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### Running command:
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###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:autonomics.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings autonomics_1.15.143.tar.gz
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/autonomics.Rcheck'
* using R Under development (unstable) (2025-01-21 r87610 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* 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 '1.15.143'
* 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 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 147.67   4.78  149.34
read_rnaseq_counts        39.42   2.24   42.16
fit_linmod                39.15   0.52   39.76
rm_diann_contaminants     30.30   1.06   30.50
plot_exprs_per_coef       27.27   0.28   27.58
plot_exprs                26.71   0.27   26.99
default_formula           21.37   0.53   21.87
plot_summary              18.14   0.13   18.29
read_somascan             17.97   0.15   18.14
read_metabolon            17.37   0.18   17.55
plot_volcano              15.57   0.21   15.80
analyze                   15.45   0.21   15.67
ftype                      9.91   0.44   10.86
read_fragpipe             10.03   0.31   10.31
plot_densities             9.05   0.29    9.47
fcluster                   8.80   0.08    8.88
extract_coef_features      8.01   0.08    8.09
plot_sample_nas            7.76   0.11    7.87
reset_fit                  7.00   0.11    7.11
fit_survival               6.54   0.08    6.97
code                       5.89   0.11    6.00
plot_subgroup_points       5.78   0.14    5.92
subtract_baseline          5.74   0.16    5.89
biplot_covariates          5.05   0.05    5.11
* 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
  'E:/biocbuild/bbs-3.21-bioc/meat/autonomics.Rcheck/00check.log'
for details.