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).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4854
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4642
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4587
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 1416/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
muscat 1.23.1  (landing page)
Helena L. Crowell
Snapshot Date: 2025-10-09 13:45 -0400 (Thu, 09 Oct 2025)
git_url: https://git.bioconductor.org/packages/muscat
git_branch: devel
git_last_commit: 38d6c84
git_last_commit_date: 2025-09-21 05:22:08 -0400 (Sun, 21 Sep 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for muscat on nebbiolo2

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.

raw results


Summary

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

Command output

##############################################################################
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###
### 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.


Installation output

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)

Tests output

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 

Example timings

muscat.Rcheck/muscat-Ex.timings

nameusersystemelapsed
aggregateData2.3490.0772.426
calcExprFreqs1.5180.0621.575
data0.0010.0000.000
gBH0.010.000.01
mmDS7.0550.1957.251
pbDS1.2640.0381.303
pbFlatten0.7690.0170.785
pbHeatmap6.6000.0726.655
pbMDS0.9810.0231.006
prepSCE0.4560.0030.459
prepSim5.8890.2216.110
resDS2.2140.0392.243
simData6.7120.0556.771
stagewise_DS_DD5.5720.0155.587