############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:gatom.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings gatom_1.5.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/gatom.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * 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 ‘gatom/DESCRIPTION’ ... OK * this is package ‘gatom’ version ‘1.5.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 global function definition for ‘pdf’ saveModuleToPdf: no visible global function definition for ‘dev.off’ 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 enzyme from gene keys metabolite metabolite.x metabolite.y na.omit name organism origin pdf pval reaction read.table rgb setNames signal signalRank species symbol tail to 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 21.403 0.741 35.528 * 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-3.21-bioc/meat/gatom.Rcheck/00check.log’ for details.