############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:autonomics.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings autonomics_1.14.8.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/autonomics.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 12.3.1 (openEuler 12.3.1-36.oe2403) * running under: openEuler 24.03 (LTS) * 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 loading without being on the library search path ... 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_rnaseq_counts 38.765 1.316 62.007 read_diann_proteingroups 34.443 0.849 42.909 plot_exprs_per_coef 34.334 0.142 43.488 plot_exprs 33.493 0.174 40.969 default_formula 22.699 0.471 30.389 read_somascan 18.850 0.063 28.260 fit 18.494 0.315 21.823 analyze 18.607 0.178 20.700 read_metabolon 18.501 0.235 24.553 plot_summary 17.850 0.135 25.850 plot_volcano 14.204 0.059 19.018 plot_densities 12.356 0.124 16.887 ftype 9.785 0.088 11.628 code 9.152 0.166 11.867 rm_diann_contaminants 8.128 0.280 15.958 fcluster 8.177 0.216 11.546 read_fragpipe 8.316 0.047 9.745 plot_sample_nas 8.242 0.024 8.898 extract_coef_features 7.526 0.259 9.613 biplot_covariates 7.046 0.179 9.451 reset_fit 6.765 0.096 11.782 fit_lmx 6.451 0.048 9.005 plot_subgroup_points 6.377 0.016 8.270 subtract_baseline 5.814 0.035 6.171 log2transform 5.492 0.063 8.211 plot_violins 5.379 0.101 7.031 modelvar 5.188 0.060 6.046 dot-plot_survival 4.955 0.163 5.636 explore_transformations 4.679 0.331 5.095 biplot 4.786 0.191 5.740 biplot_corrections 4.404 0.152 7.485 impute 4.516 0.024 9.117 plot_contrastogram 4.410 0.004 5.455 plot_heatmap 2.656 0.004 5.001 * 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 ‘/home/biocbuild/bbs-3.20-bioc/meat/autonomics.Rcheck/00check.log’ for details.