Running ‘test-all.R’ [22s/28s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > library(nat)
  Loading required package: rgl
  Registered S3 method overwritten by 'nat':
    method             from
    as.mesh3d.ashape3d rgl 
  Some nat functions depend on a CMTK installation. See ?cmtk and README.md for details.
  
  Attaching package: 'nat'
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, union
  
  > library(httr)
  > 
  > # suppress RGL in headless environments (some CRAN build machines fail otherwise)
  > if(!interactive())
  +   Sys.setenv(RGL_USE_NULL=TRUE)
  > 
  > # Is internet accessible?
  > internet.ok = identical(
  +   try(
  +     status_code(
  +       HEAD("http://flybrain.mrc-lmb.cam.ac.uk/", timeout(2))
  +     ),
  +     silent = TRUE
  +   ),
  +   200L
  + )
  > 
  > if(Sys.getenv('NOT_CRAN') == "true" && internet.ok) {
  +   # note that we want to run all tests requiring internet access
  +   Sys.setenv(NAT_INTERNET_TESTS="TRUE")
  +   # Run all test files
  +   test_check("nat")
  + } else {
  +   # We're on CRAN or flybrain is inacessible, so don't run anything involving 
  +   # remote files
  +   Sys.setenv(NAT_INTERNET_TESTS="")
  +   test_check("nat", filter="^[^.]+")
  + }
    adding: testdata/neuron/testneuron_am3d.am (deflated 45%)
    adding: testdata/neuron/testneuron_lineset.am (deflated 69%)
    adding: DA1/EBH11R.swc (deflated 53%)
    adding: DA1/EBH20R.swc (deflated 54%)
    adding: DA1/EBI12L.swc (deflated 54%)
    adding: DL3/EBH20L.swc (deflated 54%)
    adding: DL3/EBI22R.swc (deflated 53%)
  Saving _problems/test-neuronlistfh-54.R
  [ FAIL 1 | WARN 4 | SKIP 7 | PASS 785 ]
  
  ══ Skipped tests (7) ═══════════════════════════════════════════════════════════
  • On CRAN (3): 'test-cmtk.R:23:1', 'test-cmtkreg.R:58:3', 'test-ndigest.R:9:3'
  • empty test (4): 'test-neuron-io.R:992:1', 'test-neuronlist.R:90:1',
    'test-potential_synapses.R:3:1',
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-neuronlistfh.R:54:3'): we can load a previously created on disk neuronlistfh representation ──
  Error in `.local(db, key, value, ...)`: unable to insert object '1cba713a5da299980a580959163bb482'
  Backtrace:
      ▆
   1. ├─nat::as.neuronlistfh(...) at test-neuronlistfh.R:54:3
   2. └─nat:::as.neuronlistfh.neuronlist(...)
   3.   └─filehash::dumpList(x, dbName = dbdir, type = dbClass)
   4.     ├─filehash::dbInsert(db, vnames[i], data[[vnames[i]]])
   5.     └─filehash::dbInsert(db, vnames[i], data[[vnames[i]]])
   6.       └─filehash (local) .local(db, key, value, ...)
  
  [ FAIL 1 | WARN 4 | SKIP 7 | PASS 785 ]
  Error:
  ! Test failures.
  Execution halted