Luke Zappia
| Snapshot Date: 2025-08-25 13:45 -0400 (Mon, 25 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/zellkonverter |
| git_branch: devel |
| git_last_commit: 51dc46a |
| git_last_commit_date: 2025-06-19 04:01:07 -0400 (Thu, 19 Jun 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-26 12:07 -0400 (Tue, 26 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4821 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4610 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4553 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4539 |
| 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 2314/2319 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| zellkonverter 1.19.2 (landing page) Luke Zappia
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the zellkonverter package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/zellkonverter.git to reflect on this report. See Troubleshooting Build Report for more information. - 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: 1.19.2 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:zellkonverter.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings zellkonverter_1.19.2.tar.gz |
| StartedAt: 2025-08-25 22:14:14 -0400 (Mon, 25 Aug 2025) |
| EndedAt: 2025-08-25 22:20:27 -0400 (Mon, 25 Aug 2025) |
| EllapsedTime: 372.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: zellkonverter.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:zellkonverter.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings zellkonverter_1.19.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/zellkonverter.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘zellkonverter/DESCRIPTION’ ... OK
* this is package ‘zellkonverter’ version ‘1.19.2’
* 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/meat/zellkonverter.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 ... OK
* 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’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
AnnData-Conversion 8.985 0.567 9.175
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘spelling.R’
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.22-bioc/meat/zellkonverter.Rcheck/00check.log’
for details.
zellkonverter.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL zellkonverter ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘zellkonverter’ ... ** this is package ‘zellkonverter’ version ‘1.19.2’ ** 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)
zellkonverter.Rcheck/tests/spelling.Rout
R version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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.
> if (requireNamespace("spelling", quietly = TRUE)) {
+ spelling::spell_check_test(
+ vignettes = TRUE,
+ error = FALSE,
+ skip_on_cran = TRUE
+ )
+ }
All Done!
>
> proc.time()
user system elapsed
0.070 0.020 0.092
zellkonverter.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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/3.12.11/bin/python3.12
Creating virtual environment '/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.2/zellkonverterAnnDataEnv-0.10.9' ...
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/1.19.2/zellkonverterAnnDataEnv-0.10.9/lib/python3.12/site-packages (25.0.1)
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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 25.0.1
Uninstalling pip-25.0.1:
Successfully uninstalled pip-25.0.1
Successfully installed pip-25.2 setuptools-80.9.0 wheel-0.45.1
Installing packages: 'anndata==0.10.9', 'h5py==3.14.0', 'natsort==8.4.0', 'numpy==2.3.0', 'pandas==2.3.0', 'scipy==1.15.3'
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Installing collected packages: pytz, tzdata, six, packaging, numpy, natsort, array-api-compat, scipy, python-dateutil, h5py, pandas, anndata
Successfully installed anndata-0.10.9 array-api-compat-1.12.0 h5py-3.14.0 natsort-8.4.0 numpy-2.3.0 packaging-25.0 pandas-2.3.0 python-dateutil-2.9.0.post0 pytz-2025.2 scipy-1.15.3 six-1.17.0 tzdata-2025.2
Virtual environment '/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.2/zellkonverterAnnDataEnv-0.10.9' successfully created.
Using Python: /Users/biocbuild/.pyenv/versions/3.12.11/bin/python3.12
Creating virtual environment '/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.2/zellkonverterAnnDataEnv-0.10.6' ...
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/1.19.2/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages (25.0.1)
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Attempting uninstall: pip
Found existing installation: pip 25.0.1
Uninstalling pip-25.0.1:
Successfully uninstalled pip-25.0.1
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Installing packages: 'anndata==0.10.6', 'h5py==3.14.0', 'natsort==8.4.0', 'numpy==1.26.4', 'pandas==2.3.0', 'scipy==1.15.3'
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Virtual environment '/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.2/zellkonverterAnnDataEnv-0.10.6' successfully created.
Using Python: /Users/biocbuild/.pyenv/versions/3.11.13/bin/python3.11
Creating virtual environment '/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.2/zellkonverterAnnDataEnv-0.10.2' ...
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/1.19.2/zellkonverterAnnDataEnv-0.10.2/lib/python3.11/site-packages (24.0)
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Installing packages: 'anndata==0.10.2', 'h5py==3.14.0', 'natsort==8.4.0', 'numpy==1.26.4', 'pandas==2.3.0', 'scipy==1.15.3'
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Successfully installed anndata-0.10.2 array-api-compat-1.12.0 h5py-3.14.0 natsort-8.4.0 numpy-1.26.4 packaging-25.0 pandas-2.3.0 python-dateutil-2.9.0.post0 pytz-2025.2 scipy-1.15.3 six-1.17.0 tzdata-2025.2
Virtual environment '/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.2/zellkonverterAnnDataEnv-0.10.2' successfully created.
