Back to Long Tests report for BioC 3.22

This page was generated on 2025-06-14 23:55 -0400 (Sat, 14 Jun 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4807
palomino8Windows Server 2022 Datacenterx644.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six" 4548
lconwaymacOS 12.7.1 Montereyx86_644.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six" 4586
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 29/29HostnameOS / ArchCHECK
zellkonverter 1.19.1  (landing page)
Luke Zappia
Snapshot Date: 2025-06-14 09:55 -0400 (Sat, 14 Jun 2025)
git_url: https://git.bioconductor.org/packages/zellkonverter
git_branch: devel
git_last_commit: 0ed9aa2
git_last_commit_date: 2025-06-08 11:29:56 -0400 (Sun, 08 Jun 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK  
palomino8Windows Server 2022 Datacenter / x64  ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  NA  

CHECK results for zellkonverter on palomino8

To the developers/maintainers of the zellkonverter package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: zellkonverter
Version: 1.19.1
Command: F:\biocbuild\bbs-3.22-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_1.19.1.tar.gz
StartedAt: 2025-06-14 16:15:05 -0400 (Sat, 14 Jun 2025)
EndedAt: 2025-06-14 16:17:49 -0400 (Sat, 14 Jun 2025)
EllapsedTime: 163.8 seconds
RetCode: 1
Status:   ERROR  
CheckDir: zellkonverter.Rcheck
Warnings: NA

Tests output

zellkonverter.Rcheck/tests/testthat.Rout.fail


R version 4.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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Type 'license()' or 'licence()' for distribution details.

