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### Running command:
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###   /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_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/autonomics.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘autonomics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘autonomics’ version ‘1.8.0’
* 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 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 R 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 ... 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                               user system elapsed
read_rnaseq_counts           29.814  1.026  41.597
is_sig                       29.152  0.231  38.875
filter_medoid                26.314  0.502  33.050
pca                          22.703  0.467  30.630
explore_imputations          21.151  0.337  27.956
fit_limma                    20.989  0.269  26.983
read_somascan                19.742  0.354  26.683
plot_detections              19.162  0.491  25.666
biplot_covariates            17.227  0.394  23.804
read_metabolon               16.789  0.447  23.115
summarize_fit                13.430  0.325  17.610
read_rectangles              12.414  0.712  17.690
plot_features                12.274  0.290  16.524
plot_venn                    11.997  0.164  15.792
analyze                      11.561  0.564  15.671
plot_boxplots                11.233  0.276  15.147
subtract_baseline            10.603  0.374  14.537
plot_violins                 10.390  0.306  14.359
explore_transformations      10.098  0.219  12.589
log2transform                 9.370  0.199  12.639
read_proteingroups            9.177  0.219  12.576
biplot_corrections            8.932  0.390  12.988
sumexp_to_long_dt             8.332  0.535  11.789
biplot                        7.269  0.349  10.772
plot_densities                5.271  0.354   7.389
impute_systematic_nondetects  5.092  0.173   6.915
plot_volcano                  5.140  0.124   7.192
create_design                 4.879  0.137   6.401
center                        4.533  0.143   6.443
add_smiles                    4.002  0.513  11.851
weights                       4.217  0.232   5.669
contrastdefs                  4.263  0.117   5.974
limma                         4.108  0.104   5.549
make_volcano_dt               4.045  0.109   5.431
plot_data                     3.805  0.281   5.441
preprocess_rnaseq_counts      3.866  0.164   5.415
sumexp2mae                    3.630  0.317   5.235
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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
  ‘/Users/biocbuild/bbs-3.17-bioc/meat/autonomics.Rcheck/00check.log’
for details.