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CHECK report for AlphaBeta on merida1

This page was generated on 2021-05-06 12:34:17 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the AlphaBeta package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 45/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AlphaBeta 1.4.0  (landing page)
Yadollah Shahryary Dizaji
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/AlphaBeta
Branch: RELEASE_3_12
Last Commit: d67f156
Last Changed Date: 2020-10-27 11:48:09 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: AlphaBeta
Version: 1.4.0
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_1.4.0.tar.gz
StartedAt: 2021-05-05 23:07:59 -0400 (Wed, 05 May 2021)
EndedAt: 2021-05-05 23:18:08 -0400 (Wed, 05 May 2021)
EllapsedTime: 608.8 seconds
RetCode: 0
Status:   OK  
CheckDir: AlphaBeta.Rcheck
Warnings: 0

Command output

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### Running 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_1.4.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/AlphaBeta.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.4.0’
* 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
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 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      143.286  0.361 143.859
ABselectUU     127.989  0.420 128.629
ABselectMM     113.383  0.275 113.796
ABneutral       91.306  0.323  91.757
ABneutralSOMA    8.358  0.032   8.401
ABselectUUSOMA   7.991  0.036   8.043
ABselectMMSOMA   6.514  0.036   6.559
buildPedigree    0.690  0.083   5.858
rc.meth.lvl      0.542  0.019   5.827
* 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-3.12-bioc/meat/AlphaBeta.Rcheck/00check.log’
for details.



Installation output

AlphaBeta.Rcheck/00install.out

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###
### Running command:
###
###   /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)

Tests output


Example timings

AlphaBeta.Rcheck/AlphaBeta-Ex.timings

nameusersystemelapsed
ABneutral91.306 0.32391.757
ABneutralSOMA8.3580.0328.401
ABnull0.0150.0010.018
ABplot0.2880.0060.296
ABselectMM113.383 0.275113.796
ABselectMMSOMA6.5140.0366.559
ABselectUU127.989 0.420128.629
ABselectUUSOMA7.9910.0368.043
BOOTmodel143.286 0.361143.859
FtestRSS0.0170.0010.018
buildPedigree0.6900.0835.858
dMatrix0.2160.0660.292
plotPedigree0.0980.0030.102
rc.meth.lvl0.5420.0195.827