############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:netbiov.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings netbiov_1.36.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/netbiov.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-apple-darwin20 (64-bit) * 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 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘netbiov/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘netbiov’ version ‘1.36.0’ * checking package namespace information ... OK * checking package dependencies ... 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 ‘netbiov’ can be installed ... WARNING Found the following significant warnings: Warning: Package 'netbiov' is deprecated and will be removed from Bioconductor See ‘/Users/biocbuild/bbs-3.18-bioc/meat/netbiov.Rcheck/00install.out’ for details. * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R 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 startup messages can be suppressed ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .edgeCol: no visible global function definition for ‘colors’ .get.coord.abstract : dst: no visible global function definition for ‘dist’ .get.coord.mod : dst: no visible global function definition for ‘dist’ .get.coord.mod_abs : dst: no visible global function definition for ‘dist’ .getalllevels: no visible global function definition for ‘pdf’ .getalllevels: no visible global function definition for ‘dev.off’ .getcrd.mod : dst: no visible global function definition for ‘dist’ .getcrd.mod: no visible global function definition for ‘rnorm’ .getcrd.mod.nodes : dst: no visible global function definition for ‘dist’ .getcrd.mod_abs : dst: no visible global function definition for ‘dist’ .getcrd.mod_abs: no visible global function definition for ‘rnorm’ .getcrd.mod_mst : dst: no visible global function definition for ‘dist’ .getcrd.mod_mst: no visible global function definition for ‘rnorm’ .set.mst.node.col: no visible global function definition for ‘heat.colors’ .set.mst.node.col_mod: no visible global function definition for ‘heat.colors’ .set.rank.abstract: no visible global function definition for ‘colors’ .set.rank.abstract: no visible global function definition for ‘hist’ .set.rank.abstract: no visible global function definition for ‘heat.colors’ .set.rank.mod: no visible global function definition for ‘hist’ .set.rank.mod: no visible global function definition for ‘colors’ .set.rank.mod: no visible global function definition for ‘heat.colors’ .set.rank.mod_abs: no visible global function definition for ‘hist’ .set.rank.mod_abs: no visible global function definition for ‘colors’ .set.rank.mod_abs: no visible global function definition for ‘heat.colors’ .set.rank.nodes: no visible global function definition for ‘hist’ .set.rank.nodes: no visible global function definition for ‘colors’ .set.rank.nodes: no visible global function definition for ‘heat.colors’ .set.rank.spiral: no visible global function definition for ‘hist’ .set.rank.spiral: no visible global function definition for ‘colors’ .set.rank.spiral: no visible global function definition for ‘heat.colors’ .set.split.vertex.color: no visible global function definition for ‘colors’ level.plot: no visible global function definition for ‘colors’ plot.NetworkSperical: no visible global function definition for ‘colors’ plot.NetworkSperical: no visible global function definition for ‘palette’ plot.NetworkSperical.startSet: no visible global function definition for ‘colors’ plot.NetworkSperical.startSet: no visible global function definition for ‘palette’ plot.netbiov: no visible global function definition for ‘par’ plot.spiral.graph : dst: no visible global function definition for ‘dist’ tkplot.netbiov: no visible global function definition for ‘par’ Undefined global functions or variables: colors dev.off dist heat.colors hist palette par pdf rnorm Consider adding importFrom("grDevices", "colors", "dev.off", "heat.colors", "palette", "pdf") importFrom("graphics", "hist", "par") importFrom("stats", "dist", "rnorm") 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 ... WARNING Documented arguments not in \usage in documentation object 'level.plot': ‘...’ Documented arguments not in \usage in documentation object 'mst.plot': ‘...’ Documented arguments not in \usage in documentation object 'mst.plot.mod': ‘...’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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’ ... NOTE The following files are already in R: ‘Sweave.sty’ Please remove them from your package. * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed level.plot 142.481 4.301 157.847 plot.abstract.module 54.889 0.853 58.837 plot.modules 48.456 0.656 51.903 mst.plot 20.600 0.231 21.119 mst.plot.mod 16.152 0.271 17.706 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 WARNINGs, 3 NOTEs See ‘/Users/biocbuild/bbs-3.18-bioc/meat/netbiov.Rcheck/00check.log’ for details.