############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CARNIVAL.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CARNIVAL_2.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/CARNIVAL.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘CARNIVAL/DESCRIPTION’ ... OK * this is package ‘CARNIVAL’ version ‘2.2.0’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt .travis.yml 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 ‘CARNIVAL’ 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 ... OK * 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 ... NOTE Namespaces in Imports field not imported from: ‘methods’ ‘rmarkdown’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE convergenceTextToTable: no visible binding for global variable ‘.’ convergenceTextToTable: no visible binding for global variable ‘Gap’ convergenceTextToTable: no visible global function definition for ‘across’ convergenceTextToTable: no visible global function definition for ‘everything’ convergenceTextToTable: no visible binding for global variable ‘Objective’ convergenceTextToTable: no visible binding for global variable ‘Best Bound’ convergenceTextToTable: no visible global function definition for ‘n’ convergenceTextToTable: no visible binding for global variable ‘index’ defaultCbcSolveCarnivalOptions: no visible binding for global variable ‘solverPath’ exportIlpSolutionResultFromXml: no visible global function definition for ‘is’ parseCplexLog: no visible binding for global variable ‘.’ prepareLPMatrixSingle: no visible global function definition for ‘error’ solveWithCbc: no visible global function definition for ‘read.csv2’ solveWithCplex: no visible global function definition for ‘read.delim’ timeStringToTable: no visible binding for global variable ‘.’ timeStringToTable: no visible binding for global variable ‘ticks’ timeStringToTable: no visible binding for global variable ‘Solutions’ timeStringToTable: no visible global function definition for ‘across’ timeStringToTable: no visible global function definition for ‘everything’ writeCplexCommandFileFromJson: no visible global function definition for ‘fromJSON’ Undefined global functions or variables: . Best Bound Gap Objective Solutions across error everything fromJSON index is n read.csv2 read.delim solverPath ticks Consider adding importFrom("methods", "is") importFrom("utils", "read.csv2", "read.delim") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... NOTE prepare_Rd: checkData.Rd:23-25: Dropping empty section \value prepare_Rd: checkOptionsValidity.Rd:14-16: Dropping empty section \value prepare_Rd: defaultCbcSolveCarnivalOptions.Rd:12-14: Dropping empty section \value prepare_Rd: defaultCplexSpecificOptions.Rd:12-14: Dropping empty section \value prepare_Rd: defaultLpSolveCarnivalOptions.Rd:12-14: Dropping empty section \value prepare_Rd: setCarnivalOptions.Rd:14-16: Dropping empty section \value prepare_Rd: solveWithCbc.Rd:12-14: Dropping empty section \value prepare_Rd: suggestedCbcSpecificOptions.Rd:12-14: Dropping empty section \value prepare_Rd: suggestedCplexSpecificOptions.Rd:12-14: Dropping empty section \value * 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 R/sysdata.rda ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * 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: 4 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/CARNIVAL.Rcheck/00check.log’ for details.