############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BioNetStat.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BioNetStat_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/BioNetStat.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘BioNetStat/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘BioNetStat’ version ‘1.14.0’ * 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 ‘BioNetStat’ can be installed ... OK * checking installed package size ... NOTE installed size is 5.4Mb sub-directories of 1Mb or more: extdata 1.9Mb shiny 1.9Mb * 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 ... NOTE Found the following CITATION file in a non-standard place: CITATION Most likely ‘inst/CITATION’ should be used instead. * 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: ‘BiocParallel’ ‘RColorBrewer’ ‘RJSONIO’ ‘ggplot2’ ‘knitr’ ‘markdown’ ‘pheatmap’ ‘plyr’ ‘rmarkdown’ ‘stats’ ‘utils’ ‘whisker’ ‘yaml’ All declared Imports should be used. Packages in Depends field not imported from: ‘DT’ ‘shiny’ ‘shinyBS’ 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 adjacencyMatrix : : no visible global function definition for ‘cor’ adjacencyMatrix : : no visible global function definition for ‘p.adjust’ betweennessCentralityTest: no visible global function definition for ‘bplapply’ betweennessCentralityVertexTest: no visible global function definition for ‘bplapply’ closenessCentralityTest: no visible global function definition for ‘bplapply’ closenessCentralityVertexTest: no visible global function definition for ‘bplapply’ clusteringCoefficientTest : : no visible global function definition for ‘dist’ clusteringCoefficientTest : : : no visible global function definition for ‘dist’ clusteringCoefficientTest: no visible global function definition for ‘bplapply’ clusteringCoefficientVertexTest: no visible global function definition for ‘bplapply’ degreeCentralityTest: no visible global function definition for ‘bplapply’ degreeCentralityVertexTest: no visible global function definition for ‘bplapply’ degreeDistributionTest: no visible global function definition for ‘bplapply’ diffNetAnalysis: no visible binding for global variable ‘expr’ diffNetAnalysis: no visible global function definition for ‘p.adjust’ doLabels: no visible global function definition for ‘read.csv’ edgeBetweennessEdgeTest: no visible global function definition for ‘bplapply’ edgeBetweennessTest: no visible global function definition for ‘bplapply’ edgesResInt : : no visible global function definition for ‘dist’ eigenvectorCentralityTest: no visible global function definition for ‘bplapply’ eigenvectorCentralityVertexTest: no visible global function definition for ‘bplapply’ gaussianDensity: no visible global function definition for ‘bw.nrd0’ gaussianDensity: no visible global function definition for ‘density’ pathPlot: no visible binding for global variable ‘median’ readVarFile: no visible global function definition for ‘read.table’ resInt : : no visible global function definition for ‘dist’ retEdgesTable: no visible global function definition for ‘p.adjust’ retTable: no visible global function definition for ‘p.adjust’ spectralDistributionTest: no visible global function definition for ‘bplapply’ spectralEntropyTest: no visible global function definition for ‘bplapply’ var.list: no visible global function definition for ‘aggregate’ Undefined global functions or variables: aggregate bplapply bw.nrd0 cor density dist expr median p.adjust read.csv read.table Consider adding importFrom("stats", "aggregate", "bw.nrd0", "cor", "density", "dist", "median", "p.adjust") importFrom("utils", "read.csv", "read.table") 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 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 networkTest 14.921 0.232 15.296 centralityPathPlot 10.335 0.690 14.766 pathPlot 8.251 0.496 8.759 * 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-3.14-bioc/meat/BioNetStat.Rcheck/00check.log’ for details.