| Back to Long Tests report for BioC 3.22 |
This page was generated on 2025-06-07 23:55 -0400 (Sat, 07 Jun 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4795 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six" | 4536 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six" | 4574 |
| 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 29/29 | Hostname | OS / Arch | CHECK | |||||||
| zellkonverter 1.19.0 (landing page) Luke Zappia
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | ERROR | |||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | ERROR | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | ERROR | ||||||||
|
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. |
| Package: zellkonverter |
| Version: 1.19.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no zellkonverter_1.19.0.tar.gz |
| StartedAt: 2025-06-07 16:13:36 -0400 (Sat, 07 Jun 2025) |
| EndedAt: 2025-06-07 16:18:49 -0400 (Sat, 07 Jun 2025) |
| EllapsedTime: 312.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: zellkonverter.Rcheck |
| Warnings: NA |
zellkonverter.Rcheck/tests/testthat.Rout.fail
R version 4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(zellkonverter)
Registered S3 method overwritten by 'zellkonverter':
method from
py_to_r.pandas.core.arrays.categorical.Categorical reticulate
>
> test_check("zellkonverter")
Using Python: /Users/biocbuild/.pyenv/versions/3.13.2/bin/python3.13
Creating virtual environment '/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.0/zellkonverterAnnDataEnv-0.11.4' ...
Done!
Installing packages: pip, wheel, setuptools
Requirement already satisfied: pip in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.0/zellkonverterAnnDataEnv-0.11.4/lib/python3.13/site-packages (24.3.1)
Collecting pip
Using cached pip-25.1.1-py3-none-any.whl.metadata (3.6 kB)
Collecting wheel
Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
Collecting setuptools
Using cached setuptools-80.9.0-py3-none-any.whl.metadata (6.6 kB)
Using cached pip-25.1.1-py3-none-any.whl (1.8 MB)
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB)
Installing collected packages: wheel, setuptools, pip
Attempting uninstall: pip
Found existing installation: pip 24.3.1
Uninstalling pip-24.3.1:
Successfully uninstalled pip-24.3.1
Successfully installed pip-25.1.1 setuptools-80.9.0 wheel-0.45.1
Installing packages: 'anndata==0.11.4', 'h5py==3.13.0', 'hdf5==1.14.3', 'natsort==8.4.0', 'numpy==2.2.4', 'packaging==24.2', 'pandas==2.2.3', 'scipy==1.15.2'
Collecting anndata==0.11.4
Using cached anndata-0.11.4-py3-none-any.whl.metadata (9.3 kB)
Collecting h5py==3.13.0
Using cached h5py-3.13.0-cp313-cp313-macosx_10_13_x86_64.whl.metadata (2.5 kB)
ERROR: Could not find a version that satisfies the requirement hdf5==1.14.3 (from versions: none)
ERROR: No matching distribution found for hdf5==1.14.3
Using Python: /Users/biocbuild/.pyenv/versions/3.13.2/bin/python3.13
Creating virtual environment '/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.0/zellkonverterAnnDataEnv-0.11.4' ...
Done!
Installing packages: pip, wheel, setuptools
Requirement already satisfied: pip in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.0/zellkonverterAnnDataEnv-0.11.4/lib/python3.13/site-packages (24.3.1)
Collecting pip
Using cached pip-25.1.1-py3-none-any.whl.metadata (3.6 kB)
Collecting wheel
Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
Collecting setuptools
Using cached setuptools-80.9.0-py3-none-any.whl.metadata (6.6 kB)
Using cached pip-25.1.1-py3-none-any.whl (1.8 MB)
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB)
Installing collected packages: wheel, setuptools, pip
Attempting uninstall: pip
Found existing installation: pip 24.3.1
Uninstalling pip-24.3.1:
Successfully uninstalled pip-24.3.1
Successfully installed pip-25.1.1 setuptools-80.9.0 wheel-0.45.1
Installing packages: 'anndata==0.11.4', 'h5py==3.13.0', 'hdf5==1.14.3', 'natsort==8.4.0', 'numpy==2.2.4', 'packaging==24.2', 'pandas==2.2.3', 'scipy==1.15.2'
Collecting anndata==0.11.4
Using cached anndata-0.11.4-py3-none-any.whl.metadata (9.3 kB)
Collecting h5py==3.13.0
Using cached h5py-3.13.0-cp313-cp313-macosx_10_13_x86_64.whl.metadata (2.5 kB)
ERROR: Could not find a version that satisfies the requirement hdf5==1.14.3 (from versions: none)
ERROR: No matching distribution found for hdf5==1.14.3
Using Python: /Users/biocbuild/.pyenv/versions/3.13.2/bin/python3.13
Creating virtual environment '/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.0/zellkonverterAnnDataEnv-0.11.4' ...
Done!
Installing packages: pip, wheel, setuptools
Requirement already satisfied: pip in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.0/zellkonverterAnnDataEnv-0.11.4/lib/python3.13/site-packages (24.3.1)
Collecting pip
Using cached pip-25.1.1-py3-none-any.whl.metadata (3.6 kB)
Collecting wheel
Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
Collecting setuptools
Using cached setuptools-80.9.0-py3-none-any.whl.metadata (6.6 kB)
Using cached pip-25.1.1-py3-none-any.whl (1.8 MB)
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB)
Installing collected packages: wheel, setuptools, pip
Attempting uninstall: pip
Found existing installation: pip 24.3.1
Uninstalling pip-24.3.1:
Successfully uninstalled pip-24.3.1
Successfully installed pip-25.1.1 setuptools-80.9.0 wheel-0.45.1
Installing packages: 'anndata==0.11.4', 'h5py==3.13.0', 'hdf5==1.14.3', 'natsort==8.4.0', 'numpy==2.2.4', 'packaging==24.2', 'pandas==2.2.3', 'scipy==1.15.2'
Collecting anndata==0.11.4
Using cached anndata-0.11.4-py3-none-any.whl.metadata (9.3 kB)
Collecting h5py==3.13.0
Using cached h5py-3.13.0-cp313-cp313-macosx_10_13_x86_64.whl.metadata (2.5 kB)
ERROR: Could not find a version that satisfies the requirement hdf5==1.14.3 (from versions: none)
ERROR: No matching distribution found for hdf5==1.14.3
Using Python: /Users/biocbuild/.pyenv/versions/3.13.2/bin/python3.13
Creating virtual environment '/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.0/zellkonverterAnnDataEnv-0.11.4' ...
