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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, saveRDS, 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

Attaching package: 'IRanges'

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

    windows

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

C:\Users\BIOCBU~1\BASILI~1\117~1.2\SimBu\1748C3~1.0\SIMBU_~1\lib\site-packages\networkx\utils\backends.py:135: RuntimeWarning: networkx backend defined more than once: nx-loopback
  backends.update(_get_backends("networkx.backends"))
C:\Users\BIOCBU~1\BASILI~1\117~1.2\SimBu\1748C3~1.0\SIMBU_~1\lib\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)
2024-10-26 16:56:04.727593: I tensorflow/core/util/port.cc:153] oneDNN custom operations are on. You may see slightly different numerical results due to floating-point round-off errors from different computation orders. To turn them off, set the environment variable `TF_ENABLE_ONEDNN_OPTS=0`.
2024-10-26 16:56:16.316780: I tensorflow/core/util/port.cc:153] oneDNN custom operations are on. You may see slightly different numerical results due to floating-point round-off errors from different computation orders. To turn them off, set the environment variable `TF_ENABLE_ONEDNN_OPTS=0`.
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.
Could not download dataset for id.
Cannot download data and/or metadata for any of the supplied sfaira IDs. Stopping.
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.
Could not download all datasets for specified filters.
Cannot download data and/or metadata for any of the supplied sfaira IDs. Stopping.
[ FAIL 2 | WARN 2 | SKIP 0 | PASS 0 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_dataset.R:8:3'): check sfaira for single dataset ───────────────
Error in `t.default(sfaira_data$X)`: argument is not a matrix
Backtrace:
    ▆
 1. ├─testthat::expect_s4_class(...) at test_dataset.R:8:3
 2. │ └─testthat::quasi_label(enquo(object), arg = "object")
 3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
 4. └─SimBu::dataset_sfaira(...)
 5.   ├─Matrix::t(sfaira_data$X)
 6.   ├─Matrix::t(sfaira_data$X)
 7.   └─base::t.default(sfaira_data$X)
── Error ('test_dataset.R:13:3'): check sfaira for multiple datasets ───────────
Error in `t.default(sfaira_data$X)`: argument is not a matrix
Backtrace:
    ▆
 1. ├─testthat::expect_s4_class(...) at test_dataset.R:13:3
 2. │ └─testthat::quasi_label(enquo(object), arg = "object")
 3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
 4. └─SimBu::dataset_sfaira_multiple(...)
 5.   ├─Matrix::t(sfaira_data$X)
 6.   ├─Matrix::t(sfaira_data$X)
 7.   └─base::t.default(sfaira_data$X)

[ FAIL 2 | WARN 2 | SKIP 0 | PASS 0 ]
Error: Test failures
Execution halted

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no SimBu_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc-longtests/meat/SimBu.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 '1.7.0'
* 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 whether package 'SimBu' can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used
See 'F:/biocbuild/bbs-3.20-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 ('test_dataset.R:13:3'): check sfaira for multiple datasets ───────────
  Error in `t.default(sfaira_data$X)`: argument is not a matrix
  Backtrace:
      ▆
   1. ├─testthat::expect_s4_class(...) at test_dataset.R:13:3
   2. │ └─testthat::quasi_label(enquo(object), arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─SimBu::dataset_sfaira_multiple(...)
   5.   ├─Matrix::t(sfaira_data$X)
   6.   ├─Matrix::t(sfaira_data$X)
   7.   └─base::t.default(sfaira_data$X)
  
  [ FAIL 2 | WARN 2 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
* DONE

Status: 1 ERROR, 2 NOTEs
See
  'F:/biocbuild/bbs-3.20-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)