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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")
:: [Info] ::  Mirror: https://www.python.org/ftp/python
:: [Info] ::  Mirror: https://downloads.python.org/pypy/versions.json
:: [Info] ::  Mirror: https://api.github.com/repos/oracle/graalpython/releases
:: [Installing] ::  3.13.4 ...
:: [Error] :: error installing "core" component MSI.
:: [Error] :: couldn't install 3.13.4
:: [Info] ::  Mirror: https://www.python.org/ftp/python
:: [Info] ::  Mirror: https://downloads.python.org/pypy/versions.json
:: [Info] ::  Mirror: https://api.github.com/repos/oracle/graalpython/releases
:: [Installing] ::  3.13.4 ...
:: [Error] :: error installing "core" component MSI.
:: [Error] :: couldn't install 3.13.4
:: [Info] ::  Mirror: https://www.python.org/ftp/python
:: [Info] ::  Mirror: https://downloads.python.org/pypy/versions.json
:: [Info] ::  Mirror: https://api.github.com/repos/oracle/graalpython/releases
:: [Installing] ::  3.13.4 ...
:: [Error] :: error installing "core" component MSI.
:: [Error] :: couldn't install 3.13.4
:: [Info] ::  Mirror: https://www.python.org/ftp/python
:: [Info] ::  Mirror: https://downloads.python.org/pypy/versions.json
:: [Info] ::  Mirror: https://api.github.com/repos/oracle/graalpython/releases
:: [Installing] ::  3.13.4 ...
:: [Error] :: error installing "core" component MSI.
:: [Error] :: couldn't install 3.13.4
:: [Info] ::  Mirror: https://www.python.org/ftp/python
:: [Info] ::  Mirror: https://downloads.python.org/pypy/versions.json
:: [Info] ::  Mirror: https://api.github.com/repos/oracle/graalpython/releases
:: [Installing] ::  3.13.4 ...
:: [Error] :: error installing "core" component MSI.
:: [Error] :: couldn't install 3.13.4
:: [Info] ::  Mirror: https://www.python.org/ftp/python
:: [Info] ::  Mirror: https://downloads.python.org/pypy/versions.json
:: [Info] ::  Mirror: https://api.github.com/repos/oracle/graalpython/releases
:: [Installing] ::  3.13.4 ...
:: [Error] :: error installing "core" component MSI.
:: [Error] :: couldn't install 3.13.4
:: [Info] ::  Mirror: https://www.python.org/ftp/python
:: [Info] ::  Mirror: https://downloads.python.org/pypy/versions.json
:: [Info] ::  Mirror: https://api.github.com/repos/oracle/graalpython/releases
:: [Installing] ::  3.13.4 ...
:: [Error] :: error installing "core" component MSI.
:: [Error] :: couldn't install 3.13.4
:: [Info] ::  Mirror: https://www.python.org/ftp/python
:: [Info] ::  Mirror: https://downloads.python.org/pypy/versions.json
:: [Info] ::  Mirror: https://api.github.com/repos/oracle/graalpython/releases
:: [Installing] ::  3.13.4 ...
:: [Error] :: error installing "core" component MSI.
:: [Error] :: couldn't install 3.13.4
:: [Info] ::  Mirror: https://www.python.org/ftp/python
:: [Info] ::  Mirror: https://downloads.python.org/pypy/versions.json
:: [Info] ::  Mirror: https://api.github.com/repos/oracle/graalpython/releases
:: [Installing] ::  3.13.4 ...
:: [Error] :: error installing "core" component MSI.
:: [Error] :: couldn't install 3.13.4
:: [Info] ::  Mirror: https://www.python.org/ftp/python
:: [Info] ::  Mirror: https://downloads.python.org/pypy/versions.json
:: [Info] ::  Mirror: https://api.github.com/repos/oracle/graalpython/releases
:: [Installing] ::  3.13.4 ...
:: [Error] :: error installing "core" component MSI.
:: [Error] :: couldn't install 3.13.4
:: [Info] ::  Mirror: https://www.python.org/ftp/python
:: [Info] ::  Mirror: https://downloads.python.org/pypy/versions.json
:: [Info] ::  Mirror: https://api.github.com/repos/oracle/graalpython/releases
:: [Installing] ::  3.13.4 ...
:: [Error] :: error installing "core" component MSI.
:: [Error] :: couldn't install 3.13.4
:: [Info] ::  Mirror: https://www.python.org/ftp/python
:: [Info] ::  Mirror: https://downloads.python.org/pypy/versions.json
:: [Info] ::  Mirror: https://api.github.com/repos/oracle/graalpython/releases
:: [Installing] ::  3.13.4 ...
:: [Error] :: error installing "core" component MSI.
:: [Error] :: couldn't install 3.13.4
:: [Info] ::  Mirror: https://www.python.org/ftp/python
:: [Info] ::  Mirror: https://downloads.python.org/pypy/versions.json
:: [Info] ::  Mirror: https://api.github.com/repos/oracle/graalpython/releases
:: [Installing] ::  3.13.4 ...
:: [Error] :: error installing "core" component MSI.
:: [Error] :: couldn't install 3.13.4
:: [Info] ::  Mirror: https://www.python.org/ftp/python
