIP_bootstrap(atomX) at testthat/test-qSIP_atom_excess.R:41
  2: atomX$W %>% dplyr::group_by_("OTU") %>% tidyr::nest_(key_col = "data") %>% dplyr::mutate_(.dots = dots) %>% 
         dplyr::select_("-data") %>% tidyr::unnest()
  3: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  4: eval(quote(`_fseq`(`_lhs`)), env, env)
  5: eval(quote(`_fseq`(`_lhs`)), env, env)
  6: `_fseq`(`_lhs`)
  7: freduce(value, `_function_list`)
  8: function_list[[i]](value)
  9: tidyr::nest_(., key_col = "data")
  10: lifecycle::deprecate_stop("1.0.0", "nest_()", "nest()")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 107 | SKIPPED: 18 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: delta BD on rep3 dataset (@test-delta_BD.R#29) 
  2. Error: bootstrap iteration is working (@test-qSIP_atom_excess.R#41) 
  
  Error: testthat unit tests failed
  Execution halted