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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_1.11.5.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/autonomics.Rcheck’
* using R Under development (unstable) (2023-11-11 r85510)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘autonomics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘autonomics’ version ‘1.11.5’
* 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 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 R 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_rnaseq_counts           29.690  1.294  32.869
is_sig                       30.087  0.213  31.384
filter_medoid                26.603  0.796  28.287
pca                          22.855  0.691  25.198
explore_imputations          20.481  0.417  21.330
fit_limma                    20.661  0.195  21.531
read_somascan                20.096  0.455  21.925
plot_detections              17.926  0.644  20.783
biplot_covariates            16.454  0.540  18.480
read_metabolon               15.621  0.579  17.688
read_rectangles              13.197  0.677  14.380
plot_venn                    12.664  0.230  13.980
summarize_fit                12.367  0.446  13.625
plot_features                12.305  0.328  13.397
plot_boxplots                10.841  0.413  12.616
analyze                      10.695  0.511  12.218
subtract_baseline            10.349  0.459  11.005
plot_violins                 10.218  0.404  11.516
explore_transformations      10.315  0.243  10.731
read_proteingroups            9.471  0.201  10.260
log2transform                 9.397  0.208  10.137
biplot_corrections            8.550  0.500   9.766
sumexp_to_long_dt             8.373  0.668   9.376
biplot                        8.285  0.421  10.041
plot_densities                5.113  0.500   6.519
plot_volcano                  5.132  0.135   5.658
impute_systematic_nondetects  5.027  0.145   5.278
center                        4.633  0.163  12.528
add_smiles                    4.083  0.399   5.139
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/autonomics.Rcheck/00check.log’
for details.