Multiple platform build/check report for BioC 3.23 - BUILD results for StatescopeR on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.6.0 alpha (2026-04-05 r89794)	4630
kjohnson3	macOS 13.7.7 Ventura	arm64	R Under development (unstable) (2026-03-26 r89717) -- "Unsuffered Consequences"	4541
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 StatescopeR on kjohnson3

To the developers/maintainers of the StatescopeR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/StatescopeR.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: StatescopeR

Version: 0.99.35

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

StartedAt: 2026-04-06 18:06:12 -0400 (Mon, 06 Apr 2026)

EndedAt: 2026-04-06 18:06:45 -0400 (Mon, 06 Apr 2026)

EllapsedTime: 32.3 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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


* checking for file ‘StatescopeR/DESCRIPTION’ ... OK
* preparing ‘StatescopeR’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘StatescopeR.Rmd’ using rmarkdown
Requirement already satisfied: pip in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.23.0/StatescopeR/0.99.35/statescope/lib/python3.11/site-packages (24.0)
Collecting pip
  Using cached pip-26.0.1-py3-none-any.whl.metadata (4.7 kB)
Collecting wheel
  Using cached wheel-0.46.3-py3-none-any.whl.metadata (2.4 kB)
Requirement already satisfied: setuptools in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.23.0/StatescopeR/0.99.35/statescope/lib/python3.11/site-packages (79.0.1)
Collecting setuptools
  Using cached setuptools-82.0.1-py3-none-any.whl.metadata (6.5 kB)
Collecting packaging>=24.0 (from wheel)
  Using cached packaging-26.0-py3-none-any.whl.metadata (3.3 kB)
Using cached pip-26.0.1-py3-none-any.whl (1.8 MB)
Using cached wheel-0.46.3-py3-none-any.whl (30 kB)
Using cached setuptools-82.0.1-py3-none-any.whl (1.0 MB)
Using cached packaging-26.0-py3-none-any.whl (74 kB)
Installing collected packages: setuptools, pip, packaging, wheel
  Attempting uninstall: setuptools
    Found existing installation: setuptools 79.0.1
    Uninstalling setuptools-79.0.1:
      Successfully uninstalled setuptools-79.0.1
  Attempting uninstall: pip
    Found existing installation: pip 24.0
    Uninstalling pip-24.0:
      Successfully uninstalled pip-24.0
Successfully installed packaging-26.0 pip-26.0.1 setuptools-82.0.1 wheel-0.46.3
Collecting anndata==0.11.4
  Using cached anndata-0.11.4-py3-none-any.whl.metadata (9.3 kB)
Collecting deap==1.4.3
  Using cached deap-1.4.3-cp311-cp311-macosx_10_9_universal2.whl.metadata (13 kB)
Collecting cachetools==7.0.5
  Using cached cachetools-7.0.5-py3-none-any.whl.metadata (5.6 kB)
Collecting numba==0.62.1
  Using cached numba-0.62.1-cp311-cp311-macosx_11_0_arm64.whl.metadata (2.8 kB)
Collecting pandas==1.5.3
  Using cached pandas-1.5.3-cp311-cp311-macosx_11_0_arm64.whl.metadata (11 kB)
Collecting joblib==1.5.3
  Using cached joblib-1.5.3-py3-none-any.whl.metadata (5.5 kB)
Collecting numpy==1.23.5
  Using cached numpy-1.23.5-cp311-cp311-macosx_11_0_arm64.whl.metadata (2.3 kB)
Collecting scipy==1.15.3
  Using cached scipy-1.15.3-cp311-cp311-macosx_14_0_arm64.whl.metadata (61 kB)
Collecting matplotlib==3.6.3
  Using cached matplotlib-3.6.3-cp311-cp311-macosx_11_0_arm64.whl.metadata (6.8 kB)
Collecting seaborn==0.13.2
  Using cached seaborn-0.13.2-py3-none-any.whl.metadata (5.4 kB)
Collecting scikit-learn==1.5.2
  Using cached scikit_learn-1.5.2-cp311-cp311-macosx_12_0_arm64.whl.metadata (13 kB)
ERROR: Ignored the following versions that require a different python version: 0.52.0 Requires-Python >=3.6,<3.9; 0.52.0rc3 Requires-Python >=3.6,<3.9; 0.53.0 Requires-Python >=3.6,<3.10; 0.53.0rc1.post1 Requires-Python >=3.6,<3.10; 0.53.0rc2 Requires-Python >=3.6,<3.10; 0.53.0rc3 Requires-Python >=3.6,<3.10; 0.53.1 Requires-Python >=3.6,<3.10; 0.54.0 Requires-Python >=3.7,<3.10; 0.54.0rc2 Requires-Python >=3.7,<3.10; 0.54.0rc3 Requires-Python >=3.7,<3.10; 0.54.1 Requires-Python >=3.7,<3.10; 0.55.0 Requires-Python >=3.7,<3.11; 0.55.0rc1 Requires-Python >=3.7,<3.11; 0.55.1 Requires-Python >=3.7,<3.11; 0.55.2 Requires-Python >=3.7,<3.11; 1.21.2 Requires-Python >=3.7,<3.11; 1.21.3 Requires-Python >=3.7,<3.11; 1.21.4 Requires-Python >=3.7,<3.11; 1.21.5 Requires-Python >=3.7,<3.11; 1.21.6 Requires-Python >=3.7,<3.11; 1.6.2 Requires-Python >=3.7,<3.10; 1.6.3 Requires-Python >=3.7,<3.10; 1.7.0 Requires-Python >=3.7,<3.10; 1.7.1 Requires-Python >=3.7,<3.10; 1.7.2 Requires-Python >=3.7,<3.11; 1.7.3 Requires-Python >=3.7,<3.11; 1.8.0 Requires-Python >=3.8,<3.11; 1.8.0rc1 Requires-Python >=3.8,<3.11; 1.8.0rc2 Requires-Python >=3.8,<3.11; 1.8.0rc3 Requires-Python >=3.8,<3.11; 1.8.0rc4 Requires-Python >=3.8,<3.11; 1.8.1 Requires-Python >=3.8,<3.11
ERROR: Could not find a version that satisfies the requirement mkl==2025.3.0 (from versions: none)
ERROR: No matching distribution found for mkl==2025.3.0

