* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/rliger.Rcheck’
* using R Under development (unstable) (2024-04-19 r86451)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-13 (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Fedora Linux 36 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘rliger/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rliger’ version ‘2.0.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages suggested but not available for checking:
  'DoubletFinder', 'org.Hs.eg.db', 'RcppPlanc', 'reactome.db'
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘rliger’ can be installed ... [262s/205s] OK
* used C++ compiler: ‘g++-13 (GCC) 13.2.0’
* checking package directory ... OK
* checking ‘build’ 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 ... [7s/11s] OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... [8s/11s] OK
* checking whether startup messages can be suppressed ... OK
* checking use of S3 registration ... 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 ... [79s/97s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [17s/21s] ERROR
Running examples in ‘rliger-Ex.R’ failed
The error most likely occurred in:

> ### Name: ligerToSeurat
> ### Title: Convert between liger and Seurat object
> ### Aliases: ligerToSeurat
> 
> ### ** Examples
> 
> seu <- ligerToSeurat(pbmc)
Error in loadNamespace(x) : there is no package called ‘SeuratObject’
Calls: ligerToSeurat ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [50s/51s]
 [50s/51s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rliger)
  Package `rliger` has been updated massively since version 1.99.0, including the object structure which is not compatible with old versions.
  
  We recommand you backup your old analysis before overwriting any existing result.
  
  `readLiger()` is provided for reading an RDS file storing an old object and it converts the object to the up-to-date structure.
  
  Package "RcppPlanc" is required for performing integrative factorizations but is not detected. It is currently not on CRAN, so please install it with `devtools::install_github('welch-lab/RcppPlanc')`
  > 
  > test_check("rliger")
  Working ctrl H5 file path:  /tmp/Rtmp4MvZtJ/working_dir/Rtmp6C7rjl/ctrltest_4119b5e89a863.h5 
  Working stim H5 file path:  /tmp/Rtmp4MvZtJ/working_dir/Rtmp6C7rjl/stimtest_4119b199beecb.h5 
  
  
  
  
  Working ctrl H5 file path:  /tmp/Rtmp4MvZtJ/working_dir/Rtmp6C7rjl/ctrltest_4119b4ae4f6b5.h5 
  Working stim H5 file path:  /tmp/Rtmp4MvZtJ/working_dir/Rtmp6C7rjl/stimtest_4119b5823c385.h5 
  
  
  Working ctrl H5 file path:  /tmp/Rtmp4MvZtJ/working_dir/Rtmp6C7rjl/ctrltest_4119b10d6e12f.h5 
  Working stim H5 file path:  /tmp/Rtmp4MvZtJ/working_dir/Rtmp6C7rjl/stimtest_4119b528de588.h5 
  
  
  
  
  Working ctrl H5 file path:  /tmp/Rtmp4MvZtJ/working_dir/Rtmp6C7rjl/ctrltest_4119b63fdfc13.h5 
  Working stim H5 file path:  /tmp/Rtmp4MvZtJ/working_dir/Rtmp6C7rjl/stimtest_4119b71d6595a.h5 
  
  
  
  
  
  
  Working ctrl H5 file path:  /tmp/Rtmp4MvZtJ/working_dir/Rtmp6C7rjl/ctrltest_4119b5ca8d98c.h5 
  Working stim H5 file path:  /tmp/Rtmp4MvZtJ/working_dir/Rtmp6C7rjl/stimtest_4119b56540765.h5 
  
  
  
  
  
  
  
  
  
  
  [ FAIL 1 | WARN 0 | SKIP 25 | PASS 1015 ]
  
  ══ Skipped tests (25) ══════════════════════════════════════════════════════════
  • DoubletFinder cannot be loaded (1): 'test_preprocessing.R:112:5'
  • RcppPlanc cannot be loaded (16): 'test_downstream.R:69:5',
    'test_downstream.R:119:5', 'test_downstream.R:143:5',
    'test_downstream.R:190:5', 'test_downstream.R:267:5',
    'test_factorization.R:58:5', 'test_factorization.R:94:5',
    'test_factorization.R:121:5', 'test_factorization.R:154:5',
    'test_factorization.R:197:5', 'test_factorization.R:238:5',
    'test_object.R:128:5', 'test_object.R:230:5', 'test_object.R:334:5',
    'test_subset.R:62:5', 'test_subset.R:77:5'
  • Seurat cannot be loaded (4): 'test_object.R:415:5', 'test_object.R:471:5',
    'test_preprocessing.R:162:5', 'test_preprocessing.R:277:5'
  • org.Hs.eg.db cannot be loaded (1): 'test_downstream.R:244:5'
  • sankey cannot be loaded (1): 'test_visualization.R:283:5'
  • scattermore cannot be loaded (2): 'test_visualization.R:86:5',
    'test_visualization.R:108:5'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_visualization.R:161:5'): Density plot ──────────────────────────
  Error in `.checkRaster(nrow(dotCoordDF), dotRaster)`: Package scattermore is needed for rasterizing the scatter plot. Please
  install it by command: `BiocManager::install('scattermore')`
  Backtrace:
       ▆
    1. ├─rliger (local) expect_gg(...) at test_visualization.R:161:5
    2. ├─testthat::expect_message(...) at test_visualization.R:46:5
    3. │ └─testthat:::quasi_capture(enquo(object), label, capture_messages)
    4. │   ├─testthat (local) .capture(...)
    5. │   │ └─base::withCallingHandlers(...)
    6. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    7. └─rliger::plotDensityDimRed(pbmcPlot, title = letters[1:3], dotRaster = TRUE)
    8.   └─rliger:::.ggDensity(...)
    9.     └─rliger:::.checkRaster(nrow(dotCoordDF), dotRaster)
   10.       └─cli::cli_abort("Package {.pkg scattermore} is needed for rasterizing the scatter\n                plot. Please install it by command:\n                {.code BiocManager::install('scattermore')}")
   11.         └─rlang::abort(...)
  
  [ FAIL 1 | WARN 0 | SKIP 25 | PASS 1015 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... [10s/10s] OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 2 ERRORs, 1 NOTE
See
  ‘/data/gannet/ripley/R/packages/tests-Suggests/rliger.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 10:15.81, 562.18 + 38.34