############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mistyR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mistyR_1.11.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/mistyR.Rcheck’ * using R Under development (unstable) (2024-01-16 r85808) * 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 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘mistyR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘mistyR’ 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 ‘mistyR’ 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 whether startup messages can be suppressed ... 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 aggregate_results: no visible binding for global variable ‘measure’ aggregate_results: no visible binding for global variable ‘target’ aggregate_results: no visible binding for global variable ‘value’ aggregate_results: no visible binding for global variable ‘sd’ aggregate_results: no visible binding for global variable ‘view’ aggregate_results: no visible binding for global variable ‘.PT’ aggregate_results: no visible binding for global variable ‘Importance’ aggregate_results_subset: no visible binding for global variable ‘view’ aggregate_results_subset: no visible binding for global variable ‘.PT’ aggregate_results_subset: no visible binding for global variable ‘Importance’ bagged_mars_model: no visible binding for global variable ‘index’ bagged_mars_model: no visible binding for global variable ‘prediction’ collect_results : : no visible binding for global variable ‘intra.RMSE’ collect_results : : no visible binding for global variable ‘multi.RMSE’ collect_results : : no visible binding for global variable ‘multi.R2’ collect_results : : no visible binding for global variable ‘intra.R2’ collect_results: no visible binding for global variable ‘target’ collect_results : : no visible binding for global variable ‘target’ collect_results : : no visible binding for global variable ‘view’ collect_results : : : no visible binding for global variable ‘value’ collect_results : : : no visible binding for global variable ‘Predictor’ collect_results : : : no visible binding for global variable ‘Importance’ extract_signature: no visible binding for global variable ‘measure’ extract_signature: no visible binding for global variable ‘target’ extract_signature: no visible binding for global variable ‘ts’ extract_signature: no visible binding for global variable ‘view’ extract_signature: no visible binding for global variable ‘value’ extract_signature : : no visible binding for global variable ‘Importance’ extract_signature : : no visible binding for global variable ‘Target’ extract_signature : : no visible binding for global variable ‘ts’ extract_signature : : no visible binding for global variable ‘Predictor’ gradient_boosting_model: no visible binding for global variable ‘index’ linear_model: no visible binding for global variable ‘index’ mars_model: no visible binding for global variable ‘index’ mlp_model: no visible binding for global variable ‘index’ plot_contrast_heatmap: no visible binding for global variable ‘view’ plot_contrast_heatmap: no visible binding for global variable ‘measure’ plot_contrast_heatmap: no visible binding for global variable ‘target’ plot_contrast_heatmap: no visible binding for global variable ‘Target’ plot_contrast_heatmap: no visible binding for global variable ‘nsamples’ plot_contrast_heatmap: no visible binding for global variable ‘Predictor’ plot_contrast_heatmap: no visible binding for global variable ‘Importance’ plot_contrast_results: no visible binding for global variable ‘view’ plot_contrast_results : : no visible binding for global variable ‘view’ plot_contrast_results : : no visible binding for global variable ‘Predictor’ plot_contrast_results : : no visible binding for global variable ‘Target’ plot_contrast_results: no visible binding for global variable ‘measure’ plot_contrast_results: no visible binding for global variable ‘target’ plot_contrast_results : : no visible binding for global variable ‘nsamples’ plot_contrast_results : : no visible binding for global variable ‘Importance’ plot_improvement_stats: no visible binding for global variable ‘target’ plot_improvement_stats: no visible binding for global variable ‘sd’ plot_interaction_communities: no visible binding for global variable ‘nsamples’ plot_interaction_communities: no visible binding for global variable ‘Predictor’ plot_interaction_heatmap: no visible binding for global variable ‘measure’ plot_interaction_heatmap: no visible binding for global variable ‘target’ plot_interaction_heatmap: no visible binding for global variable ‘Target’ plot_interaction_heatmap: no visible binding for global variable ‘Importance’ plot_interaction_heatmap: no visible binding for global variable ‘Predictor’ plot_interaction_heatmap: no visible binding for global variable ‘total’ plot_view_contributions: no visible binding for global variable ‘measure’ plot_view_contributions: no visible binding for global variable ‘target’ plot_view_contributions: no visible binding for global variable ‘fraction’ plot_view_contributions: no visible binding for global variable ‘view’ run_misty : : no visible binding for global variable ‘p’ run_misty : : no visible binding for global variable ‘intra.RMSE’ run_misty : : no visible binding for global variable ‘multi.RMSE’ run_misty : : no visible binding for global variable ‘intra.R2’ run_misty : : no visible binding for global variable ‘multi.R2’ svm_model: no visible binding for global variable ‘index’ Undefined global functions or variables: .PT Importance Predictor Target fraction index intra.R2 intra.RMSE measure multi.R2 multi.RMSE nsamples p prediction sd target total ts value view Consider adding importFrom("stats", "sd", "ts") 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed collect_results 267.595 17.516 334.758 reexports 88.846 5.958 110.484 run_misty 87.847 5.147 105.169 remove_views 57.370 5.270 72.497 add_paraview 46.301 2.719 57.213 add_juxtaview 13.588 0.524 16.488 create_view 13.882 0.170 17.337 plot_improvement_stats 8.444 0.450 10.897 plot_contrast_results 5.676 0.233 7.191 plot_contrast_heatmap 5.415 0.241 6.907 plot_interaction_heatmap 4.458 0.226 5.509 plot_view_contributions 4.205 0.227 5.300 plot_interaction_communities 4.201 0.229 5.286 extract_signature 3.894 0.223 5.052 * 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: 1 NOTE See ‘/Users/biocbuild/bbs-3.19-bioc/meat/mistyR.Rcheck/00check.log’ for details.