############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:CellNOptR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings CellNOptR_1.52.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/CellNOptR.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 ‘CellNOptR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CellNOptR’ version ‘1.52.0’ * 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' NOTE Depends: includes the non-default packages: 'RBGL', 'graph', 'RCurl', 'Rgraphviz', 'XML', 'ggplot2', 'rmarkdown' Adding so many packages to the search path is excessive and importing selectively is preferable. * 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 ‘CellNOptR’ can be installed ... OK * used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * 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 Package in Depends field not imported from: ‘rmarkdown’ 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 .error.bar: no visible global function definition for ‘arrows’ CNORwrap: no visible global function definition for ‘pdf’ CNORwrap: no visible global function definition for ‘dev.off’ build_sif_table_from_rule : rename_gates: no visible binding for global variable ‘node_in’ build_sif_table_from_rule : rename_gates: no visible binding for global variable ‘node_out’ build_sif_table_from_rule : simplify_gates: no visible global function definition for ‘filter’ build_sif_table_from_rule : simplify_gates: no visible binding for global variable ‘node_in’ build_sif_table_from_rule : simplify_gates: no visible binding for global variable ‘node_out’ build_sif_table_from_rule : interpret_sif_list: no visible global function definition for ‘setNames’ build_sif_table_from_rule : interpret_sif_list: no visible binding for global variable ‘num_or’ build_sif_table_from_rule : interpret_sif_list: no visible binding for global variable ‘node_out’ build_sif_table_from_rule : interpret_sif_list: no visible binding for global variable ‘new_node_out’ build_sif_table_from_rule : interpret_sif_list: no visible binding for global variable ‘node_in’ build_sif_table_from_rule : interpret_sif_list: no visible binding for global variable ‘new_node_in’ build_sif_table_from_rule : interpret_sif_list: no visible global function definition for ‘filter’ build_sif_table_from_rule : interpret_sif_list: no visible global function definition for ‘distinct’ build_sif_table_from_rule : interpret_sif_list: no visible binding for global variable ‘or_members’ build_sif_table_from_rule : write_sif: no visible binding for global variable ‘node_in’ build_sif_table_from_rule : write_sif: no visible binding for global variable ‘node_out’ build_sif_table_from_rule : write_sif: no visible binding for global variable ‘sign1’ build_sif_table_from_rule : write_sif: no visible binding for global variable ‘sign2’ createEdgeAttrs: no visible global function definition for ‘rgb’ crossvalidateBoolean: no visible global function definition for ‘error’ expandGates: no visible global function definition for ‘combn’ gaBinaryT1: no visible global function definition for ‘runif’ gaBinaryTN: no visible global function definition for ‘runif’ graph2sif: no visible global function definition for ‘write.table’ makeCNOlist: no visible binding for global variable ‘var’ mapBack: no visible global function definition for ‘write.table’ plotCNOlist: no visible global function definition for ‘par’ plotCNOlist: no visible global function definition for ‘text’ plotCNOlist: no visible global function definition for ‘axis’ plotCNOlist: no visible global function definition for ‘barplot’ plotCNOlistLarge: no visible global function definition for ‘par’ plotCNOlistLarge: no visible global function definition for ‘dev.new’ plotCNOlistLarge: no visible global function definition for ‘text’ plotCNOlistLarge: no visible global function definition for ‘axis’ plotCNOlistLarge: no visible global function definition for ‘image’ plotCNOlistLargePDF: no visible global function definition for ‘pdf’ plotCNOlistLargePDF: no visible global function definition for ‘dev.off’ plotCNOlistPDF: no visible global function definition for ‘pdf’ plotCNOlistPDF: no visible global function definition for ‘dev.off’ plotFit: no visible global function definition for ‘par’ plotFit: no visible global function definition for ‘pdf’ plotFit: no visible global function definition for ‘dev.off’ plotModel: no visible global function definition for ‘pdf’ plotModel: no visible global function definition for ‘png’ plotModel: no visible global function definition for ‘svg’ plotModel: no visible global function definition for ‘read.table’ plotModel: no visible global function definition for ‘installed.packages’ plotModel: no visible global function definition for ‘dev.off’ plotOptimResults: no visible global function definition for ‘par’ plotOptimResults: no visible global function definition for ‘text’ plotOptimResults: no visible global function definition for ‘rect’ plotOptimResults: no visible global