############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rBiopaxParser.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rBiopaxParser_2.46.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/rBiopaxParser.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘rBiopaxParser/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘rBiopaxParser’ version ‘2.46.0’ * 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 ‘rBiopaxParser’ 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 dependencies in R code ... NOTE 'library' or 'require' calls in package code: ‘RBGL’ ‘RCurl’ ‘Rgraphviz’ ‘graph’ ‘igraph’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE addBiopaxInstance: no visible binding for global variable ‘property’ addBiopaxInstances: no visible binding for global variable ‘id’ addBiopaxInstances: no visible binding for global variable ‘property’ addPropertiesToBiopaxInstance: no visible binding for global variable ‘property’ colorGraphNodes: no visible global function definition for ‘hcl’ createBiopax: no visible binding for global variable ‘id’ createBiopax: no visible binding for global variable ‘property’ getReferencedIDs: no visible binding for global variable ‘property_attr’ getReferencedIDs: no visible binding for global variable ‘property’ getReferencingIDs: no visible binding for global variable ‘property_attr’ getReferencingIDs: no visible binding for global variable ‘property’ internal_XMLInstance2DF: no visible binding for global variable ‘i’ internal_XMLInstance2DF: no visible binding for global variable ‘p’ internal_generateXMLfromBiopax: no visible binding for global variable ‘id’ internal_getBiopaxModelAsDataFrame: no visible binding for global variable ‘property’ internal_propertyListToDF: no visible binding for global variable ‘property’ layoutRegulatoryGraph: no visible global function definition for ‘nodes’ listInstances: no visible binding for global variable ‘property_value’ listInstances: no visible binding for global variable ‘property’ pathway2AdjacancyMatrix: no visible global function definition for ‘as’ pathway2Graph: no visible global function definition for ‘new’ pathway2Graph: no visible global function definition for ‘getClassDef’ pathway2Graph: no visible binding for global variable ‘id’ pathway2Graph: no visible binding for global variable ‘property’ pathway2RegulatoryGraph: no visible global function definition for ‘new’ pathway2RegulatoryGraph: no visible global function definition for ‘getClassDef’ pathway2RegulatoryGraph: no visible binding for global variable ‘id’ pathway2RegulatoryGraph: no visible binding for global variable ‘property’ plotRegulatoryGraph: no visible global function definition for ‘nodes’ removeDisconnectedParts: no visible global function definition for ‘removeNode’ removeNodes: no visible global function definition for ‘edgeWeights’ removeNodes: no visible global function definition for ‘na.omit’ removeNodes: no visible global function definition for ‘removeNode’ removeNodes: no visible global function definition for ‘addEdge’ removeProperties: no visible binding for global variable ‘property’ selectInstances: no visible binding for global variable ‘property_value’ Undefined global functions or variables: addEdge as edgeWeights getClassDef hcl i id na.omit new nodes p property property_attr property_value removeNode Consider adding importFrom("grDevices", "hcl") importFrom("methods", "as", "getClassDef", "new") importFrom("stats", "na.omit") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 ... NOTE Note: found 1 marked UTF-8 string * checking data for ASCII and uncompressed saves ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/rBiopaxParser.Rcheck/00check.log’ for details.