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This page was generated on 2025-10-11 12:03 -0400 (Sat, 11 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4864
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4652
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4597
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4586
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1014/2346HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Ibex 0.99.31  (landing page)
Nick Borcherding
Snapshot Date: 2025-10-10 13:45 -0400 (Fri, 10 Oct 2025)
git_url: https://git.bioconductor.org/packages/Ibex
git_branch: devel
git_last_commit: cd6ffd6
git_last_commit_date: 2025-09-23 14:58:00 -0400 (Tue, 23 Sep 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  YES
taishanLinux (openEuler 24.03 LTS) / aarch64  NA    NA    NA  


CHECK results for Ibex on nebbiolo2

To the developers/maintainers of the Ibex package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Ibex.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: Ibex
Version: 0.99.31
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:Ibex.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings Ibex_0.99.31.tar.gz
StartedAt: 2025-10-11 01:01:15 -0400 (Sat, 11 Oct 2025)
EndedAt: 2025-10-11 01:08:22 -0400 (Sat, 11 Oct 2025)
EllapsedTime: 426.5 seconds
RetCode: 1
Status:   ERROR  
CheckDir: Ibex.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:Ibex.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings Ibex_0.99.31.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/Ibex.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘Ibex/DESCRIPTION’ ... OK
* this is package ‘Ibex’ version ‘0.99.31’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Ibex’ can be installed ... OK
* checking installed package size ... OK
* 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 ... 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 ... OK
* checking whether startup messages can be suppressed ... 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 ... 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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘Ibex-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CoNGAfy
> ### Title: Reduce a Single-Cell Object to Representative Cells
> ### Aliases: CoNGAfy
> 
> ### ** Examples
> 
> #' # Get Data
> ibex_example <- get(data("ibex_example"))
> 
> ibex.clones <- CoNGAfy(ibex_example, 
+                        method = "dist")
Loading required namespace: GenomeInfoDb
Failed with error:  ‘there is no package called ‘GenomeInfoDb’’
Error in .requirePackage(package) : 
  unable to load required package ‘GenomeInfoDb’
Calls: CoNGAfy ... .extendsForS3 -> extends -> getClassDef -> .requirePackage
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘spelling.R’
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   12. │       ├─methods::callNextMethod()
   13. │       └─SummarizedExperiment (local) .nextMethod(object = object)
   14. │         ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose)
   15. │         └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
   16. │           ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
   17. │           └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
   18. │             └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
   19. └─methods:::.extendsForS3(`<chr>`)
   20.   └─methods::extends(Class, maybe = FALSE)
   21.     └─methods::getClassDef(class1)
   22.       └─methods:::.requirePackage(package)
  
  [ FAIL 8 | WARN 0 | SKIP 2 | PASS 23 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘Ibex.Rmd’ using knitr
2025-10-11 01:08:10.462500: 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`.
2025-10-11 01:08:10.477811: I external/local_xla/xla/tsl/cuda/cudart_stub.cc:32] Could not find cuda drivers on your machine, GPU will not be used.
2025-10-11 01:08:10.699780: I external/local_xla/xla/tsl/cuda/cudart_stub.cc:32] Could not find cuda drivers on your machine, GPU will not be used.
2025-10-11 01:08:10.838425: E external/local_xla/xla/stream_executor/cuda/cuda_fft.cc:477] Unable to register cuFFT factory: Attempting to register factory for plugin cuFFT when one has already been registered
WARNING: All log messages before absl::InitializeLog() is called are written to STDERR
E0000 00:00:1760159290.955305 3046012 cuda_dnn.cc:8310] Unable to register cuDNN factory: Attempting to register factory for plugin cuDNN when one has already been registered
E0000 00:00:1760159290.988614 3046012 cuda_blas.cc:1418] Unable to register cuBLAS factory: Attempting to register factory for plugin cuBLAS when one has already been registered
2025-10-11 01:08:11.268204: I tensorflow/core/platform/cpu_feature_guard.cc:210] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
To enable the following instructions: AVX2 AVX512F AVX512_VNNI FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
2025-10-11 01:08:14.377469: E external/local_xla/xla/stream_executor/cuda/cuda_driver.cc:152] failed call to cuInit: INTERNAL: CUDA error: Failed call to cuInit: UNKNOWN ERROR (303)
Failed with error:  'there is no package called 'GenomeInfoDb''

