##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:tLOH.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings tLOH_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/tLOH.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘tLOH/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘tLOH’ version ‘1.7.0’
* 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 for sufficient/correct file permissions ... 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 ... 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 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 99.809  2.003 101.817
regionAnalysis       72.477  0.300  72.779
runHMM_2             67.479  0.292  67.773
runHMM_3             66.030  0.312  78.995
runHMM_1             38.618  0.072  38.690
prepareHMMdataframes 36.132  0.168  36.300
tLOHCalcUpdate       34.659  0.092  34.752
splitByChromosome    34.541  0.184  34.727
aggregateCHRPlot      9.937  0.160  10.096
alleleFrequencyPlot   8.519  0.096   8.615
tLOHCalc              6.544  0.020   6.563
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘tLOH_vignette.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/tLOH.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL tLOH
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-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)