############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PDATK.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PDATK_1.11.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/PDATK.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘PDATK/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘PDATK’ version ‘1.11.0’ * 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 ... WARNING Found the following significant warnings: Warning: replacing previous import ‘survival::brier’ by ‘verification::brier’ when loading ‘PDATK’ See ‘/Users/biocbuild/bbs-3.20-bioc/meat/PDATK.Rcheck/00install.out’ for details. * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * 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 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 ... WARNING Missing link or links in Rd file 'rankFeatures-MultiAssayExperiment-method.Rd': ‘[dplyr:ranking]{dplyr::dense_rank}’ See section 'Cross-references' in the 'Writing R Extensions' manual. * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... NOTE Documented arguments not in \usage in Rd file 'dot-randomSampleIndex.Rd': ‘numSamples’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed ModelComparison 5.787 0.085 7.177 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * 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: 2 WARNINGs, 3 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/PDATK.Rcheck/00check.log’ for details.