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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:escape.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings escape_2.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/escape.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 ‘escape/DESCRIPTION’ ... OK
* this is package ‘escape’ version ‘2.6.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘escape’ 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* 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 ‘escape-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: densityEnrichment
> ### Title: Visualize Mean Density Ranking of Genes Across Gene Sets
> ### Aliases: densityEnrichment
> 
> ### ** Examples
> 
> gs <- list(Bcells = c("MS4A1", "CD79B", "CD79A", "IGH1", "IGH2"),
+            Tcells = c("CD3E", "CD3D", "CD3G", "CD7","CD8A"))
>            
> pbmc_small <- SeuratObject::pbmc_small
>                         
> densityEnrichment(pbmc_small, 
+                   gene.set.use = "Tcells",
+                   gene.sets = gs)
Error in .kcdfvals_sparse_to_dense(expr, Gaussk, verbose) : 
  is.logical(Gaussk) is not TRUE
Calls: densityEnrichment
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘spelling.R’
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    is.logical(Gaussk) is not TRUE
  ── Error ('test-densityEnrichment.R:60:3'): group.by selects an alternative metadata column ──
  Error in `.kcdfvals_sparse_to_dense(expr, Gaussk, verbose)`: is.logical(Gaussk) is not TRUE
  Backtrace:
      ▆
   1. └─escape::densityEnrichment(...) at test-densityEnrichment.R:60:3
   2.   ├─base::suppressWarnings(...)
   3.   │ └─base::withCallingHandlers(...)
   4.   └─GSVA (local) compute.cdf(tmp, seq_len(ncol(tmp)), TRUE, FALSE)
   5.     └─GSVA:::.kcdfvals_sparse_to_dense(expr, Gaussk, verbose)
   6.       └─base::stopifnot(is.logical(Gaussk))
  
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 161 ]
  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
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/escape.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL escape
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘escape’ ...
** this is package ‘escape’ version ‘2.6.0’
** 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 (escape)

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.

> if(requireNamespace('spelling', quietly = TRUE))
+   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+                              skip_on_cran = TRUE)
All Done!
> 
> proc.time()
   user  system elapsed 
  0.149   0.037   0.176 

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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(escape)
> 
> test_check("escape")
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 161 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-densityEnrichment.R:15:3'): densityEnrichment() returns a patchwork / ggplot object ──
Error in `.kcdfvals_sparse_to_dense(expr, Gaussk, verbose)`: is.logical(Gaussk) is not TRUE
Backtrace:
    ▆
 1. └─escape::densityEnrichment(...) at test-densityEnrichment.R:15:3
 2.   ├─base::suppressWarnings(...)
 3.   │ └─base::withCallingHandlers(...)
 4.   └─GSVA (local) compute.cdf(tmp, seq_len(ncol(tmp)), TRUE, FALSE)
 5.     └─GSVA:::.kcdfvals_sparse_to_dense(expr, Gaussk, verbose)
 6.       └─base::stopifnot(is.logical(Gaussk))
── Error ('test-densityEnrichment.R:28:3'): all groups appear once in the density layer ──
Error in `.kcdfvals_sparse_to_dense(expr, Gaussk, verbose)`: is.logical(Gaussk) is not TRUE
Backtrace:
    ▆
 1. └─escape::densityEnrichment(pbmc, "Tcells", GS) at test-densityEnrichment.R:28:3
 2.   ├─base::suppressWarnings(...)
 3.   │ └─base::withCallingHandlers(...)
 4.   └─GSVA (local) compute.cdf(tmp, seq_len(ncol(tmp)), TRUE, FALSE)
 5.     └─GSVA:::.kcdfvals_sparse_to_dense(expr, Gaussk, verbose)
 6.       └─base::stopifnot(is.logical(Gaussk))
── Failure ('test-densityEnrichment.R:37:3'): custom palette works ─────────────
Expected `densityEnrichment(...)` to run without any errors.
ℹ Actually got a <simpleError> with text:
  is.logical(Gaussk) is not TRUE
── Error ('test-densityEnrichment.R:60:3'): group.by selects an alternative metadata column ──
Error in `.kcdfvals_sparse_to_dense(expr, Gaussk, verbose)`: is.logical(Gaussk) is not TRUE
Backtrace:
    ▆
 1. └─escape::densityEnrichment(...) at test-densityEnrichment.R:60:3
 2.   ├─base::suppressWarnings(...)
 3.   │ └─base::withCallingHandlers(...)
 4.   └─GSVA (local) compute.cdf(tmp, seq_len(ncol(tmp)), TRUE, FALSE)
 5.     └─GSVA:::.kcdfvals_sparse_to_dense(expr, Gaussk, verbose)
 6.       └─base::stopifnot(is.logical(Gaussk))

[ FAIL 4 | WARN 0 | SKIP 0 | PASS 161 ]
Error: Test failures
Execution halted