Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Fix test failure in R 4.1 for c.neuronlist #444

Closed
jefferis opened this issue Sep 9, 2020 · 0 comments
Closed

Fix test failure in R 4.1 for c.neuronlist #444

jefferis opened this issue Sep 9, 2020 · 0 comments

Comments

@jefferis
Copy link
Collaborator

jefferis commented Sep 9, 2020

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
jefferis added a commit that referenced this issue Sep 22, 2020
* we weren't relying on the old behaviour beyond this test
* closes #444
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant