############################################################################## ############################################################################## ### ### 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_1.14.8.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 ‘1.14.8’ * 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 239.007 3.196 255.237 read_rnaseq_counts 66.040 2.898 69.818 plot_exprs_per_coef 62.849 0.324 63.887 plot_exprs 62.787 0.344 70.349 rm_diann_contaminants 50.588 0.646 49.843 default_formula 38.371 0.751 41.767 analyze 33.877 0.235 35.380 fit 32.594 0.490 35.035 plot_summary 32.439 0.174 34.267 read_somascan 31.600 0.174 32.893 read_metabolon 31.261 0.204 32.837 plot_volcano 24.868 0.180 26.840 plot_densities 21.137 0.339 23.344 ftype 17.257 0.622 19.242 read_fragpipe 16.867 0.593 18.851 code 16.956 0.139 17.692 plot_sample_nas 14.926 0.081 15.720 fcluster 13.870 0.112 14.784 extract_coef_features 13.718 0.131 14.494 biplot_covariates 12.692 0.115 13.095 reset_fit 12.151 0.141 13.261 fit_lmx 11.489 0.172 11.947 plot_subgroup_points 11.415 0.114 11.947 subtract_baseline 11.004 0.190 11.965 plot_violins 9.158 0.119 10.072 modelvar 9.017 0.119 9.703 biplot 8.878 0.111 9.360 log2transform 8.834 0.082 9.451 explore_transformations 8.445 0.279 9.307 dot-plot_survival 8.175 0.535 9.156 plot_contrastogram 7.947 0.247 8.578 biplot_corrections 7.790 0.102 8.184 impute 7.334 0.063 7.705 pca 7.208 0.109 7.766 plot_contrast_venn 5.998 0.111 6.639 add_facetvars 5.260 0.121 5.543 plot_fit_summary 4.720 0.100 5.019 sumexp_to_longdt 4.579 0.228 5.080 download_contaminants 0.082 0.013 7.885 * 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.