Quitting from Ibex.Rmd:235-242 [unnamed-chunk-8]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.requirePackage()`:
! unable to load required package 'GenomeInfoDb'
---
Backtrace:
     ▆
  1. ├─Ibex::runIbex(...)
  2. │ └─Ibex:::filter.cells(sc.data, chain)
  3. │   ├─sc.obj[, cells.index]
  4. │   └─sc.obj[, cells.index]
  5. │     ├─BiocGenerics::updateObject(x)
  6. │     └─SingleCellExperiment::updateObject(x)
  7. │       ├─methods::callNextMethod()
  8. │       └─SummarizedExperiment (local) .nextMethod(object = object)
  9. │         ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose)
 10. │         └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
 11. │           ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
 12. │           └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
 13. │             └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
 14. └─methods:::.extendsForS3(`<chr>`)
 15.   └─methods::extends(Class, maybe = FALSE)
 16.     └─methods::getClassDef(class1)
 17.       └─methods:::.requirePackage(package)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Ibex.Rmd' failed with diagnostics:
unable to load required package 'GenomeInfoDb'
--- failed re-building ‘Ibex.Rmd’

SUMMARY: processing the following file failed:
  ‘Ibex.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 3 ERRORs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/Ibex.Rcheck/00check.log’
for details.


Installation output

Ibex.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL Ibex
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘Ibex’ ...
** this is package ‘Ibex’ version ‘0.99.31’
** using staged installation
** R
** data
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Ibex)

Tests output

Ibex.Rcheck/tests/spelling.Rout


R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> if(requireNamespace('spelling', quietly = TRUE))
+   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+                              skip_on_cran = TRUE)
All Done!
> 
> proc.time()
   user  system elapsed 
  0.147   0.039   0.175 

Ibex.Rcheck/tests/testthat.Rout.fail


R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(Ibex)
> 
> test_check("Ibex")
Failed with error:  'there is no package called 'GenomeInfoDb''
Failed with error:  'there is no package called 'GenomeInfoDb''
Failed with error:  'there is no package called 'GenomeInfoDb''
[1] "Performing geometric transformation..."
Failed with error:  'there is no package called 'GenomeInfoDb''
Failed with error:  'there is no package called 'GenomeInfoDb''
Failed with error:  'there is no package called 'GenomeInfoDb''
Failed with error:  'there is no package called 'GenomeInfoDb''
Failed with error:  'there is no package called 'GenomeInfoDb''
[ FAIL 8 | WARN 0 | SKIP 2 | PASS 23 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• Required Python modules (Keras, NumPy) are not available. (2):
  'test-Ibex_matrix.R:24:5', 'test-runIbex.R:24:5'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-CoNGAfy.R:6:3'): CoNGAfy works with Seurat object ──────────────
Error in `.requirePackage(package)`: unable to load required package 'GenomeInfoDb'
Backtrace:
     ▆
  1. ├─Ibex::CoNGAfy(ibex_example, method = "mean") at test-CoNGAfy.R:6:3
  2. │ ├─input.data[, which(colnames(input.data) %in% cells.chains)]
  3. │ └─input.data[, which(colnames(input.data) %in% cells.chains)]
  4. │   ├─BiocGenerics::updateObject(x)
  5. │   └─SingleCellExperiment::updateObject(x)
  6. │     ├─methods::callNextMethod()
  7. │     └─SummarizedExperiment (local) .nextMethod(object = object)
  8. │       ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose)
  9. │       └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
 10. │         ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
 11. │         └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
 12. │           └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
 13. └─methods:::.extendsForS3(`<chr>`)
 14.   └─methods::extends(Class, maybe = FALSE)
 15.     └─methods::getClassDef(class1)
 16.       └─methods:::.requirePackage(package)
── Error ('test-CoNGAfy.R:15:3'): CoNGAfy works with dist method ───────────────
Error in `.requirePackage(package)`: unable to load required package 'GenomeInfoDb'
Backtrace:
     ▆
  1. ├─Ibex::CoNGAfy(ibex_example, method = "dist") at test-CoNGAfy.R:15:3
  2. │ ├─input.data[, which(colnames(input.data) %in% cells.chains)]
  3. │ └─input.data[, which(colnames(input.data) %in% cells.chains)]
  4. │   ├─BiocGenerics::updateObject(x)
  5. │   └─SingleCellExperiment::updateObject(x)
  6. │     ├─methods::callNextMethod()
  7. │     └─SummarizedExperiment (local) .nextMethod(object = object)
  8. │       ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose)
  9. │       └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
 10. │         ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
 11. │         └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
 12. │           └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
 13. └─methods:::.extendsForS3(`<chr>`)
 14.   └─methods::extends(Class, maybe = FALSE)
 15.     └─methods::getClassDef(class1)
 16.       └─methods:::.requirePackage(package)
── Error ('test-CoNGAfy.R:23:3'): CoNGAfy filters cells correctly ──────────────
Error in `.requirePackage(package)`: unable to load required package 'GenomeInfoDb'
Backtrace:
     ▆
  1. ├─Ibex::CoNGAfy(ibex_example, method = "mean") at test-CoNGAfy.R:23:3
  2. │ ├─input.data[, which(colnames(input.data) %in% cells.chains)]
  3. │ └─input.data[, which(colnames(input.data) %in% cells.chains)]
  4. │   ├─BiocGenerics::updateObject(x)
  5. │   └─SingleCellExperiment::updateObject(x)
  6. │     ├─methods::callNextMethod()
  7. │     └─SummarizedExperiment (local) .nextMethod(object = object)
  8. │       ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose)
  9. │       └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
 10. │         ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
 11. │         └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
 12. │           └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
 13. └─methods:::.extendsForS3(`<chr>`)
 14.   └─methods::extends(Class, maybe = FALSE)
 15.     └─methods::getClassDef(class1)
 16.       └─methods:::.requirePackage(package)
── Failure ('test-runIbex.R:6:3'): runIbex handles incorrect inputs gracefully ──
`runIbex(sc.data = ibex_example, chain = "Middle", method = "encoder")` threw an error with unexpected message.
Expected match: "'arg' should be one of \"Heavy\", \"Light\""
Actual message: "unable to load required package 'GenomeInfoDb'"
Backtrace:
     ▆
  1. ├─testthat::expect_error(...) at test-runIbex.R:6:3
  2. │ └─testthat:::quasi_capture(...)
  3. │   ├─testthat (local) .capture(...)
  4. │   │ └─base::withCallingHandlers(...)
  5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  6. ├─Ibex::runIbex(sc.data = ibex_example, chain = "Middle", method = "encoder")
  7. │ └─Ibex:::filter.cells(sc.data, chain)
  8. │   ├─sc.obj[, cells.index]
  9. │   └─sc.obj[, cells.index]
 10. │     ├─BiocGenerics::updateObject(x)
 11. │     └─SingleCellExperiment::updateObject(x)
 12. │       ├─methods::callNextMethod()
 13. │       └─SummarizedExperiment (local) .nextMethod(object = object)
 14. │         ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose)
 15. │         └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
 16. │           ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
 17. │           └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
 18. │             └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
 19. └─methods:::.extendsForS3(`<chr>`)
 20.   └─methods::extends(Class, maybe = FALSE)
 21.     └─methods::getClassDef(class1)
 22.       └─methods:::.requirePackage(package)
── Failure ('test-runIbex.R:8:3'): runIbex handles incorrect inputs gracefully ──
