R version 4.4.1 (2024-06-14) -- "Race for Your Life"
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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

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, 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

/private/var/cache/basilisk/1.16.0/SimBu/1.6.0/SimBu_env_1_1_1/lib/python3.9/site-packages/threadpoolctl.py:1214: RuntimeWarning: 
Found Intel OpenMP ('libiomp') and LLVM OpenMP ('libomp') loaded at
the same time. Both libraries are known to be incompatible and this
can cause random crashes or deadlocks on Linux when loaded in the
same Python program.
Using threadpoolctl may cause crashes or deadlocks. For more
information and possible workarounds, please see
    https://github.com/joblib/threadpoolctl/blob/master/multiple_openmp.md

  warnings.warn(msg, RuntimeWarning)
/private/var/cache/basilisk/1.16.0/SimBu/1.6.0/SimBu_env_1_1_1/lib/python3.9/site-packages/dask/dataframe/__init__.py:31: 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
/private/var/cache/basilisk/1.16.0/SimBu/1.6.0/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...
/private/var/cache/basilisk/1.16.0/SimBu/1.6.0/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)
/private/var/cache/basilisk/1.16.0/SimBu/1.6.0/SimBu_env_1_1_1/lib/python3.9/site-packages/anndata/_core/anndata.py:1820: 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...
/private/var/cache/basilisk/1.16.0/SimBu/1.6.0/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)
/private/var/cache/basilisk/1.16.0/SimBu/1.6.0/SimBu_env_1_1_1/lib/python3.9/site-packages/anndata/_core/anndata.py:1820: 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...
/private/var/cache/basilisk/1.16.0/SimBu/1.6.0/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)
/private/var/cache/basilisk/1.16.0/SimBu/1.6.0/SimBu_env_1_1_1/lib/python3.9/site-packages/anndata/_core/anndata.py:1820: 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...
/private/var/cache/basilisk/1.16.0/SimBu/1.6.0/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)
/private/var/cache/basilisk/1.16.0/SimBu/1.6.0/SimBu_env_1_1_1/lib/python3.9/site-packages/anndata/_core/anndata.py:1820: 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 
712.363  81.714 882.062 

##############################################################################
##############################################################################
###
### 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_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-longtests/meat/SimBu.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* 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 ‘1.6.0’
* 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-3.19-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-3.19-bioc-longtests/meat/SimBu.Rcheck/00check.log’
for details.

* installing *source* package ‘SimBu’ ...
** 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)