############################################################################## ############################################################################## ### ### 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 38.068 1.511 47.010 plot_exprs_per_coef 34.013 0.235 35.363 plot_exprs 34.035 0.123 35.734 read_diann_proteingroups 33.021 0.337 43.531 default_formula 21.825 0.255 22.288 read_somascan 19.136 0.338 25.548 fit 17.978 0.144 18.945 plot_summary 17.655 0.211 18.637 analyze 17.516 0.112 17.675 read_metabolon 17.325 0.032 19.139 plot_volcano 13.861 0.087 15.453 plot_densities 12.150 0.096 12.699 ftype 9.608 0.099 10.164 code 9.439 0.008 9.561 read_fragpipe 8.358 0.108 10.293 plot_sample_nas 8.071 0.020 9.381 fcluster 7.861 0.024 8.067 extract_coef_features 7.367 0.032 7.732 rm_diann_contaminants 7.182 0.123 9.866 reset_fit 6.737 0.016 7.136 biplot_covariates 6.652 0.032 6.789 plot_subgroup_points 6.188 0.079 7.071 subtract_baseline 5.793 0.127 6.497 fit_lmx 5.868 0.024 5.905 plot_violins 5.240 0.024 5.283 modelvar 5.055 0.024 5.268 log2transform 4.983 0.028 5.057 explore_transformations 4.756 0.139 5.256 annotate_uniprot_rest 0.225 0.004 5.222 * 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.