############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:netbiov.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings netbiov_1.28.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/netbiov.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘netbiov/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘netbiov’ version ‘1.28.0’ * 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 ... OK * 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 dependencies in R code ... OK * checking S3 generic/method consistency ... NOTE Found the following apparent S3 methods exported but not registered: plot.NetworkSperical plot.NetworkSperical.startSet plot.abstract.module plot.abstract.nodes plot.modules plot.netbiov plot.spiral.graph See section ‘Registering S3 methods’ in the ‘Writing R Extensions’ manual. * 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 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 plot.abstract.module 23.850 0.387 24.239 level.plot 22.769 0.263 23.034 plot.modules 18.489 0.012 18.501 mst.plot 8.277 0.087 8.366 * 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: 1 WARNING, 4 NOTEs See ‘/home/biocbuild/bbs-3.14-bioc/meat/netbiov.Rcheck/00check.log’ for details.