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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_1.14.7.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/autonomics.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* 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 ‘1.14.7’
* 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 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 241.655  3.900 264.588
read_rnaseq_counts        66.183  2.990  74.330
plot_exprs_per_coef       63.059  0.358  65.548
plot_exprs                62.883  0.448  69.019
rm_diann_contaminants     49.464  0.721  53.614
default_formula           38.414  0.886  41.995
analyze                   34.137  0.331  36.602
plot_summary              32.698  0.247  35.056
fit                       32.238  0.516  36.068
read_somascan             31.953  0.173  34.728
read_metabolon            31.520  0.276  32.903
plot_volcano              25.300  0.291  27.508
plot_densities            21.360  0.359  24.718
ftype                     17.555  0.832  20.299
code                      17.262  0.191  18.970
read_fragpipe             16.890  0.374  17.164
plot_sample_nas           15.017  0.086  16.121
fcluster                  14.213  0.132  15.424
biplot_covariates         13.676  0.144  12.531
extract_coef_features     13.470  0.159  14.655
reset_fit                 12.338  0.190  11.833
plot_subgroup_points      11.514  0.138  12.474
subtract_baseline         11.124  0.211  12.692
fit_lmx                   10.999  0.156  12.375
modelvar                   9.356  0.136  10.545
plot_violins               9.351  0.133  10.101
biplot                     9.024  0.128   9.721
log2transform              8.853  0.079   9.471
dot-plot_survival          8.341  0.586   9.580
explore_transformations    8.466  0.283   9.556
plot_contrastogram         7.940  0.273   9.401
biplot_corrections         7.991  0.110   8.537
pca                        7.276  0.131   8.221
impute                     7.339  0.056   7.550
plot_contrast_venn         5.953  0.125   7.123
sumexp_to_longdt           5.048  0.424   5.613
add_facetvars              5.300  0.130   5.827
plot_fit_summary           4.719  0.103   5.329
* 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-3.20-bioc/meat/autonomics.Rcheck/00check.log’
for details.