Using Python: /Users/biocbuild/.pyenv/versions/3.11.13/bin/python3.11
Creating virtual environment '/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.2/zellkonverterAnnDataEnv-0.9.2' ...
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/1.19.2/zellkonverterAnnDataEnv-0.9.2/lib/python3.11/site-packages (24.0)
Collecting pip
Using cached pip-25.2-py3-none-any.whl.metadata (4.7 kB)
Collecting wheel
Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
Requirement already satisfied: setuptools in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.2/zellkonverterAnnDataEnv-0.9.2/lib/python3.11/site-packages (65.5.0)
Collecting setuptools
Using cached setuptools-80.9.0-py3-none-any.whl.metadata (6.6 kB)
Using cached pip-25.2-py3-none-any.whl (1.8 MB)
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Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB)
Installing collected packages: wheel, setuptools, pip
Attempting uninstall: setuptools
Found existing installation: setuptools 65.5.0
Uninstalling setuptools-65.5.0:
Successfully uninstalled setuptools-65.5.0
Attempting uninstall: pip
Found existing installation: pip 24.0
Uninstalling pip-24.0:
Successfully uninstalled pip-24.0
Successfully installed pip-25.2 setuptools-80.9.0 wheel-0.45.1
Installing packages: 'anndata==0.9.2', 'h5py==3.14.0', 'natsort==8.4.0', 'numpy==1.26.4', 'pandas==2.3.0', 'scipy==1.15.3'
Collecting anndata==0.9.2
Using cached anndata-0.9.2-py3-none-any.whl.metadata (6.1 kB)
Collecting h5py==3.14.0
Using cached h5py-3.14.0-cp311-cp311-macosx_11_0_arm64.whl.metadata (2.7 kB)
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Using cached natsort-8.4.0-py3-none-any.whl.metadata (21 kB)
Collecting numpy==1.26.4
Using cached numpy-1.26.4-cp311-cp311-macosx_11_0_arm64.whl.metadata (114 kB)
Collecting pandas==2.3.0
Using cached pandas-2.3.0-cp311-cp311-macosx_11_0_arm64.whl.metadata (91 kB)
Collecting scipy==1.15.3
Using cached scipy-1.15.3-cp311-cp311-macosx_12_0_arm64.whl.metadata (61 kB)
Collecting packaging>=20 (from anndata==0.9.2)
Using cached packaging-25.0-py3-none-any.whl.metadata (3.3 kB)
Collecting python-dateutil>=2.8.2 (from pandas==2.3.0)
Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
Collecting pytz>=2020.1 (from pandas==2.3.0)
Using cached pytz-2025.2-py2.py3-none-any.whl.metadata (22 kB)
Collecting tzdata>=2022.7 (from pandas==2.3.0)
Using cached tzdata-2025.2-py2.py3-none-any.whl.metadata (1.4 kB)
Collecting six>=1.5 (from python-dateutil>=2.8.2->pandas==2.3.0)
Using cached six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB)
Using cached anndata-0.9.2-py3-none-any.whl (104 kB)
Using cached h5py-3.14.0-cp311-cp311-macosx_11_0_arm64.whl (2.9 MB)
Using cached natsort-8.4.0-py3-none-any.whl (38 kB)
Using cached numpy-1.26.4-cp311-cp311-macosx_11_0_arm64.whl (14.0 MB)
Using cached pandas-2.3.0-cp311-cp311-macosx_11_0_arm64.whl (10.8 MB)
Using cached scipy-1.15.3-cp311-cp311-macosx_12_0_arm64.whl (30.1 MB)
Using cached packaging-25.0-py3-none-any.whl (66 kB)
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Using cached tzdata-2025.2-py2.py3-none-any.whl (347 kB)
Installing collected packages: pytz, tzdata, six, packaging, numpy, natsort, scipy, python-dateutil, h5py, pandas, anndata
Successfully installed anndata-0.9.2 h5py-3.14.0 natsort-8.4.0 numpy-1.26.4 packaging-25.0 pandas-2.3.0 python-dateutil-2.9.0.post0 pytz-2025.2 scipy-1.15.3 six-1.17.0 tzdata-2025.2
Virtual environment '/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.2/zellkonverterAnnDataEnv-0.9.2' successfully created.
