############################################################################## ############################################################################## ### ### 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_1.12.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/autonomics.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 ‘1.12.1’ * 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 ... NOTE checkRd: (-1) dequantify.Rd:24: Lost braces; missing escapes or markup? 24 | Encode {channel} as suffix. | ^ * 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 245.496 3.908 302.357 read_rnaseq_counts 62.243 3.109 77.865 plot_exprs 54.504 0.504 66.605 plot_exprs_per_coef 51.037 0.515 62.908 rm_diann_contaminants 49.941 0.685 60.978 default_formula 40.937 0.996 49.700 analyze 33.014 0.329 38.727 fit 31.617 0.488 38.423 read_somascan 31.702 0.231 39.159 plot_summary 31.373 0.350 38.670 read_metabolon 30.900 0.285 37.959 plot_volcano 26.015 0.300 32.069 plot_densities 21.314 0.446 26.329 read_fragpipe 16.671 0.366 20.541 plot_sample_nas 15.591 0.172 19.600 code 13.430 0.170 15.876 biplot_covariates 13.281 0.166 16.949 extract_coef_features 12.475 0.174 14.628 subtract_baseline 11.647 0.460 13.947 plot_subgroup_points 11.505 0.197 14.858 fit_lmx 11.359 0.217 14.513 reset_fit 10.575 0.168 13.850 plot_violins 9.772 0.182 12.082 biplot 9.368 0.144 11.841 log2transform 9.189 0.097 11.084 dot-plot_survival 8.347 0.724 10.803 explore_transformations 8.619 0.094 10.306 biplot_corrections 8.299 0.128 10.065 impute 7.768 0.084 9.398 pca 7.559 0.134 9.258 plot_contrastogram 5.900 0.263 7.869 sumexp_to_longdt 4.754 0.211 6.008 plot_contrast_venn 4.838 0.124 6.546 plot_fit_summary 4.631 0.120 5.791 add_facetvars 4.375 0.201 5.490 plot_heatmap 4.480 0.044 5.410 modelvar 4.316 0.130 5.413 read_olink 3.804 0.215 5.062 * 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/autonomics.Rcheck/00check.log’ for details.