Done!
Installing packages: pip, wheel, setuptools
Requirement already satisfied: pip in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.0/zellkonverterAnnDataEnv-0.11.4/lib/python3.13/site-packages (24.3.1)
Collecting pip
Using cached pip-25.1.1-py3-none-any.whl.metadata (3.6 kB)
Collecting wheel
Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
Collecting setuptools
Using cached setuptools-80.9.0-py3-none-any.whl.metadata (6.6 kB)
Using cached pip-25.1.1-py3-none-any.whl (1.8 MB)
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB)
Installing collected packages: wheel, setuptools, pip
Attempting uninstall: pip
Found existing installation: pip 24.3.1
Uninstalling pip-24.3.1:
Successfully uninstalled pip-24.3.1
Successfully installed pip-25.1.1 setuptools-80.9.0 wheel-0.45.1
Installing packages: 'anndata==0.11.4', 'h5py==3.13.0', 'hdf5==1.14.3', 'natsort==8.4.0', 'numpy==2.2.4', 'packaging==24.2', 'pandas==2.2.3', 'scipy==1.15.2'
Collecting anndata==0.11.4
Using cached anndata-0.11.4-py3-none-any.whl.metadata (9.3 kB)
Collecting h5py==3.13.0
Using cached h5py-3.13.0-cp313-cp313-macosx_10_13_x86_64.whl.metadata (2.5 kB)
ERROR: Could not find a version that satisfies the requirement hdf5==1.14.3 (from versions: none)
ERROR: No matching distribution found for hdf5==1.14.3
Using Python: /Users/biocbuild/.pyenv/versions/3.13.2/bin/python3.13
Creating virtual environment '/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.0/zellkonverterAnnDataEnv-0.11.4' ...
Done!
Installing packages: pip, wheel, setuptools
Requirement already satisfied: pip in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.0/zellkonverterAnnDataEnv-0.11.4/lib/python3.13/site-packages (24.3.1)
Collecting pip
Using cached pip-25.1.1-py3-none-any.whl.metadata (3.6 kB)
Collecting wheel
Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
Collecting setuptools
Using cached setuptools-80.9.0-py3-none-any.whl.metadata (6.6 kB)
Using cached pip-25.1.1-py3-none-any.whl (1.8 MB)
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB)
Installing collected packages: wheel, setuptools, pip
Attempting uninstall: pip
Found existing installation: pip 24.3.1
Uninstalling pip-24.3.1:
Successfully uninstalled pip-24.3.1
Successfully installed pip-25.1.1 setuptools-80.9.0 wheel-0.45.1
Installing packages: 'anndata==0.11.4', 'h5py==3.13.0', 'hdf5==1.14.3', 'natsort==8.4.0', 'numpy==2.2.4', 'packaging==24.2', 'pandas==2.2.3', 'scipy==1.15.2'
Collecting anndata==0.11.4
Using cached anndata-0.11.4-py3-none-any.whl.metadata (9.3 kB)
Collecting h5py==3.13.0
Using cached h5py-3.13.0-cp313-cp313-macosx_10_13_x86_64.whl.metadata (2.5 kB)
ERROR: Could not find a version that satisfies the requirement hdf5==1.14.3 (from versions: none)
ERROR: No matching distribution found for hdf5==1.14.3
Using Python: /Users/biocbuild/.pyenv/versions/3.13.2/bin/python3.13
Creating virtual environment '/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.0/zellkonverterAnnDataEnv-0.11.4' ...
Done!
Installing packages: pip, wheel, setuptools
Requirement already satisfied: pip in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.0/zellkonverterAnnDataEnv-0.11.4/lib/python3.13/site-packages (24.3.1)
Collecting pip
Using cached pip-25.1.1-py3-none-any.whl.metadata (3.6 kB)
Collecting wheel
Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
Collecting setuptools
Using cached setuptools-80.9.0-py3-none-any.whl.metadata (6.6 kB)
Using cached pip-25.1.1-py3-none-any.whl (1.8 MB)
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB)
Installing collected packages: wheel, setuptools, pip
Attempting uninstall: pip
Found existing installation: pip 24.3.1
Uninstalling pip-24.3.1:
Successfully uninstalled pip-24.3.1
Successfully installed pip-25.1.1 setuptools-80.9.0 wheel-0.45.1
Installing packages: 'anndata==0.11.4', 'h5py==3.13.0', 'hdf5==1.14.3', 'natsort==8.4.0', 'numpy==2.2.4', 'packaging==24.2', 'pandas==2.2.3', 'scipy==1.15.2'
Collecting anndata==0.11.4
Using cached anndata-0.11.4-py3-none-any.whl.metadata (9.3 kB)
Collecting h5py==3.13.0
Using cached h5py-3.13.0-cp313-cp313-macosx_10_13_x86_64.whl.metadata (2.5 kB)
ERROR: Could not find a version that satisfies the requirement hdf5==1.14.3 (from versions: none)
ERROR: No matching distribution found for hdf5==1.14.3
Using Python: /Users/biocbuild/.pyenv/versions/3.13.2/bin/python3.13
Creating virtual environment '/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.0/zellkonverterAnnDataEnv-0.11.4' ...
