############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:timeOmics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings timeOmics_1.19.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/timeOmics.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * using platform: aarch64-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 Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘timeOmics/DESCRIPTION’ ... OK * this is package ‘timeOmics’ version ‘1.19.0’ * package encoding: UTF-8 * 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' 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: .travis.yml 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 ‘timeOmics’ 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 ... NOTE Problems with news in ‘NEWS.md’: No news entries found. * 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 whether startup messages can be suppressed ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... WARNING getCluster: function(X, user.block, user.cluster) getCluster.UpDown: function(X, user.block, user.cluster, .by, .preserve, ...) filter: function(.data, ..., .by, .preserve) filter.cluster.df: function(.data, user.block, user.cluster) See section ‘Generic functions and methods’ in the ‘Writing R Extensions’ manual. * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .mutate_cluster: no visible binding for global variable ‘cluster’ .mutate_cluster: no visible binding for global variable ‘contrib.max’ check_legend.block.name: no visible global function definition for ‘is’ dmatrix.spearman.dissimilarity: no visible global function definition for ‘cor’ filter.cluster.df: no visible binding for global variable ‘block’ filter.cluster.df: no visible binding for global variable ‘cluster’ getCluster.block.pls: no visible binding for global variable ‘block’ getCluster.block.pls: no visible binding for global variable ‘molecule’ getCluster.block.pls: no visible binding for global variable ‘comp’ getCluster.block.spls: no visible binding for global variable ‘block’ getCluster.block.spls: no visible binding for global variable ‘molecule’ getCluster.block.spls: no visible binding for global variable ‘comp’ getCluster.mixo_pls: no visible binding for global variable ‘comp’ getCluster.mixo_spls: no visible binding for global variable ‘comp’ getCluster.pca: no visible binding for global variable ‘comp’ getCluster.spca: no visible binding for global variable ‘comp’ getNcomp: no visible global function definition for ‘is’ getUpDownCluster: no visible global function definition for ‘is’ get_MSE: no visible binding for global variable ‘feature’ get_MSE: no visible global function definition for ‘na.omit’ get_MSE: no visible binding for global variable ‘Y_i’ get_MSE: no visible binding for global variable ‘Y_hat’ get_MSE: no visible binding for global variable ‘error’ lmms.filter.lines: no visible global function definition for ‘is’ lmms.filter.lines: no visible global function definition for ‘slot’ lmms.filter.lines: no visible binding for global variable ‘feature’ lmms.filter.lines: no visible binding for global variable ‘BP.test’ lmms.filter.lines: no visible binding for global variable ‘MSE’ lmms.filter.lines: no visible binding for global variable ‘val’ lmms.filter.lines: no visible global function definition for ‘all_of’ plot.ncomp.tune.silhouette: no visible global function definition for ‘is’ plot.ncomp.tune.silhouette: no visible binding for global variable ‘ncomp’ plot.proportionality: no visible binding for global variable ‘cluster1’ plot.proportionality: no visible binding for global variable ‘value’ plot.proportionality: no visible binding for global variable ‘insideout’ plot.spca.tune.silhouette: no visible binding for global variable ‘comp’ plot.spca.tune.silhouette: no visible binding for global variable ‘X’ plot.spca.tune.silhouette: no visible binding for global variable ‘na.omit’ plot.spca.tune.silhouette: no visible binding for global variable ‘contrib’ plot.spca.tune.silhouette: no visible binding for global variable ‘value’ plotLong: no visible binding for global variable ‘block’ plotLong: no visible binding for global variable ‘new.block’ plotLong: no visible global function definition for ‘is’ plotLong: no visible binding for global variable ‘.’ plotLong: no visible binding for global variable ‘value’ plotLong: no visible binding for global variable ‘molecule’ proportionality: no visible binding for global variable ‘molecule’ proportionality: no visible binding for global variable ‘cluster’ proportionality: no visible binding for global variable ‘.’ proportionality : : no visible binding for global variable ‘.’ proportionality: no visible binding for global variable ‘feature1’ proportionality: no visible binding for global variable ‘feature2’ proportionality: no visible binding for global variable ‘cluster1’ proportionality: no visible binding for global variable ‘cluster2’ proportionality: no visible global function definition for ‘na.omit’ remove.low.cv: no visible global function definition for ‘is’ remove.low.cv : : no visible global function definition for ‘sd’ sd_new: no visible global function definition for ‘sd’ silhouette: no visible binding for global variable ‘silhouette.coef’ stat_median: no visible binding for global variable ‘cluster1’ stat_median: no visible binding for global variable ‘cluster2’ stat_median: no visible binding for global variable ‘value’ stat_median: no visible global function definition for ‘median’ stat_median: no visible binding for global variable ‘Pvalue’ stat_median: no visible binding for global variable ‘na.omit’ to_lr2phs: no visible global function definition for ‘var’ tune.silhouette.get_choice_keepX: no visible binding for global variable ‘comp’ tune.silhouette.get_choice_keepX: no visible binding for global variable ‘direction’ tune.silhouette.get_choice_keepX: no visible binding for global variable ‘Pval.pos’ tune.silhouette.get_choice_keepX: no visible binding for global variable ‘Pval.neg’ tune.silhouette.get_choice_keepX: no visible binding for global variable ‘distance_from_origin’ tune.silhouette.get_choice_keepX: no visible binding for global variable ‘Pval.dir’ tune.silhouette.get_choice_keepX: no visible binding for global variable ‘Pval.value’ tune.silhouette.get_choice_keepX: no visible global function definition for ‘na.omit’ tune.silhouette.get_choice_keepX : : no visible binding for global variable ‘Pval.value’ tune.silhouette.get_choice_keepX : : no visible binding for global variable ‘distance_from_origin’ tune.silhouette.get_choice_keepX : : no visible binding for global variable ‘.’ tune.silhouette.get_slopes: no visible global function definition for ‘is’ tune.silhouette.get_slopes: no visible binding for global variable ‘origin’ tune.silhouette.get_slopes: no visible binding for global variable ‘destination’ tune.silhouette.get_slopes: no visible binding for global variable ‘.’ tune.silhouette.get_slopes: no visible binding for global variable ‘comp’ tune.silhouette.get_slopes: no visible binding for global variable ‘direction’ tune.silhouette.get_slopes: no visible binding for global variable ‘slope.pos’ tune.silhouette.get_slopes: no visible binding for global variable ‘slope.neg’ tune.silhouette.get_slopes: no visible binding for global variable ‘Z_score.pos’ tune.silhouette.get_slopes: no visible global function definition for ‘pnorm’ tune.silhouette.get_slopes: no visible binding for global variable ‘Z_score.neg’ tuneCluster.block.spls: no visible binding for global variable ‘silhouette.coef’ tuneCluster.spca: no visible binding for global variable ‘silhouette.coef’ tuneCluster.spls: no visible binding for global variable ‘silhouette.coef’ unscale: no visible global function definition for ‘is’ Undefined global functions or variables: . BP.test MSE Pval.dir Pval.neg Pval.pos Pval.value Pvalue X Y_hat Y_i Z_score.neg Z_score.pos all_of block cluster cluster1 cluster2 comp contrib contrib.max cor destination direction distance_from_origin error feature feature1 feature2 insideout is median molecule na.omit ncomp new.block origin pnorm sd silhouette.coef slope.neg slope.pos slot val value var Consider adding importFrom("methods", "is", "slot") importFrom("stats", "cor", "median", "na.omit", "pnorm", "sd", "var") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: getNcomp.Rd: silhouette Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * checking for missing documentation entries ... WARNING Undocumented code objects: ‘timeOmics.simdata’ Undocumented data sets: ‘timeOmics.simdata’ All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 R/sysdata.rda ... 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 ... 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, 4 NOTEs See ‘/Users/biocbuild/bbs-3.21-bioc/meat/timeOmics.Rcheck/00check.log’ for details.