R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
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Platform: x86_64-apple-darwin20

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> library(testthat)
> library(SimBu)
> 
> test_check("SimBu")
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:Matrix':

    expand, unname

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: Seqinfo
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

Using Python: /Users/biocbuild/.pyenv/versions/3.9.24/bin/python3.9
Creating virtual environment '/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/SimBu/1.11.0/SimBu_env_1_1_1' ... 
+ /Users/biocbuild/.pyenv/versions/3.9.24/bin/python3.9 -m venv /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/SimBu/1.11.0/SimBu_env_1_1_1
Done!
Installing packages: pip, wheel, setuptools
+ /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/SimBu/1.11.0/SimBu_env_1_1_1/bin/python -m pip install --upgrade pip wheel setuptools
Requirement already satisfied: pip in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/SimBu/1.11.0/SimBu_env_1_1_1/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/SimBu/1.11.0/SimBu_env_1_1_1/lib/python3.9/site-packages (79.0.1)
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 79.0.1
    Uninstalling setuptools-79.0.1:
      Successfully uninstalled setuptools-79.0.1
  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==3.2.1', 'hdf5==1.10.6', 'natsort==7.1.1', 'numpy==1.20.2', 'packaging==20.9', 'pandas==1.2.4', 'scipy==1.6.3', 'sqlite==3.35.5', 'sfaira==0.3.12', 'tables==3.7.0'
+ /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/SimBu/1.11.0/SimBu_env_1_1_1/bin/python -m pip install --upgrade --no-user 'anndata==0.7.6' 'h5py==3.2.1' 'hdf5==1.10.6' 'natsort==7.1.1' 'numpy==1.20.2' 'packaging==20.9' 'pandas==1.2.4' 'scipy==1.6.3' 'sqlite==3.35.5' 'sfaira==0.3.12' 'tables==3.7.0'
Collecting anndata==0.7.6
  Using cached anndata-0.7.6-py3-none-any.whl.metadata (4.0 kB)
Collecting h5py==3.2.1
  Using cached h5py-3.2.1-cp39-cp39-macosx_10_9_x86_64.whl.metadata (2.0 kB)
ERROR: Ignored the following versions that require a different python version: 0.11.0 Requires-Python >=3.10; 0.11.0rc3 Requires-Python >=3.10; 0.11.1 Requires-Python >=3.10; 0.11.2 Requires-Python >=3.10; 0.11.3 Requires-Python >=3.10; 0.11.4 Requires-Python >=3.10; 0.12.0 Requires-Python >=3.11; 0.12.0rc1 Requires-Python >=3.11; 0.12.0rc2 Requires-Python >=3.11; 0.12.0rc3 Requires-Python >=3.11; 0.12.0rc4 Requires-Python >=3.11; 0.12.1 Requires-Python >=3.11; 0.12.2 Requires-Python >=3.11; 0.12.3 Requires-Python >=3.11; 3.15.0 Requires-Python >=3.10; 3.15.1 Requires-Python >=3.10
ERROR: Could not find a version that satisfies the requirement hdf5==1.10.6 (from versions: none)
ERROR: No matching distribution found for hdf5==1.10.6
Error installing package(s): "'anndata==0.7.6'", "'h5py==3.2.1'", "'hdf5==1.10.6'", "'natsort==7.1.1'", "'numpy==1.20.2'", "'packaging==20.9'", "'pandas==1.2.4'", "'scipy==1.6.3'", "'sqlite==3.35.5'", "'sfaira==0.3.12'", "'tables==3.7.0'"
[ FAIL 2 | WARN 4 | SKIP 0 | PASS 0 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_dataset.R:8:3'): check sfaira for single dataset ─────────────
SimBu::dataset_sfaira(...) is not an S4 object
── Failure ('test_dataset.R:13:3'): check sfaira for multiple datasets ─────────
SimBu::dataset_sfaira_multiple(...) is not an S4 object

[ FAIL 2 | WARN 4 | 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 SimBu_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc-longtests/meat/SimBu.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* 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 ‘SimBu/DESCRIPTION’ ... OK
* this is package ‘SimBu’ version ‘1.11.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
  .pre-commit-config.yaml
  .prettierignore
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SimBu’ can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used
See ‘/Users/biocbuild/bbs-3.22-bioc-longtests/meat/SimBu.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 ... OK
* 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:
  ERROR: Ignored the following versions that require a different python version: 0.11.0 Requires-Python >=3.10; 0.11.0rc3 Requires-Python >=3.10; 0.11.1 Requires-Python >=3.10; 0.11.2 Requires-Python >=3.10; 0.11.3 Requires-Python >=3.10; 0.11.4 Requires-Python >=3.10; 0.12.0 Requires-Python >=3.11; 0.12.0rc1 Requires-Python >=3.11; 0.12.0rc2 Requires-Python >=3.11; 0.12.0rc3 Requires-Python >=3.11; 0.12.0rc4 Requires-Python >=3.11; 0.12.1 Requires-Python >=3.11; 0.12.2 Requires-Python >=3.11; 0.12.3 Requires-Python >=3.11; 3.15.0 Requires-Python >=3.10; 3.15.1 Requires-Python >=3.10
  ERROR: Could not find a version that satisfies the requirement hdf5==1.10.6 (from versions: none)
  ERROR: No matching distribution found for hdf5==1.10.6
  Error installing package(s): "'anndata==0.7.6'", "'h5py==3.2.1'", "'hdf5==1.10.6'", "'natsort==7.1.1'", "'numpy==1.20.2'", "'packaging==20.9'", "'pandas==1.2.4'", "'scipy==1.6.3'", "'sqlite==3.35.5'", "'sfaira==0.3.12'", "'tables==3.7.0'"
  [ FAIL 2 | WARN 4 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_dataset.R:8:3'): check sfaira for single dataset ─────────────
  SimBu::dataset_sfaira(...) is not an S4 object
  ── Failure ('test_dataset.R:13:3'): check sfaira for multiple datasets ─────────
  SimBu::dataset_sfaira_multiple(...) is not an S4 object
  
  [ FAIL 2 | WARN 4 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc-longtests/meat/SimBu.Rcheck/00check.log’
for details.

* installing *source* package ‘SimBu’ ...
** this is package ‘SimBu’ version ‘1.11.0’
** using non-staged installation via StagedInstall field
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (SimBu)