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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:monaLisa.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings monaLisa_1.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/monaLisa.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘monaLisa/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘monaLisa’ 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 ‘monaLisa’ 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 R 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* 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:
  `res2` not identical to list(bestScore = 0.631460077278843, bestOffset = 0L, bestDirection = "revcomp").
  Objects equal but not identical
  ── Failure ('test_pfm_comparison.R:25:5'): .compareMotifPair works as expected ──
  `res3` not identical to list(bestScore = 0.631460077278843, bestOffset = 7L, bestDirection = "forward").
  Objects equal but not identical
  ── Failure ('test_pfm_comparison.R:83:5'): motifSimilarity works as expected ───
  res1[c(4, 7, 8)] not identical to c(1, 0.631460077278843, 0.631460077278843).
  Objects equal but not identical
  ── Failure ('test_pfm_comparison.R:88:5'): motifSimilarity works as expected ───
  `res1` not identical to `res5`.
  Objects equal but not identical
  
  [ FAIL 4 | WARN 1 | SKIP 1 | PASS 533 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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
See
  ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/monaLisa.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL monaLisa
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘monaLisa’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (monaLisa)

R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)

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(monaLisa)

> 
> test_check("monaLisa")
[ FAIL 4 | WARN 1 | SKIP 1 | PASS 533 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test_Homer.R:116:1'

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_pfm_comparison.R:24:5'): .compareMotifPair works as expected ──
`res2` not identical to list(bestScore = 0.631460077278843, bestOffset = 0L, bestDirection = "revcomp").
Objects equal but not identical
── Failure ('test_pfm_comparison.R:25:5'): .compareMotifPair works as expected ──
`res3` not identical to list(bestScore = 0.631460077278843, bestOffset = 7L, bestDirection = "forward").
Objects equal but not identical
── Failure ('test_pfm_comparison.R:83:5'): motifSimilarity works as expected ───
res1[c(4, 7, 8)] not identical to c(1, 0.631460077278843, 0.631460077278843).
Objects equal but not identical
── Failure ('test_pfm_comparison.R:88:5'): motifSimilarity works as expected ───
`res1` not identical to `res5`.
Objects equal but not identical

[ FAIL 4 | WARN 1 | SKIP 1 | PASS 533 ]
Error: Test failures
Execution halted