R version 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
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")
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: C:\Users\biocbuild\AppData\Local\R\cache\R\basilisk\1.16.0\zellkonverter\1.14.1\zellkonverterAnnDataEnv-0.10.6

  added / updated specs:
    - python=3.12.2


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    setuptools-70.1.0          |     pyhd8ed1ab_0         484 KB  conda-forge
    ------------------------------------------------------------
                                           Total:         484 KB

The following NEW packages will be INSTALLED:

  bzip2              conda-forge/win-64::bzip2-1.0.8-hcfcfb64_5
  ca-certificates    conda-forge/win-64::ca-certificates-2024.6.2-h56e8100_0
  libexpat           conda-forge/win-64::libexpat-2.6.2-h63175ca_0
  libffi             conda-forge/win-64::libffi-3.4.2-h8ffe710_5
  libsqlite          conda-forge/win-64::libsqlite-3.46.0-h2466b09_0
  libzlib            conda-forge/win-64::libzlib-1.3.1-h2466b09_1
  openssl            conda-forge/win-64::openssl-3.3.1-h2466b09_0
  pip                conda-forge/noarch::pip-24.0-pyhd8ed1ab_0
  python             conda-forge/win-64::python-3.12.2-h2628c8c_0_cpython
  setuptools         conda-forge/noarch::setuptools-70.1.0-pyhd8ed1ab_0
  tk                 conda-forge/win-64::tk-8.6.13-h5226925_1
  tzdata             conda-forge/noarch::tzdata-2024a-h0c530f3_0
  ucrt               conda-forge/win-64::ucrt-10.0.22621.0-h57928b3_0
  vc                 conda-forge/win-64::vc-14.3-h8a93ad2_20
  vc14_runtime       conda-forge/win-64::vc14_runtime-14.40.33810-ha82c5b3_20
  vs2015_runtime     conda-forge/win-64::vs2015_runtime-14.40.33810-h3bf8584_20
  wheel              conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1
  xz                 conda-forge/win-64::xz-5.2.6-h8d14728_0


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done


==> WARNING: A newer version of conda exists. <==
  current version: 4.12.0
  latest version: 24.5.0

Please update conda by running

    $ conda update -n base -c defaults conda



# All requested packages already installed.

Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done


==> WARNING: A newer version of conda exists. <==
  current version: 4.12.0
  latest version: 24.5.0

Please update conda by running

    $ conda update -n base -c defaults conda



## Package Plan ##

  environment location: C:\Users\biocbuild\AppData\Local\R\cache\R\basilisk\1.16.0\zellkonverter\1.14.1\zellkonverterAnnDataEnv-0.10.6

  added / updated specs:
    - anndata=0.10.6
    - h5py=3.10.0
    - hdf5=1.14.3
    - natsort=8.4.0
    - numpy=1.26.4
    - packaging=24.0
    - pandas=2.2.1
    - python[version='3.12.2.*,3.12.2.*']
    - scipy=1.12.0


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    array-api-compat-1.7.1     |     pyhd8ed1ab_0          32 KB  conda-forge
    hdf5-1.14.3                |nompi_h2b43c12_105         1.9 MB  conda-forge
    ------------------------------------------------------------
                                           Total:         2.0 MB

The following NEW packages will be INSTALLED:

  anndata            conda-forge/noarch::anndata-0.10.6-pyhd8ed1ab_0
  array-api-compat   conda-forge/noarch::array-api-compat-1.7.1-pyhd8ed1ab_0
  cached-property    conda-forge/noarch::cached-property-1.5.2-hd8ed1ab_1
  cached_property    conda-forge/noarch::cached_property-1.5.2-pyha770c72_1
  exceptiongroup     conda-forge/noarch::exceptiongroup-1.2.0-pyhd8ed1ab_2
  h5py               conda-forge/win-64::h5py-3.10.0-nompi_py312h1751c5b_101
  hdf5               conda-forge/win-64::hdf5-1.14.3-nompi_h2b43c12_105
  intel-openmp       conda-forge/win-64::intel-openmp-2024.1.0-h57928b3_966
  krb5               conda-forge/win-64::krb5-1.21.2-heb0366b_0
  libaec             conda-forge/win-64::libaec-1.1.3-h63175ca_0
  libblas            conda-forge/win-64::libblas-3.9.0-22_win64_mkl
  libcblas           conda-forge/win-64::libcblas-3.9.0-22_win64_mkl
  libcurl            conda-forge/win-64::libcurl-8.8.0-hd5e4a3a_0
  libhwloc           conda-forge/win-64::libhwloc-2.10.0-default_h8125262_1001
  libiconv           conda-forge/win-64::libiconv-1.17-hcfcfb64_2
  liblapack          conda-forge/win-64::liblapack-3.9.0-22_win64_mkl
  libssh2            conda-forge/win-64::libssh2-1.11.0-h7dfc565_0
  libxml2            conda-forge/win-64::libxml2-2.12.7-h283a6d9_1
  mkl                conda-forge/win-64::mkl-2024.1.0-h66d3029_692
  natsort            conda-forge/noarch::natsort-8.4.0-pyhd8ed1ab_0
  numpy              conda-forge/win-64::numpy-1.26.4-py312h8753938_0
  packaging          conda-forge/noarch::packaging-24.0-pyhd8ed1ab_0
  pandas             conda-forge/win-64::pandas-2.2.1-py312h2ab9e98_0
  pthreads-win32     conda-forge/win-64::pthreads-win32-2.9.1-hfa6e2cd_3
  python-dateutil    conda-forge/noarch::python-dateutil-2.9.0-pyhd8ed1ab_0
  python-tzdata      conda-forge/noarch::python-tzdata-2024.1-pyhd8ed1ab_0
  python_abi         conda-forge/win-64::python_abi-3.12-4_cp312
  pytz               conda-forge/noarch::pytz-2024.1-pyhd8ed1ab_0
  scipy              conda-forge/win-64::scipy-1.12.0-py312h8753938_2
  six                conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
  tbb                conda-forge/win-64::tbb-2021.12.0-hc790b64_1



