############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:AlphaBeta.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings AlphaBeta_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/AlphaBeta.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘AlphaBeta/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘AlphaBeta’ version ‘1.16.0’ * 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 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 149.296 7.679 165.118 ABselectUU 140.054 5.210 150.667 ABselectMM 111.148 0.124 111.493 ABneutral 92.520 1.886 96.861 ABselectUUSOMA 9.604 0.051 9.675 ABneutralSOMA 8.550 0.047 8.619 ABselectMMSOMA 6.500 0.000 6.515 buildPedigree 1.173 0.027 5.823 rc.meth.lvl 0.877 0.017 7.038 * 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-3.18-bioc/meat/AlphaBeta.Rcheck/00check.log’ for details.