############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:autonomics.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings autonomics_1.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/autonomics.Rcheck' * using R version 4.1.3 (2022-03-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'autonomics/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'autonomics' version '1.2.0' * 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 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 R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 ... WARNING Undocumented arguments in documentation object 'normimpute' 'ref' 'pos' Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed read_rnaseq_counts 22.15 0.86 22.57 pca 15.64 0.09 15.73 is_sig 13.05 0.11 13.00 filter_medoid 12.36 0.15 12.78 explore_imputations 11.50 0.14 11.50 biplot_covariates 11.06 0.17 11.24 plot_detections 11.01 0.19 10.86 read_somascan 10.67 0.19 10.85 read_rectangles 9.60 0.39 10.32 fit_limma 8.88 0.03 8.86 summarize_fit 7.32 0.47 7.52 read_metabolon 7.50 0.16 7.65 sumexp_to_long_dt 6.16 0.24 6.09 biplot_corrections 6.05 0.19 6.23 analyze 5.44 0.25 7.72 explore_transformations 5.36 0.13 5.40 read_proteingroups 5.36 0.12 5.33 plot_violins 5.19 0.08 5.26 plot_venn 5.17 0.08 5.22 add_smiles 3.05 0.22 5.89 counts 2.99 0.11 19.87 download_data 2.79 0.14 9.42 merge_sfile 2.64 0.25 30.36 center 2.59 0.25 162.87 analysis 2.30 0.19 16.36 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed read_rnaseq_counts 20.43 0.84 20.89 is_sig 12.39 0.08 12.34 filter_medoid 12.03 0.05 12.07 pca 11.64 0.07 11.72 explore_imputations 11.48 0.13 11.47 read_somascan 10.07 0.08 10.55 read_rectangles 9.28 0.42 9.70 plot_detections 8.50 0.22 8.44 fit_limma 8.28 0.05 8.29 biplot_covariates 7.68 0.13 7.81 read_metabolon 7.18 0.11 7.60 summarize_fit 6.36 0.25 6.44 read_proteingroups 5.90 0.14 5.87 explore_transformations 5.69 0.07 5.77 subtract_baseline 5.58 0.10 7.38 analyze 5.43 0.20 7.41 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'testthat.R' OK ** running tests for arch 'x64' ... Running 'testthat.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 1 NOTE See 'C:/Users/biocbuild/bbs-3.14-bioc/meat/autonomics.Rcheck/00check.log' for details.