############################################################################## ############################################################################## ### ### 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 235.820 3.529 259.598 read_rnaseq_counts 65.486 3.068 69.886 plot_exprs 61.847 0.352 66.127 plot_exprs_per_coef 61.646 0.333 63.955 rm_diann_contaminants 48.305 0.626 55.915 default_formula 38.031 0.719 41.167 analyze 33.620 0.266 35.337 fit 32.072 0.426 36.983 plot_summary 32.180 0.200 34.322 read_metabolon 31.701 0.284 37.321 read_somascan 31.601 0.182 32.866 plot_volcano 25.037 0.235 29.417 plot_densities 21.239 0.320 24.203 ftype 17.195 0.784 19.814 read_fragpipe 17.122 0.606 18.144 code 16.834 0.137 18.095 plot_sample_nas 14.711 0.069 15.790 fcluster 13.736 0.120 14.926 extract_coef_features 13.315 0.132 14.529 biplot_covariates 12.612 0.120 13.128 reset_fit 12.402 0.248 12.936 plot_subgroup_points 11.376 0.122 12.511 fit_lmx 11.012 0.152 12.978 subtract_baseline 10.854 0.174 12.267 plot_violins 9.119 0.135 9.947 modelvar 8.994 0.123 10.803 log2transform 8.861 0.074 9.913 biplot 8.791 0.111 9.432 dot-plot_survival 8.196 0.563 9.422 explore_transformations 8.402 0.283 9.677 plot_contrastogram 8.078 0.243 9.686 biplot_corrections 7.805 0.103 8.016 impute 7.330 0.054 7.846 pca 7.156 0.108 8.228 plot_contrast_venn 5.710 0.103 6.864 add_facetvars 5.218 0.120 5.806 sumexp_to_longdt 4.924 0.230 4.743 plot_fit_summary 4.724 0.100 5.083 summarize_fit 4.136 0.143 5.679 annotate_uniprot_rest 0.148 0.023 7.717 * 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.