############################################################################## ############################################################################## ### ### 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 243.482 5.162 276.764 read_rnaseq_counts 66.615 3.017 74.859 plot_exprs_per_coef 64.229 0.536 68.593 plot_exprs 63.337 0.836 74.804 rm_diann_contaminants 50.040 1.003 55.243 default_formula 38.571 0.949 43.811 analyze 34.195 0.398 37.472 fit 32.620 0.623 37.802 plot_summary 32.924 0.299 36.414 read_metabolon 31.895 0.622 35.106 read_somascan 32.241 0.276 36.603 plot_volcano 25.562 0.430 28.911 plot_densities 20.043 0.358 23.323 ftype 17.470 0.663 20.618 code 17.433 0.224 19.628 read_fragpipe 16.390 0.381 18.116 plot_sample_nas 15.024 0.129 16.682 fcluster 14.204 0.197 15.861 extract_coef_features 13.602 0.186 15.087 biplot_covariates 12.913 0.192 14.002 reset_fit 12.304 0.203 12.024 subtract_baseline 11.517 0.499 13.735 plot_subgroup_points 11.599 0.181 13.120 fit_lmx 11.185 0.250 13.008 log2transform 10.132 0.228 11.339 plot_violins 9.397 0.170 10.488 modelvar 9.079 0.154 10.300 biplot 9.012 0.151 10.005 dot-plot_survival 8.350 0.713 10.341 explore_transformations 8.542 0.330 9.852 biplot_corrections 8.004 0.126 8.699 plot_contrastogram 7.778 0.305 9.059 impute 7.363 0.098 8.395 pca 7.194 0.152 8.290 plot_contrast_venn 5.870 0.138 6.752 add_facetvars 5.270 0.140 5.896 sumexp_to_longdt 4.682 0.245 5.598 plot_fit_summary 4.619 0.117 5.009 download_contaminants 0.082 0.012 9.261 * 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.