Done!
Installing packages: pip, wheel, setuptools
Requirement already satisfied: pip in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.0/zellkonverterAnnDataEnv-0.11.4/lib/python3.13/site-packages (24.3.1)
Collecting pip
Using cached pip-25.1.1-py3-none-any.whl.metadata (3.6 kB)
Collecting wheel
Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
Collecting setuptools
Using cached setuptools-80.9.0-py3-none-any.whl.metadata (6.6 kB)
Using cached pip-25.1.1-py3-none-any.whl (1.8 MB)
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB)
Installing collected packages: wheel, setuptools, pip
Attempting uninstall: pip
Found existing installation: pip 24.3.1
Uninstalling pip-24.3.1:
Successfully uninstalled pip-24.3.1
Successfully installed pip-25.1.1 setuptools-80.9.0 wheel-0.45.1
Installing packages: 'anndata==0.11.4', 'h5py==3.13.0', 'hdf5==1.14.3', 'natsort==8.4.0', 'numpy==2.2.4', 'packaging==24.2', 'pandas==2.2.3', 'scipy==1.15.2'
Collecting anndata==0.11.4
Using cached anndata-0.11.4-py3-none-any.whl.metadata (9.3 kB)
Collecting h5py==3.13.0
Using cached h5py-3.13.0-cp313-cp313-macosx_10_13_x86_64.whl.metadata (2.5 kB)
ERROR: Could not find a version that satisfies the requirement hdf5==1.14.3 (from versions: none)
ERROR: No matching distribution found for hdf5==1.14.3
Using Python: /Users/biocbuild/.pyenv/versions/3.13.2/bin/python3.13
Creating virtual environment '/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.0/zellkonverterAnnDataEnv-0.11.4' ...
Done!
Installing packages: pip, wheel, setuptools
Requirement already satisfied: pip in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.0/zellkonverterAnnDataEnv-0.11.4/lib/python3.13/site-packages (24.3.1)
Collecting pip
Using cached pip-25.1.1-py3-none-any.whl.metadata (3.6 kB)
Collecting wheel
Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
Collecting setuptools
Using cached setuptools-80.9.0-py3-none-any.whl.metadata (6.6 kB)
Using cached pip-25.1.1-py3-none-any.whl (1.8 MB)
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB)
Installing collected packages: wheel, setuptools, pip
Attempting uninstall: pip
Found existing installation: pip 24.3.1
Uninstalling pip-24.3.1:
Successfully uninstalled pip-24.3.1
Successfully installed pip-25.1.1 setuptools-80.9.0 wheel-0.45.1
Installing packages: 'anndata==0.11.4', 'h5py==3.13.0', 'hdf5==1.14.3', 'natsort==8.4.0', 'numpy==2.2.4', 'packaging==24.2', 'pandas==2.2.3', 'scipy==1.15.2'
Collecting anndata==0.11.4
Using cached anndata-0.11.4-py3-none-any.whl.metadata (9.3 kB)
Collecting h5py==3.13.0
Using cached h5py-3.13.0-cp313-cp313-macosx_10_13_x86_64.whl.metadata (2.5 kB)
ERROR: Could not find a version that satisfies the requirement hdf5==1.14.3 (from versions: none)
ERROR: No matching distribution found for hdf5==1.14.3
Using Python: /Users/biocbuild/.pyenv/versions/3.13.2/bin/python3.13
Creating virtual environment '/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.0/zellkonverterAnnDataEnv-0.11.4' ...
Done!
Installing packages: pip, wheel, setuptools
Requirement already satisfied: pip in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.0/zellkonverterAnnDataEnv-0.11.4/lib/python3.13/site-packages (24.3.1)
Collecting pip
Using cached pip-25.1.1-py3-none-any.whl.metadata (3.6 kB)
Collecting wheel
Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
Collecting setuptools
Using cached setuptools-80.9.0-py3-none-any.whl.metadata (6.6 kB)
Using cached pip-25.1.1-py3-none-any.whl (1.8 MB)
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB)
Installing collected packages: wheel, setuptools, pip
Attempting uninstall: pip
Found existing installation: pip 24.3.1
Uninstalling pip-24.3.1:
Successfully uninstalled pip-24.3.1
Successfully installed pip-25.1.1 setuptools-80.9.0 wheel-0.45.1
Installing packages: 'anndata==0.11.4', 'h5py==3.13.0', 'hdf5==1.14.3', 'natsort==8.4.0', 'numpy==2.2.4', 'packaging==24.2', 'pandas==2.2.3', 'scipy==1.15.2'
Collecting anndata==0.11.4
Using cached anndata-0.11.4-py3-none-any.whl.metadata (9.3 kB)
Collecting h5py==3.13.0
Using cached h5py-3.13.0-cp313-cp313-macosx_10_13_x86_64.whl.metadata (2.5 kB)
ERROR: Could not find a version that satisfies the requirement hdf5==1.14.3 (from versions: none)
ERROR: No matching distribution found for hdf5==1.14.3
Using Python: /Users/biocbuild/.pyenv/versions/3.13.2/bin/python3.13
Creating virtual environment '/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.0/zellkonverterAnnDataEnv-0.11.4' ...
Done!
