Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-10 12:04 -0400 (Fri, 10 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" | 4854 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4642 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4587 |
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 1416/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
muscat 1.23.1 (landing page) Helena L. Crowell
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the muscat package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/muscat.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: muscat |
Version: 1.23.1 |
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:muscat.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings muscat_1.23.1.tar.gz |
StartedAt: 2025-10-10 02:18:53 -0400 (Fri, 10 Oct 2025) |
EndedAt: 2025-10-10 02:29:08 -0400 (Fri, 10 Oct 2025) |
EllapsedTime: 614.8 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: muscat.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:muscat.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings muscat_1.23.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/muscat.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 ‘muscat/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘muscat’ version ‘1.23.1’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 26 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ‘muscat’ 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 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 ... NOTE bbhw: warning in SerialParam(progress = verbose): partial argument match of 'progress' to 'progressbar' pbHeatmap: no visible global function definition for ‘hcl.colors’ pbHeatmap: no visible binding for global variable ‘gene’ pbHeatmap: no visible binding for global variable ‘p_adj.loc’ pbHeatmap: no visible binding for global variable ‘logFC’ Undefined global functions or variables: gene hcl.colors logFC p_adj.loc Consider adding importFrom("grDevices", "hcl.colors") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Non-topic package-anchored link(s) in Rd file 'mmDS.Rd': ‘[limma:dupcor]{duplicateCorrelation}’ See section 'Cross-references' in the 'Writing R Extensions' manual. Found the following Rd file(s) with Rd \link{} targets missing package anchors: pbHeatmap.Rd: HeatmapList-class prepSCE.Rd: SingleCellExperiment-class Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed mmDS 7.055 0.195 7.251 simData 6.712 0.055 6.771 pbHeatmap 6.600 0.072 6.655 prepSim 5.889 0.221 6.110 stagewise_DS_DD 5.572 0.015 5.587 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * 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 ‘analysis.Rmd’ using rmarkdown The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/muscat.Rcheck/vign_test/muscat/vignettes/analysis_files/figure-html/dr-ids-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/muscat.Rcheck/vign_test/muscat/vignettes/analysis_files/figure-html/dr-ids-2.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/muscat.Rcheck/vign_test/muscat/vignettes/analysis_files/figure-html/pb-mds-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/muscat.Rcheck/vign_test/muscat/vignettes/analysis_files/figure-html/unnamed-chunk-5-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/muscat.Rcheck/vign_test/muscat/vignettes/analysis_files/figure-html/upset-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/muscat.Rcheck/vign_test/muscat/vignettes/analysis_files/figure-html/unnamed-chunk-12-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/muscat.Rcheck/vign_test/muscat/vignettes/analysis_files/figure-html/violins-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/muscat.Rcheck/vign_test/muscat/vignettes/analysis_files/figure-html/pb-hm-1-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/muscat.Rcheck/vign_test/muscat/vignettes/analysis_files/figure-html/pb-hm-2-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/muscat.Rcheck/vign_test/muscat/vignettes/analysis_files/figure-html/pb-hm-3-1.png" but not available. --- finished re-building ‘analysis.Rmd’ --- re-building ‘bbhw.Rmd’ using rmarkdown Failed with error: 'there is no package called 'GenomeInfoDb'' Quitting from bbhw.Rmd:166-184 [unnamed-chunk-3] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `.requirePackage()`: ! unable to load required package 'GenomeInfoDb' --- Backtrace: ▆ 1. ├─BiocGenerics::rbind(example_sce, example_sce) 2. │ ├─BiocGenerics (local) standardGeneric("rbind") 3. │ │ ├─BiocGenerics::eval(mc, env) 4. │ │ └─base::eval(mc, env) 5. │ │ └─base::eval(mc, env) 6. │ └─SingleCellExperiment::rbind(...) 7. │ ├─BiocGenerics::lapply(args, updateObject) 8. │ └─base::lapply(args, updateObject) 9. │ ├─BiocGenerics (local) FUN(X[[i]], ...) 10. │ └─SingleCellExperiment (local) FUN(X[[i]], ...) 11. │ ├─methods::callNextMethod() 12. │ └─SummarizedExperiment (local) .nextMethod(object = object) 13. │ ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose) 14. │ └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose) 15. │ ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose) 16. │ └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose) 17. │ └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose) 18. └─methods:::.extendsForS3(`<chr>`) 19. └─methods::extends(Class, maybe = FALSE) 20. └─methods::getClassDef(class1) 21. └─methods:::.requirePackage(package) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'bbhw.Rmd' failed with diagnostics: unable to load required package 'GenomeInfoDb' --- failed re-building ‘bbhw.Rmd’ --- re-building ‘detection.Rmd’ using rmarkdown The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/muscat.Rcheck/vign_test/muscat/vignettes/detection_files/figure-html/pbs-mds-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/muscat.Rcheck/vign_test/muscat/vignettes/detection_files/figure-html/unnamed-chunk-5-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/muscat.Rcheck/vign_test/muscat/vignettes/detection_files/figure-html/unnamed-chunk-8-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/muscat.Rcheck/vign_test/muscat/vignettes/detection_files/figure-html/upset-1.png" but not available. --- finished re-building ‘detection.Rmd’ --- re-building ‘simulation.Rmd’ using rmarkdown Failed with error: 'there is no package called 'GenomeInfoDb'' Quitting from simulation.Rmd:106-117 [prepSim] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `h()`: ! error in evaluating the argument 'x' in selecting a method for function 'assay': unable to load required package 'GenomeInfoDb' --- Backtrace: ▆ 1. ├─SummarizedExperiment::assay(example_sce[rownames(ref), colnames(ref)]) 2. ├─example_sce[rownames(ref), colnames(ref)] 3. ├─example_sce[rownames(ref), colnames(ref)] 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) 17. │ └─base::stop(...) 18. └─base::.handleSimpleError(...) 19. └─base (local) h(simpleError(msg, call)) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'simulation.Rmd' failed with diagnostics: error in evaluating the argument 'x' in selecting a method for function 'assay': unable to load required package 'GenomeInfoDb' --- failed re-building ‘simulation.Rmd’ SUMMARY: processing the following files failed: ‘bbhw.Rmd’ ‘simulation.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 2 NOTEs See ‘/home/biocbuild/bbs-3.22-bioc/meat/muscat.Rcheck/00check.log’ for details.
muscat.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL muscat ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘muscat’ ... ** this is package ‘muscat’ version ‘1.23.1’ ** 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 (muscat)
muscat.Rcheck/tests/testthat.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. > library(testthat) > library(muscat) > > test_check("muscat") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 555 ] > > proc.time() user system elapsed 94.948 1.594 96.396
muscat.Rcheck/muscat-Ex.timings
name | user | system | elapsed | |
aggregateData | 2.349 | 0.077 | 2.426 | |
calcExprFreqs | 1.518 | 0.062 | 1.575 | |
data | 0.001 | 0.000 | 0.000 | |
gBH | 0.01 | 0.00 | 0.01 | |
mmDS | 7.055 | 0.195 | 7.251 | |
pbDS | 1.264 | 0.038 | 1.303 | |
pbFlatten | 0.769 | 0.017 | 0.785 | |
pbHeatmap | 6.600 | 0.072 | 6.655 | |
pbMDS | 0.981 | 0.023 | 1.006 | |
prepSCE | 0.456 | 0.003 | 0.459 | |
prepSim | 5.889 | 0.221 | 6.110 | |
resDS | 2.214 | 0.039 | 2.243 | |
simData | 6.712 | 0.055 | 6.771 | |
stagewise_DS_DD | 5.572 | 0.015 | 5.587 | |