Running ‘misctests.R’ [3s/5s]
  Running ‘phylo4dtests.R’ [2s/4s]
  Running ‘phylosubtest.R’ [2s/4s]
  Running ‘phylotorture.R’ [2s/4s]
  Running ‘plottest.R’ [2s/4s]
  Running ‘roundtrip.R’ [2s/4s]
  Running ‘test-all.R’ [12s/16s]
  Running ‘testprune.R’ [2s/3s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > ## This script is only run during R CMD check, so we can set an environment
  > ## variable that will only run tests during R CMD check (or `devtools::check()`)
  > ## and not during `devtools::test()`.
  > 
  > ## Thus in the tests, we can request the NEXUS files that are stored in the
  > ## `inst/` folder, but during the checks, we test the files that have been
  > ## installed (using the `system.file()` function).
  > 
  > library(testthat)
  > 
  > Sys.setenv("R_CMD_CHECK" = "true")
  > 
  > test_check("phylobase")
  Loading required package: phylobase
  ── 1. Failure: phylo4d can be built from phylo4 (@test.class-phylo4d.R#112)  ───
  tdata(phyd, "tip") not equal to data.frame(c = factor(tipDt$c, levels = letters[nid.all]), row.names = lab.tip).
  Component "c": Modes: character, numeric
  Component "c": Attributes: < target is NULL, current is list >
  Component "c": target is character, current is factor
  
  ── 2. Failure: phylo4d can be built from phylo4 (@test.class-phylo4d.R#114)  ───
  tdata(phyd, "internal") not equal to data.frame(c = factor(nodDt$c, levels = letters[nid.all]), row.names = lab.int).
  Component "c": Modes: character, numeric
  Component "c": Attributes: < target is NULL, current is list >
  Component "c": target is character, current is factor
  
  ── 3. Failure: phylo4d can be built from phylo object (@test.class-phylo4d.R#276
  tdata(phyd, "internal")$labelValues not equal to as.factor(tr$node.label).
  Types not compatible: character is not integer
  
  ── 4. Failure: works factors (@test.formatData.R#66)  ──────────────────────────
  phylobase:::formatData(phy.alt, factor(letters[1:5])) not equal to phylobase:::formatData(phy.alt, data.frame(dt = letters[1:5])).
  Component "dt": 'current' is not a factor
  
  ── 5. Failure: formatData works with duplicated labels (@test.formatData.R#302) 
  phylobase:::formatData(phy.dup, factor(letters[1:5])) not equal to phylobase:::formatData(phy.dup, data.frame(dt = letters[1:5])).
  Component "dt": Modes: numeric, character
  Component "dt": target is numeric, current is character
  
  ── 6. Failure: check.node.labels='asdata' with readNCL (@test.readNCL.R#537)  ──
  tdata(newTr)$labelValues not equal to factor(c(NA, NA, NA, "yy", "xx")).
  Types not compatible: character is not integer
  
  ── 7. Failure: check.node.labels='asdata' with readNewick (@test.readNCL.R#543) 
  tdata(newTr)$labelValues not equal to factor(c(NA, NA, NA, "yy", "xx")).
  Types not compatible: character is not integer
  
  ── 8. Failure: phylo4 to data.frame (@test.setAs-Methods.R#169)  ───────────────
  phy.show$node.type not equal to factor(unname(nodeType(phy))).
  Types not compatible: character is not integer
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 625 | SKIPPED: 0 | WARNINGS: 10 | FAILED: 8 ]
  1. Failure: phylo4d can be built from phylo4 (@test.class-phylo4d.R#112) 
  2. Failure: phylo4d can be built from phylo4 (@test.class-phylo4d.R#114) 
  3. Failure: phylo4d can be built from phylo object (@test.class-phylo4d.R#276) 
  4. Failure: works factors (@test.formatData.R#66) 
  5. Failure: formatData works with duplicated labels (@test.formatData.R#302) 
  6. Failure: check.node.labels='asdata' with readNCL (@test.readNCL.R#537) 
  7. Failure: check.node.labels='asdata' with readNewick (@test.readNCL.R#543) 
  8. Failure: phylo4 to data.frame (@test.setAs-Methods.R#169) 
  
  Error: testthat unit tests failed
  Execution halted