Using Python: /Users/biocbuild/.pyenv/versions/3.9.23/bin/python3.9
Creating virtual environment '/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.2/zellkonverterAnnDataEnv-0.8.0' ...
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/1.19.2/zellkonverterAnnDataEnv-0.8.0/lib/python3.9/site-packages (23.0.1)
Collecting pip
Using cached pip-25.2-py3-none-any.whl (1.8 MB)
Collecting wheel
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Requirement already satisfied: setuptools in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.2/zellkonverterAnnDataEnv-0.8.0/lib/python3.9/site-packages (58.1.0)
Collecting setuptools
Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB)
Installing collected packages: wheel, setuptools, pip
Attempting uninstall: setuptools
Found existing installation: setuptools 58.1.0
Uninstalling setuptools-58.1.0:
Successfully uninstalled setuptools-58.1.0
Attempting uninstall: pip
Found existing installation: pip 23.0.1
Uninstalling pip-23.0.1:
Successfully uninstalled pip-23.0.1
Successfully installed pip-25.2 setuptools-80.9.0 wheel-0.45.1
Installing packages: 'anndata==0.8.0', 'h5py==3.14.0', 'natsort==8.4.0', 'numpy==1.26.4', 'pandas==1.5.3', 'scipy==1.13.1'
Collecting anndata==0.8.0
Using cached anndata-0.8.0-py3-none-any.whl.metadata (4.6 kB)
Collecting h5py==3.14.0
Using cached h5py-3.14.0-cp39-cp39-macosx_11_0_arm64.whl.metadata (2.7 kB)
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Using cached natsort-8.4.0-py3-none-any.whl.metadata (21 kB)
Collecting numpy==1.26.4
Using cached numpy-1.26.4-cp39-cp39-macosx_11_0_arm64.whl.metadata (61 kB)
Collecting pandas==1.5.3
Using cached pandas-1.5.3-cp39-cp39-macosx_11_0_arm64.whl.metadata (11 kB)
Collecting scipy==1.13.1
Using cached scipy-1.13.1-cp39-cp39-macosx_12_0_arm64.whl.metadata (60 kB)
Collecting packaging>=20 (from anndata==0.8.0)
Using cached packaging-25.0-py3-none-any.whl.metadata (3.3 kB)
Collecting python-dateutil>=2.8.1 (from pandas==1.5.3)
Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
Collecting pytz>=2020.1 (from pandas==1.5.3)
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Installing collected packages: pytz, six, packaging, numpy, natsort, scipy, python-dateutil, h5py, pandas, anndata
Successfully installed anndata-0.8.0 h5py-3.14.0 natsort-8.4.0 numpy-1.26.4 packaging-25.0 pandas-1.5.3 python-dateutil-2.9.0.post0 pytz-2025.2 scipy-1.13.1 six-1.17.0
Virtual environment '/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.2/zellkonverterAnnDataEnv-0.8.0' successfully created.
Using Python: /Users/biocbuild/.pyenv/versions/3.9.23/bin/python3.9
Creating virtual environment '/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.2/zellkonverterAnnDataEnv-0.7.6' ...