:: [Info] ::  Mirror: https://downloads.python.org/pypy/versions.json
:: [Info] ::  Mirror: https://api.github.com/repos/oracle/graalpython/releases
:: [Installing] ::  3.13.4 ...
:: [Error] :: error installing "core" component MSI.
:: [Error] :: couldn't install 3.13.4
:: [Info] ::  Mirror: https://www.python.org/ftp/python
:: [Info] ::  Mirror: https://downloads.python.org/pypy/versions.json
:: [Info] ::  Mirror: https://api.github.com/repos/oracle/graalpython/releases
:: [Installing] ::  3.13.4 ...
:: [Error] :: error installing "core" component MSI.
:: [Error] :: couldn't install 3.13.4
:: [Info] ::  Mirror: https://www.python.org/ftp/python
:: [Info] ::  Mirror: https://downloads.python.org/pypy/versions.json
:: [Info] ::  Mirror: https://api.github.com/repos/oracle/graalpython/releases
:: [Installing] ::  3.13.4 ...
:: [Error] :: error installing "core" component MSI.
:: [Error] :: couldn't install 3.13.4
:: [Info] ::  Mirror: https://www.python.org/ftp/python
:: [Info] ::  Mirror: https://downloads.python.org/pypy/versions.json
:: [Info] ::  Mirror: https://api.github.com/repos/oracle/graalpython/releases
:: [Installing] ::  3.13.4 ...
:: [Error] :: error installing "core" component MSI.
:: [Error] :: couldn't install 3.13.4
:: [Info] ::  Mirror: https://www.python.org/ftp/python
:: [Info] ::  Mirror: https://downloads.python.org/pypy/versions.json
:: [Info] ::  Mirror: https://api.github.com/repos/oracle/graalpython/releases
:: [Installing] ::  3.13.4 ...
:: [Error] :: error installing "core" component MSI.
:: [Error] :: couldn't install 3.13.4
:: [Info] ::  Mirror: https://www.python.org/ftp/python
:: [Info] ::  Mirror: https://downloads.python.org/pypy/versions.json
:: [Info] ::  Mirror: https://api.github.com/repos/oracle/graalpython/releases
:: [Installing] ::  3.13.4 ...
:: [Error] :: error installing "core" component MSI.
:: [Error] :: couldn't install 3.13.4
:: [Info] ::  Mirror: https://www.python.org/ftp/python
:: [Info] ::  Mirror: https://downloads.python.org/pypy/versions.json
:: [Info] ::  Mirror: https://api.github.com/repos/oracle/graalpython/releases
:: [Installing] ::  3.13.4 ...
:: [Error] :: error installing "core" component MSI.
:: [Error] :: couldn't install 3.13.4
[ FAIL 20 | WARN 0 | SKIP 0 | PASS 0 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-cellrank_pancreas.R:45:10'): Reading H5AD works ────────────────
Error in `pyenv_python(version = version)`: Python 3.13.4 does not appear to be installed.
Try installing it with install_python(version = "3.13.4").
Backtrace:
     ▆
  1. ├─testthat::expect_warning(...) at test-cellrank_pancreas.R:44:5
  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-cellrank_pancreas.R:45:10
  7.   └─basilisk::basiliskRun(...)
  8.     └─basilisk::basiliskStart(...)
  9.       └─basilisk::obtainEnvironmentPath(env)
 10.         └─basilisk::setupBasiliskEnv(...)
 11.           ├─base::suppressMessages(install_python(version))
 12.           │ └─base::withCallingHandlers(...)
 13.           └─reticulate::install_python(version)
 14.             └─reticulate:::pyenv_python(version = version)
── Error ('test-cellrank_pancreas.R:51:1'): (code run outside of `test_that()`) ──
Error in `pyenv_python(version = version)`: Python 3.13.4 does not appear to be installed.
Try installing it with install_python(version = "3.13.4").
Backtrace:
     ▆
  1. ├─base::suppressWarnings(readH5AD(file)) at test-cellrank_pancreas.R:51:1
  2. │ └─base::withCallingHandlers(...)
  3. └─zellkonverter::readH5AD(file)
  4.   └─basilisk::basiliskRun(...)
  5.     └─basilisk::basiliskStart(...)
  6.       └─basilisk::obtainEnvironmentPath(env)
  7.         └─basilisk::setupBasiliskEnv(...)
  8.           ├─base::suppressMessages(install_python(version))
  9.           │ └─base::withCallingHandlers(...)
 10.           └─reticulate::install_python(version)
 11.             └─reticulate:::pyenv_python(version = version)
── Error ('test-example_anndata.R:21:5'): Reading H5AD works ───────────────────
Error in `pyenv_python(version = version)`: Python 3.13.4 does not appear to be installed.
Try installing it with install_python(version = "3.13.4").
Backtrace:
    ▆
 1. └─zellkonverter::readH5AD(file) at test-example_anndata.R:21:5
 2.   └─basilisk::basiliskRun(...)
 3.     └─basilisk::basiliskStart(...)
 4.       └─basilisk::obtainEnvironmentPath(env)
 5.         └─basilisk::setupBasiliskEnv(...)
