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This page was generated on 2025-10-16 12:07 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4867
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4655
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4600
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4610
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 1417/2346HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
muscat 1.23.2  (landing page)
Helena L. Crowell
Snapshot Date: 2025-10-15 13:45 -0400 (Wed, 15 Oct 2025)
git_url: https://git.bioconductor.org/packages/muscat
git_branch: devel
git_last_commit: 8bb91e1
git_last_commit_date: 2025-10-15 04:02:09 -0400 (Wed, 15 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  YES
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  YES
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  YES
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    ERROR  


CHECK results for muscat on taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: muscat
Version: 1.23.1
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:muscat.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings muscat_1.23.1.tar.gz
StartedAt: 2025-10-14 10:42:01 -0000 (Tue, 14 Oct 2025)
EndedAt: 2025-10-14 10:50:20 -0000 (Tue, 14 Oct 2025)
EllapsedTime: 498.8 seconds
RetCode: 1
Status:   ERROR  
CheckDir: muscat.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:muscat.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings muscat_1.23.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/muscat.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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            9.490  0.239   9.974
pbHeatmap       9.403  0.103  10.487
simData         9.165  0.107  10.098
prepSim         7.227  0.135   7.725
stagewise_DS_DD 6.762  0.080   6.892
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-simData.R:60:9'): pbDS() gets at least 50% right for 10% DE genes ──
  sum(re$id[seq_len(n_de)] %in% gi$id[de]) is not more than round(n_de/2). Difference: -2
  Backtrace:
      ▆
   1. └─base::replicate(...) at test-simData.R:49:5
   2.   └─base::sapply(...)
   3.     └─base::lapply(X = X, FUN = FUN, ...)
   4.       └─muscat (local) FUN(X[[i]], ...)
   5.         └─testthat::expect_gte(...) at test-simData.R:60:9
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 554 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* 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/R/R/bin/R CMD INSTALL muscat
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/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
Warning in check_dep_version(dep_pkg = "TMB") :
  package version mismatch: 
glmmTMB was built with TMB package version 1.9.17
Current TMB package version is 1.9.18
Please re-install glmmTMB from source or restore original ‘TMB’ package (see '?reinstalling' for more information)
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in check_dep_version(dep_pkg = "TMB") :
  package version mismatch: 
glmmTMB was built with TMB package version 1.9.17
Current TMB package version is 1.9.18
Please re-install glmmTMB from source or restore original ‘TMB’ package (see '?reinstalling' for more information)
** testing if installed package can be loaded from final location
Warning in check_dep_version(dep_pkg = "TMB") :
  package version mismatch: 
glmmTMB was built with TMB package version 1.9.17
Current TMB package version is 1.9.18
Please re-install glmmTMB from source or restore original ‘TMB’ package (see '?reinstalling' for more information)
** testing if installed package keeps a record of temporary installation path
* DONE (muscat)

Tests output

muscat.Rcheck/tests/testthat.Rout.fail


R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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)
Warning message:
In check_dep_version(dep_pkg = "TMB") : package version mismatch: 
glmmTMB was built with TMB package version 1.9.17
Current TMB package version is 1.9.18
Please re-install glmmTMB from source or restore original 'TMB' package (see '?reinstalling' for more information)
> 
> test_check("muscat")
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 554 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-simData.R:60:9'): pbDS() gets at least 50% right for 10% DE genes ──
sum(re$id[seq_len(n_de)] %in% gi$id[de]) is not more than round(n_de/2). Difference: -2
Backtrace:
    ▆
 1. └─base::replicate(...) at test-simData.R:49:5
 2.   └─base::sapply(...)
 3.     └─base::lapply(X = X, FUN = FUN, ...)
 4.       └─muscat (local) FUN(X[[i]], ...)
 5.         └─testthat::expect_gte(...) at test-simData.R:60:9

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 554 ]
Error: Test failures
Execution halted

Example timings

muscat.Rcheck/muscat-Ex.timings

nameusersystemelapsed
aggregateData2.3100.1432.459
calcExprFreqs1.2140.0161.233
data000
gBH0.0130.0000.013
mmDS9.4900.2399.974
pbDS1.6380.0361.678
pbFlatten0.9250.0120.938
pbHeatmap 9.403 0.10310.487
pbMDS1.2420.0121.260
prepSCE0.5940.0040.663
prepSim7.2270.1357.725
resDS2.9810.0683.059
simData 9.165 0.10710.098
stagewise_DS_DD6.7620.0806.892