############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:RBioinf.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings RBioinf_1.67.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/RBioinf.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * 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 ‘RBioinf/DESCRIPTION’ ... OK * this is package ‘RBioinf’ version ‘1.67.0’ * 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' 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 ‘RBioinf’ can be installed ... OK * used C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ * checking installed package size ... INFO installed size is 5.7Mb sub-directories of 1Mb or more: extdata 5.5Mb * 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 Packages in Depends field not imported from: ‘graph’ ‘methods’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. Unexported object imported by a ':::' call: ‘methods:::.getMethodsTable’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE class2Graph: warning in matrix(0, nr = nN, nc = nN): partial argument match of 'nr' to 'nrow' class2Graph: warning in matrix(0, nr = nN, nc = nN): partial argument match of 'nc' to 'ncol' LPO: no visible global function definition for ‘getClass’ OLDcplList: no visible global function definition for ‘getAllSuperClasses’ OLDcplList: no visible global function definition for ‘getClass’ S4Help: no visible global function definition for ‘isClass’ S4Help: no visible global function definition for ‘getAllSuperClasses’ S4Help: no visible global function definition for ‘getClass’ S4Help: no visible global function definition for ‘menu’ S4Help: no visible global function definition for ‘isGeneric’ S4Help: no visible global function definition for ‘getGeneric’ S4Help: no visible binding for global variable ‘help’ candidateDirectSC: no visible global function definition for ‘getClass’ class2Graph: no visible global function definition for ‘is’ class2Graph: no visible global function definition for ‘getClass’ class2Graph: no visible global function definition for ‘getAllSuperClasses’ class2Graph: no visible global function definition for ‘new’ class2Graph: no visible global function definition for ‘as’ classList2Graph: no visible global function definition for ‘join’ computeClassLinearization: no visible global function definition for ‘getClass’ printWithNumbers: no visible global function definition for ‘is’ subClassNames: no visible global function definition for ‘isClassDef’ subClassNames: no visible global function definition for ‘getClass’ superClassNames: no visible global function definition for ‘isClassDef’ superClassNames: no visible global function definition for ‘getClass’ superClasses: no visible global function definition for ‘is’ traceMethods: no visible global function definition for ‘isGeneric’ traceMethods: no visible global function definition for ‘showMethods’ Undefined global functions or variables: as getAllSuperClasses getClass getGeneric help is isClass isClassDef isGeneric join menu new showMethods Consider adding importFrom("methods", "as", "getAllSuperClasses", "getClass", "getGeneric", "is", "isClass", "isClassDef", "isGeneric", "new", "showMethods") importFrom("utils", "help", "menu") 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/bbs-3.21-bioc/R/site-library/RBioinf/libs/RBioinf.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 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 * 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: 3 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/RBioinf.Rcheck/00check.log’ for details.