Installing packages: pip, wheel, setuptools
Requirement already satisfied: pip in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.0/zellkonverterAnnDataEnv-0.11.4/lib/python3.13/site-packages (24.3.1)
Collecting pip
Using cached pip-25.1.1-py3-none-any.whl.metadata (3.6 kB)
Collecting wheel
Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
Collecting setuptools
Using cached setuptools-80.9.0-py3-none-any.whl.metadata (6.6 kB)
Using cached pip-25.1.1-py3-none-any.whl (1.8 MB)
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB)
Installing collected packages: wheel, setuptools, pip
Attempting uninstall: pip
Found existing installation: pip 24.3.1
Uninstalling pip-24.3.1:
Successfully uninstalled pip-24.3.1
Successfully installed pip-25.1.1 setuptools-80.9.0 wheel-0.45.1
Installing packages: 'anndata==0.11.4', 'h5py==3.13.0', 'hdf5==1.14.3', 'natsort==8.4.0', 'numpy==2.2.4', 'packaging==24.2', 'pandas==2.2.3', 'scipy==1.15.2'
Collecting anndata==0.11.4
Using cached anndata-0.11.4-py3-none-any.whl.metadata (9.3 kB)
Collecting h5py==3.13.0
Using cached h5py-3.13.0-cp313-cp313-macosx_10_13_x86_64.whl.metadata (2.5 kB)
ERROR: Could not find a version that satisfies the requirement hdf5==1.14.3 (from versions: none)
ERROR: No matching distribution found for hdf5==1.14.3
Using Python: /Users/biocbuild/.pyenv/versions/3.13.2/bin/python3.13
Creating virtual environment '/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.0/zellkonverterAnnDataEnv-0.11.4' ...
Done!
Installing packages: pip, wheel, setuptools
Requirement already satisfied: pip in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.0/zellkonverterAnnDataEnv-0.11.4/lib/python3.13/site-packages (24.3.1)
Collecting pip
Using cached pip-25.1.1-py3-none-any.whl.metadata (3.6 kB)
Collecting wheel
Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
Collecting setuptools
Using cached setuptools-80.9.0-py3-none-any.whl.metadata (6.6 kB)
Using cached pip-25.1.1-py3-none-any.whl (1.8 MB)
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB)
Installing collected packages: wheel, setuptools, pip
Attempting uninstall: pip
Found existing installation: pip 24.3.1
Uninstalling pip-24.3.1:
Successfully uninstalled pip-24.3.1
Successfully installed pip-25.1.1 setuptools-80.9.0 wheel-0.45.1
Installing packages: 'anndata==0.11.4', 'h5py==3.13.0', 'hdf5==1.14.3', 'natsort==8.4.0', 'numpy==2.2.4', 'packaging==24.2', 'pandas==2.2.3', 'scipy==1.15.2'
Collecting anndata==0.11.4
Using cached anndata-0.11.4-py3-none-any.whl.metadata (9.3 kB)
Collecting h5py==3.13.0
Using cached h5py-3.13.0-cp313-cp313-macosx_10_13_x86_64.whl.metadata (2.5 kB)
ERROR: Could not find a version that satisfies the requirement hdf5==1.14.3 (from versions: none)
ERROR: No matching distribution found for hdf5==1.14.3
Using Python: /Users/biocbuild/.pyenv/versions/3.13.2/bin/python3.13
Creating virtual environment '/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.0/zellkonverterAnnDataEnv-0.11.4' ...
Done!
Installing packages: pip, wheel, setuptools
Requirement already satisfied: pip in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.0/zellkonverterAnnDataEnv-0.11.4/lib/python3.13/site-packages (24.3.1)
Collecting pip
Using cached pip-25.1.1-py3-none-any.whl.metadata (3.6 kB)
Collecting wheel
Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
Collecting setuptools
Using cached setuptools-80.9.0-py3-none-any.whl.metadata (6.6 kB)
Using cached pip-25.1.1-py3-none-any.whl (1.8 MB)
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB)
Installing collected packages: wheel, setuptools, pip
Attempting uninstall: pip
Found existing installation: pip 24.3.1
Uninstalling pip-24.3.1:
Successfully uninstalled pip-24.3.1
Successfully installed pip-25.1.1 setuptools-80.9.0 wheel-0.45.1
Installing packages: 'anndata==0.11.4', 'h5py==3.13.0', 'hdf5==1.14.3', 'natsort==8.4.0', 'numpy==2.2.4', 'packaging==24.2', 'pandas==2.2.3', 'scipy==1.15.2'
Collecting anndata==0.11.4
Using cached anndata-0.11.4-py3-none-any.whl.metadata (9.3 kB)
Collecting h5py==3.13.0
Using cached h5py-3.13.0-cp313-cp313-macosx_10_13_x86_64.whl.metadata (2.5 kB)
ERROR: Could not find a version that satisfies the requirement hdf5==1.14.3 (from versions: none)
ERROR: No matching distribution found for hdf5==1.14.3
Using Python: /Users/biocbuild/.pyenv/versions/3.13.2/bin/python3.13
Creating virtual environment '/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.0/zellkonverterAnnDataEnv-0.11.4' ...
Done!
Installing packages: pip, wheel, setuptools
Requirement already satisfied: pip in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.0/zellkonverterAnnDataEnv-0.11.4/lib/python3.13/site-packages (24.3.1)
Collecting pip
Using cached pip-25.1.1-py3-none-any.whl.metadata (3.6 kB)
Collecting wheel
Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
Collecting setuptools
Using cached setuptools-80.9.0-py3-none-any.whl.metadata (6.6 kB)
Using cached pip-25.1.1-py3-none-any.whl (1.8 MB)
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB)
Installing collected packages: wheel, setuptools, pip
Attempting uninstall: pip
Found existing installation: pip 24.3.1
Uninstalling pip-24.3.1:
Successfully uninstalled pip-24.3.1
Successfully installed pip-25.1.1 setuptools-80.9.0 wheel-0.45.1
Installing packages: 'anndata==0.11.4', 'h5py==3.13.0', 'hdf5==1.14.3', 'natsort==8.4.0', 'numpy==2.2.4', 'packaging==24.2', 'pandas==2.2.3', 'scipy==1.15.2'
Collecting anndata==0.11.4
Using cached anndata-0.11.4-py3-none-any.whl.metadata (9.3 kB)
Collecting h5py==3.13.0
Using cached h5py-3.13.0-cp313-cp313-macosx_10_13_x86_64.whl.metadata (2.5 kB)
ERROR: Could not find a version that satisfies the requirement hdf5==1.14.3 (from versions: none)
ERROR: No matching distribution found for hdf5==1.14.3
Using Python: /Users/biocbuild/.pyenv/versions/3.13.2/bin/python3.13
Creating virtual environment '/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.0/zellkonverterAnnDataEnv-0.11.4' ...
