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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_1.24.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/muscat.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 ‘1.24.0’
* 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 ... ERROR
Running examples in ‘muscat-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mmDS
> ### Title: DS analysis using mixed-models (MM)
> ### Aliases: mmDS .mm_dream .mm_dream2 .mm_vst .mm_glmm
> 
> ### ** Examples
> 
> # subset "B cells" cluster
> data(example_sce)
> b_cells <- example_sce$cluster_id == "B cells"
> sub <- example_sce[, b_cells]
> sub$cluster_id <- droplevels(sub$cluster_id)
> 
> # downsample to 100 genes
> gs <- sample(nrow(sub), 100)
> sub <- sub[gs, ]
> 
> # run DS analysis using cell-level mixed-model
> res <- mmDS(sub, method = "dream", verbose = FALSE)
Error in dream(v, as.formula(formula), cd, contrast, ddf, BPPARAM = BPPARAM,  : 
  All models failed.  The first model fails with:
 Error in as_lmerModLmerTest2(x): Unable to extract deviance function from model fit
Calls: mmDS -> lapply -> FUN -> do.call -> <Anonymous>
Execution halted
* 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:
  ── Error ('test-mmDS.R:70:9'): mmDS-utils; .mm_dream2 ──────────────────────────
  Error in `dream(v, formula, cd, BPPARAM = BPPARAM, ddf = ddf, suppressWarnings = !verbose, quiet = !verbose)`: All models failed.  The first model fails with:
   Error in as_lmerModLmerTest2(x): Unable to extract deviance function from model fit
  
  Backtrace:
      ▆
   1. ├─base::suppressWarnings(get(fun)(x[gs, cs], verbose = FALSE)) at test-mmDS.R:70:9
   2. │ └─base::withCallingHandlers(...)
   3. └─get(fun)(x[gs, cs], verbose = FALSE)
   4.   └─variancePartition::dream(...)
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 545 ]
  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: 2 ERRORs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/muscat.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL muscat
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘muscat’ ...
** this is package ‘muscat’ version ‘1.24.0’
** 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)

R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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")
Saving _problems/test-mmDS-44.R
Saving _problems/test-mmDS-71.R
Saving _problems/test-mmDS-71.R
[ FAIL 3 | WARN 0 | SKIP 0 | PASS 545 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-mmDS.R:43:5'): mmDS() - filtering ──────────────────────────────
Error in `dream(v, formula, cd, BPPARAM = BPPARAM, ddf = ddf, suppressWarnings = !verbose, quiet = !verbose)`: All models failed.  The first model fails with:
 Error in as_lmerModLmerTest2(x): Unable to extract deviance function from model fit

Backtrace:
    ▆
 1. ├─base::suppressWarnings(mmDS(x[gs, cs], verbose = FALSE)) at test-mmDS.R:43:5
 2. │ └─base::withCallingHandlers(...)
 3. └─muscat::mmDS(x[gs, cs], verbose = FALSE)
 4.   └─base::lapply(...)
 5.     └─muscat (local) FUN(X[[i]], ...)
 6.       ├─base::do.call(fun, args)
 7.       └─muscat (local) `<fn>`(...)
 8.         └─variancePartition::dream(...)
── Error ('test-mmDS.R:70:9'): mmDS-utils; .mm_dream ───────────────────────────
Error in `dream(v, as.formula(formula), cd, contrast, ddf, BPPARAM = BPPARAM, suppressWarnings = !verbose, quiet = !verbose)`: All models failed.  The first model fails with:
 Error in as_lmerModLmerTest2(x): Unable to extract deviance function from model fit

Backtrace:
    ▆
 1. ├─base::suppressWarnings(get(fun)(x[gs, cs], verbose = FALSE)) at test-mmDS.R:70:9
 2. │ └─base::withCallingHandlers(...)
 3. └─get(fun)(x[gs, cs], verbose = FALSE)
 4.   ├─base::suppressWarnings(fit <- eval(.dream))
 5.   │ └─base::withCallingHandlers(...)
 6.   ├─base::eval(.dream)
 7.   │ └─base::eval(.dream)
 8.   └─variancePartition::dream(...)
── Error ('test-mmDS.R:70:9'): mmDS-utils; .mm_dream2 ──────────────────────────
Error in `dream(v, formula, cd, BPPARAM = BPPARAM, ddf = ddf, suppressWarnings = !verbose, quiet = !verbose)`: All models failed.  The first model fails with:
 Error in as_lmerModLmerTest2(x): Unable to extract deviance function from model fit

Backtrace:
    ▆
 1. ├─base::suppressWarnings(get(fun)(x[gs, cs], verbose = FALSE)) at test-mmDS.R:70:9
 2. │ └─base::withCallingHandlers(...)
 3. └─get(fun)(x[gs, cs], verbose = FALSE)
 4.   └─variancePartition::dream(...)

[ FAIL 3 | WARN 0 | SKIP 0 | PASS 545 ]
Error:
! Test failures.
Execution halted