############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:DrugVsDisease.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings DrugVsDisease_2.49.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/DrugVsDisease.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 ‘DrugVsDisease/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘DrugVsDisease’ version ‘2.49.0’ * 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' INFO Depends: includes the non-default packages: 'affy', 'limma', 'biomaRt', 'ArrayExpress', 'GEOquery', 'DrugVsDiseasedata', 'cMap2data', 'qvalue' 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 ‘DrugVsDisease’ 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: ‘ArrayExpress’ ‘DrugVsDiseasedata’ ‘GEOquery’ ‘affy’ ‘biomaRt’ ‘limma’ ‘qvalue’ Please remove these calls from your code. Namespaces in Imports field not imported from: ‘BiocGenerics’ ‘RUnit’ ‘annotate’ ‘hgu133a.db’ ‘hgu133a2.db’ ‘hgu133plus2.db’ ‘xtable’ All declared Imports should be used. Packages in Depends field not imported from: ‘ArrayExpress’ ‘DrugVsDiseasedata’ ‘GEOquery’ ‘affy’ ‘biomaRt’ ‘cMap2data’ ‘limma’ ‘qvalue’ 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 .averagecluster: no visible binding for global variable ‘drugClusters’ .averagecluster: no visible binding for global variable ‘diseaseClusters’ .calculateES: no visible binding for global variable ‘drugRL’ .calculateES: no visible binding for global variable ‘diseaseRL’ .calculateES : : no visible global function definition for ‘qvalue’ .convertEnsembl: no visible binding for global variable ‘annotationlist’ .convertEnsembl: no visible global function definition for ‘useMart’ .convertEnsembl: no visible global function definition for ‘getBM’ .datafromAE: no visible global function definition for ‘ArrayExpress’ .datafromAE: no visible global function definition for ‘annotation’ .datafromAE: no visible global function definition for ‘pData’ .datafromGEO: no visible global function definition for ‘getGEO’ .datafromGEO: no visible global function definition for ‘GDS2eSet’ .datafromGEO: no visible global function definition for ‘pData’ .datafromGEO: no visible global function definition for ‘annotation’ .datafromGEO: no visible binding for global variable ‘GEOfactorvalues’ .datafromGEO: no visible global function definition for ‘exprs’ .findCluster: no visible binding for global variable ‘drugClusters’ .findCluster: no visible binding for global variable ‘diseaseClusters’ .findSignifCompounds: no visible global function definition for ‘qvalue’ .fitlms: no visible global function definition for ‘lmFit’ .multcontrast: no visible global function definition for ‘contrasts.fit’ .multcontrast: no visible global function definition for ‘eBayes’ .normalisedata: no visible global function definition for ‘rma’ .normalisedata: no visible global function definition for ‘mas5’ .readlocalAE: no visible global function definition for ‘ReadAffy’ .readlocalCEL: no visible global function definition for ‘ReadAffy’ .singlecontrast: no visible global function definition for ‘lmFit’ .singlecontrast: no visible global function definition for ‘contrasts.fit’ .singlecontrast: no visible global function definition for ‘eBayes’ .treatmentonlyfit: no visible global function definition for ‘lmFit’ .writecytoscape: no visible binding for global variable ‘drugClusters’ .writecytoscape: no visible binding for global variable ‘cytodrug’ .writecytoscape: no visible binding for global variable ‘druglabels’ .writecytoscape: no visible binding for global variable ‘diseaseClusters’ .writecytoscape: no visible binding for global variable ‘cytodisease’ .writecytoscape: no visible binding for global variable ‘diseaselabels’ generateprofiles: no visible binding for global variable ‘genelist’ generateprofiles: no visible global function definition for ‘exprs’ Undefined global functions or variables: ArrayExpress GDS2eSet GEOfactorvalues ReadAffy annotation annotationlist contrasts.fit cytodisease cytodrug diseaseClusters diseaseRL diseaselabels drugClusters drugRL druglabels eBayes exprs genelist getBM getGEO lmFit mas5 pData qvalue rma useMart * 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 LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed classifyprofile 16.207 2.594 18.803 selectrankedlists 10.971 1.312 12.285 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ 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: 2 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/DrugVsDisease.Rcheck/00check.log’ for details.