############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:GraphPAC.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings GraphPAC_1.48.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/GraphPAC.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 ‘GraphPAC/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘GraphPAC’ version ‘1.48.0’ * 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 ‘GraphPAC’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Title field: should not end in a period. * 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 Packages in Depends field not imported from: ‘RMallow’ ‘TSP’ ‘iPAC’ ‘igraph’ 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 Find.TSP.Path: no visible global function definition for ‘dist’ Find.TSP.Path: no visible global function definition for ‘ATSP’ Find.TSP.Path: no visible global function definition for ‘insert_dummy’ Find.TSP.Path: no visible global function definition for ‘solve_TSP’ Find.TSP.Path: no visible global function definition for ‘cut_tour’ GraphClust: no visible global function definition for ‘graph.empty’ GraphClust: no visible global function definition for ‘V’ GraphClust: no visible global function definition for ‘V<-’ GraphClust: no visible global function definition for ‘add.edges’ GraphClust: no visible global function definition for ‘nmc’ Plot.Protein: no visible global function definition for ‘heat.colors’ Plot.Protein: no visible global function definition for ‘vcount’ Plot.Protein: no visible global function definition for ‘gray’ Plot.Protein: no visible global function definition for ‘topo.colors’ Plot.Protein: no visible global function definition for ‘cm.colors’ Plot.Protein: no visible global function definition for ‘V’ Plot.Protein: no visible global function definition for ‘tkplot’ Plot.Protein: no visible binding for global variable ‘layout.circle’ Undefined global functions or variables: ATSP V V<- add.edges cm.colors cut_tour dist graph.empty gray heat.colors insert_dummy layout.circle nmc solve_TSP tkplot topo.colors vcount Consider adding importFrom("grDevices", "cm.colors", "gray", "heat.colors", "topo.colors") importFrom("stats", "dist") to your NAMESPACE file. * checking Rd files ... NOTE checkRd: (-1) Plot.Protein.Rd:33: Lost braces 33 | This function is based on the ``tkplot" function in \emph{igraph}. Please see the documentation for that package for the necessary requirements. Special thanks to Dr. G\'{a}bor Cs\'{a}rdi (creator of the \emph{igraph} package) for his help. | ^ checkRd: (-1) Plot.Protein.Rd:33: Lost braces 33 | This function is based on the ``tkplot" function in \emph{igraph}. Please see the documentation for that package for the necessary requirements. Special thanks to Dr. G\'{a}bor Cs\'{a}rdi (creator of the \emph{igraph} package) for his help. | ^ * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed Find.TSP.Path 2.649 0.528 6.411 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/GraphPAC.Rcheck/00check.log’ for details.