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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:signifinder.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings signifinder_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/signifinder.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘signifinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘signifinder’ version ‘1.8.0’
* 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 ‘signifinder’ 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 ... 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘signifinder-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ADOSign
> ### Title: Adenosine Signaling Signature
> ### Aliases: ADOSign
> 
> ### ** Examples
> 
> data(ovse)
> ADOSign(dataset = ovse)
ADOSign is using 100% of signature genes
! 3 genes with constant values throughout the samples
! Genes with constant values are discarded
Error in `.mapGeneSetsToFeatures()`:
✖ No identifiers in the gene sets could be matched to the identifiers in
  the expression data.
Backtrace:
     ▆
  1. └─signifinder::ADOSign(dataset = ovse)
  2.   ├─base::as.vector(gsva(gsvaPar, verbose = FALSE))
  3.   ├─GSVA::gsva(gsvaPar, verbose = FALSE)
  4.   └─GSVA::gsva(gsvaPar, verbose = FALSE)
  5.     └─GSVA (local) .local(param, ...)
  6.       ├─GSVA::gsvaScores(param = rankspar, verbose = verbose, BPPARAM = BPPARAM)
  7.       └─GSVA::gsvaScores(param = rankspar, verbose = verbose, BPPARAM = BPPARAM)
  8.         └─GSVA (local) .local(param, ...)
  9.           └─GSVA:::.filterAndMapGeneSets(...)
 10.             └─GSVA:::.mapGeneSetsToFeatures(geneSets, rownames(filteredDataMatrix))
 11.               └─cli::cli_abort(c(x = msg))
 12.                 └─rlang::abort(...)
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:
    2.   ├─base::as.vector(gsva(gsvaPar, verbose = FALSE))
    3.   ├─GSVA::gsva(gsvaPar, verbose = FALSE)
    4.   └─GSVA::gsva(gsvaPar, verbose = FALSE)
    5.     └─GSVA (local) .local(param, ...)
    6.       ├─GSVA::gsvaScores(param = rankspar, verbose = verbose, BPPARAM = BPPARAM)
    7.       └─GSVA::gsvaScores(param = rankspar, verbose = verbose, BPPARAM = BPPARAM)
    8.         └─GSVA (local) .local(param, ...)
    9.           └─GSVA:::.filterAndMapGeneSets(...)
   10.             └─GSVA:::.mapGeneSetsToFeatures(geneSets, rownames(filteredDataMatrix))
   11.               └─cli::cli_abort(c(x = msg))
   12.                 └─rlang::abort(...)
  
  [ FAIL 2 | WARN 9 | SKIP 0 | PASS 260 ]
  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: 2 ERRORs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/signifinder.Rcheck/00check.log’
for details.