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### Running command:
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###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:autonomics.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings autonomics_1.14.8.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/autonomics.Rcheck'
* using R version 4.4.2 (2024-10-31 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 '1.14.8'
* 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 143.37   5.75  145.40
read_rnaseq_counts        37.20   1.77   39.20
rm_diann_contaminants     31.48   1.46   32.52
plot_exprs                30.86   0.36   31.22
plot_exprs_per_coef       30.61   0.37   31.02
default_formula           18.69   0.60   19.30
read_metabolon            16.74   0.33   17.04
fit                       16.39   0.39   17.77
read_somascan             16.58   0.18   16.76
analyze                   16.23   0.17   17.01
plot_summary              16.17   0.19   16.36
plot_volcano              13.80   0.25   14.06
plot_densities            11.89   0.31   12.21
read_fragpipe             10.95   0.30   11.08
code                       8.96   0.11    9.07
ftype                      7.97   0.28    8.44
fcluster                   7.75   0.20    9.01
plot_sample_nas            7.72   0.04    7.77
extract_coef_features      6.41   0.11    6.51
plot_subgroup_points       6.30   0.16    6.47
reset_fit                  6.28   0.14    6.44
biplot_covariates          6.07   0.08    6.26
subtract_baseline          5.85   0.17    6.00
dot-plot_survival          5.13   0.65    6.39
plot_violins               5.39   0.19    5.58
fit_lmx                    5.45   0.11    5.57
* 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
  'F:/biocbuild/bbs-3.20-bioc/meat/autonomics.Rcheck/00check.log'
for details.