Done!
Installing packages: pip, wheel, setuptools
Requirement already satisfied: pip in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.0/zellkonverterAnnDataEnv-0.11.4/lib/python3.13/site-packages (24.3.1)
Collecting pip
Using cached pip-25.1.1-py3-none-any.whl.metadata (3.6 kB)
Collecting wheel
Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
Collecting setuptools
Using cached setuptools-80.9.0-py3-none-any.whl.metadata (6.6 kB)
Using cached pip-25.1.1-py3-none-any.whl (1.8 MB)
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB)
Installing collected packages: wheel, setuptools, pip
Attempting uninstall: pip
Found existing installation: pip 24.3.1
Uninstalling pip-24.3.1:
Successfully uninstalled pip-24.3.1
Successfully installed pip-25.1.1 setuptools-80.9.0 wheel-0.45.1
Installing packages: 'anndata==0.11.4', 'h5py==3.13.0', 'hdf5==1.14.3', 'natsort==8.4.0', 'numpy==2.2.4', 'packaging==24.2', 'pandas==2.2.3', 'scipy==1.15.2'
Collecting anndata==0.11.4
Using cached anndata-0.11.4-py3-none-any.whl.metadata (9.3 kB)
Collecting h5py==3.13.0
Using cached h5py-3.13.0-cp313-cp313-macosx_10_13_x86_64.whl.metadata (2.5 kB)
ERROR: Could not find a version that satisfies the requirement hdf5==1.14.3 (from versions: none)
ERROR: No matching distribution found for hdf5==1.14.3
Using Python: /Users/biocbuild/.pyenv/versions/3.13.2/bin/python3.13
Creating virtual environment '/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.0/zellkonverterAnnDataEnv-0.11.4' ...
Done!
Installing packages: pip, wheel, setuptools
Requirement already satisfied: pip in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.0/zellkonverterAnnDataEnv-0.11.4/lib/python3.13/site-packages (24.3.1)
Collecting pip
Using cached pip-25.1.1-py3-none-any.whl.metadata (3.6 kB)
Collecting wheel
Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
Collecting setuptools
Using cached setuptools-80.9.0-py3-none-any.whl.metadata (6.6 kB)
Using cached pip-25.1.1-py3-none-any.whl (1.8 MB)
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB)
Installing collected packages: wheel, setuptools, pip
Attempting uninstall: pip
Found existing installation: pip 24.3.1
Uninstalling pip-24.3.1:
Successfully uninstalled pip-24.3.1
Successfully installed pip-25.1.1 setuptools-80.9.0 wheel-0.45.1
Installing packages: 'anndata==0.11.4', 'h5py==3.13.0', 'hdf5==1.14.3', 'natsort==8.4.0', 'numpy==2.2.4', 'packaging==24.2', 'pandas==2.2.3', 'scipy==1.15.2'
Collecting anndata==0.11.4
Using cached anndata-0.11.4-py3-none-any.whl.metadata (9.3 kB)
Collecting h5py==3.13.0
Using cached h5py-3.13.0-cp313-cp313-macosx_10_13_x86_64.whl.metadata (2.5 kB)
ERROR: Could not find a version that satisfies the requirement hdf5==1.14.3 (from versions: none)
ERROR: No matching distribution found for hdf5==1.14.3
Using Python: /Users/biocbuild/.pyenv/versions/3.13.2/bin/python3.13
Creating virtual environment '/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.0/zellkonverterAnnDataEnv-0.11.4' ...
Done!
Installing packages: pip, wheel, setuptools
Requirement already satisfied: pip in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.0/zellkonverterAnnDataEnv-0.11.4/lib/python3.13/site-packages (24.3.1)
Collecting pip
Using cached pip-25.1.1-py3-none-any.whl.metadata (3.6 kB)
Collecting wheel
Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
Collecting setuptools
Using cached setuptools-80.9.0-py3-none-any.whl.metadata (6.6 kB)
Using cached pip-25.1.1-py3-none-any.whl (1.8 MB)
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB)
Installing collected packages: wheel, setuptools, pip
Attempting uninstall: pip
Found existing installation: pip 24.3.1
Uninstalling pip-24.3.1:
Successfully uninstalled pip-24.3.1
Successfully installed pip-25.1.1 setuptools-80.9.0 wheel-0.45.1
Installing packages: 'anndata==0.11.4', 'h5py==3.13.0', 'hdf5==1.14.3', 'natsort==8.4.0', 'numpy==2.2.4', 'packaging==24.2', 'pandas==2.2.3', 'scipy==1.15.2'
Collecting anndata==0.11.4
Using cached anndata-0.11.4-py3-none-any.whl.metadata (9.3 kB)
Collecting h5py==3.13.0
Using cached h5py-3.13.0-cp313-cp313-macosx_10_13_x86_64.whl.metadata (2.5 kB)
ERROR: Could not find a version that satisfies the requirement hdf5==1.14.3 (from versions: none)
ERROR: No matching distribution found for hdf5==1.14.3
Using Python: /Users/biocbuild/.pyenv/versions/3.13.2/bin/python3.13
Creating virtual environment '/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.0/zellkonverterAnnDataEnv-0.11.4' ...
Done!
