############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:autonomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings autonomics_1.14.7.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/autonomics.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘autonomics/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘autonomics’ version ‘1.14.7’ * 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 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 ‘autonomics’ 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 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 ... OK * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed read_diann_proteingroups 239.612 3.536 256.631 read_rnaseq_counts 65.958 2.767 71.764 plot_exprs_per_coef 62.422 0.325 63.299 plot_exprs 62.173 0.326 66.233 rm_diann_contaminants 49.335 0.656 51.365 default_formula 38.565 0.744 41.773 analyze 33.713 0.275 35.695 fit 32.278 0.471 34.892 plot_summary 32.448 0.176 34.444 read_metabolon 31.552 0.252 34.838 read_somascan 31.065 0.128 31.079 plot_volcano 24.741 0.193 26.584 plot_densities 21.368 0.334 24.486 ftype 17.497 0.799 21.022 read_fragpipe 16.923 0.518 17.562 code 17.231 0.156 18.469 plot_sample_nas 14.847 0.079 15.660 fcluster 13.990 0.116 14.758 extract_coef_features 13.224 0.130 14.077 biplot_covariates 12.739 0.133 13.232 reset_fit 12.450 0.223 12.019 plot_subgroup_points 11.318 0.116 12.180 subtract_baseline 10.918 0.146 11.513 fit_lmx 10.901 0.154 12.436 modelvar 9.230 0.139 10.354 plot_violins 9.217 0.117 9.873 biplot 8.966 0.110 9.396 log2transform 8.821 0.072 9.288 dot-plot_survival 8.262 0.553 9.444 explore_transformations 8.464 0.261 9.319 plot_contrastogram 7.920 0.268 9.302 biplot_corrections 7.953 0.101 8.462 impute 7.270 0.050 7.617 pca 7.135 0.115 8.031 plot_contrast_venn 5.787 0.106 6.573 add_facetvars 5.261 0.122 5.602 * 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-3.20-bioc/meat/autonomics.Rcheck/00check.log’ for details.