Downloading and Extracting Packages

array-api-compat-1.7 | 32 KB     |            |   0% 
array-api-compat-1.7 | 32 KB     | ########## | 100% 
array-api-compat-1.7 | 32 KB     | ########## | 100% 

hdf5-1.14.3          | 1.9 MB    |            |   0% 
hdf5-1.14.3          | 1.9 MB    | ########## | 100% 
hdf5-1.14.3          | 1.9 MB    | ########## | 100% 
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
C:\Users\BIOCBU~1\AppData\Local\R\cache\R\basilisk\116~1.0\ZELLKO~1\114~1.1\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\116~1.0\ZELLKO~1\114~1.1\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\116~1.0\ZELLKO~1\114~1.1\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\116~1.0\ZELLKO~1\114~1.1\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\116~1.0\ZELLKO~1\114~1.1\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\116~1.0\ZELLKO~1\114~1.1\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\116~1.0\ZELLKO~1\114~1.1\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\116~1.0\ZELLKO~1\114~1.1\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\116~1.0\ZELLKO~1\114~1.1\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\116~1.0\ZELLKO~1\114~1.1\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\116~1.0\ZELLKO~1\114~1.1\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\116~1.0\ZELLKO~1\114~1.1\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\116~1.0\ZELLKO~1\114~1.1\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 0 | SKIP 0 | PASS 178 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-gtex_8tissues.R:53:10'): Reading H5AD works ────────────────────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'colnames': INTEGER() can only be applied to a 'integer', not a 'double'
Backtrace:
     ▆
  1. ├─testthat::expect_warning(...) at test-gtex_8tissues.R:52:5
  2. │ └─testthat:::quasi_capture(...)
  3. │   ├─testthat (local) .capture(...)
  4. │   │ └─base::withCallingHandlers(...)
  5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  6. ├─zellkonverter::readH5AD(file) at test-gtex_8tissues.R:53:10
  7. │ └─basilisk::basiliskRun(...)
  8. │   └─zellkonverter (local) fun(...)
  9. │     └─zellkonverter::AnnData2SCE(...)
 10. │       ├─zellkonverter:::.convert_anndata_df(...)
 11. │       │ └─BiocGenerics::colnames(adata_df)
 12. │       ├─reticulate::py_to_r(adata$obs)
 13. │       └─reticulate:::py_to_r.pandas.core.frame.DataFrame(adata$obs)
 14. │         └─reticulate:::py_convert_pandas_df(x)
 15. └─base::.handleSimpleError(...)
 16.   └─base (local) h(simpleError(msg, call))
── Error ('test-gtex_8tissues.R:59:1'): (code run outside of `test_that()`) ────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'colnames': INTEGER() can only be applied to a 'integer', not a 'double'
Backtrace:
     ▆
  1. ├─base::suppressWarnings(readH5AD(file)) at test-gtex_8tissues.R:59:1
  2. │ └─base::withCallingHandlers(...)
  3. ├─zellkonverter::readH5AD(file)
  4. │ └─basilisk::basiliskRun(...)
  5. │   └─zellkonverter (local) fun(...)
  6. │     └─zellkonverter::AnnData2SCE(...)
  7. │       ├─zellkonverter:::.convert_anndata_df(...)
  8. │       │ └─BiocGenerics::colnames(adata_df)
  9. │       ├─reticulate::py_to_r(adata$obs)
 10. │       └─reticulate:::py_to_r.pandas.core.frame.DataFrame(adata$obs)
 11. │         └─reticulate:::py_convert_pandas_df(x)
 12. └─base::.handleSimpleError(...)
 13.   └─base (local) h(simpleError(msg, call))
── 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 0 | SKIP 0 | PASS 178 ]
Error: Test failures
Execution halted

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-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_1.14.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc-longtests/meat/zellkonverter.Rcheck'
* using R version 4.4.0 (2024-04-24 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 '1.14.1'
* 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-3.19-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:
   10. │       └─reticulate:::py_to_r.pandas.core.frame.DataFrame(adata$obs)
   11. │         └─reticulate:::py_convert_pandas_df(x)
   12. └─base::.handleSimpleError(...)
   13.   └─base (local) h(simpleError(msg, call))
  ── 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 0 | SKIP 0 | PASS 178 ]
  Error: Test failures
  Execution halted
* DONE

Status: 1 ERROR, 1 NOTE
See
  'F:/biocbuild/bbs-3.19-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)