 6.           ├─base::suppressMessages(install_python(version))
 7.           │ └─base::withCallingHandlers(...)
 8.           └─reticulate::install_python(version)
 9.             └─reticulate:::pyenv_python(version = version)
── Error ('test-example_anndata.R:25:1'): (code run outside of `test_that()`) ──
Error in `pyenv_python(version = version)`: Python 3.13.4 does not appear to be installed.
Try installing it with install_python(version = "3.13.4").
Backtrace:
     ▆
  1. ├─base::suppressWarnings(readH5AD(file)) at test-example_anndata.R:25:1
  2. │ └─base::withCallingHandlers(...)
  3. └─zellkonverter::readH5AD(file)
  4.   └─basilisk::basiliskRun(...)
  5.     └─basilisk::basiliskStart(...)
  6.       └─basilisk::obtainEnvironmentPath(env)
  7.         └─basilisk::setupBasiliskEnv(...)
  8.           ├─base::suppressMessages(install_python(version))
  9.           │ └─base::withCallingHandlers(...)
 10.           └─reticulate::install_python(version)
 11.             └─reticulate:::pyenv_python(version = version)
── Error ('test-gtex_8tissues.R:53:10'): Reading H5AD works ────────────────────
Error in `pyenv_python(version = version)`: Python 3.13.4 does not appear to be installed.
Try installing it with install_python(version = "3.13.4").
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.     └─basilisk::basiliskStart(...)
  9.       └─basilisk::obtainEnvironmentPath(env)
 10.         └─basilisk::setupBasiliskEnv(...)
 11.           ├─base::suppressMessages(install_python(version))
 12.           │ └─base::withCallingHandlers(...)
 13.           └─reticulate::install_python(version)
 14.             └─reticulate:::pyenv_python(version = version)
── Error ('test-gtex_8tissues.R:59:1'): (code run outside of `test_that()`) ────
Error in `pyenv_python(version = version)`: Python 3.13.4 does not appear to be installed.
Try installing it with install_python(version = "3.13.4").
Backtrace:
     ▆
  1. ├─base::suppressWarnings(readH5AD(file)) at test-gtex_8tissues.R:59:1
  2. │ └─base::withCallingHandlers(...)
  3. └─zellkonverter::readH5AD(file)
  4.   └─basilisk::basiliskRun(...)
  5.     └─basilisk::basiliskStart(...)
  6.       └─basilisk::obtainEnvironmentPath(env)
  7.         └─basilisk::setupBasiliskEnv(...)
  8.           ├─base::suppressMessages(install_python(version))
  9.           │ └─base::withCallingHandlers(...)
 10.           └─reticulate::install_python(version)
 11.             └─reticulate:::pyenv_python(version = version)
── Error ('test-pegasus_marrow.R:30:5'): Reading H5AD works ────────────────────
Error in `pyenv_python(version = version)`: Python 3.13.4 does not appear to be installed.
Try installing it with install_python(version = "3.13.4").
Backtrace:
    ▆
 1. └─zellkonverter::readH5AD(file) at test-pegasus_marrow.R:30:5
 2.   └─basilisk::basiliskRun(...)
 3.     └─basilisk::basiliskStart(...)
 4.       └─basilisk::obtainEnvironmentPath(env)
 5.         └─basilisk::setupBasiliskEnv(...)
 6.           ├─base::suppressMessages(install_python(version))
 7.           │ └─base::withCallingHandlers(...)
 8.           └─reticulate::install_python(version)
 9.             └─reticulate:::pyenv_python(version = version)
── Error ('test-pegasus_marrow.R:34:1'): (code run outside of `test_that()`) ───
Error in `pyenv_python(version = version)`: Python 3.13.4 does not appear to be installed.
Try installing it with install_python(version = "3.13.4").
Backtrace:
     ▆
  1. ├─base::suppressWarnings(readH5AD(file)) at test-pegasus_marrow.R:34:1
  2. │ └─base::withCallingHandlers(...)
  3. └─zellkonverter::readH5AD(file)
  4.   └─basilisk::basiliskRun(...)
  5.     └─basilisk::basiliskStart(...)
  6.       └─basilisk::obtainEnvironmentPath(env)
  7.         └─basilisk::setupBasiliskEnv(...)
  8.           ├─base::suppressMessages(install_python(version))
  9.           │ └─base::withCallingHandlers(...)
 10.           └─reticulate::install_python(version)
 11.             └─reticulate:::pyenv_python(version = version)
── Error ('test-scIB_pancreas.R:15:5'): Reading H5AD works ─────────────────────
Error in `pyenv_python(version = version)`: Python 3.13.4 does not appear to be installed.
Try installing it with install_python(version = "3.13.4").
Backtrace:
    ▆
 1. └─zellkonverter::readH5AD(file) at test-scIB_pancreas.R:15:5
 2.   └─basilisk::basiliskRun(...)
 3.     └─basilisk::basiliskStart(...)
