############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:GeneGA.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings GeneGA_1.56.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/GeneGA.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 ‘GeneGA/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘GeneGA’ version ‘1.56.0’ * 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 ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘GeneGA’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Non-standard license specification: GPL version 2 Standardizable: TRUE Standardized license specification: GPL-2 * checking top-level files ... OK * 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 ... NOTE Warning: no function found corresponding to methods exports from ‘GeneGA’ for: ‘show’ A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start. Probably some imports need to be declared in the NAMESPACE file. * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... NOTE Packages in Depends field not imported from: ‘hash’ ‘methods’ ‘seqinr’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE GeneCodon: no visible global function definition for ‘s2c’ GeneCodon: no visible global function definition for ‘data’ GeneCodon: no visible binding for global variable ‘wSet’ GeneCodon: no visible global function definition for ‘hash’ GeneCodon: no visible global function definition for ‘translate’ GeneCodon: no visible global function definition for ‘invert’ GeneFoldGA: no visible global function definition for ‘s2c’ GeneFoldGA: no visible global function definition for ‘hash’ GeneFoldGA: no visible global function definition for ‘translate’ GeneFoldGA: no visible global function definition for ‘invert’ GeneFoldGA: no visible global function definition for ‘runif’ GeneFoldGA: no visible global function definition for ‘new’ GeneGA: no visible global function definition for ‘s2c’ GeneGA: no visible global function definition for ‘data’ GeneGA: no visible binding for global variable ‘wSet’ GeneGA: no visible global function definition for ‘hash’ GeneGA: no visible global function definition for ‘translate’ GeneGA: no visible global function definition for ‘invert’ GeneGA: no visible global function definition for ‘runif’ GeneGA: no visible global function definition for ‘new’ GeneGA_internal: no visible global function definition for ‘s2c’ GeneGA_internal: no visible global function definition for ‘data’ GeneGA_internal: no visible binding for global variable ‘wSet’ GeneGA_internal: no visible global function definition for ‘hash’ GeneGA_internal: no visible global function definition for ‘translate’ GeneGA_internal: no visible global function definition for ‘invert’ GeneGA_internal: no visible global function definition for ‘runif’ GeneGA_internal: no visible global function definition for ‘new’ evaluationFoldFunction: no visible global function definition for ‘s2c’ evaluationFunction: no visible global function definition for ‘s2c’ evaluationFunction: no visible global function definition for ‘cai’ evaluationFunction_internal: no visible global function definition for ‘s2c’ evaluationFunction_internal: no visible global function definition for ‘cai’ fold: no visible global function definition for ‘s2c’ plotGeneGA,GeneFoldGA: no visible global function definition for ‘par’ plotGeneGA,GeneGA: no visible global function definition for ‘par’ Undefined global functions or variables: cai data hash invert new par runif s2c translate wSet Consider adding importFrom("graphics", "par") importFrom("methods", "new") importFrom("stats", "runif") importFrom("utils", "data") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed GeneGA 27.684 10.582 60.428 GeneGA-package 8.062 6.364 22.624 plotGeneGA-methods 6.714 6.404 21.734 GeneFoldGA 6.335 5.765 16.416 * 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: 5 NOTEs See ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/GeneGA.Rcheck/00check.log’ for details.