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### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:autonomics.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings autonomics_1.17.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/autonomics.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'autonomics/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'autonomics' version '1.17.0'
* 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 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
read_diann_proteingroups 153.29   6.40  156.38
read_rnaseq_counts        41.83   2.45   49.78
fit_linmod                38.92   0.47   39.56
rm_diann_contaminants     30.69   1.25   31.10
plot_exprs_per_coef       28.41   0.31   28.74
plot_exprs                26.62   0.33   27.48
default_formula           19.47   0.61   19.94
plot_summary              18.92   0.25   19.17
read_metabolon            18.77   0.16   18.92
read_somascan             18.83   0.05   18.87
analyze                   17.14   0.31   17.48
plot_volcano              16.50   0.27   16.94
ftype                     11.50   0.46   12.03
read_fragpipe             10.71   0.27   10.91
fcluster                   8.83   0.14    9.02
extract_coef_features      8.36   0.11    8.50
plot_densities             7.97   0.20    8.18
plot_sample_nas            7.66   0.08    7.75
code                       7.01   0.11    7.12
biplot_covariates          6.87   0.11    6.98
fit_survival               6.77   0.12    7.39
reset_fit                  6.55   0.11    6.68
subtract_baseline          6.20   0.13    6.33
plot_subgroup_points       6.06   0.07    6.14
plot_violins               5.08   0.19    5.26
biplot                     5.17   0.08    5.25
plot_survival              5.10   0.08    5.20
* 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
  'F:/biocbuild/bbs-3.22-bioc/meat/autonomics.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL autonomics
###
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* installing to library 'F:/biocbuild/bbs-3.22-bioc/R/library'
* installing *source* package 'autonomics' ...
** this is package 'autonomics' version '1.17.0'
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** 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 (2025-06-13 ucrt) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 2 | SKIP 0 | PASS 158 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 158 ]
> 
> proc.time()
   user  system elapsed 
 190.85   13.92  214.36