 4.       └─basilisk::obtainEnvironmentPath(env)
 5.         └─basilisk::setupBasiliskEnv(...)
 6.           ├─base::suppressMessages(install_python(version))
 7.           │ └─base::withCallingHandlers(...)
 8.           └─reticulate::install_python(version)
 9.             └─reticulate:::pyenv_python(version = version)
── Error ('test-scIB_pancreas.R:19:1'): (code run outside of `test_that()`) ────
Error in `pyenv_python(version = version)`: Python 3.13.4 does not appear to be installed.
Try installing it with install_python(version = "3.13.4").
Backtrace:
     ▆
  1. ├─base::suppressWarnings(readH5AD(file)) at test-scIB_pancreas.R:19:1
  2. │ └─base::withCallingHandlers(...)
  3. └─zellkonverter::readH5AD(file)
  4.   └─basilisk::basiliskRun(...)
  5.     └─basilisk::basiliskStart(...)
  6.       └─basilisk::obtainEnvironmentPath(env)
  7.         └─basilisk::setupBasiliskEnv(...)
  8.           ├─base::suppressMessages(install_python(version))
  9.           │ └─base::withCallingHandlers(...)
 10.           └─reticulate::install_python(version)
 11.             └─reticulate:::pyenv_python(version = version)
── Error ('test-scanpy_pbmc3k.R:25:5'): Reading H5AD works ─────────────────────
Error in `pyenv_python(version = version)`: Python 3.13.4 does not appear to be installed.
Try installing it with install_python(version = "3.13.4").
Backtrace:
    ▆
 1. └─zellkonverter::readH5AD(file) at test-scanpy_pbmc3k.R:25:5
 2.   └─basilisk::basiliskRun(...)
 3.     └─basilisk::basiliskStart(...)
 4.       └─basilisk::obtainEnvironmentPath(env)
 5.         └─basilisk::setupBasiliskEnv(...)
 6.           ├─base::suppressMessages(install_python(version))
 7.           │ └─base::withCallingHandlers(...)
 8.           └─reticulate::install_python(version)
 9.             └─reticulate:::pyenv_python(version = version)
── Error ('test-scanpy_pbmc3k.R:29:1'): (code run outside of `test_that()`) ────
Error in `pyenv_python(version = version)`: Python 3.13.4 does not appear to be installed.
Try installing it with install_python(version = "3.13.4").
Backtrace:
     ▆
  1. ├─base::suppressWarnings(readH5AD(file)) at test-scanpy_pbmc3k.R:29:1
  2. │ └─base::withCallingHandlers(...)
  3. └─zellkonverter::readH5AD(file)
  4.   └─basilisk::basiliskRun(...)
  5.     └─basilisk::basiliskStart(...)
  6.       └─basilisk::obtainEnvironmentPath(env)
  7.         └─basilisk::setupBasiliskEnv(...)
  8.           ├─base::suppressMessages(install_python(version))
  9.           │ └─base::withCallingHandlers(...)
 10.           └─reticulate::install_python(version)
 11.             └─reticulate:::pyenv_python(version = version)
── Error ('test-scanpy_trajectory.R:22:5'): Reading H5AD works ─────────────────
Error in `pyenv_python(version = version)`: Python 3.13.4 does not appear to be installed.
Try installing it with install_python(version = "3.13.4").
Backtrace:
    ▆
 1. └─zellkonverter::readH5AD(file) at test-scanpy_trajectory.R:22:5
 2.   └─basilisk::basiliskRun(...)
 3.     └─basilisk::basiliskStart(...)
 4.       └─basilisk::obtainEnvironmentPath(env)
 5.         └─basilisk::setupBasiliskEnv(...)
 6.           ├─base::suppressMessages(install_python(version))
 7.           │ └─base::withCallingHandlers(...)
 8.           └─reticulate::install_python(version)
 9.             └─reticulate:::pyenv_python(version = version)
── Error ('test-scanpy_trajectory.R:26:1'): (code run outside of `test_that()`) ──
Error in `pyenv_python(version = version)`: Python 3.13.4 does not appear to be installed.
Try installing it with install_python(version = "3.13.4").
Backtrace:
     ▆
  1. ├─base::suppressWarnings(readH5AD(file)) at test-scanpy_trajectory.R:26:1
  2. │ └─base::withCallingHandlers(...)
  3. └─zellkonverter::readH5AD(file)
  4.   └─basilisk::basiliskRun(...)
  5.     └─basilisk::basiliskStart(...)
  6.       └─basilisk::obtainEnvironmentPath(env)
  7.         └─basilisk::setupBasiliskEnv(...)
  8.           ├─base::suppressMessages(install_python(version))
  9.           │ └─base::withCallingHandlers(...)
 10.           └─reticulate::install_python(version)
 11.             └─reticulate:::pyenv_python(version = version)
── Error ('test-scvelo_pancreas.R:38:5'): Reading H5AD works ───────────────────
Error in `pyenv_python(version = version)`: Python 3.13.4 does not appear to be installed.
Try installing it with install_python(version = "3.13.4").
