[ Started: 2022-04-26 15:56:05 ] * using log directory ‘/home/omnipath/testing/carnival/bioc-3.15/2022-04-26_1553/CARNIVAL/CARNIVAL.Rcheck’ * using R version 4.2.0 RC (2022-04-21 r82226) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * checking for file ‘CARNIVAL/DESCRIPTION’ ... OK * this is package ‘CARNIVAL’ version ‘2.5.1’ * 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 executable files ... OK * checking for hidden files and directories ... NOTE Found the following hidden files and directories: .github 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE checkSolverPathInSystem: no visible global function definition for ‘searchForSolver’ convergenceTextToTable: no visible binding for global variable ‘.’ convergenceTextToTable: no visible binding for global variable ‘Gap’ convergenceTextToTable: no visible binding for global variable ‘Objective’ convergenceTextToTable: no visible binding for global variable ‘Best Bound’ convergenceTextToTable: no visible binding for global variable ‘index’ createInternalDataRepresentation: no visible global function definition for ‘buildDataVector’ createInternalDataRepresentation: no visible global function definition for ‘createVariables’ exportIlpSolutionFromSolutionMatrix: no visible binding for global variable ‘nodes’ exportIlpSolutionFromSolutionMatrix: no visible binding for global variable ‘nodesValue’ exportIlpSolutionFromSolutionMatrix: no visible binding for global variable ‘solution’ exportIlpSolutionFromSolutionMatrix: no visible binding for global variable ‘Node2Value’ exportIlpSolutionFromSolutionMatrix: no visible binding for global variable ‘edgesUpValue’ exportIlpSolutionFromSolutionMatrix: no visible binding for global variable ‘edgesDownValue’ exportIlpSolutionFromSolutionMatrix: no visible binding for global variable ‘presents’ exportIlpSolutionFromSolutionMatrix: no visible binding for global variable ‘Node1’ exportIlpSolutionFromSolutionMatrix: no visible binding for global variable ‘Sign’ exportIlpSolutionFromSolutionMatrix: no visible binding for global variable ‘Node2’ exportIlpSolutionFromSolutionMatrix: no visible binding for global variable ‘Activity’ exportIlpSolutionFromSolutionMatrix: no visible binding for global variable ‘nodesType’ exportIlpSolutionFromSolutionMatrix: no visible binding for global variable ‘zeroActivity’ exportIlpSolutionFromSolutionMatrix: no visible binding for global variable ‘activityUp’ exportIlpSolutionFromSolutionMatrix: no visible binding for global variable ‘activityDown’ exportIlpSolutionFromSolutionMatrix: no visible binding for global variable ‘UpAct’ exportIlpSolutionFromSolutionMatrix: no visible binding for global variable ‘DownAct’ getSolutionMatrixGurobi: no visible global function definition for ‘read.csv2’ parseCplexLog: no visible binding for global variable ‘.’ prepareForCarnivalRun: no visible global function definition for ‘createLpFormulation’ processSolution: no visible global function definition for ‘exportIlpSolutionResultFromXml’ sendTaskToSolver: no visible global function definition for ‘transformVariables’ 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’ Undefined global functions or variables: . Activity activityDown activityUp Best Bound buildDataVector createLpFormulation createVariables DownAct edgesDownValue edgesUpValue exportIlpSolutionResultFromXml Gap index Node1 Node2 Node2Value nodes nodesType nodesValue Objective presents read.csv2 read.delim searchForSolver Sign solution Solutions ticks transformVariables UpAct zeroActivity Consider adding importFrom("utils", "read.csv2", "read.delim") to your NAMESPACE file. * 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 R/sysdata.rda ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘CARNIVAL.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/omnipath/testing/carnival/bioc-3.15/2022-04-26_1553/CARNIVAL/CARNIVAL.Rcheck/00check.log’ for details. [ Finished: 2022-04-26 15:57:00 ]