############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:iBBiG.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings iBBiG_1.50.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/iBBiG.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘iBBiG/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘iBBiG’ version ‘1.50.0’ * checking package namespace information ... NOTE Found export directives that require package ‘methods’: ‘exportClasses’ ‘exportMethods’ Remove all such namespace directives (if obsolete) or ensure that the DESCRIPTION Depends or Imports field contains ‘methods’. * 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 ‘iBBiG’ can be installed ... OK * used C compiler: ‘gcc (conda-forge gcc 14.2.0-1) 14.2.0’ * 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 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 'library' or 'require' call to ‘biclust’ which was already attached by Depends. Please remove these calls from your code. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE addSignal: no visible global function definition for ‘runif’ iBBiG: no visible global function definition for ‘new’ makeArtificial: no visible global function definition for ‘runif’ makeArtificial: no visible global function definition for ‘new’ Clusterscores,iBBiG: no visible global function definition for ‘slot’ Clusterscores<-,iBBiG: no visible global function definition for ‘slot<-’ Clusterscores<-,iBBiG: no visible global function definition for ‘validObject’ Number,iBBiG: no visible global function definition for ‘slot’ Number<-,iBBiG: no visible global function definition for ‘slot<-’ Number<-,iBBiG: no visible global function definition for ‘validObject’ NumberxCol,iBBiG: no visible global function definition for ‘slot’ NumberxCol<-,iBBiG: no visible global function definition for ‘slot<-’ NumberxCol<-,iBBiG: no visible global function definition for ‘validObject’ Parameters,iBBiG: no visible global function definition for ‘slot’ Parameters<-,iBBiG: no visible global function definition for ‘slot<-’ Parameters<-,iBBiG: no visible global function definition for ‘validObject’ RowScorexNumber,iBBiG: no visible global function definition for ‘slot’ RowScorexNumber<-,iBBiG: no visible global function definition for ‘slot<-’ RowScorexNumber<-,iBBiG: no visible global function definition for ‘validObject’ RowxNumber,iBBiG: no visible global function definition for ‘slot’ RowxNumber<-,iBBiG: no visible global function definition for ‘slot<-’ RowxNumber<-,iBBiG: no visible global function definition for ‘validObject’ Seeddata,iBBiG: no visible global function definition for ‘slot’ Seeddata<-,iBBiG: no visible global function definition for ‘slot<-’ Seeddata<-,iBBiG: no visible global function definition for ‘validObject’ analyzeClust,Biclust-iBBiG: no visible global function definition for ‘as’ analyzeClust,list-iBBiG: no visible global function definition for ‘new’ coerce,Biclust-iBBiG: no visible global function definition for ‘new’ info,iBBiG: no visible global function definition for ‘slot’ info<-,iBBiG: no visible global function definition for ‘slot<-’ info<-,iBBiG: no visible global function definition for ‘validObject’ plot,iBBiG-ANY: no visible global function definition for ‘layout’ plot,iBBiG-ANY: no visible global function definition for ‘colors’ plot,iBBiG-ANY: no visible global function definition for ‘image’ plot,iBBiG-ANY: no visible global function definition for ‘legend’ plot,iBBiG-ANY: no visible binding for global variable ‘title’ plot,iBBiG-ANY: no visible global function definition for ‘title’ plot,iBBiG-ANY: no visible global function definition for ‘barplot’ Undefined global functions or variables: as barplot colors image layout legend new runif slot slot<- title validObject Consider adding importFrom("grDevices", "colors") importFrom("graphics", "barplot", "image", "layout", "legend", "title") importFrom("methods", "as", "new", "slot", "slot<-", "validObject") importFrom("stats", "runif") 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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available File ‘/home/biocbuild/R/R-4.4.1/site-library/iBBiG/libs/iBBiG.so’: Found ‘rand’, possibly from ‘rand’ (C) Found ‘srand’, possibly from ‘srand’ (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 nor [v]sprintf. 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 iBBiG-class 29.679 0.080 29.806 iBBiG-package 29.660 0.028 29.796 iBBiG 28.396 0.036 28.532 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 5 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/iBBiG.Rcheck/00check.log’ for details.