function definition for ‘points’ plotOptimResults: no visible global function definition for ‘axis’ plotOptimResults: no visible global function definition for ‘image’ plotOptimResultsPDF: no visible global function definition for ‘pdf’ plotOptimResultsPDF: no visible global function definition for ‘dev.off’ plotOptimResultsPan: no visible global function definition for ‘par’ plotOptimResultsPan: no visible global function definition for ‘split.screen’ plotOptimResultsPan: no visible global function definition for ‘heat.colors’ plotOptimResultsPan: no visible global function definition for ‘screen’ plotOptimResultsPan: no visible global function definition for ‘text’ plotOptimResultsPan: no visible global function definition for ‘rect’ plotOptimResultsPan: no visible global function definition for ‘points’ plotOptimResultsPan: no visible global function definition for ‘axis’ plotOptimResultsPan: no visible global function definition for ‘barplot’ plotOptimResultsPan: no visible global function definition for ‘image’ plotOptimResultsPan: no visible global function definition for ‘plot.new’ plotOptimResultsPan: no visible global function definition for ‘segments’ plotOptimResultsPan: no visible global function definition for ‘close.screen’ plotOptimResultsPan: no visible global function definition for ‘dev.off’ randomizeCNOlist: no visible global function definition for ‘rnorm’ randomizeCNOlist: no visible global function definition for ‘runif’ readBND: no visible global function definition for ‘write.table’ readBNET: no visible global function definition for ‘mutate’ readBNET: no visible binding for global variable ‘factors’ readBNET: no visible binding for global variable ‘i_and_gates’ readBNET: no visible binding for global variable ‘.’ readBNET: no visible binding for global variable ‘sif_df’ readBNET: no visible global function definition for ‘write.table’ readMIDAS: no visible global function definition for ‘count.fields’ readMIDAS: no visible global function definition for ‘read.csv’ readMIDAS: no visible global function definition for ‘read.table’ readSBMLQual: no visible global function definition for ‘write.table’ readSIF: no visible global function definition for ‘read.table’ sif2graph: no visible global function definition for ‘read.table’ writeMIDAS: no visible global function definition for ‘write.table’ writeNetworkW: no visible global function definition for ‘write.table’ writeSIF: no visible global function definition for ‘write.table’ writeScaffoldW: no visible global function definition for ‘write.table’ Undefined global functions or variables: . arrows axis barplot close.screen combn count.fields dev.new dev.off distinct error factors filter heat.colors i_and_gates image installed.packages mutate new_node_in new_node_out node_in node_out num_or or_members par pdf plot.new png points read.csv read.table rect rgb rnorm runif screen segments setNames sif_df sign1 sign2 split.screen svg text var write.table Consider adding importFrom("grDevices", "dev.new", "dev.off", "heat.colors", "pdf", "png", "rgb", "svg") importFrom("graphics", "arrows", "axis", "barplot", "close.screen", "image", "par", "plot.new", "points", "rect", "screen", "segments", "split.screen", "text") importFrom("stats", "filter", "rnorm", "runif", "setNames", "var") importFrom("utils", "combn", "count.fields", "installed.packages", "read.csv", "read.table", "write.table") to your NAMESPACE file. * checking Rd files ... NOTE checkRd: (-1) computeScoreT1.Rd:27: Lost braces 27 | a model structure, as created by code{readSIF}, normally pre-processed | ^ checkRd: (-1) computeScoreTN.Rd:26: Lost braces 26 | a model structure, as created by code{readSIF}, normally pre-processed | ^ checkRd: (-1) plotModel.Rd:59: Lost braces in \itemize; meant \describe ? checkRd: (-1) plotModel.Rd:60: Lost braces in \itemize; meant \describe ? checkRd: (-1) plotModel.Rd:61: Lost braces in \itemize; meant \describe ? checkRd: (-1) plotModel.Rd:62: Lost braces in \itemize; meant \describe ? checkRd: (-1) plotModel.Rd:63: Lost braces in \itemize; meant \describe ? checkRd: (-1) plotModel.Rd:64: Lost braces in \itemize; meant \describe ? checkRd: (-1) plotModel.Rd:65: Lost braces in \itemize; meant \describe ? checkRd: (-1) plotModel.Rd:66: Lost braces in \itemize; meant \describe ? checkRd: (-1) plotModel.Rd:67: Lost braces in \itemize; meant \describe ? checkRd: (-1) plotModel.Rd:68: Lost braces in \itemize; meant \describe ? checkRd: (-1) plotModel.Rd:69: Lost braces in \itemize; meant \describe ? * 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 data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘test_gaBinaryT1.R’ Running ‘test_gaBinaryT2.R’ Running ‘test_gaBinaryT3.R’ Running ‘test_import_rules.R’ Running ‘test_manySteadyStates.R’ Running ‘test_priorBitString.R’ Running ‘test_simulateTN.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: 5 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/CellNOptR.Rcheck/00check.log’ for details.