Running ‘testthat.R’ [13s/20s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(corncob)
  > 
  > test_check("corncob")
  [ FAIL 10 | WARN 0 | SKIP 0 | PASS 17 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_bbdml.R:32:1): (code run outside of `test_that()`) ──────────────
  Error in `if (detectseparation::detect_separation(y = cbind(W, M - W), 
      x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
      warning(paste("Separation detected in abundance model!", 
          "Likely, one of your covariates/experimental conditions is such that", 
          "there are all zero counts within a group. Consider identifying and removing", 
          "this covariate from your model. The results of this model are not to be", 
          "trusted because there is not enough data. \n", sep = "\n"), 
          immediate. = TRUE)
      sep_da <- TRUE
  }`: argument is of length zero
  Backtrace:
      ▆
   1. └─corncob::bbdml(...) at test_bbdml.R:32:0
  ── Error (test_differentialTest.R:11:1): (code run outside of `test_that()`) ───
  Error in `differentialTest(formula = ~Plants + DayAmdmt, phi.formula = ~Plants + 
      DayAmdmt, formula_null = ~1, phi.formula_null = ~1, data = subsoil, 
      boot = FALSE, test = "LRT", inits = rbind(rep(0.01, 6)), 
      inits_null = rbind(rep(0.01, 2)))`: All models failed to converge! 
  
             If you are seeing this, it is likely that your model is overspecified. This occurs when your sample size is not large enough to estimate all the parameters of your model. This is most commonly due to categorical variables that include many categories. 
  
             Alternatively, double-check your values for the arguments `link`, `phi.link`, and `method` to makes sure that they follow the specified options. 
  
             To confirm you have fixed the issue, try running a model for a single taxon with bbdml.
  Backtrace:
      ▆
   1. └─corncob::differentialTest(...) at test_differentialTest.R:11:0
  ── Error (test_getRestrictionTerms.R:12:1): (code run outside of `test_that()`) ──
  Error in `if (detectseparation::detect_separation(y = cbind(W, M - W), 
      x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
      warning(paste("Separation detected in abundance model!", 
          "Likely, one of your covariates/experimental conditions is such that", 
          "there are all zero counts within a group. Consider identifying and removing", 
          "this covariate from your model. The results of this model are not to be", 
          "trusted because there is not enough data. \n", sep = "\n"), 
          immediate. = TRUE)
      sep_da <- TRUE
  }`: argument is of length zero
  Backtrace:
      ▆
   1. └─corncob::bbdml(...) at test_getRestrictionTerms.R:12:0
  ── Error (test_lrtest.R:19:1): (code run outside of `test_that()`) ─────────────
  Error in `if (detectseparation::detect_separation(y = cbind(W, M - W), 
      x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
      warning(paste("Separation detected in abundance model!", 
          "Likely, one of your covariates/experimental conditions is such that", 
          "there are all zero counts within a group. Consider identifying and removing", 
          "this covariate from your model. The results of this model are not to be", 
          "trusted because there is not enough data. \n", sep = "\n"), 
          immediate. = TRUE)
      sep_da <- TRUE
  }`: argument is of length zero
  Backtrace:
      ▆
   1. └─corncob::bbdml(...) at test_lrtest.R:19:0
  ── Error (test_pb.R:14:1): (code run outside of `test_that()`) ─────────────────
  Error in `if (detectseparation::detect_separation(y = cbind(W, M - W), 
      x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
      warning(paste("Separation detected in abundance model!", 
          "Likely, one of your covariates/experimental conditions is such that", 
          "there are all zero counts within a group. Consider identifying and removing", 
          "this covariate from your model. The results of this model are not to be", 
          "trusted because there is not enough data. \n", sep = "\n"), 
          immediate. = TRUE)
      sep_da <- TRUE
  }`: argument is of length zero
  Backtrace:
      ▆
   1. └─corncob::bbdml(...) at test_pb.R:14:0
  ── Error (test_s3.R:12:1): (code run outside of `test_that()`) ─────────────────
  Error in `if (detectseparation::detect_separation(y = cbind(W, M - W), 
      x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
      warning(paste("Separation detected in abundance model!", 
          "Likely, one of your covariates/experimental conditions is such that", 
          "there are all zero counts within a group. Consider identifying and removing", 
          "this covariate from your model. The results of this model are not to be", 
          "trusted because there is not enough data. \n", sep = "\n"), 
          immediate. = TRUE)
      sep_da <- TRUE
  }`: argument is of length zero
  Backtrace:
      ▆
   1. └─corncob::bbdml(...) at test_s3.R:12:0
  ── Error (test_sandwich.R:12:1): (code run outside of `test_that()`) ───────────
  Error in `if (detectseparation::detect_separation(y = cbind(W, M - W), 
      x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
      warning(paste("Separation detected in abundance model!", 
          "Likely, one of your covariates/experimental conditions is such that", 
          "there are all zero counts within a group. Consider identifying and removing", 
          "this covariate from your model. The results of this model are not to be", 
          "trusted because there is not enough data. \n", sep = "\n"), 
          immediate. = TRUE)
      sep_da <- TRUE
  }`: argument is of length zero
  Backtrace:
      ▆
   1. └─corncob::bbdml(...) at test_sandwich.R:12:0
  ── Error (test_scorehessian.R:12:1): (code run outside of `test_that()`) ───────
  Error in `if (detectseparation::detect_separation(y = cbind(W, M - W), 
      x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
      warning(paste("Separation detected in abundance model!", 
          "Likely, one of your covariates/experimental conditions is such that", 
          "there are all zero counts within a group. Consider identifying and removing", 
          "this covariate from your model. The results of this model are not to be", 
          "trusted because there is not enough data. \n", sep = "\n"), 
          immediate. = TRUE)
      sep_da <- TRUE
  }`: argument is of length zero
  Backtrace:
      ▆
   1. └─corncob::bbdml(...) at test_scorehessian.R:12:0
  ── Error (test_simulate.R:12:1): (code run outside of `test_that()`) ───────────
  Error in `if (detectseparation::detect_separation(y = cbind(W, M - W), 
      x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
      warning(paste("Separation detected in abundance model!", 
          "Likely, one of your covariates/experimental conditions is such that", 
          "there are all zero counts within a group. Consider identifying and removing", 
          "this covariate from your model. The results of this model are not to be", 
          "trusted because there is not enough data. \n", sep = "\n"), 
          immediate. = TRUE)
      sep_da <- TRUE
  }`: argument is of length zero
  Backtrace:
      ▆
   1. └─corncob::bbdml(...) at test_simulate.R:12:0
  ── Error (test_waldtest.R:18:1): (code run outside of `test_that()`) ───────────
  Error in `if (detectseparation::detect_separation(y = cbind(W, M - W), 
      x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
      warning(paste("Separation detected in abundance model!", 
          "Likely, one of your covariates/experimental conditions is such that", 
          "there are all zero counts within a group. Consider identifying and removing", 
          "this covariate from your model. The results of this model are not to be", 
          "trusted because there is not enough data. \n", sep = "\n"), 
          immediate. = TRUE)
      sep_da <- TRUE
  }`: argument is of length zero
  Backtrace:
      ▆
   1. └─corncob::bbdml(...) at test_waldtest.R:18:0
  
  [ FAIL 10 | WARN 0 | SKIP 0 | PASS 17 ]
  Error: Test failures
  Execution halted