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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:muscat.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings muscat_1.21.0.tar.gz
###
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/muscat.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'muscat/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'muscat' version '1.21.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 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 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
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
simData         12.72   0.30   13.11
prepSim         11.03   0.07   11.10
mmDS             9.25   0.15    9.41
pbHeatmap        7.99   0.70    7.87
stagewise_DS_DD  6.68   0.12    6.80
* 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:
    2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ ├─withr::with_output_sink(...)
    5. │   │ │ └─base::force(code)
    6. │   │ ├─base::withCallingHandlers(...)
    7. │   │ └─base::withVisible(code)
    8. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    9. └─muscat::pbDS(pbs, verbose = FALSE, min_cells = 0, filter = "none")
   10.   ├─BiocParallel::bplapply(...)
   11.   └─BiocParallel::bplapply(...)
   12.     └─BiocParallel:::.bpinit(...)
  
  [ 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
  'E:/biocbuild/bbs-3.21-bioc/meat/muscat.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL muscat
###
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* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'muscat' ...
** 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 Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 1 | WARN 0 | SKIP 0 | PASS 554 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-pbDS.R:101:3'): pbDS() filtering ───────────────────────────────
<bplist_error/bperror/error/condition>
Error: BiocParallel errors
  1 remote errors, element index: 1
  4 unevaluated and other errors
  first remote error:
Error in glmFit.default(sely, design, offset = seloffset, dispersion = 0.05, : Design matrix not of full rank.  The following coefficients not estimable:
 g2

Backtrace:
     ▆
  1. ├─testthat::expect_silent(...) at test-pbDS.R:101:3
  2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
  3. │   ├─testthat (local) .capture(...)
  4. │   │ ├─withr::with_output_sink(...)
  5. │   │ │ └─base::force(code)
  6. │   │ ├─base::withCallingHandlers(...)
  7. │   │ └─base::withVisible(code)
  8. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  9. └─muscat::pbDS(pbs, verbose = FALSE, min_cells = 0, filter = "none")
 10.   ├─BiocParallel::bplapply(...)
 11.   └─BiocParallel::bplapply(...)
 12.     └─BiocParallel:::.bpinit(...)

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