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/1.19.2/zellkonverterAnnDataEnv-0.7.6/lib/python3.9/site-packages (23.0.1)
Collecting pip
Using cached pip-25.2-py3-none-any.whl (1.8 MB)
Collecting wheel
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Requirement already satisfied: setuptools in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.2/zellkonverterAnnDataEnv-0.7.6/lib/python3.9/site-packages (58.1.0)
Collecting setuptools
Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB)
Installing collected packages: wheel, setuptools, pip
Attempting uninstall: setuptools
Found existing installation: setuptools 58.1.0
Uninstalling setuptools-58.1.0:
Successfully uninstalled setuptools-58.1.0
Attempting uninstall: pip
Found existing installation: pip 23.0.1
Uninstalling pip-23.0.1:
Successfully uninstalled pip-23.0.1
Successfully installed pip-25.2 setuptools-80.9.0 wheel-0.45.1
Installing packages: 'anndata==0.7.6', 'h5py==3.14.0', 'natsort==8.4.0', 'numpy==1.26.4', 'pandas==1.5.3', 'scipy==1.13.1'
Collecting anndata==0.7.6
Using cached anndata-0.7.6-py3-none-any.whl.metadata (4.0 kB)
Collecting h5py==3.14.0
Using cached h5py-3.14.0-cp39-cp39-macosx_11_0_arm64.whl.metadata (2.7 kB)
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Using cached natsort-8.4.0-py3-none-any.whl.metadata (21 kB)
Collecting numpy==1.26.4
Using cached numpy-1.26.4-cp39-cp39-macosx_11_0_arm64.whl.metadata (61 kB)
Collecting pandas==1.5.3
Using cached pandas-1.5.3-cp39-cp39-macosx_11_0_arm64.whl.metadata (11 kB)
Collecting scipy==1.13.1
Using cached scipy-1.13.1-cp39-cp39-macosx_12_0_arm64.whl.metadata (60 kB)
Collecting packaging>=20 (from anndata==0.7.6)
Using cached packaging-25.0-py3-none-any.whl.metadata (3.3 kB)
Collecting xlrd<2.0 (from anndata==0.7.6)
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Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
Collecting pytz>=2020.1 (from pandas==1.5.3)
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Collecting six>=1.5 (from python-dateutil>=2.8.1->pandas==1.5.3)
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Installing collected packages: pytz, xlrd, six, packaging, numpy, natsort, scipy, python-dateutil, h5py, pandas, anndata
Successfully installed anndata-0.7.6 h5py-3.14.0 natsort-8.4.0 numpy-1.26.4 packaging-25.0 pandas-1.5.3 python-dateutil-2.9.0.post0 pytz-2025.2 scipy-1.13.1 six-1.17.0 xlrd-1.2.0
Virtual environment '/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.2/zellkonverterAnnDataEnv-0.7.6' successfully created.
sys:1: FutureWarning: X.dtype being converted to np.float32 from float64. In the next version of anndata (0.9) conversion will not be automatic. Pass dtype explicitly to avoid this warning. Pass `AnnData(X, dtype=X.dtype, ...)` to get the future behavour.
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.2/zellkonverterAnnDataEnv-0.7.6/lib/python3.9/site-packages/anndata/_core/anndata.py:1220: FutureWarning: The `inplace` parameter in pandas.Categorical.reorder_categories is deprecated and will be removed in a future version. Reordering categories will always return a new Categorical object.
c.reorder_categories(natsorted(c.categories), inplace=True)
... storing 'tissue' as categorical
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.2/zellkonverterAnnDataEnv-0.7.6/lib/python3.9/site-packages/anndata/_core/anndata.py:1220: FutureWarning: The `inplace` parameter in pandas.Categorical.reorder_categories is deprecated and will be removed in a future version. Reordering categories will always return a new Categorical object.
c.reorder_categories(natsorted(c.categories), inplace=True)
... storing 'level1class' as categorical
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.2/zellkonverterAnnDataEnv-0.7.6/lib/python3.9/site-packages/anndata/_core/anndata.py:1220: FutureWarning: The `inplace` parameter in pandas.Categorical.reorder_categories is deprecated and will be removed in a future version. Reordering categories will always return a new Categorical object.
c.reorder_categories(natsorted(c.categories), inplace=True)
... storing 'level2class' as categorical
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/zellkonverter/1.19.2/zellkonverterAnnDataEnv-0.7.6/lib/python3.9/site-packages/anndata/_core/anndata.py:1220: FutureWarning: The `inplace` parameter in pandas.Categorical.reorder_categories is deprecated and will be removed in a future version. Reordering categories will always return a new Categorical object.
c.reorder_categories(natsorted(c.categories), inplace=True)
... storing 'featureType' as categorical
[ FAIL 0 | WARN 20 | SKIP 4 | PASS 198 ]
══ Skipped tests (4) ═══════════════════════════════════════════════════════════
• On CRAN (4): 'test-read.R:197:5', 'test-read.R:239:5',
'test-zzz-anndata.R:6:5', 'test-zzz-anndata.R:63:5'
[ FAIL 0 | WARN 20 | SKIP 4 | PASS 198 ]
>
> proc.time()
user system elapsed
73.562 16.222 300.813
zellkonverter.Rcheck/zellkonverter-Ex.timings
| name | user | system | elapsed | |
| AnnData-Conversion | 8.985 | 0.567 | 9.175 | |
| AnnData-Environment | 0.001 | 0.001 | 0.002 | |
| readH5AD | 0.211 | 0.024 | 0.246 | |
| setZellkonverterVerbose | 0 | 0 | 0 | |
| writeH5AD | 1.035 | 0.216 | 1.273 | |