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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PureCN.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PureCN_2.15.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/PureCN.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘PureCN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PureCN’ version ‘2.15.3’
* checking package namespace information ... OK
* checking package dependencies ... INFO
Package which this enhances but not available for checking: ‘genomicsdb’
* 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 ‘PureCN’ 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                user system elapsed
callAmplificationsInLowPurity 55.877  0.415  56.629
segmentationPSCBS             51.705  0.645  52.787
filterIntervals               26.032  0.339  26.528
runAbsoluteCN                 24.644  0.413  25.283
segmentationHclust            21.736  0.399  22.350
findFocal                     15.619  0.115  15.836
segmentationCBS               11.614  0.117  11.840
annotateTargets                7.120  0.317   7.500
* 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:
  FATAL [2025-07-22 23:15:59] parameters (PureCN 2.15.3). 
  
  [ FAIL 1 | WARN 12 | SKIP 2 | PASS 398 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • gatk binary > 4.1.7.0 required (1): 'test_segmentation.R:25:4'
  • genomicsdb required (1): 'test_setMappingBiasVcf.R:45:5'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_getSexFromCoverage.R:7:1'): (code run outside of `test_that()`) ──
  Error in `renameSeqlevels(chr22, c(chr22 = "chrX"))`: could not find function "renameSeqlevels"
  
  [ FAIL 1 | WARN 12 | SKIP 2 | PASS 398 ]
  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
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/PureCN.Rcheck/00check.log’
for details.