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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_1.15.36.tar.gz
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/autonomics.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* 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 '1.15.36'
* 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 167.18   4.50  168.40
rm_diann_contaminants     36.90   1.32   38.11
read_rnaseq_counts        35.83   1.84   37.95
fit                       25.92   0.33   26.26
plot_exprs_per_coef       24.47   0.31   24.80
plot_exprs                23.39   0.30   23.69
default_formula           21.76   0.80   22.47
plot_volcano              19.03   0.33   19.37
read_somascan             16.35   0.05   16.41
read_metabolon            15.75   0.19   15.94
plot_summary              14.89   0.24   15.14
analyze                   13.50   0.27   13.78
read_fragpipe             11.42   0.20   11.49
plot_densities            10.57   0.13   10.72
ftype                      9.16   0.21    9.39
fcluster                   7.49   0.19    7.67
extract_coef_features      6.76   0.09    6.86
code                       6.34   0.11    6.45
biplot_covariates          6.27   0.09    6.36
plot_sample_nas            6.20   0.10    6.46
reset_fit                  5.47   0.11    5.58
dot-plot_survival          4.78   0.66    5.43
subtract_baseline          5.07   0.14    5.23
log2transform              5.03   0.04    5.09
* 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.