Running ‘testthat.R’ [364s/421s]
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
  could not find function ".makeSortEnum"
  1: physeq_list_betaDiv(physeq_S2D2_l) at testthat/test-BD_ordinations.R:2
  2: plyr::llply(physeq_l, phyloseq::distance, method = method, weighted = weighted, fast = fast, 
         normalized = normalized, parallel = parallel)
  3: structure(lapply(pieces, .fun, ...), dim = dim(pieces))
  4: lapply(pieces, .fun, ...)
  5: FUN(X[[i]], ...)
  6: FUN(X[[i]], ...)
  7: UniFrac(physeq, ...)
  8: UniFrac(physeq, ...)
  9: fastUniFrac(physeq, weighted, normalized, parallel)
  10: matrix(tree$edge[order(tree$edge[, 1]), ][, 2], byrow = TRUE, ncol = 2)
  11: order(tree$edge[, 1])
  12: standardGeneric("order")
  13: eval(mc, env)
  14: eval(mc, env)
  15: eval(mc, env)
  16: order(...)
  
  ── 2. Error: Beta diversity from a list of phyloseq objects (parallel) (@test-BD
  could not find function ".makeSortEnum"
  1: physeq_list_betaDiv(physeq_S2D2_l, parallel = TRUE) at testthat/test-BD_ordinations.R:9
  2: plyr::llply(physeq_l, phyloseq::distance, method = method, weighted = weighted, fast = fast, 
         normalized = normalized, parallel = parallel)
  3: structure(lapply(pieces, .fun, ...), dim = dim(pieces))
  4: lapply(pieces, .fun, ...)
  5: FUN(X[[i]], ...)
  6: FUN(X[[i]], ...)
  7: UniFrac(physeq, ...)
  8: UniFrac(physeq, ...)
  9: fastUniFrac(physeq, weighted, normalized, parallel)
  10: matrix(tree$edge[order(tree$edge[, 1]), ][, 2], byrow = TRUE, ncol = 2)
  11: order(tree$edge[, 1])
  12: standardGeneric("order")
  13: eval(mc, env)
  14: eval(mc, env)
  15: eval(mc, env)
  16: order(...)
  
  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 
  ── 3. Error: phyloseq sim (@test-HTSSIP_sim.R#59)  ─────────────────────────────
  could not find function "sample_data"
  1: physeq %>% sample_data %>% .$Buoyant_density at testthat/test-HTSSIP_sim.R:59
  2: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  3: eval(quote(`_fseq`(`_lhs`)), env, env)
  4: eval(quote(`_fseq`(`_lhs`)), env, env)
  5: `_fseq`(`_lhs`)
  6: freduce(value, `_function_list`)
  7: function_list[[i]](value)
  
  ── 4. Error: phyloseq sim w/ metadata (@test-HTSSIP_sim.R#75)  ─────────────────
  could not find function "sample_data"
  1: physeq %>% sample_data %>% .$Buoyant_density at testthat/test-HTSSIP_sim.R:75
  2: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  3: eval(quote(`_fseq`(`_lhs`)), env, env)
  4: eval(quote(`_fseq`(`_lhs`)), env, env)
  5: `_fseq`(`_lhs`)
  6: freduce(value, `_function_list`)
  7: function_list[[i]](value)
  
  ── 5. Error: phyloseq sample_data can be converted to dataframe (@test-Util.R#10
  could not find function "sample_data"
  1: suppressWarnings(as.data.frame(as.matrix(sample_data(physeq_S2D2)))) at testthat/test-Util.R:10
  2: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
  3: as.data.frame(as.matrix(sample_data(physeq_S2D2)))
  4: as.matrix(sample_data(physeq_S2D2))
  
  ── 6. Error: phyloseq tax_table can be converted to dataframe (@test-Util.R#18) 
  could not find function "tax_table"
  1: suppressWarnings(as.data.frame(as.matrix(tax_table(physeq_S2D2)))) at testthat/test-Util.R:18
  2: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
  3: as.data.frame(as.matrix(tax_table(physeq_S2D2)))
  4: as.matrix(tax_table(physeq_S2D2))
  
  ── 7. Error: phyloseq otu_table can be converted to dataframe (@test-Util.R#25) 
  could not find function "otu_table"
  1: suppressWarnings(as.data.frame(as.matrix(otu_table(physeq_S2D2)))) at testthat/test-Util.R:25
  2: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
  3: as.data.frame(as.matrix(otu_table(physeq_S2D2)))
  4: as.matrix(otu_table(physeq_S2D2))
  
  ── 8. Error: phyloseq_re sample_data can be converted to dataframe (@test-Util.R
  could not find function "sample_data"
  1: suppressWarnings(as.data.frame(as.matrix(sample_data(physeq_rep3)))) at testthat/test-Util.R:35
  2: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
  3: as.data.frame(as.matrix(sample_data(physeq_rep3)))
  4: as.matrix(sample_data(physeq_rep3))
  
  ── 9. Error: phyloseq otu_table can be converted to dataframe (@test-Util.R#48) 
  could not find function "otu_table"
  1: suppressWarnings(as.data.frame(as.matrix(otu_table(physeq_rep3)))) at testthat/test-Util.R:48
  2: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
  3: as.data.frame(as.matrix(otu_table(physeq_rep3)))
  4: as.matrix(otu_table(physeq_rep3))
  
  ── 10. Error: physeq_format runs (@test-chk.R#5)  ──────────────────────────────
  could not find function "sample_data"
  1: expect_equal(x %>% sample_data %>% colnames, physeq_S2D2 %>% sample_data %>% colnames) at testthat/test-chk.R:5
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: x %>% sample_data %>% colnames
  5: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  6: eval(quote(`_fseq`(`_lhs`)), env, env)
  7: eval(quote(`_fseq`(`_lhs`)), env, env)
  8: `_fseq`(`_lhs`)
  9: freduce(value, `_function_list`)
  10: function_list[[i]](value)
  
  ── 11. Error: qPCR OTU table transformation (@test-qSIP_trans.R#39)  ───────────
  could not find function "otu_table"
  1: physeq_rep3 %>% otu_table %>% colnames at testthat/test-qSIP_trans.R:39
  2: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  3: eval(quote(`_fseq`(`_lhs`)), env, env)
  4: eval(quote(`_fseq`(`_lhs`)), env, env)
  5: `_fseq`(`_lhs`)
  6: freduce(value, `_function_list`)
  7: function_list[[i]](value)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 83 SKIPPED: 17 FAILED: 11
  1. Error: Beta diversity from a list of phyloseq objects (@test-BD_ordinations.R#2) 
  2. Error: Beta diversity from a list of phyloseq objects (parallel) (@test-BD_ordinations.R#9) 
  3. Error: phyloseq sim (@test-HTSSIP_sim.R#59) 
  4. Error: phyloseq sim w/ metadata (@test-HTSSIP_sim.R#75) 
  5. Error: phyloseq sample_data can be converted to dataframe (@test-Util.R#10) 
  6. Error: phyloseq tax_table can be converted to dataframe (@test-Util.R#18) 
  7. Error: phyloseq otu_table can be converted to dataframe (@test-Util.R#25) 
  8. Error: phyloseq_re sample_data can be converted to dataframe (@test-Util.R#35) 
  9. Error: phyloseq otu_table can be converted to dataframe (@test-Util.R#48) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted