Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-11 12:03 -0400 (Sat, 11 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4864 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4652 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4597 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (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 1014/2346 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Ibex 0.99.31 (landing page) Nick Borcherding
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | NA | NA | NA | ||||||||||
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. |
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 |
############################################################################## ############################################################################## ### ### 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.
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)
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
Ibex.Rcheck/Ibex-Ex.timings
name | user | system | elapsed |