Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-17 13:07:16 -0500 (Mon, 17 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for AlphaBeta on machv2


To the developers/maintainers of the AlphaBeta package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/AlphaBeta.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 43/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AlphaBeta 1.8.0  (landing page)
Yadollah Shahryary Dizaji
Snapshot Date: 2022-01-16 01:55:05 -0500 (Sun, 16 Jan 2022)
git_url: https://git.bioconductor.org/packages/AlphaBeta
git_branch: RELEASE_3_14
git_last_commit: da93a7f
git_last_commit_date: 2021-10-26 12:53:27 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: AlphaBeta
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:AlphaBeta.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings AlphaBeta_1.8.0.tar.gz
StartedAt: 2022-01-16 10:02:12 -0500 (Sun, 16 Jan 2022)
EndedAt: 2022-01-16 10:15:31 -0500 (Sun, 16 Jan 2022)
EllapsedTime: 798.7 seconds
RetCode: 0
Status:   OK  
CheckDir: AlphaBeta.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:AlphaBeta.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings AlphaBeta_1.8.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/AlphaBeta.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.8.0’
* 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      187.518  0.391 188.121
ABselectUU     180.152  0.320 180.634
ABselectMM     146.373  0.278 146.786
ABneutral      119.214  0.301 119.628
ABselectUUSOMA  12.657  0.039  12.712
ABneutralSOMA   10.828  0.028  10.864
ABselectMMSOMA   8.184  0.018   8.209
buildPedigree    0.878  0.113   7.141
rc.meth.lvl      0.584  0.022   6.623
* 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-3.14-bioc/meat/AlphaBeta.Rcheck/00check.log’
for details.



Installation output

AlphaBeta.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL AlphaBeta
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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
ABneutral119.214 0.301119.628
ABneutralSOMA10.828 0.02810.864
ABnull0.0090.0010.010
ABplot0.3790.0080.389
ABselectMM146.373 0.278146.786
ABselectMMSOMA8.1840.0188.209
ABselectUU180.152 0.320180.634
ABselectUUSOMA12.657 0.03912.712
BOOTmodel187.518 0.391188.121
FtestRSS0.0190.0020.022
buildPedigree0.8780.1137.141
dMatrix0.2840.0880.381
plotPedigree0.0970.0030.099
rc.meth.lvl0.5840.0226.623