Installing packages: pip, wheel, setuptools
Requirement already satisfied: pip in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.0/zellkonverterAnnDataEnv-0.11.4/lib/python3.13/site-packages (24.3.1)
Collecting pip
Using cached pip-25.1.1-py3-none-any.whl.metadata (3.6 kB)
Collecting wheel
Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
Collecting setuptools
Using cached setuptools-80.9.0-py3-none-any.whl.metadata (6.6 kB)
Using cached pip-25.1.1-py3-none-any.whl (1.8 MB)
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB)
Installing collected packages: wheel, setuptools, pip
Attempting uninstall: pip
Found existing installation: pip 24.3.1
Uninstalling pip-24.3.1:
Successfully uninstalled pip-24.3.1
Successfully installed pip-25.1.1 setuptools-80.9.0 wheel-0.45.1
Installing packages: 'anndata==0.11.4', 'h5py==3.13.0', 'hdf5==1.14.3', 'natsort==8.4.0', 'numpy==2.2.4', 'packaging==24.2', 'pandas==2.2.3', 'scipy==1.15.2'
Collecting anndata==0.11.4
Using cached anndata-0.11.4-py3-none-any.whl.metadata (9.3 kB)
Collecting h5py==3.13.0
Using cached h5py-3.13.0-cp313-cp313-macosx_10_13_x86_64.whl.metadata (2.5 kB)
ERROR: Could not find a version that satisfies the requirement hdf5==1.14.3 (from versions: none)
ERROR: No matching distribution found for hdf5==1.14.3
Using Python: /Users/biocbuild/.pyenv/versions/3.13.2/bin/python3.13
Creating virtual environment '/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.0/zellkonverterAnnDataEnv-0.11.4' ...
Done!
Installing packages: pip, wheel, setuptools
Requirement already satisfied: pip in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.0/zellkonverterAnnDataEnv-0.11.4/lib/python3.13/site-packages (24.3.1)
Collecting pip
Using cached pip-25.1.1-py3-none-any.whl.metadata (3.6 kB)
Collecting wheel
Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
Collecting setuptools
Using cached setuptools-80.9.0-py3-none-any.whl.metadata (6.6 kB)
Using cached pip-25.1.1-py3-none-any.whl (1.8 MB)
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB)
Installing collected packages: wheel, setuptools, pip
Attempting uninstall: pip
Found existing installation: pip 24.3.1
Uninstalling pip-24.3.1:
Successfully uninstalled pip-24.3.1
Successfully installed pip-25.1.1 setuptools-80.9.0 wheel-0.45.1
Installing packages: 'anndata==0.11.4', 'h5py==3.13.0', 'hdf5==1.14.3', 'natsort==8.4.0', 'numpy==2.2.4', 'packaging==24.2', 'pandas==2.2.3', 'scipy==1.15.2'
Collecting anndata==0.11.4
Using cached anndata-0.11.4-py3-none-any.whl.metadata (9.3 kB)
Collecting h5py==3.13.0
Using cached h5py-3.13.0-cp313-cp313-macosx_10_13_x86_64.whl.metadata (2.5 kB)
ERROR: Could not find a version that satisfies the requirement hdf5==1.14.3 (from versions: none)
ERROR: No matching distribution found for hdf5==1.14.3
Using Python: /Users/biocbuild/.pyenv/versions/3.13.2/bin/python3.13
Creating virtual environment '/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.0/zellkonverterAnnDataEnv-0.11.4' ...
Done!
Installing packages: pip, wheel, setuptools
Requirement already satisfied: pip in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.0/zellkonverterAnnDataEnv-0.11.4/lib/python3.13/site-packages (24.3.1)
Collecting pip
Using cached pip-25.1.1-py3-none-any.whl.metadata (3.6 kB)
Collecting wheel
Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
Collecting setuptools
Using cached setuptools-80.9.0-py3-none-any.whl.metadata (6.6 kB)
Using cached pip-25.1.1-py3-none-any.whl (1.8 MB)
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB)
Installing collected packages: wheel, setuptools, pip
Attempting uninstall: pip
Found existing installation: pip 24.3.1
Uninstalling pip-24.3.1:
Successfully uninstalled pip-24.3.1
Successfully installed pip-25.1.1 setuptools-80.9.0 wheel-0.45.1
Installing packages: 'anndata==0.11.4', 'h5py==3.13.0', 'hdf5==1.14.3', 'natsort==8.4.0', 'numpy==2.2.4', 'packaging==24.2', 'pandas==2.2.3', 'scipy==1.15.2'
Collecting anndata==0.11.4
Using cached anndata-0.11.4-py3-none-any.whl.metadata (9.3 kB)
Collecting h5py==3.13.0
Using cached h5py-3.13.0-cp313-cp313-macosx_10_13_x86_64.whl.metadata (2.5 kB)
ERROR: Could not find a version that satisfies the requirement hdf5==1.14.3 (from versions: none)
ERROR: No matching distribution found for hdf5==1.14.3
Using Python: /Users/biocbuild/.pyenv/versions/3.13.2/bin/python3.13
Creating virtual environment '/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.0/zellkonverterAnnDataEnv-0.11.4' ...
Done!
