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CHECK report for AlphaBeta on merida1

This page was generated on 2020-04-15 12:49:49 -0400 (Wed, 15 Apr 2020).

Package 44/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AlphaBeta 1.0.0
Yadollah Shahryary Dizaji
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/AlphaBeta
Branch: RELEASE_3_10
Last Commit: ce752ca
Last Changed Date: 2019-10-29 13:11:52 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: AlphaBeta
Version: 1.0.0
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_1.0.0.tar.gz
StartedAt: 2020-04-15 00:19:10 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 00:29:54 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 643.6 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_1.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/AlphaBeta.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.0.0’
* 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 or elapsed time > 5s
                  user system elapsed
BOOTmodel      164.045  0.464 165.884
ABselectUU     137.687  0.494 139.500
ABselectMM     114.580  0.340 116.022
ABneutral       99.419  0.258 100.397
ABneutralSOMA   12.730  0.045  12.945
ABselectUUSOMA   9.123  0.030   9.232
ABselectMMSOMA   7.465  0.046   7.587
* 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-3.10-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/3.6/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
ABneutral 99.419 0.258100.397
ABneutralSOMA12.730 0.04512.945
ABnull0.0200.0010.021
ABselectMM114.580 0.340116.022
ABselectMMSOMA7.4650.0467.587
ABselectUU137.687 0.494139.500
ABselectUUSOMA9.1230.0309.232
BOOTmodel164.045 0.464165.884
FtestRSS0.0150.0010.015
convertDMATRIX0.1640.0010.166
dMatrix1.0511.8230.373
makePHYLO0.1200.1770.037
rc.meth.lvl0.5660.4884.451