Multiple platform build/check report for BioC 3.21 - BUILD results for zellkonverter on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences"	4777
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences"	4545
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4576
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4528
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4458
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*

BUILD results for zellkonverter on kjohnson3

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.

raw results

Summary

Package: zellkonverter

Version: 1.17.1

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data zellkonverter

StartedAt: 2025-03-19 18:04:41 -0400 (Wed, 19 Mar 2025)

EndedAt: 2025-03-19 18:08:24 -0400 (Wed, 19 Mar 2025)

EllapsedTime: 222.2 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data zellkonverter
###
##############################################################################
##############################################################################


* checking for file ‘zellkonverter/DESCRIPTION’ ... OK
* preparing ‘zellkonverter’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘zellkonverter.Rmd’ using rmarkdown
python-build: use openssl@3 from homebrew
python-build: use readline from homebrew
Downloading Python-3.12.7.tar.xz...
-> https://www.python.org/ftp/python/3.12.7/Python-3.12.7.tar.xz
Installing Python-3.12.7...
python-build: use tcl-tk from homebrew
python-build: use readline from homebrew
python-build: use zlib from xcode sdk
Installed Python-3.12.7 to /Users/biocbuild/.pyenv/versions/3.12.7
Requirement already satisfied: pip in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.19.2/zellkonverter/1.17.1/zellkonverterAnnDataEnv-0.10.9/lib/python3.12/site-packages (24.2)
Collecting pip
  Using cached pip-25.0.1-py3-none-any.whl.metadata (3.7 kB)
Collecting wheel
  Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
Collecting setuptools
  Using cached setuptools-77.0.1-py3-none-any.whl.metadata (6.7 kB)
Using cached pip-25.0.1-py3-none-any.whl (1.8 MB)
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Using cached setuptools-77.0.1-py3-none-any.whl (1.3 MB)
Installing collected packages: wheel, setuptools, pip
  Attempting uninstall: pip
    Found existing installation: pip 24.2
    Uninstalling pip-24.2:
      Successfully uninstalled pip-24.2
Successfully installed pip-25.0.1 setuptools-77.0.1 wheel-0.45.1
Collecting anndata==0.10.9
  Using cached anndata-0.10.9-py3-none-any.whl.metadata (6.9 kB)
Collecting h5py==3.12.1
  Downloading h5py-3.12.1-cp312-cp312-macosx_11_0_arm64.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

Quitting from zellkonverter.Rmd:41-50 [read]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! Error installing package(s): "'anndata==0.10.9'", "'h5py==3.12.1'", "'hdf5==1.14.3'", "'natsort==8.4.0'", "'numpy==2.1.2'", "'packaging==24.1'", "'pandas==2.2.3'", "'python==3.12.7'", "'scipy==1.14.1'"
---
Backtrace:
    ▆
 1. └─zellkonverter::readH5AD(example_h5ad)
 2.   └─basilisk::basiliskRun(...)
 3.     └─basilisk::basiliskStart(...)
 4.       └─basilisk::obtainEnvironmentPath(env)
 5.         └─basilisk::setupBasiliskEnv(...)
 6.           └─reticulate::virtualenv_install(...)
 7.             └─reticulate:::pip_install(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'zellkonverter.Rmd' failed with diagnostics:
Error installing package(s): "'anndata==0.10.9'", "'h5py==3.12.1'", "'hdf5==1.14.3'", "'natsort==8.4.0'", "'numpy==2.1.2'", "'packaging==24.1'", "'pandas==2.2.3'", "'python==3.12.7'", "'scipy==1.14.1'"
--- failed re-building ‘zellkonverter.Rmd’

SUMMARY: processing the following file failed:
  ‘zellkonverter.Rmd’

Error: Vignette re-building failed.
Execution halted