Backtrace:
    ▆
 1. └─zellkonverter::readH5AD(file) at test-scvelo_pancreas.R:38:5
 2.   └─basilisk::basiliskRun(...)
 3.     └─basilisk::basiliskStart(...)
 4.       └─basilisk::obtainEnvironmentPath(env)
 5.         └─basilisk::setupBasiliskEnv(...)
 6.           ├─base::suppressMessages(install_python(version))
 7.           │ └─base::withCallingHandlers(...)
 8.           └─reticulate::install_python(version)
 9.             └─reticulate:::pyenv_python(version = version)
── Error ('test-scvelo_pancreas.R:42:1'): (code run outside of `test_that()`) ──
Error in `pyenv_python(version = version)`: Python 3.13.4 does not appear to be installed.
Try installing it with install_python(version = "3.13.4").
Backtrace:
     ▆
  1. ├─base::suppressWarnings(readH5AD(file)) at test-scvelo_pancreas.R:42:1
  2. │ └─base::withCallingHandlers(...)
  3. └─zellkonverter::readH5AD(file)
  4.   └─basilisk::basiliskRun(...)
  5.     └─basilisk::basiliskStart(...)
  6.       └─basilisk::obtainEnvironmentPath(env)
  7.         └─basilisk::setupBasiliskEnv(...)
  8.           ├─base::suppressMessages(install_python(version))
  9.           │ └─base::withCallingHandlers(...)
 10.           └─reticulate::install_python(version)
 11.             └─reticulate:::pyenv_python(version = version)
── Error ('test-scvi_citeseq.R:24:5'): Reading H5AD works ──────────────────────
Error in `pyenv_python(version = version)`: Python 3.13.4 does not appear to be installed.
Try installing it with install_python(version = "3.13.4").
Backtrace:
     ▆
  1. ├─testthat::expect_warning(readH5AD(file)) at test-scvi_citeseq.R:24:5
  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)
  7.   └─basilisk::basiliskRun(...)
  8.     └─basilisk::basiliskStart(...)
  9.       └─basilisk::obtainEnvironmentPath(env)
 10.         └─basilisk::setupBasiliskEnv(...)
 11.           ├─base::suppressMessages(install_python(version))
 12.           │ └─base::withCallingHandlers(...)
 13.           └─reticulate::install_python(version)
 14.             └─reticulate:::pyenv_python(version = version)
── Error ('test-scvi_citeseq.R:28:1'): (code run outside of `test_that()`) ─────
Error in `pyenv_python(version = version)`: Python 3.13.4 does not appear to be installed.
Try installing it with install_python(version = "3.13.4").
Backtrace:
     ▆
  1. ├─base::suppressWarnings(readH5AD(file)) at test-scvi_citeseq.R:28:1
  2. │ └─base::withCallingHandlers(...)
  3. └─zellkonverter::readH5AD(file)
  4.   └─basilisk::basiliskRun(...)
  5.     └─basilisk::basiliskStart(...)
  6.       └─basilisk::obtainEnvironmentPath(env)
  7.         └─basilisk::setupBasiliskEnv(...)
  8.           ├─base::suppressMessages(install_python(version))
  9.           │ └─base::withCallingHandlers(...)
 10.           └─reticulate::install_python(version)
 11.             └─reticulate:::pyenv_python(version = version)
── Error ('test-squidpy_visium.R:37:5'): Reading H5AD works ────────────────────
Error in `pyenv_python(version = version)`: Python 3.13.4 does not appear to be installed.
Try installing it with install_python(version = "3.13.4").
Backtrace:
    ▆
 1. └─zellkonverter::readH5AD(file) at test-squidpy_visium.R:37:5
 2.   └─basilisk::basiliskRun(...)
 3.     └─basilisk::basiliskStart(...)
 4.       └─basilisk::obtainEnvironmentPath(env)
 5.         └─basilisk::setupBasiliskEnv(...)
 6.           ├─base::suppressMessages(install_python(version))
 7.           │ └─base::withCallingHandlers(...)
 8.           └─reticulate::install_python(version)
 9.             └─reticulate:::pyenv_python(version = version)
── Error ('test-squidpy_visium.R:41:1'): (code run outside of `test_that()`) ───
Error in `pyenv_python(version = version)`: Python 3.13.4 does not appear to be installed.
Try installing it with install_python(version = "3.13.4").
Backtrace:
     ▆
  1. ├─base::suppressWarnings(readH5AD(file)) at test-squidpy_visium.R:41:1
  2. │ └─base::withCallingHandlers(...)
  3. └─zellkonverter::readH5AD(file)
  4.   └─basilisk::basiliskRun(...)
  5.     └─basilisk::basiliskStart(...)
  6.       └─basilisk::obtainEnvironmentPath(env)
  7.         └─basilisk::setupBasiliskEnv(...)
  8.           ├─base::suppressMessages(install_python(version))
  9.           │ └─base::withCallingHandlers(...)
 10.           └─reticulate::install_python(version)
 11.             └─reticulate:::pyenv_python(version = version)

