############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DaMiRseq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DaMiRseq_2.4.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/DaMiRseq.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘DaMiRseq/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘DaMiRseq’ version ‘2.4.3’ * 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 ... NOTE Found the following hidden files and directories: .BBSoptions .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘DaMiRseq’ can be installed ... OK * checking installed package size ... NOTE installed size is 6.4Mb sub-directories of 1Mb or more: data 6.0Mb * 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 DaMiR.Allplot: warning in pheatmap(sampleDistMatrix, clustering_distance_rows = mydist, clustering_distance_cols = mydist, col = colors, breaks = seque, annotation_col = df): partial argument match of 'col' to 'color' DaMiR.Clustplot: warning in pheatmap(count_data, clustering_distance_rows = d_r, clustering_distance_cols = d_c, scale = "row", col = colors, annotation_col = df): partial argument match of 'col' to 'color' DaMiR.Allplot: no visible binding for global variable ‘X1’ DaMiR.Allplot: no visible binding for global variable ‘X2’ DaMiR.Allplot: no visible binding for global variable ‘value’ DaMiR.Allplot: no visible binding for global variable ‘variable’ DaMiR.EnsembleLearning2cl: no visible binding for global variable ‘Classifiers’ DaMiR.EnsembleLearning2cl: no visible binding for global variable ‘Accuracy’ DaMiR.EnsembleLearning2cl: no visible binding for global variable ‘MCC’ DaMiR.EnsembleLearning2cl: no visible binding for global variable ‘Specificity’ DaMiR.EnsembleLearning2cl: no visible binding for global variable ‘Sensitivity’ DaMiR.EnsembleLearning2cl: no visible binding for global variable ‘PPV’ DaMiR.EnsembleLearning2cl: no visible binding for global variable ‘NPV’ DaMiR.EnsembleLearning2cl: no visible global function definition for ‘colSds’ DaMiR.EnsembleLearningNcl: no visible binding for global variable ‘Classifiers’ DaMiR.EnsembleLearningNcl: no visible binding for global variable ‘Accuracy’ DaMiR.EnsembleLearningNcl: no visible global function definition for ‘colSds’ DaMiR.MDSplot: no visible binding for global variable ‘X1’ DaMiR.MDSplot: no visible binding for global variable ‘X2’ DaMiR.ModelSelect: no visible binding for global variable ‘Accuracy’ DaMiR.ModelSelect: no visible binding for global variable ‘N.predictors’ DaMiR.ModelSelect: no visible binding for global variable ‘counts’ DaMiR.iTSadjust: no visible binding for global variable ‘value’ DaMiR.iTSadjust: no visible binding for global variable ‘variable’ DaMiR.iTSnorm: no visible binding for global variable ‘value’ DaMiR.iTSnorm: no visible binding for global variable ‘variable’ Undefined global functions or variables: Accuracy Classifiers MCC N.predictors NPV PPV Sensitivity Specificity X1 X2 colSds counts value variable * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... WARNING Missing link or links in documentation object 'DaMiR.normalization.Rd': ‘estimateDispersions’ 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 ... 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 ... WARNING LazyData DB of 5.5 MB without LazyDataCompression set See §1.1.6 of 'Writing R Extensions' * checking data for ASCII and uncompressed saves ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed DaMiR.Allplot 6.26 0.267 6.528 * 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: 2 WARNINGs, 3 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/DaMiRseq.Rcheck/00check.log’ for details.