############################################################################## ############################################################################## ### ### 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_1.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/mistyR.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 ‘mistyR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘mistyR’ version ‘1.13.0’ * 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 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 ... 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 ... NOTE checkRd: (-1) collect_results.Rd:32: Lost braces; missing escapes or markup? 32 | for all performance measures for each {target} over all samples.} | ^ * 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 276.486 17.622 321.078 reexports 91.614 6.756 107.568 run_misty 90.962 5.875 102.072 remove_views 61.092 5.825 73.118 add_paraview 49.386 2.966 58.729 add_juxtaview 14.612 0.556 17.297 create_view 14.973 0.109 17.088 plot_improvement_stats 8.879 0.416 9.917 plot_contrast_results 6.186 0.228 7.184 plot_contrast_heatmap 5.807 0.224 6.770 plot_interaction_heatmap 4.768 0.212 5.470 plot_interaction_communities 4.482 0.216 5.153 plot_view_contributions 4.453 0.209 5.112 * 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 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/mistyR.Rcheck/00check.log’ for details.