Package: AlphaBeta

Version: 1.1.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:AlphaBeta.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings AlphaBeta_1.1.0.tar.gz

StartedAt: 2020-01-16 01:37:46 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 01:51:26 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 819.6 seconds

RetCode: 0

Status:  OK

CheckDir: AlphaBeta.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:AlphaBeta.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings AlphaBeta_1.1.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/AlphaBeta.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AlphaBeta/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AlphaBeta’ version ‘1.1.0’
* 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 ‘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
BOOTmodel: multiple local function definitions for ‘divergence’ with
  different formal arguments
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
BOOTmodel      207.406  0.451 207.874
ABselectUU     179.748  0.501 180.256
ABselectMM     147.326  0.425 147.856
ABneutral      128.328  0.528 128.873
ABneutralSOMA   15.596  0.073  15.670
ABselectUUSOMA  11.015  0.032  11.048
ABselectMMSOMA  10.258  0.051  10.310
rc.meth.lvl      0.651  0.178   7.172
* 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
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/AlphaBeta.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL AlphaBeta
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘AlphaBeta’ ...
** using staged installation
** R
** 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 (AlphaBeta)

name	user	system	elapsed
ABneutral	128.328	0.528	128.873
ABneutralSOMA	15.596	0.073	15.670
ABnull	0.011	0.001	0.013
ABselectMM	147.326	0.425	147.856
ABselectMMSOMA	10.258	0.051	10.310
ABselectUU	179.748	0.501	180.256
ABselectUUSOMA	11.015	0.032	11.048
BOOTmodel	207.406	0.451	207.874
FtestRSS	0.012	0.001	0.015
convertDMATRIX	0.220	0.002	0.225
dMatrix	2.065	1.020	0.550
makePHYLO	0.081	0.053	0.033
rc.meth.lvl	0.651	0.178	7.172