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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_1.15.143.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/autonomics.Rcheck’
* using R Under development (unstable) (2025-01-22 r87618)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* 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 ‘1.15.143’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 30 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ... 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_diann_proteingroups 105.834  2.033 108.868
read_rnaseq_counts        36.416  3.238  40.226
fit_linmod                32.479  0.283  32.913
plot_exprs_per_coef       25.334  0.164  25.617
plot_exprs                24.165  0.211  24.522
rm_diann_contaminants     21.864  0.448  22.544
default_formula           18.789  0.339  19.304
read_somascan             15.950  0.104  16.190
read_metabolon            15.746  0.146  16.008
analyze                   15.530  0.162  15.795
plot_summary              15.379  0.124  15.571
plot_volcano              12.976  0.120  13.153
plot_densities             8.541  0.231   8.844
ftype                      8.472  0.243   8.785
extract_coef_features      7.322  0.069   7.420
plot_sample_nas            6.623  0.085   6.759
fcluster                   6.569  0.062   6.656
read_fragpipe              6.190  0.101   6.360
code                       5.482  0.080   5.599
biplot_covariates          5.469  0.085   5.590
reset_fit                  5.397  0.080   5.524
fit_survival               5.318  0.054   5.403
plot_subgroup_points       5.041  0.080   5.151
subtract_baseline          4.923  0.196   5.179
* 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
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/autonomics.Rcheck/00check.log’
for details.