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### Running command:
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###   E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:tLOH.install-out.txt --library=E:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings tLOH_1.12.0.tar.gz
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* using log directory 'E:/biocbuild/bbs-3.19-bioc/meat/tLOH.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* 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 '1.12.0'
* 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 90.83   5.45   98.49
regionAnalysis       62.01   1.39   63.42
runHMM_2             58.84   1.23   60.09
runHMM_3             56.75   1.45   58.20
runHMM_1             38.03   0.93   38.94
tLOHCalcUpdate       35.33   0.66   35.98
splitByChromosome    34.72   0.54   35.25
prepareHMMdataframes 33.35   0.65   34.02
alleleFrequencyPlot   8.39   0.11    8.50
aggregateCHRPlot      7.87   0.28    8.16
tLOHCalc              6.30   0.21    6.52
* 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
  'E:/biocbuild/bbs-3.19-bioc/meat/tLOH.Rcheck/00check.log'
for details.

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### Running command:
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###   E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL tLOH
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* installing to library 'E:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'tLOH' ...
** using staged installation
** R
** data
** 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 (tLOH)