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This page was generated on 2025-01-27 12:04 -0500 (Mon, 27 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4746
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4494
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4517
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4469
taishanLinux (openEuler 24.03 LTS)aarch644.4.2 (2024-10-31) -- "Pile of Leaves" 4395
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

Package 56/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AlphaBeta 1.20.0  (landing page)
Yadollah Shahryary Dizaji
Snapshot Date: 2025-01-23 13:00 -0500 (Thu, 23 Jan 2025)
git_url: https://git.bioconductor.org/packages/AlphaBeta
git_branch: RELEASE_3_20
git_last_commit: e7d6512
git_last_commit_date: 2024-10-29 10:39:08 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for AlphaBeta on nebbiolo2

To the developers/maintainers of the AlphaBeta package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: AlphaBeta
Version: 1.20.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:AlphaBeta.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings AlphaBeta_1.20.0.tar.gz
StartedAt: 2025-01-23 19:50:41 -0500 (Thu, 23 Jan 2025)
EndedAt: 2025-01-23 20:00:19 -0500 (Thu, 23 Jan 2025)
EllapsedTime: 577.8 seconds
RetCode: 0
Status:   OK  
CheckDir: AlphaBeta.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:AlphaBeta.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings AlphaBeta_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/AlphaBeta.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘AlphaBeta/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AlphaBeta’ version ‘1.20.0’
* 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 code 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 loading without being on the library search path ... 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      83.965  0.023  83.993
ABselectUU     81.016  0.063  81.085
ABselectMM     65.187  0.145  65.334
ABneutral      52.634  0.329  52.968
ABselectUUSOMA  5.567  0.006   5.573
ABneutralSOMA   5.190  0.018   5.209
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/AlphaBeta.Rcheck/00check.log’
for details.


Installation output

AlphaBeta.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL AlphaBeta
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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
ABneutral52.634 0.32952.968
ABneutralSOMA5.1900.0185.209
ABnull0.0060.0010.007
ABplot0.2500.0050.267
ABselectMM65.187 0.14565.334
ABselectMMSOMA3.8910.0093.901
ABselectUU81.016 0.06381.085
ABselectUUSOMA5.5670.0065.573
BOOTmodel83.965 0.02383.993
FtestRSS0.010.000.01
buildPedigree0.8090.0433.930
dMatrix0.1020.0200.121
plotPedigree0.0620.0000.062
rc.meth.lvl0.6160.0363.983