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### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:muscat.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings muscat_1.22.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/muscat.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘1.22.0’
* 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
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 logFC p_adj.loc
* 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      7.733  0.237   7.969
simData   7.270  0.045   7.317
pbHeatmap 6.306  0.084   6.372
prepSim   5.655  0.176   5.831
* 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: -1
  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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/muscat.Rcheck/00check.log’
for details.

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###
### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL muscat
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘muscat’ ...
** this is package ‘muscat’ version ‘1.22.0’
** 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)

R version 4.5.1 (2025-06-13) -- "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)
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: -1
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