############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:PDATK.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings PDATK_1.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/PDATK.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘PDATK/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘PDATK’ version ‘1.2.0’ * package encoding: UTF-8 * 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 ‘PDATK’ 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 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 dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .calculateMSMthresholds: no visible binding for global variable ‘funContext’ .plotNetwork: no visible global function definition for ‘legend’ NCSModel: no visible binding for global variable ‘metric’ NCSModel: no visible binding for global variable ‘comparison’ NCSModel: no visible binding for global variable ‘centroid_K’ NCSModel: no visible binding for global variable ‘assay_K’ NetworkCommunitySearchModel: no visible binding for global variable ‘metric’ NetworkCommunitySearchModel: no visible binding for global variable ‘comparison’ NetworkCommunitySearchModel: no visible binding for global variable ‘centroid_K’ NetworkCommunitySearchModel: no visible binding for global variable ‘assay_K’ predictClasses,ConsensusMetaclusteringModel-ANY: no visible global function definition for ‘.error’ predictClasses,NCSModel-ANY: no visible binding for global variable ‘centroid_cohort’ predictClasses,NCSModel-ANY: no visible binding for global variable ‘centroid_K’ predictClasses,NCSModel-ANY: no visible binding for global variable ‘assay_cohort’ predictClasses,NCSModel-ANY: no visible binding for global variable ‘assay_K’ predictClasses,NCSModel-ANY: no visible binding for global variable ‘tmp’ predictClasses,NCSModel-ANY: no visible binding for global variable ‘cluster_label’ rankFeatures,MultiAssayExperiment: no visible binding for global variable ‘feature’ rankFeatures,MultiAssayExperiment: no visible binding for global variable ‘missignAssays’ rankFeatures,MultiAssayExperiment: no visible binding for global variable ‘feature_score’ rankFeatures,MultiAssayExperiment: no visible binding for global variable ‘feature_rank’ trainModel,ConsensusMetaclusteringModel: no visible global function definition for ‘pdf’ trainModel,ConsensusMetaclusteringModel: no visible global function definition for ‘dev.off’ trainModel,NCSModel: no visible binding for global variable ‘ingroup_proportion’ trainModel,NCSModel: no visible binding for global variable ‘cor_threshold’ Undefined global functions or variables: .error assay_K assay_cohort centroid_K centroid_cohort cluster_label comparison cor_threshold dev.off feature feature_rank feature_score funContext ingroup_proportion legend metric missignAssays pdf tmp Consider adding importFrom("grDevices", "dev.off", "pdf") importFrom("graphics", "legend") 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.14-bioc/meat/PDATK.Rcheck/00check.log’ for details.