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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_1.14.8.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/autonomics.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘autonomics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘autonomics’ version ‘1.14.8’
* 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 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 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 107.679  3.557  96.072
read_rnaseq_counts        32.517  1.394  32.393
plot_exprs_per_coef       24.446  0.304  23.218
rm_diann_contaminants     23.368  0.923  19.621
plot_exprs                23.907  0.332  23.038
fit                       18.536  0.921  13.656
default_formula           17.578  0.748  15.954
analyze                   13.798  0.305  12.719
read_metabolon            13.745  0.253  12.934
plot_summary              13.680  0.197  13.413
read_somascan             13.209  0.161  12.526
plot_densities            11.055  0.344  10.111
plot_volcano              10.600  0.177  10.136
ftype                      9.158  0.741   7.598
read_fragpipe              7.875  0.305   6.264
fit_lmx                    6.303  0.332   4.570
fcluster                   6.478  0.142   5.975
plot_sample_nas            6.448  0.071   6.567
code                       6.333  0.112   6.226
reset_fit                  5.705  0.192   4.838
log2transform              5.487  0.086   5.598
dot-plot_survival          5.130  0.307   5.459
biplot_covariates          5.198  0.109   5.109
extract_coef_features      5.018  0.115   4.899
plot_subgroup_points       4.812  0.087   5.068
* 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
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/autonomics.Rcheck/00check.log’
for details.