Installing packages: pip, wheel, setuptools
Requirement already satisfied: pip in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.0/zellkonverterAnnDataEnv-0.11.4/lib/python3.13/site-packages (24.3.1)
Collecting pip
Using cached pip-25.1.1-py3-none-any.whl.metadata (3.6 kB)
Collecting wheel
Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
Collecting setuptools
Using cached setuptools-80.9.0-py3-none-any.whl.metadata (6.6 kB)
Using cached pip-25.1.1-py3-none-any.whl (1.8 MB)
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB)
Installing collected packages: wheel, setuptools, pip
Attempting uninstall: pip
Found existing installation: pip 24.3.1
Uninstalling pip-24.3.1:
Successfully uninstalled pip-24.3.1
Successfully installed pip-25.1.1 setuptools-80.9.0 wheel-0.45.1
Installing packages: 'anndata==0.11.4', 'h5py==3.13.0', 'hdf5==1.14.3', 'natsort==8.4.0', 'numpy==2.2.4', 'packaging==24.2', 'pandas==2.2.3', 'scipy==1.15.2'
Collecting anndata==0.11.4
Using cached anndata-0.11.4-py3-none-any.whl.metadata (9.3 kB)
Collecting h5py==3.13.0
Using cached h5py-3.13.0-cp313-cp313-macosx_10_13_x86_64.whl.metadata (2.5 kB)
ERROR: Could not find a version that satisfies the requirement hdf5==1.14.3 (from versions: none)
ERROR: No matching distribution found for hdf5==1.14.3
[ FAIL 20 | WARN 0 | SKIP 0 | PASS 0 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-cellrank_pancreas.R:45:10'): Reading H5AD works ────────────────
Error: Error installing package(s): "'anndata==0.11.4'", "'h5py==3.13.0'", "'hdf5==1.14.3'", "'natsort==8.4.0'", "'numpy==2.2.4'", "'packaging==24.2'", "'pandas==2.2.3'", "'scipy==1.15.2'"
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. └─reticulate::virtualenv_create(...)
12. └─reticulate:::pip_install(python, packages)
── Error ('test-cellrank_pancreas.R:51:1'): (code run outside of `test_that()`) ──
Error: Error installing package(s): "'anndata==0.11.4'", "'h5py==3.13.0'", "'hdf5==1.14.3'", "'natsort==8.4.0'", "'numpy==2.2.4'", "'packaging==24.2'", "'pandas==2.2.3'", "'scipy==1.15.2'"
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. └─reticulate::virtualenv_create(...)
9. └─reticulate:::pip_install(python, packages)
── Error ('test-example_anndata.R:21:5'): Reading H5AD works ───────────────────
Error: Error installing package(s): "'anndata==0.11.4'", "'h5py==3.13.0'", "'hdf5==1.14.3'", "'natsort==8.4.0'", "'numpy==2.2.4'", "'packaging==24.2'", "'pandas==2.2.3'", "'scipy==1.15.2'"
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. └─reticulate::virtualenv_create(...)
7. └─reticulate:::pip_install(python, packages)
── Error ('test-example_anndata.R:25:1'): (code run outside of `test_that()`) ──
Error: Error installing package(s): "'anndata==0.11.4'", "'h5py==3.13.0'", "'hdf5==1.14.3'", "'natsort==8.4.0'", "'numpy==2.2.4'", "'packaging==24.2'", "'pandas==2.2.3'", "'scipy==1.15.2'"
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. └─reticulate::virtualenv_create(...)
9. └─reticulate:::pip_install(python, packages)
── Error ('test-gtex_8tissues.R:53:10'): Reading H5AD works ────────────────────
Error: Error installing package(s): "'anndata==0.11.4'", "'h5py==3.13.0'", "'hdf5==1.14.3'", "'natsort==8.4.0'", "'numpy==2.2.4'", "'packaging==24.2'", "'pandas==2.2.3'", "'scipy==1.15.2'"
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. └─reticulate::virtualenv_create(...)
12. └─reticulate:::pip_install(python, packages)
── Error ('test-gtex_8tissues.R:59:1'): (code run outside of `test_that()`) ────
Error: Error installing package(s): "'anndata==0.11.4'", "'h5py==3.13.0'", "'hdf5==1.14.3'", "'natsort==8.4.0'", "'numpy==2.2.4'", "'packaging==24.2'", "'pandas==2.2.3'", "'scipy==1.15.2'"
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. └─reticulate::virtualenv_create(...)
9. └─reticulate:::pip_install(python, packages)
── Error ('test-pegasus_marrow.R:30:5'): Reading H5AD works ────────────────────
Error: Error installing package(s): "'anndata==0.11.4'", "'h5py==3.13.0'", "'hdf5==1.14.3'", "'natsort==8.4.0'", "'numpy==2.2.4'", "'packaging==24.2'", "'pandas==2.2.3'", "'scipy==1.15.2'"
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. └─reticulate::virtualenv_create(...)
7. └─reticulate:::pip_install(python, packages)
── Error ('test-pegasus_marrow.R:34:1'): (code run outside of `test_that()`) ───
Error: Error installing package(s): "'anndata==0.11.4'", "'h5py==3.13.0'", "'hdf5==1.14.3'", "'natsort==8.4.0'", "'numpy==2.2.4'", "'packaging==24.2'", "'pandas==2.2.3'", "'scipy==1.15.2'"
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. └─reticulate::virtualenv_create(...)
9. └─reticulate:::pip_install(python, packages)
── Error ('test-scIB_pancreas.R:15:5'): Reading H5AD works ─────────────────────
Error: Error installing package(s): "'anndata==0.11.4'", "'h5py==3.13.0'", "'hdf5==1.14.3'", "'natsort==8.4.0'", "'numpy==2.2.4'", "'packaging==24.2'", "'pandas==2.2.3'", "'scipy==1.15.2'"
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. └─reticulate::virtualenv_create(...)
7. └─reticulate:::pip_install(python, packages)
── Error ('test-scIB_pancreas.R:19:1'): (code run outside of `test_that()`) ────
Error: Error installing package(s): "'anndata==0.11.4'", "'h5py==3.13.0'", "'hdf5==1.14.3'", "'natsort==8.4.0'", "'numpy==2.2.4'", "'packaging==24.2'", "'pandas==2.2.3'", "'scipy==1.15.2'"
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. └─reticulate::virtualenv_create(...)
