natverse / nat

NeuroAnatomy Toolbox: An R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons.
https://natverse.org/nat/
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Fix test failure in R 4.1 for c.neuronlist #444

Closed jefferis closed 3 years ago

jefferis commented 3 years ago

related to https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17900

Dear maintainer,

Please see the problems shown on
<https://cran.r-project.org/web/checks/check_results_nat.html>.

Please correct before 2020-09-20 to safely retain your package on CRAN.

Best,
-k
checking tests ... [35s/39s] ERROR
  Running 'test-all.R' [34s/38s]
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%)
  -- 1. Failure: c.neuronlist behaves (@test-neuronlist.R#26) -------------------
  `c(Cell07PNs[1:5], NULL)` did not throw an error.

  == testthat results ===========================================================
  [ OK: 787 | SKIPPED: 5 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: c.neuronlist behaves (@test-neuronlist.R#26)

  Error: testthat unit tests failed
  Execution halted
checking for unstated dependencies in vignettes ... OK
checking package vignettes in 'inst/doc' ... OK
checking re-building of vignette outputs ... [9s/11s] OK
checking PDF version of manual ... OK
checking for non-standard things in the check directory ... OK
DONE