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### Running command:
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###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:tLOH.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings tLOH_1.6.0.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/tLOH.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'tLOH/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'tLOH' version '1.6.0'
* 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 ... 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 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 73.02   3.77   76.81
regionAnalysis       61.84   0.52   65.66
runHMM_3             49.72   0.25   49.97
runHMM_2             47.66   0.27   47.95
runHMM_1             37.95   0.09   38.48
prepareHMMdataframes 30.10   0.15   30.25
splitByChromosome    28.58   0.04   28.61
tLOHCalcUpdate       28.10   0.10   28.20
alleleFrequencyPlot   7.00   0.20    7.20
aggregateCHRPlot      6.53   0.05    6.56
* 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: OK

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### Running command:
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###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL tLOH
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* installing to library 'F:/biocbuild/bbs-3.16-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)