############################################################################## ############################################################################## ### ### 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 238.857 3.518 267.422 read_rnaseq_counts 66.431 2.764 72.304 plot_exprs 62.617 0.341 70.377 plot_exprs_per_coef 62.591 0.365 65.862 rm_diann_contaminants 50.018 0.957 56.254 default_formula 38.270 0.747 42.909 analyze 33.957 0.260 37.248 plot_summary 32.419 0.196 35.615 fit 32.120 0.438 37.123 read_metabolon 31.431 0.282 37.394 read_somascan 31.424 0.211 34.493 plot_volcano 25.033 0.210 28.171 plot_densities 21.351 0.319 25.602 ftype 17.557 0.767 20.837 code 17.235 0.159 19.069 read_fragpipe 16.715 0.566 20.281 plot_sample_nas 14.962 0.081 16.747 fcluster 14.015 0.116 15.443 extract_coef_features 13.402 0.141 14.815 biplot_covariates 12.947 0.127 14.193 reset_fit 11.923 0.261 13.319 plot_subgroup_points 11.575 0.123 13.019 fit_lmx 10.948 0.144 12.564 subtract_baseline 10.916 0.135 11.293 plot_violins 9.188 0.123 10.226 modelvar 9.149 0.131 10.835 biplot 8.912 0.110 9.540 log2transform 8.903 0.069 9.815 dot-plot_survival 8.279 0.553 9.646 explore_transformations 8.498 0.263 9.662 biplot_corrections 7.992 0.107 8.695 plot_contrastogram 7.852 0.241 9.403 impute 7.401 0.055 8.059 pca 7.226 0.113 8.462 plot_contrast_venn 5.828 0.100 6.965 add_facetvars 5.249 0.111 5.906 plot_fit_summary 4.705 0.093 5.270 plot_heatmap 4.518 0.024 5.047 read_olink 2.484 0.093 5.001 download_contaminants 0.082 0.012 7.641 * 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.