R version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
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Platform: x86_64-w64-mingw32/x64

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> library(testthat)
> library(zellkonverter)
Registered S3 method overwritten by 'zellkonverter':
  method                                             from      
  py_to_r.pandas.core.arrays.categorical.Categorical reticulate
> 
> test_check("zellkonverter")
C:\Users\BIOCBU~1\AppData\Local\R\cache\R\basilisk\117~1.0\ZELLKO~1\115~1.0\ZELLKO~1.6\Lib\site-packages\anndata\_core\anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
  warnings.warn(
C:\Users\BIOCBU~1\AppData\Local\R\cache\R\basilisk\117~1.0\ZELLKO~1\115~1.0\ZELLKO~1.6\Lib\site-packages\anndata\_core\anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
  warnings.warn(
C:\Users\BIOCBU~1\AppData\Local\R\cache\R\basilisk\117~1.0\ZELLKO~1\115~1.0\ZELLKO~1.6\Lib\site-packages\anndata\_core\anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
  warnings.warn(
C:\Users\BIOCBU~1\AppData\Local\R\cache\R\basilisk\117~1.0\ZELLKO~1\115~1.0\ZELLKO~1.6\Lib\site-packages\anndata\_core\anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
  warnings.warn(
C:\Users\BIOCBU~1\AppData\Local\R\cache\R\basilisk\117~1.0\ZELLKO~1\115~1.0\ZELLKO~1.6\Lib\site-packages\anndata\_core\anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
  warnings.warn(
C:\Users\BIOCBU~1\AppData\Local\R\cache\R\basilisk\117~1.0\ZELLKO~1\115~1.0\ZELLKO~1.6\Lib\site-packages\anndata\_core\anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
  warnings.warn(
C:\Users\BIOCBU~1\AppData\Local\R\cache\R\basilisk\117~1.0\ZELLKO~1\115~1.0\ZELLKO~1.6\Lib\site-packages\anndata\_core\anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
  warnings.warn(
C:\Users\BIOCBU~1\AppData\Local\R\cache\R\basilisk\117~1.0\ZELLKO~1\115~1.0\ZELLKO~1.6\Lib\site-packages\anndata\_core\anndata.py:1818: UserWarning: Observation names are not unique. To make them unique, call `.obs_names_make_unique`.
  utils.warn_names_duplicates("obs")
C:\Users\BIOCBU~1\AppData\Local\R\cache\R\basilisk\117~1.0\ZELLKO~1\115~1.0\ZELLKO~1.6\Lib\site-packages\anndata\_core\anndata.py:1818: UserWarning: Observation names are not unique. To make them unique, call `.obs_names_make_unique`.
  utils.warn_names_duplicates("obs")
C:\Users\BIOCBU~1\AppData\Local\R\cache\R\basilisk\117~1.0\ZELLKO~1\115~1.0\ZELLKO~1.6\Lib\site-packages\anndata\_core\anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
  warnings.warn(
C:\Users\BIOCBU~1\AppData\Local\R\cache\R\basilisk\117~1.0\ZELLKO~1\115~1.0\ZELLKO~1.6\Lib\site-packages\anndata\_core\anndata.py:1818: UserWarning: Observation names are not unique. To make them unique, call `.obs_names_make_unique`.
  utils.warn_names_duplicates("obs")
C:\Users\BIOCBU~1\AppData\Local\R\cache\R\basilisk\117~1.0\ZELLKO~1\115~1.0\ZELLKO~1.6\Lib\site-packages\anndata\_core\anndata.py:1818: UserWarning: Observation names are not unique. To make them unique, call `.obs_names_make_unique`.
  utils.warn_names_duplicates("obs")
C:\Users\BIOCBU~1\AppData\Local\R\cache\R\basilisk\117~1.0\ZELLKO~1\115~1.0\ZELLKO~1.6\Lib\site-packages\anndata\_core\anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
  warnings.warn(
[ FAIL 3 | WARN 18 | SKIP 0 | PASS 177 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-gtex_8tissues.R:6:1'): (code run outside of `test_that()`) ─────
Error in `bfcrpath(cache, "https://storage.googleapis.com/gtex_analysis_v9/snrna_seq_data/GTEx_8_tissues_snRNAseq_atlas_071421.public_obs.h5ad")`: not all 'rnames' found or unique.
Backtrace:
    ▆
 1. ├─BiocFileCache::bfcrpath(cache, "https://storage.googleapis.com/gtex_analysis_v9/snrna_seq_data/GTEx_8_tissues_snRNAseq_atlas_071421.public_obs.h5ad") at test-gtex_8tissues.R:6:1
 2. └─BiocFileCache::bfcrpath(cache, "https://storage.googleapis.com/gtex_analysis_v9/snrna_seq_data/GTEx_8_tissues_snRNAseq_atlas_071421.public_obs.h5ad")
── Failure ('test-pegasus_marrow.R:37:5'): SCE is valid ────────────────────────
varm names not identical to `correct_names`.
Lengths differ: 4 is not 5
Backtrace:
    ▆
 1. └─zellkonverter:::validateH5ADSCE(sce, names, missing) at test-pegasus_marrow.R:37:5
 2.   └─zellkonverter:::.names_validator(...)
 3.     └─testthat::expect_identical(actual_names, correct_names, label = label)
── Failure ('test-scvi_citeseq.R:45:5'): Round trip is as expected ─────────────
SummarizedExperiment::colData(sce) not identical to SummarizedExperiment::colData(expected).
Objects equal but not identical
Backtrace:
    ▆
 1. └─zellkonverter:::expectSCE(out, sce) at test-scvi_citeseq.R:45:5
 2.   └─testthat::expect_identical(...)

[ FAIL 3 | WARN 18 | SKIP 0 | PASS 177 ]
Error: Test failures
Execution halted

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no zellkonverter_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc-longtests/meat/zellkonverter.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using options '--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error'
* checking for file 'zellkonverter/DESCRIPTION' ... OK
* this is package 'zellkonverter' version '1.15.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'zellkonverter' can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used
See 'F:/biocbuild/bbs-3.20-bioc-longtests/meat/zellkonverter.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking files in 'vignettes' ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in 'longtests' ... OK
* checking tests in 'longtests' ...
  Running 'testthat.R'
 ERROR
Running the tests in 'longtests/testthat.R' failed.
Last 13 lines of output:
      ▆
   1. └─zellkonverter:::validateH5ADSCE(sce, names, missing) at test-pegasus_marrow.R:37:5
   2.   └─zellkonverter:::.names_validator(...)
   3.     └─testthat::expect_identical(actual_names, correct_names, label = label)
  ── Failure ('test-scvi_citeseq.R:45:5'): Round trip is as expected ─────────────
  SummarizedExperiment::colData(sce) not identical to SummarizedExperiment::colData(expected).
  Objects equal but not identical
  Backtrace:
      ▆
   1. └─zellkonverter:::expectSCE(out, sce) at test-scvi_citeseq.R:45:5
   2.   └─testthat::expect_identical(...)
  
  [ FAIL 3 | WARN 18 | SKIP 0 | PASS 177 ]
  Error: Test failures
  Execution halted
* DONE

Status: 1 ERROR, 1 NOTE
See
  'F:/biocbuild/bbs-3.20-bioc-longtests/meat/zellkonverter.Rcheck/00check.log'
for details.

* installing *source* package 'zellkonverter' ...
** using non-staged installation via StagedInstall field
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (zellkonverter)