############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:BicARE.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings BicARE_1.56.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/BicARE.Rcheck’ * using R version 4.2.3 (2023-03-15) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * checking for file ‘BicARE/DESCRIPTION’ ... OK * this is package ‘BicARE’ version ‘1.56.0’ * 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 ‘BicARE’ 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 loading without being on the library search path ... OK * checking dependencies in R code ... NOTE Packages in Depends field not imported from: ‘Biobase’ ‘GSEABase’ ‘multtest’ 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 FLOC: no visible global function definition for ‘new’ FLOC: no visible global function definition for ‘exprs’ FLOC: no visible global function definition for ‘runif’ FLOC: no visible binding for global variable ‘var’ bicluster: no visible global function definition for ‘exprs’ bicluster: no visible global function definition for ‘featureNames’ bicluster: no visible global function definition for ‘sampleNames’ makeReport: no visible global function definition for ‘annotation’ makeReport: no visible global function definition for ‘png’ makeReport: no visible global function definition for ‘dev.off’ makeReport: no visible global function definition for ‘getSYMBOL’ makeReport: no visible global function definition for ‘setName’ makeReport: no visible global function definition for ‘browseURL’ plot.bicluster: no visible global function definition for ‘par’ plot.bicluster: no visible global function definition for ‘matplot’ plot.bicluster: no visible global function definition for ‘axis’ residue: no visible global function definition for ‘new’ residue: no visible global function definition for ‘exprs’ testAnnot: no visible global function definition for ‘pData’ testAnnot: no visible global function definition for ‘phenoData’ testAnnot: no visible global function definition for ‘chisq.test’ testAnnot: no visible global function definition for ‘mt.rawp2adjp’ testSet: no visible global function definition for ‘exprs’ testSet: no visible global function definition for ‘GeneSet’ testSet: no visible global function definition for ‘geneIdType’ testSet: no visible global function definition for ‘geneIds’ testSet: no visible global function definition for ‘mapIdentifiers’ testSet: no visible global function definition for ‘phyper’ testSet: no visible global function definition for ‘mt.rawp2adjp’ Undefined global functions or variables: GeneSet annotation axis browseURL chisq.test dev.off exprs featureNames geneIdType geneIds getSYMBOL mapIdentifiers matplot mt.rawp2adjp new pData par phenoData phyper png runif sampleNames setName var Consider adding importFrom("grDevices", "dev.off", "png") importFrom("graphics", "axis", "matplot", "par") importFrom("methods", "new") importFrom("stats", "chisq.test", "phyper", "runif", "var") importFrom("utils", "browseURL") 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 ... 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 compiled code ... NOTE Note: information on .o files is not available File ‘/home/biocbuild/bbs-3.16-bioc/R/site-library/BicARE/libs/BicARE.so’: Found ‘__printf_chk’, possibly from ‘printf’ (C) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs. The detected symbols are linked into the code but might come from libraries and not actually be called. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed testSet 384.710 1.092 385.805 FLOC 21.858 0.059 21.918 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘BicARE.Rnw’... OK OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See ‘/home/biocbuild/bbs-3.16-bioc/meat/BicARE.Rcheck/00check.log’ for details.