############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CNORfeeder.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CNORfeeder_1.47.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/CNORfeeder.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * using platform: x86_64-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 Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘CNORfeeder/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CNORfeeder’ version ‘1.47.0’ * 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 ‘CNORfeeder’ 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 ... WARNING '::' or ':::' import not declared from: ‘catnet’ 'loadNamespace' or 'requireNamespace' call not declared from: ‘catnet’ 'library' or 'require' call to ‘MEIGOR’ in package code. 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 Binference: no visible global function definition for ‘write.table’ MIinference: no visible global function definition for ‘as’ MIinference: no visible global function definition for ‘write.table’ gaBinaryT1W: no visible global function definition for ‘runif’ getLBodeContObjFunctionWeighted: no visible global function definition for ‘incidence2Adjacency’ getLBodeContObjFunctionWeighted: no visible global function definition for ‘getLBodeSimFunction’ integrateLinks: no visible global function definition for ‘write.table’ linksRanking: no visible global function definition for ‘write.table’ makeBTables: no visible global function definition for ‘na.omit’ mapBTables2model: no visible global function definition for ‘new’ parEstimationLBodeSSmWeighted: no visible global function definition for ‘incidence2Adjacency’ parEstimationLBodeSSmWeighted: no visible global function definition for ‘createLBodeContPars’ parEstimationLBodeSSmWeighted: no visible global function definition for ‘essR’ parEstimationLBodeWeighted: no visible global function definition for ‘defaultParametersSSm’ parEstimationLBodeWeighted: no visible global function definition for ‘defaultParametersGA’ parEstimationLBodeWeighted: no visible global function definition for ‘parEstimationLBodeGA’ preprocessingWeighted: no visible global function definition for ‘graph_from_graphnel’ preprocessingWeighted: no visible global function definition for ‘get.adjacency’ preprocessingWeighted: no visible global function definition for ‘all_simple_paths’ preprocessingWeighted: no visible global function definition for ‘write.table’ runDynamicFeeder: no visible global function definition for ‘defaultParametersSSm’ shift: no visible global function definition for ‘tail’ shift: no visible global function definition for ‘head’ Undefined global functions or variables: all_simple_paths as createLBodeContPars defaultParametersGA defaultParametersSSm essR get.adjacency getLBodeSimFunction graph_from_graphnel head incidence2Adjacency na.omit new parEstimationLBodeGA runif tail write.table Consider adding importFrom("methods", "as", "new") importFrom("stats", "na.omit", "runif") importFrom("utils", "head", "tail", "write.table") 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 ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: Binference.Rd: makeCNOlist MIinference.Rd: makeCNOlist, sif2graph, model2sif buildFeederObjectDynamic.Rd: makeCNOlist gaBinaryT1W.Rd: gaBinaryT1 identifyMisfitIndices.Rd: makeCNOlist integrateLinks.Rd: makeCNOlist linksRanking.Rd: makeCNOlist makeBTables.Rd: makeCNOlist mapBTables2model.Rd: readSif, readMIDAS mapDDN2model.Rd: readSif, makeCNOlist, readMIDAS runDynamicFeeder.Rd: makeCNOlist weighting.Rd: makeCNOlist Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 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: 1 WARNING, 2 NOTEs See ‘/Users/biocbuild/bbs-3.21-bioc/meat/CNORfeeder.Rcheck/00check.log’ for details.