`runIbex(sc.data = ibex_example, chain = "Heavy", method = "xyz")` threw an error with unexpected message.
Expected match: "'arg' should be one of \"encoder\", \"geometric\""
Actual message: "unable to load required package 'GenomeInfoDb'"
Backtrace:
     ▆
  1. ├─testthat::expect_error(...) at test-runIbex.R:8:3
  2. │ └─testthat:::quasi_capture(...)
  3. │   ├─testthat (local) .capture(...)
  4. │   │ └─base::withCallingHandlers(...)
  5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  6. ├─Ibex::runIbex(sc.data = ibex_example, chain = "Heavy", method = "xyz")
  7. │ └─Ibex:::filter.cells(sc.data, chain)
  8. │   ├─sc.obj[, cells.index]
  9. │   └─sc.obj[, cells.index]
 10. │     ├─BiocGenerics::updateObject(x)
 11. │     └─SingleCellExperiment::updateObject(x)
 12. │       ├─methods::callNextMethod()
 13. │       └─SummarizedExperiment (local) .nextMethod(object = object)
 14. │         ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose)
 15. │         └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
 16. │           ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
 17. │           └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
 18. │             └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
 19. └─methods:::.extendsForS3(`<chr>`)
 20.   └─methods::extends(Class, maybe = FALSE)
 21.     └─methods::getClassDef(class1)
 22.       └─methods:::.requirePackage(package)
── Failure ('test-runIbex.R:10:3'): runIbex handles incorrect inputs gracefully ──
`runIbex(...)` threw an error with unexpected message.
Expected match: "'arg' should be one of \"CNN\", \"VAE\", \"CNN.EXP\", \"VAE.EXP\""
Actual message: "unable to load required package 'GenomeInfoDb'"
Backtrace:
     ▆
  1. ├─testthat::expect_error(...) at test-runIbex.R:10:3
  2. │ └─testthat:::quasi_capture(...)
  3. │   ├─testthat (local) .capture(...)
  4. │   │ └─base::withCallingHandlers(...)
  5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  6. ├─Ibex::runIbex(...)
  7. │ └─Ibex:::filter.cells(sc.data, chain)
  8. │   ├─sc.obj[, cells.index]
  9. │   └─sc.obj[, cells.index]
 10. │     ├─BiocGenerics::updateObject(x)
 11. │     └─SingleCellExperiment::updateObject(x)
 12. │       ├─methods::callNextMethod()
 13. │       └─SummarizedExperiment (local) .nextMethod(object = object)
 14. │         ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose)
 15. │         └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
 16. │           ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
 17. │           └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
 18. │             └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
 19. └─methods:::.extendsForS3(`<chr>`)
 20.   └─methods::extends(Class, maybe = FALSE)
 21.     └─methods::getClassDef(class1)
 22.       └─methods:::.requirePackage(package)
── Failure ('test-runIbex.R:12:3'): runIbex handles incorrect inputs gracefully ──
`runIbex(...)` threw an error with unexpected message.
Expected match: "arg' should be one of \"atchleyFactors\", \"crucianiProperties\", \"kideraFactors\", \"MSWHIM\", \"tScales\", \"OHE\""
Actual message: "unable to load required package 'GenomeInfoDb'"
Backtrace:
     ▆
  1. ├─testthat::expect_error(...) at test-runIbex.R:12:3
  2. │ └─testthat:::quasi_capture(...)
  3. │   ├─testthat (local) .capture(...)
  4. │   │ └─base::withCallingHandlers(...)
  5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  6. ├─Ibex::runIbex(...)
  7. │ └─Ibex:::filter.cells(sc.data, chain)
  8. │   ├─sc.obj[, cells.index]
  9. │   └─sc.obj[, cells.index]
 10. │     ├─BiocGenerics::updateObject(x)
 11. │     └─SingleCellExperiment::updateObject(x)
 12. │       ├─methods::callNextMethod()
 13. │       └─SummarizedExperiment (local) .nextMethod(object = object)
 14. │         ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose)
 15. │         └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
 16. │           ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
 17. │           └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
 18. │             └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
 19. └─methods:::.extendsForS3(`<chr>`)
 20.   └─methods::extends(Class, maybe = FALSE)
 21.     └─methods::getClassDef(class1)
 22.       └─methods:::.requirePackage(package)
── Failure ('test-runIbex.R:14:3'): runIbex handles incorrect inputs gracefully ──
`runIbex(...)` threw an error with unexpected message.
Expected match: "non-numeric argument to mathematical function"
Actual message: "unable to load required package 'GenomeInfoDb'"
Backtrace:
     ▆
  1. ├─testthat::expect_error(...) at test-runIbex.R:14:3
  2. │ └─testthat:::quasi_capture(...)
  3. │   ├─testthat (local) .capture(...)
  4. │   │ └─base::withCallingHandlers(...)
  5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  6. ├─Ibex::runIbex(...)
  7. │ └─Ibex:::filter.cells(sc.data, chain)
  8. │   ├─sc.obj[, cells.index]
  9. │   └─sc.obj[, cells.index]
 10. │     ├─BiocGenerics::updateObject(x)
 11. │     └─SingleCellExperiment::updateObject(x)
 12. │       ├─methods::callNextMethod()
 13. │       └─SummarizedExperiment (local) .nextMethod(object = object)
 14. │         ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose)
 15. │         └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
 16. │           ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
 17. │           └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
 18. │             └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
 19. └─methods:::.extendsForS3(`<chr>`)
 20.   └─methods::extends(Class, maybe = FALSE)
 21.     └─methods::getClassDef(class1)
 22.       └─methods:::.requirePackage(package)

[ FAIL 8 | WARN 0 | SKIP 2 | PASS 23 ]
Error: Test failures
Execution halted

Example timings

Ibex.Rcheck/Ibex-Ex.timings

nameusersystemelapsed