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### Running command:
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###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:tLOH.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings tLOH_1.14.0.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/tLOH.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'tLOH/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'tLOH' version '1.14.0'
* 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 whether package 'tLOH' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
hiddenMarkovAnalysis 96.84   5.83  105.27
regionAnalysis       63.21   1.69   64.89
runHMM_3             61.82   1.99   63.79
runHMM_2             60.89   1.86   62.72
prepareHMMdataframes 40.17   1.05   41.98
runHMM_1             38.07   0.73   38.80
tLOHCalcUpdate       34.71   0.75   35.46
splitByChromosome    33.59   0.66   34.25
aggregateCHRPlot      9.23   0.19    9.42
alleleFrequencyPlot   8.34   0.17    8.52
tLOHCalc              5.95   0.11    6.06
* 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 NOTEs
See
  'F:/biocbuild/bbs-3.20-bioc/meat/tLOH.Rcheck/00check.log'
for details.