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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_1.17.16.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/autonomics.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* 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 ‘1.17.16’
* 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                  173.515 11.247 254.738
read_diann_proteingroups  117.651  3.850 127.954
awblinmod                  48.420  0.295  49.007
read_rnaseq_counts         35.969  3.792  40.909
rm_diann_contaminants      26.818  0.529  27.660
LINMOD                     25.764  0.346  26.268
plot_exprs                 22.498  0.233  23.033
plot_exprs_per_coef        22.014  0.198  22.376
default_formula            19.758  0.630  20.568
read_somascan              16.105  0.148  16.420
plot_volcano               16.057  0.166  16.306
read_metabolon             15.582  0.190  15.967
analyze                    15.224  0.234  15.575
plot_summary               14.878  0.118  15.063
fit_survival               13.114  0.122  13.316
explore-transforms         12.992  0.124  13.211
fcluster                   11.952  0.098  12.142
plot_densities             10.391  0.418  12.357
ftype                       9.283  0.302   9.675
read_fragpipe               8.335  0.205   8.651
biplot_covariates           8.282  0.080   8.413
plot_xy_density             7.978  0.066   8.100
plot_detections             7.944  0.060   8.077
plot_subgroup_points        6.542  0.145   6.935
subtract_baseline           6.239  0.146   6.462
code                        5.740  0.092   5.971
plot_violins                5.609  0.117   5.769
reset_fit                   5.414  0.152   5.657
extract_contrast_features   5.341  0.101   5.485
log2transform               5.214  0.045   5.286
sbind                       5.010  0.102   5.244
* 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.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL autonomics
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘autonomics’ ...
** this is package ‘autonomics’ version ‘1.17.16’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Note: wrong number of arguments to 'seq_along' 
Note: wrong number of arguments to 'sqrt' 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (autonomics)

R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(autonomics)

Attaching package: 'autonomics'

The following objects are masked from 'package:stats':

    biplot, loadings

The following object is masked from 'package:base':

    beta

> 
> test_check("autonomics")
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 158 ]

[ FAIL 0 | WARN 3 | SKIP 0 | PASS 158 ]
> 
> proc.time()
   user  system elapsed 
139.173  19.606 272.143