9. └─reticulate:::pip_install(python, packages)
── Error ('test-scanpy_pbmc3k.R:25:5'): Reading H5AD works ─────────────────────
Error: Error installing package(s): "'anndata==0.11.4'", "'h5py==3.13.0'", "'hdf5==1.14.3'", "'natsort==8.4.0'", "'numpy==2.2.4'", "'packaging==24.2'", "'pandas==2.2.3'", "'scipy==1.15.2'"
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. └─reticulate::virtualenv_create(...)
7. └─reticulate:::pip_install(python, packages)
── Error ('test-scanpy_pbmc3k.R:29:1'): (code run outside of `test_that()`) ────
Error: Error installing package(s): "'anndata==0.11.4'", "'h5py==3.13.0'", "'hdf5==1.14.3'", "'natsort==8.4.0'", "'numpy==2.2.4'", "'packaging==24.2'", "'pandas==2.2.3'", "'scipy==1.15.2'"
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. └─reticulate::virtualenv_create(...)
9. └─reticulate:::pip_install(python, packages)
── Error ('test-scanpy_trajectory.R:22:5'): Reading H5AD works ─────────────────
Error: Error installing package(s): "'anndata==0.11.4'", "'h5py==3.13.0'", "'hdf5==1.14.3'", "'natsort==8.4.0'", "'numpy==2.2.4'", "'packaging==24.2'", "'pandas==2.2.3'", "'scipy==1.15.2'"
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. └─reticulate::virtualenv_create(...)
7. └─reticulate:::pip_install(python, packages)
── Error ('test-scanpy_trajectory.R:26:1'): (code run outside of `test_that()`) ──
Error: Error installing package(s): "'anndata==0.11.4'", "'h5py==3.13.0'", "'hdf5==1.14.3'", "'natsort==8.4.0'", "'numpy==2.2.4'", "'packaging==24.2'", "'pandas==2.2.3'", "'scipy==1.15.2'"
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. └─reticulate::virtualenv_create(...)
9. └─reticulate:::pip_install(python, packages)
── Error ('test-scvelo_pancreas.R:38:5'): Reading H5AD works ───────────────────
Error: Error installing package(s): "'anndata==0.11.4'", "'h5py==3.13.0'", "'hdf5==1.14.3'", "'natsort==8.4.0'", "'numpy==2.2.4'", "'packaging==24.2'", "'pandas==2.2.3'", "'scipy==1.15.2'"
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. └─reticulate::virtualenv_create(...)
7. └─reticulate:::pip_install(python, packages)
── Error ('test-scvelo_pancreas.R:42:1'): (code run outside of `test_that()`) ──
Error: Error installing package(s): "'anndata==0.11.4'", "'h5py==3.13.0'", "'hdf5==1.14.3'", "'natsort==8.4.0'", "'numpy==2.2.4'", "'packaging==24.2'", "'pandas==2.2.3'", "'scipy==1.15.2'"
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. └─reticulate::virtualenv_create(...)
9. └─reticulate:::pip_install(python, packages)
── Error ('test-scvi_citeseq.R:24:5'): Reading H5AD works ──────────────────────
Error: Error installing package(s): "'anndata==0.11.4'", "'h5py==3.13.0'", "'hdf5==1.14.3'", "'natsort==8.4.0'", "'numpy==2.2.4'", "'packaging==24.2'", "'pandas==2.2.3'", "'scipy==1.15.2'"
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. └─reticulate::virtualenv_create(...)
12. └─reticulate:::pip_install(python, packages)
── Error ('test-scvi_citeseq.R:28:1'): (code run outside of `test_that()`) ─────
Error: Error installing package(s): "'anndata==0.11.4'", "'h5py==3.13.0'", "'hdf5==1.14.3'", "'natsort==8.4.0'", "'numpy==2.2.4'", "'packaging==24.2'", "'pandas==2.2.3'", "'scipy==1.15.2'"
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. └─reticulate::virtualenv_create(...)
9. └─reticulate:::pip_install(python, packages)
── Error ('test-squidpy_visium.R:37:5'): Reading H5AD works ────────────────────
Error: Error installing package(s): "'anndata==0.11.4'", "'h5py==3.13.0'", "'hdf5==1.14.3'", "'natsort==8.4.0'", "'numpy==2.2.4'", "'packaging==24.2'", "'pandas==2.2.3'", "'scipy==1.15.2'"
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. └─reticulate::virtualenv_create(...)
7. └─reticulate:::pip_install(python, packages)
── Error ('test-squidpy_visium.R:41:1'): (code run outside of `test_that()`) ───
Error: Error installing package(s): "'anndata==0.11.4'", "'h5py==3.13.0'", "'hdf5==1.14.3'", "'natsort==8.4.0'", "'numpy==2.2.4'", "'packaging==24.2'", "'pandas==2.2.3'", "'scipy==1.15.2'"
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. └─reticulate::virtualenv_create(...)
9. └─reticulate:::pip_install(python, packages)
[ FAIL 20 | WARN 0 | SKIP 0 | PASS 0 ]
Error: Test failures
Execution halted
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no zellkonverter_1.19.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc-longtests/meat/zellkonverter.Rcheck’
* using R version 4.5.0 Patched (2025-04-21 r88169)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* 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 ‘1.19.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘zellkonverter’ can be installed ... NOTE
Found the following notes/warnings:
Non-staged installation was used
See ‘/Users/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:
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. └─reticulate::virtualenv_create(...)
9. └─reticulate:::pip_install(python, packages)
[ FAIL 20 | WARN 0 | SKIP 0 | PASS 0 ]
Error: Test failures
Execution halted
* DONE
Status: 1 ERROR, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.22-bioc-longtests/meat/zellkonverter.Rcheck/00check.log’
for details.
zellkonverter.Rcheck/00install.out
* installing *source* package ‘zellkonverter’ ... ** this is package ‘zellkonverter’ version ‘1.19.0’ ** 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)