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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_1.18.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/autonomics.Rcheck’
* using R version 4.5.2 Patched (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘autonomics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘autonomics’ version ‘1.18.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 32 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 ... NOTE
Non-topic package-anchored link(s) in Rd file 'reexports.Rd':
  ‘[magrittr:compound]{%<>%}’ ‘[magrittr:pipe]{%>%}’
  ‘[magrittr:aliases]{extract}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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
write_xl                  193.788  5.991 311.897
read_diann_proteingroups  116.733  1.998 184.390
awblinmod                  46.396  0.440  74.014
read_rnaseq_counts         35.199  1.288  58.168
LINMOD                     26.936  0.406  42.490
rm_diann_contaminants      24.232  0.429  42.267
plot_exprs                 23.871  0.229  40.743
plot_exprs_per_coef        22.608  0.201  38.455
default_formula            20.217  0.456  33.967
plot_volcano               15.876  0.178  27.549
analyze                    15.283  0.223  24.017
plot_summary               15.331  0.166  26.325
read_metabolon             14.327  0.176  24.490
read_somascan              14.255  0.111  25.184
fit_survival               13.778  0.181  21.634
plot_densities             11.967  0.262  18.686
explore-transforms         11.608  0.129  18.275
fcluster                   10.432  0.109  15.944
ftype                       8.542  0.319  13.928
plot_detections             8.636  0.079  13.357
read_fragpipe               8.439  0.185  14.528
biplot_covariates           8.061  0.112  13.079
plot_xy_density             7.472  0.072  12.852
plot_subgroup_points        6.893  0.108  11.938
plot_violins                5.929  0.110  10.150
subtract_baseline           5.682  0.091   9.033
log2transform               5.448  0.072   8.748
code                        5.278  0.084   8.809
reset_fit                   5.081  0.121   9.600
extract_contrast_features   5.011  0.082   7.805
sbind                       4.807  0.055   8.557
biplot                      4.339  0.084   6.927
biplot_corrections          3.995  0.075   6.318
modelvar                    3.709  0.078   5.778
impute                      3.737  0.046   6.020
pca                         3.624  0.078   5.627
plot_contrastogram          3.231  0.139   5.240
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/autonomics.Rcheck/00check.log’
for details.