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### Running command:
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###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:AlphaBeta.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings AlphaBeta_1.9.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/AlphaBeta.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'AlphaBeta/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'AlphaBeta' version '1.9.0'
* 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 'AlphaBeta' 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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... NOTE
ABplot: no visible binding for global variable 'delta.t'
ABplot: no visible binding for global variable 'div.obs'
BOOTmodel : LSE_intercept: no visible binding for global variable 'sel'
BOOTmodel: no visible binding for global variable 'sel'
BOOTmodel: multiple local function definitions for 'divergence' with
  different formal arguments
plotPedigree: no visible binding for global variable 'meth'
plotPedigree: no visible binding for global variable 'V1'
plotPedigree: no visible binding for global variable 'V2'
Undefined global functions or variables:
  V1 V2 delta.t div.obs meth sel
* 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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
ABselectUU     81.65   0.01   81.68
BOOTmodel      76.28   0.00   76.29
ABselectMM     64.20   0.00   64.20
ABneutral      50.62   0.02   50.65
ABselectUUSOMA  5.24   0.02    5.25
buildPedigree   1.13   0.03    5.20
* 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: 2 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/AlphaBeta.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL AlphaBeta
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'AlphaBeta' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'AlphaBeta'
    finding HTML links ... done
    ABneutral                               html  
    ABneutralSOMA                           html  
    ABnull                                  html  
    ABplot                                  html  
    ABselectMM                              html  
    ABselectMMSOMA                          html  
    ABselectUU                              html  
    ABselectUUSOMA                          html  
    BOOTmodel                               html  
    FtestRSS                                html  
    buildPedigree                           html  
    dMatrix                                 html  
    plotPedigree                            html  
    rc.meth.lvl                             html  
** 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 (AlphaBeta)
Making 'packages.html' ... done