[ FAIL 20 | WARN 0 | SKIP 0 | PASS 0 ]
Error: Test failures
Execution halted

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.22-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_1.19.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.22-bioc-longtests/meat/zellkonverter.Rcheck'
* using R version 4.5.0 (2025-04-11 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* 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 '1.19.1'
* 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-3.22-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 ... NOTE
Non-topic package-anchored link(s) in Rd file 'AnnData-Conversion.Rd':
  '[SingleCellExperiment:internals]{int_metadata()}'

Non-topic package-anchored link(s) in Rd file 'AnnData-Environment.Rd':
  '[basilisk:basiliskOptions]{basilisk::setBasiliskShared()}'

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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. ├─base::suppressWarnings(readH5AD(file)) at test-squidpy_visium.R:41:1
    2. │ └─base::withCallingHandlers(...)
    3. └─zellkonverter::readH5AD(file)
    4.   └─basilisk::basiliskRun(...)
    5.     └─basilisk::basiliskStart(...)
    6.       └─basilisk::obtainEnvironmentPath(env)
    7.         └─basilisk::setupBasiliskEnv(...)
    8.           ├─base::suppressMessages(install_python(version))
    9.           │ └─base::withCallingHandlers(...)
   10.           └─reticulate::install_python(version)
   11.             └─reticulate:::pyenv_python(version = version)
  
  [ FAIL 20 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
* DONE

Status: 1 ERROR, 2 NOTEs
See
  'F:/biocbuild/bbs-3.22-bioc-longtests/meat/zellkonverter.Rcheck/00check.log'
for details.

Installation output

zellkonverter.Rcheck/00install.out

* installing *source* package 'zellkonverter' ...
** this is package 'zellkonverter' version '1.19.1'
** 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)