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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: aarch64-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 Ventura 13.7.1
* 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 102.442  3.169  95.666
read_rnaseq_counts        33.387  1.413  32.652
plot_exprs                26.177  0.393  24.740
plot_exprs_per_coef       24.934  0.346  23.458
rm_diann_contaminants     24.323  0.813  20.319
fit                       18.681  0.939  13.713
default_formula           17.636  0.785  15.992
analyze                   13.867  0.304  12.705
read_metabolon            13.660  0.243  12.841
read_somascan             13.354  0.232  12.446
plot_summary              13.054  0.265  11.898
plot_densities            11.213  0.349  10.417
plot_volcano              10.287  0.206   9.802
ftype                      9.837  0.642   8.211
read_fragpipe              7.865  0.378   6.825
plot_sample_nas            6.883  0.126   6.193
fcluster                   6.490  0.148   6.033
fit_lmx                    6.269  0.333   4.588
code                       6.208  0.102   6.095
reset_fit                  5.695  0.216   4.722
dot-plot_survival          5.092  0.298   5.402
biplot_covariates          5.249  0.100   5.123
plot_subgroup_points       5.186  0.136   4.676
extract_coef_features      4.918  0.109   4.806
* 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.