Back to Multiple platform build/check report for BioC 3.12
[A]BCDEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for AlphaBeta on malbec1

This page was generated on 2020-08-06 11:46:07 -0400 (Thu, 06 Aug 2020).

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 43/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AlphaBeta 1.3.3
Yadollah Shahryary Dizaji
Snapshot Date: 2020-08-05 14:50:59 -0400 (Wed, 05 Aug 2020)
URL: https://git.bioconductor.org/packages/AlphaBeta
Branch: master
Last Commit: 3497a14
Last Changed Date: 2020-06-06 09:46:58 -0400 (Sat, 06 Jun 2020)
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 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: AlphaBeta
Version: 1.3.3
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:AlphaBeta.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings AlphaBeta_1.3.3.tar.gz
StartedAt: 2020-08-06 04:49:32 -0400 (Thu, 06 Aug 2020)
EndedAt: 2020-08-06 04:58:50 -0400 (Thu, 06 Aug 2020)
EllapsedTime: 558.0 seconds
RetCode: 0
Status:  OK 
CheckDir: AlphaBeta.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:AlphaBeta.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings AlphaBeta_1.3.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/AlphaBeta.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-pc-linux-gnu (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 ‘1.3.3’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
ABselectUU     136.140  0.064 136.394
BOOTmodel      128.828  0.268 129.458
ABselectMM      95.368  0.008  95.491
ABneutral       81.128  0.012  81.772
ABselectUUSOMA   9.240  0.032   9.285
ABneutralSOMA    8.508  0.004   8.630
buildPedigree    0.864  0.360   6.234
rc.meth.lvl      0.532  0.128   5.273
* 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
  ‘/home/biocbuild/bbs-3.12-bioc/meat/AlphaBeta.Rcheck/00check.log’
for details.



Installation output

AlphaBeta.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL AlphaBeta
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/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
ABneutral81.128 0.01281.772
ABneutralSOMA8.5080.0048.630
ABnull0.0200.0000.019
ABplot0.3560.0040.398
ABselectMM95.368 0.00895.491
ABselectMMSOMA4.6120.0044.620
ABselectUU136.140 0.064136.394
ABselectUUSOMA9.2400.0329.285
BOOTmodel128.828 0.268129.458
FtestRSS0.0120.0000.038
buildPedigree0.8640.3606.234
dMatrix0.1720.2600.494
plotPedigree0.1240.0000.123
rc.meth.lvl0.5320.1285.273