Quitting from StatescopeR.Rmd:106-135 [Prepare StatescopeR input]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! Error installing package(s): "'anndata==0.11.4'", "'deap==1.4.3'", "'cachetools==7.0.5'", "'numba==0.62.1'", "'pandas==1.5.3'", "'joblib==1.5.3'", "'numpy==1.23.5'", "'scipy==1.15.3'", "'matplotlib==3.6.3'", "'seaborn==0.13.2'", "'scikit-learn==1.5.2'", "'mkl==2025.3.0'", "'torch==2.8.0'", "'dill==0.3.4'", "'statescope-autogenes==1.0.4.post2'", "'psutil==7.2.2'"
---
Backtrace:
    ▆
 1. └─StatescopeR::select_genes(scRNAseq, 30L, 50L, labels = scRNAseq$`cell type`)
 2.   └─basilisk::basiliskStart(statescope)
 3.     └─basilisk::obtainEnvironmentPath(env)
 4.       └─basilisk::setupBasiliskEnv(...)
 5.         └─reticulate::virtualenv_create(...)
 6.           └─reticulate:::pip_install(python, packages)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'StatescopeR.Rmd' failed with diagnostics:
Error installing package(s): "'anndata==0.11.4'", "'deap==1.4.3'", "'cachetools==7.0.5'", "'numba==0.62.1'", "'pandas==1.5.3'", "'joblib==1.5.3'", "'numpy==1.23.5'", "'scipy==1.15.3'", "'matplotlib==3.6.3'", "'seaborn==0.13.2'", "'scikit-learn==1.5.2'", "'mkl==2025.3.0'", "'torch==2.8.0'", "'dill==0.3.4'", "'statescope-autogenes==1.0.4.post2'", "'psutil==7.2.2'"
--- failed re-building ‘StatescopeR.Rmd’

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

Error: Vignette re-building failed.
Execution halted