##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:chipenrich.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings chipenrich_2.31.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/chipenrich.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘chipenrich/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘chipenrich’ version ‘2.31.0’
* 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 ‘chipenrich’ 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 ... NOTE
checkRd: (-1) broadenrich.Rd:134: Escaped LaTeX specials: \&
checkRd: (-1) chipenrich.Rd:148: Escaped LaTeX specials: \&
checkRd: (-1) hybridenrich.Rd:111: Escaped LaTeX specials: \&
checkRd: (-1) polyenrich.Rd:148: Escaped LaTeX specials: \&
checkRd: (-1) proxReg.Rd:117: Escaped LaTeX specials: \&
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
broadenrich 7.039  0.336   7.465
polyenrich  5.499  0.362   5.931
* 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 in ``.rowNamesDF<-`(x, value = value)`: invalid 'row.names' length
  Backtrace:
      ▆
   1. ├─base::suppressWarnings(...) at test_5_chipenrich.R:84:9
   2. │ └─base::withCallingHandlers(...)
   3. └─chipenrich::chipenrich(...)
   4.   └─chipenrich:::post_process_enrichments(enrich)
   5.     └─base::`rownames<-`(`*tmp*`, value = c(1:nrow(enrich)))
   6.       ├─base::`row.names<-`(`*tmp*`, value = value)
   7.       └─base::`row.names<-.data.frame`(`*tmp*`, value = value)
   8.         └─base::`.rowNamesDF<-`(x, value = value)
  
  [ FAIL 1 | WARN 0 | SKIP 3 | PASS 169 ]
  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, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/chipenrich.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL chipenrich
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘chipenrich’ ...
** this is package ‘chipenrich’ version ‘2.31.0’
** using staged installation
** R
** 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 (chipenrich)

R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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(chipenrich)





> 
> test_check("chipenrich")
[ FAIL 1 | WARN 0 | SKIP 3 | PASS 169 ]

══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• empty test (3): 'test_5_chipenrich.R:199:1', 'test_5_chipenrich.R:232:1',
  'test_5_chipenrich.R:236:1'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_5_chipenrich.R:84:2'): Test old chipapprox method ──────────────
Error in ``.rowNamesDF<-`(x, value = value)`: invalid 'row.names' length
Backtrace:
    ▆
 1. ├─base::suppressWarnings(...) at test_5_chipenrich.R:84:9
 2. │ └─base::withCallingHandlers(...)
 3. └─chipenrich::chipenrich(...)
 4.   └─chipenrich:::post_process_enrichments(enrich)
 5.     └─base::`rownames<-`(`*tmp*`, value = c(1:nrow(enrich)))
 6.       ├─base::`row.names<-`(`*tmp*`, value = value)
 7.       └─base::`row.names<-.data.frame`(`*tmp*`, value = value)
 8.         └─base::`.rowNamesDF<-`(x, value = value)

[ FAIL 1 | WARN 0 | SKIP 3 | PASS 169 ]
Error: Test failures
Execution halted