############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:maPredictDSC.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings maPredictDSC_1.44.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/maPredictDSC.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 ‘maPredictDSC/DESCRIPTION’ ... OK * this is package ‘maPredictDSC’ version ‘1.44.0’ * 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' NOTE Depends: includes the non-default packages: 'MASS', 'affy', 'limma', 'gcrma', 'ROC', 'class', 'e1071', 'caret', 'hgu133plus2.db', 'ROCR', 'AnnotationDbi', 'LungCancerACvsSCCGEO' Adding so many packages to the search path is excessive and importing selectively is preferable. * 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 ‘maPredictDSC’ can be installed ... OK * checking installed package size ... OK * 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 'library' or 'require' calls to packages already attached by Depends: ‘ROC’ ‘ROCR’ ‘affy’ ‘caret’ ‘class’ ‘e1071’ ‘gcrma’ ‘limma’ Please remove these calls from your code. 'library' or 'require' call to ‘parallel’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Packages in Depends field not imported from: ‘LungCancerACvsSCCGEO’ ‘ROC’ ‘ROCR’ ‘affy’ ‘caret’ ‘class’ ‘e1071’ ‘gcrma’ ‘hgu133plus2.db’ ‘limma’ 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 maPredictDSC: no visible global function definition for ‘installed.packages’ maPredictDSC: no visible global function definition for ‘ReadAffy’ maPredictDSC: no visible global function definition for ‘rma’ maPredictDSC: no visible global function definition for ‘mas5’ maPredictDSC: no visible global function definition for ‘gcrma’ maPredictDSC: no visible global function definition for ‘exprs’ maPredictDSC: no visible global function definition for ‘mas5calls’ maPredictDSC: no visible global function definition for ‘createFolds’ maPredictDSC : mff: no visible global function definition for ‘model.matrix’ maPredictDSC : mff: no visible global function definition for ‘formula’ maPredictDSC : mff: no visible global function definition for ‘lmFit’ maPredictDSC : mff: no visible global function definition for ‘makeContrasts’ maPredictDSC : mff: no visible global function definition for ‘contrasts.fit’ maPredictDSC : mff: no visible global function definition for ‘eBayes’ maPredictDSC : mff: no visible global function definition for ‘topTable’ maPredictDSC : mff: no visible global function definition for ‘pt’ maPredictDSC : mff : wf: no visible global function definition for ‘wilcox.test’ maPredictDSC : mff: no visible global function definition for ‘predict’ maPredictDSC : mff: no visible global function definition for ‘knn’ maPredictDSC : mff: no visible global function definition for ‘svm’ maPredictDSC : mff: no visible global function definition for ‘rocdemo.sca’ maPredictDSC : mff: no visible binding for global variable ‘dxrule.sca’ maPredictDSC : mff: no visible global function definition for ‘AUC’ maPredictDSC: no visible global function definition for ‘mclapply’ maPredictDSC: no visible global function definition for ‘sd’ maPredictDSC: no visible global function definition for ‘model.matrix’ maPredictDSC: no visible global function definition for ‘formula’ maPredictDSC: no visible global function definition for ‘lmFit’ maPredictDSC: no visible global function definition for ‘makeContrasts’ maPredictDSC: no visible global function definition for ‘contrasts.fit’ maPredictDSC: no visible global function definition for ‘eBayes’ maPredictDSC: no visible global function definition for ‘topTable’ maPredictDSC: no visible global function definition for ‘pt’ maPredictDSC : wf: no visible global function definition for ‘wilcox.test’ maPredictDSC: no visible global function definition for ‘predict’ maPredictDSC: no visible global function definition for ‘knn’ maPredictDSC: no visible global function definition for ‘svm’ perfDSC: no visible global function definition for ‘prediction’ perfDSC: no visible global function definition for ‘performance’ perfDSC: no visible global function definition for ‘na.omit’ perfDSC: no visible global function definition for ‘trapezint’ perfDSC: no visible global function definition for ‘rocdemo.sca’ perfDSC: no visible binding for global variable ‘dxrule.sca’ perfDSC: no visible global function definition for ‘AUC’ Undefined global functions or variables: AUC ReadAffy contrasts.fit createFolds dxrule.sca eBayes exprs formula gcrma installed.packages knn lmFit makeContrasts mas5 mas5calls mclapply model.matrix na.omit performance predict prediction pt rma rocdemo.sca sd svm topTable trapezint wilcox.test Consider adding importFrom("stats", "formula", "model.matrix", "na.omit", "predict", "pt", "sd", "wilcox.test") importFrom("utils", "installed.packages") 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 ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed predictDSC 153.164 12.09 114.786 * 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-3.20-bioc/meat/maPredictDSC.Rcheck/00check.log’ for details.