[R-pkg-devel] R-CMD-check works locally and on github, but windows automatic checks fail

[Cyril Lagger]

Hi all,

I am trying to submit our package scDiffCom (
https://github.com/CyrilLagger/scDiffCom) to CRAN. However, it does not
pass the windows automatic checks for some unclear reason to me. Any help
would be really appreciated!

Basically, the output from R-CMD-check is fine locally and for the github
actions I specified, but not for the automatic windows tests. Please see
below:

------------
1)
no ERRORs, no WARNINGs, no NOTEs when running devtools:check() locally
(windows 10, R 4.1.0)

2)
no ERRORs, no WARNINGs, no NOTEs when running github-actions
<https://github.com/CyrilLagger/scDiffCom/blob/master/.github/workflows/check-standard.yaml>
for windows-latest (release), macOS-latest (release), ubuntu-20.04
(release), ubuntu-20.04 (devel)

3)
1 ERROR when running devtools:check_win_devel: *Running the tests in
'tests/testthat.R' failed.* However, testthat.Rout.fail is not informative
to me, it only contains:

> library(testthat)
> library(scDiffCom)
>
> test_check("scDiffCom")
Loading required package: SeuratObject

4)
2 ERRORs when running devtools:check_win_release. As follows:

** running tests for arch 'i386' ... [5s] ERROR
  Running 'spelling.R' [0s]
  Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(scDiffCom)
  >
  > test_check("scDiffCom")
  Loading required package: SeuratObject
  == Failed tests
================================================================
  -- Error (test-everything.R:171:1): (code run outside of
`test_that()`) --------
  Error: error in load action .__A__.1 for package RcppAnnoy:
loadModule(module = "AnnoyAngular", what = TRUE, env = ns, loadNow =
TRUE): Unable to load module "AnnoyAngular": bad binding access
  Backtrace:
       x
    1. +-base::lapply(...) test-everything.R:171:0
    2. | \-scDiffCom:::FUN(X[[i]], ...)
    3. |   \-scDiffCom:::extract_analysis_inputs(...) test-everything.R:174:4
    4. |     \-scDiffCom:::extract_seurat_inputs(...)
    5. \-base::loadNamespace(x)
    6.   +-base::namespaceImportFrom(...)
    7.   | \-base::asNamespace(ns)
    8.   \-base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()),
versionCheck = vI[[j]])
    9.     \-methods::cacheMetaData(ns, TRUE, ns)
   10.       \-methods:::.doLoadActions(where, attach)

  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 6 ]
  Error: Test failures
  Execution halted
** running tests for arch 'x64' ... [5s] ERROR
  Running 'spelling.R' [0s]
  Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(scDiffCom)
  >
  > test_check("scDiffCom")
  Loading required package: SeuratObject

-----------

Since I have no error locally on my machine, I don't know what I could
change for the automatic tests to work. Also, I don't understand why
the github-action for windows-latest (release) works but not
devtools:check_win_release().

By the way, I installed R devel on my machine in addition to R 4.1.0,
but it turns out I cannot test our package installation because it has
Bioconductor dependencies and "Bioconductor does not yet build and
check packages for R version 4.2" as reported here
<https://github.com/r-hub/rhub/issues/471>. The exact same error
actually also occurs when I run devtools:check_rhub(). It does not
seem to be related to the failure of testthat I reported above, but I
thought it might be useful to mention it.

Thanks in advance for any help/suggestions!

Cyril

	[[alternative HTML version deleted]]