Back to Multiple platform build/check report for BioC 3.17
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This page was generated on 2022-12-06 11:05:26 -0500 (Tue, 06 Dec 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences" 4277
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-11-30 r83393 ucrt) -- "Unsuffered Consequences" 4193
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences" 4236
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 nebbiolo1


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? 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 40/2155HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AlphaBeta 1.13.0  (landing page)
Yadollah Shahryary Dizaji
Snapshot Date: 2022-12-05 14:00:11 -0500 (Mon, 05 Dec 2022)
git_url: https://git.bioconductor.org/packages/AlphaBeta
git_branch: master
git_last_commit: fb92321
git_last_commit_date: 2022-11-01 11:20:18 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  NO, package depends on 'BiocParallel' which is not available

Summary

Package: AlphaBeta
Version: 1.13.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:AlphaBeta.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings AlphaBeta_1.13.0.tar.gz
StartedAt: 2022-12-05 18:43:45 -0500 (Mon, 05 Dec 2022)
EndedAt: 2022-12-05 18:54:13 -0500 (Mon, 05 Dec 2022)
EllapsedTime: 628.7 seconds
RetCode: 0
Status:   OK  
CheckDir: AlphaBeta.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:AlphaBeta.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings AlphaBeta_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/AlphaBeta.Rcheck’
* using R Under development (unstable) (2022-11-30 r83393)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘AlphaBeta/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AlphaBeta’ version ‘1.13.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
BOOTmodel      84.233  0.052  84.286
ABselectUU     79.657  0.088  79.748
ABselectMM     63.855  0.104  63.960
ABneutral      52.776  0.332  53.108
ABselectUUSOMA  5.739  0.004   5.743
ABneutralSOMA   5.137  0.036   5.173
buildPedigree   1.737  0.059   6.163
rc.meth.lvl     0.957  0.000   5.204
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘AlphaBeta.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/AlphaBeta.Rcheck/00check.log’
for details.



Installation output

AlphaBeta.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL AlphaBeta
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-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
ABneutral52.776 0.33253.108
ABneutralSOMA5.1370.0365.173
ABnull0.010.000.01
ABplot0.2440.0190.264
ABselectMM63.855 0.10463.960
ABselectMMSOMA4.2080.0044.213
ABselectUU79.657 0.08879.748
ABselectUUSOMA5.7390.0045.743
BOOTmodel84.233 0.05284.286
FtestRSS0.0120.0000.011
buildPedigree1.7370.0596.163
dMatrix0.6400.0210.660
plotPedigree0.0780.0000.077
rc.meth.lvl0.9570.0005.204