R version 4.5.1 RC (2025-06-05 r88288) -- "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: GenomeInfoDb
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

/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.20.0/SimBu/1.10.0/SimBu_env_1_1_1/lib/python3.9/site-packages/dask/dataframe/__init__.py:42: FutureWarning: 
Dask dataframe query planning is disabled because dask-expr is not installed.

You can install it with `pip install dask[dataframe]` or `conda install dask`.
This will raise in a future version.

  warnings.warn(msg, FutureWarning)
Sucessfully loaded sfaira.
Starting to download dataset from Sfaria with id: 
homosapiens_lungparenchyma_2019_10x3v2_madissoon_001_10.1186/s13059-019-1906-x
Ontology <class 'sfaira.versions.metadata.base.OntologyMondo'> is not a DAG, treat child-parent reasoning with care.
Ontology <class 'sfaira.versions.metadata.base.OntologyUberon'> is not a DAG, treat child-parent reasoning with care.
Ontology <class 'sfaira.versions.metadata.base.OntologyUberonLifecyclestage'> is not a DAG, treat child-parent reasoning with care.
Checking file accessibility for id: 
homosapiens_lungparenchyma_2019_10x3v2_madissoon_001_10.1186/s13059-019-1906-x
Checking if IDs contain datasets which are currently known to be broken.
Downloading datasets...
Downloading: madissoon19_lung.processed.h5ad
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.20.0/SimBu/1.10.0/SimBu_env_1_1_1/lib/python3.9/site-packages/anndata/__init__.py:55: FutureWarning: `anndata.read` is deprecated, use `anndata.read_h5ad` instead. `ad.read` will be removed in mid 2024.
  warnings.warn(
loading homosapiens_lungparenchyma_2019_10x3v2_madissoon_001_10.1186/s13059-019-1906-x
Streamlining features & meta-data...
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.20.0/SimBu/1.10.0/SimBu_env_1_1_1/lib/python3.9/site-packages/scipy/sparse/_index.py:142: SparseEfficiencyWarning: Changing the sparsity structure of a csc_matrix is expensive. lil_matrix is more efficient.
  self._set_arrayXarray_sparse(i, j, x)
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.20.0/SimBu/1.10.0/SimBu_env_1_1_1/lib/python3.9/site-packages/anndata/_core/anndata.py:1756: UserWarning: Variable names are not unique. To make them unique, call `.var_names_make_unique`.
  utils.warn_names_duplicates("var")
WARNING:root:name and ontology keys are both missing
Using rownames for cell-IDs.
Filtering genes...
Created dataset.
Starting to download dataset from Sfaria with id: 
homosapiens_lungparenchyma_2019_10x3v2_madissoon_001_10.1186/s13059-019-1906-x
Checking file accessibility for id: 
homosapiens_lungparenchyma_2019_10x3v2_madissoon_001_10.1186/s13059-019-1906-x
Checking if IDs contain datasets which are currently known to be broken.
Downloading datasets...
loading homosapiens_lungparenchyma_2019_10x3v2_madissoon_001_10.1186/s13059-019-1906-x
Streamlining features & meta-data...
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.20.0/SimBu/1.10.0/SimBu_env_1_1_1/lib/python3.9/site-packages/scipy/sparse/_index.py:142: SparseEfficiencyWarning: Changing the sparsity structure of a csc_matrix is expensive. lil_matrix is more efficient.
  self._set_arrayXarray_sparse(i, j, x)
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.20.0/SimBu/1.10.0/SimBu_env_1_1_1/lib/python3.9/site-packages/anndata/_core/anndata.py:1756: UserWarning: Variable names are not unique. To make them unique, call `.var_names_make_unique`.
  utils.warn_names_duplicates("var")
Using rownames for cell-IDs.
Filtering genes...
Created dataset.
Starting to download datasets from Sfaria...
Removing datasets without cell-type annotation...
Checking file accessibility for id: 
homosapiens_lungparenchyma_2019_10x3v2_madissoon_001_10.1186/s13059-019-1906-x
Checking if IDs contain datasets which are currently known to be broken.
Downloading datasets...
loading homosapiens_lungparenchyma_2019_10x3v2_madissoon_001_10.1186/s13059-019-1906-x
Streamlining features & meta-data...
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.20.0/SimBu/1.10.0/SimBu_env_1_1_1/lib/python3.9/site-packages/scipy/sparse/_index.py:142: SparseEfficiencyWarning: Changing the sparsity structure of a csc_matrix is expensive. lil_matrix is more efficient.
  self._set_arrayXarray_sparse(i, j, x)
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.20.0/SimBu/1.10.0/SimBu_env_1_1_1/lib/python3.9/site-packages/anndata/_core/anndata.py:1756: UserWarning: Variable names are not unique. To make them unique, call `.var_names_make_unique`.
  utils.warn_names_duplicates("var")
Using rownames for cell-IDs.
Filtering genes...
Created dataset.
Starting to download datasets from Sfaria...
Removing datasets without cell-type annotation...
Checking file accessibility for id: 
homosapiens_lungparenchyma_2019_10x3v2_madissoon_001_10.1186/s13059-019-1906-x
Checking if IDs contain datasets which are currently known to be broken.
Downloading datasets...
loading homosapiens_lungparenchyma_2019_10x3v2_madissoon_001_10.1186/s13059-019-1906-x
Streamlining features & meta-data...
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.20.0/SimBu/1.10.0/SimBu_env_1_1_1/lib/python3.9/site-packages/scipy/sparse/_index.py:142: SparseEfficiencyWarning: Changing the sparsity structure of a csc_matrix is expensive. lil_matrix is more efficient.
  self._set_arrayXarray_sparse(i, j, x)
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.20.0/SimBu/1.10.0/SimBu_env_1_1_1/lib/python3.9/site-packages/anndata/_core/anndata.py:1756: UserWarning: Variable names are not unique. To make them unique, call `.var_names_make_unique`.
  utils.warn_names_duplicates("var")
Using rownames for cell-IDs.
Filtering genes...
Created dataset.
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 2 ]

[ FAIL 0 | WARN 4 | SKIP 0 | PASS 2 ]
> 
> proc.time()
   user  system elapsed 
680.564  72.031 877.050 
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.20.0/SimBu/1.10.0/SimBu_env_1_1_1/lib/python3.9/multiprocessing/resource_tracker.py:216: UserWarning: resource_tracker: There appear to be 1 leaked semaphore objects to clean up at shutdown
  warnings.warn('resource_tracker: There appear to be %d '

##############################################################################
##############################################################################
###
### 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_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc-longtests/meat/SimBu.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* 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 ‘1.10.0’
* 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-3.21-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’
 OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc-longtests/meat/SimBu.Rcheck/00check.log’
for details.

* installing *source* package ‘SimBu’ ...
** this is package ‘SimBu’ version ‘1.10.0’
** 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)