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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biscuiteer.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biscuiteer_1.17.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/biscuiteer.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biscuiteer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘biscuiteer’ version ‘1.17.3’
* 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 ‘biscuiteer’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘BiocParallel::bpstart’ by ‘QDNAseq::bpstart’ when loading ‘biscuiteer’
See ‘/Users/biocbuild/bbs-3.19-bioc/meat/biscuiteer.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data      1.1Mb
    extdata   3.4Mb
* 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 ... NOTE
Problems with news in ‘NEWS.md’:
No news entries found.
* 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘QDNAseq:::expectedVariance’
  See the note in ?`:::` about the use of this operator.
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
RRBSeq              15.527  0.709  20.139
WGBSage             11.821  0.587  14.573
byExtremality       10.889  0.482  13.223
filterLoci          10.660  0.488  12.925
unionize             9.646  0.567  12.059
WGBSeq               8.961  0.204  10.458
binCoverage          7.898  0.323   9.601
readEpibed           6.911  0.102   9.550
getLogitFracMeth     5.031  0.224   5.436
byChromArm           4.332  0.216   5.255
simplifySampleNames  3.883  0.242   5.009
readBiscuit          3.638  0.198   5.073
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/biscuiteer.Rcheck/00check.log’
for details.