############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:gatom.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings gatom_1.9.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/gatom.Rcheck’ * using R Under development (unstable) (2025-10-20 r88955) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.3 LTS * using session charset: UTF-8 * checking for file ‘gatom/DESCRIPTION’ ... OK * this is package ‘gatom’ version ‘1.9.2’ * 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 ‘gatom’ 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 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 ... 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 ... NOTE Unexported object imported by a ':::' call: ‘htmlwidgets:::createWidgetId’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .makeEdgeTable: no visible binding for global variable ‘gene’ .makeEdgeTable: no visible binding for global variable ‘ID’ .makeEdgeTable: no visible binding for global variable ‘pval’ .makeEdgeTable: no visible binding for global variable ‘enzyme’ .makeEdgeTable: no visible binding for global variable ‘reaction’ .makeEdgeTable: no visible binding for global variable ‘origin’ .makeEdgeTable: no visible binding for global variable ‘atom.x’ .makeEdgeTable: no visible binding for global variable ‘atom.y’ .makeVertexTable: no visible binding for global variable ‘ID’ .makeVertexTable: no visible binding for global variable ‘pval’ .makeVertexTable: no visible binding for global variable ‘metabolite’ .makeVertexTable: no visible binding for global variable ‘base_metabolite’ .makeVertexTable: no visible binding for global variable ‘atom’ .makeVertexTable: no visible binding for global variable ‘origin’ addHighlyExpressedEdges: no visible binding for global variable ‘from’ addHighlyExpressedEdges: no visible binding for global variable ‘to’ addHighlyExpressedEdges: no visible binding for global variable ‘signalRank’ collapseAtomsIntoMetabolites: no visible global function definition for ‘setNames’ collapseAtomsIntoMetabolites: no visible binding for global variable ‘metabolite’ collapseAtomsIntoMetabolites: no visible binding for global variable ‘name’ collapseAtomsIntoMetabolites: no visible binding for global variable ‘from’ collapseAtomsIntoMetabolites: no visible binding for global variable ‘to’ convertPvalDT: no visible binding for global variable ‘pval’ findColumn: no visible global function definition for ‘na.omit’ force_alg: no visible global function definition for ‘aggregate’ getDotColor: no visible global function definition for ‘rgb’ getEdgeDotStrings : : no visible global function definition for ‘na.omit’ getEdgeXmlStrings : : no visible global function definition for ‘na.omit’ getMetabolicPathways: no visible global function definition for ‘na.omit’ getMetabolicPathways: no visible binding for global variable ‘PATHNAME’ getMetabolicPathways: no visible global function definition for ‘read.table’ getModulePdfLayout: no visible global function definition for ‘pdf’ getModulePdfLayout: no visible global function definition for ‘dev.off’ getNodeDotStrings : : no visible global function definition for ‘na.omit’ getNodeXmlStrings : : no visible global function definition for ‘na.omit’ makeMetabolicGraph: no visible binding for global variable ‘signalRank’ makeMetabolicGraph: no visible binding for global variable ‘atom.x’ makeMetabolicGraph: no visible binding for global variable ‘atom.y’ makeMetabolicGraph: no visible binding for global variable ‘metabolite.x’ makeMetabolicGraph: no visible binding for global variable ‘metabolite.y’ makeMetabolicGraph: no visible binding for global variable ‘metabolite’ makeOrgGatomAnnotation: no visible binding for global variable ‘species’ makeOrgGatomAnnotation: no visible binding for global variable ‘organism’ makeOrgGatomAnnotation: no visible global function definition for ‘keys’ makeOrgGatomAnnotation: no visible binding for global variable ‘gene’ makeOrgGatomAnnotation: no visible binding for global variable ‘symbol’ makeOrgGatomAnnotation: no visible binding for global variable ‘enzyme’ makeOrgGatomAnnotation: no visible global function definition for ‘tail’ makeOrgGatomAnnotation: no visible global function definition for ‘na.omit’ prepareDEColumn: no visible binding for global variable ‘ID’ prepareDEColumn: no visible binding for global variable ‘pval’ saveModuleToPdf: no visible binding for global variable ‘x’ saveModuleToPdf: no visible binding for global variable ‘y’ saveModuleToPdf: no visible binding for global variable ‘xend’ saveModuleToPdf: no visible binding for global variable ‘yend’ saveModuleToPdf: no visible binding for global variable ‘edge_size’ saveModuleToPdf: no visible binding for global variable ‘edge_color’ saveModuleToPdf: no visible binding for global variable ‘edge_label’ saveModuleToPdf: no visible binding for global variable ‘node_size’ saveModuleToPdf: no visible binding for global variable ‘node_color’ saveModuleToPdf: no visible binding for global variable ‘node_label’ scoreGraph: no visible binding for global variable ‘pval’ scoreGraph: no visible binding for global variable ‘signal’ scoreGraph: no visible global function definition for ‘setNames’ Undefined global functions or variables: ID PATHNAME aggregate atom atom.x atom.y base_metabolite dev.off edge_color edge_label edge_size enzyme from gene keys metabolite metabolite.x metabolite.y na.omit name node_color node_label node_size organism origin pdf pval reaction read.table rgb setNames signal signalRank species symbol tail to x xend y yend Consider adding importFrom("grDevices", "dev.off", "pdf", "rgb") importFrom("stats", "aggregate", "na.omit", "setNames") importFrom("utils", "read.table", "tail") 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 LazyData ... 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 makeOrgGatomAnnotation 26.264 0.592 44.35 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * 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: 2 NOTEs See ‘/home/biocbuild/bbs-3.23-bioc/meat/gatom.Rcheck/00check.log’ for details.