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###
### Running command:
###
###   /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_1.14.9.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/autonomics.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-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 Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘autonomics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘autonomics’ version ‘1.14.9’
* 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 234.118  3.068 253.092
read_rnaseq_counts        63.325  2.672  67.292
plot_exprs_per_coef       62.093  0.248  63.025
plot_exprs                62.030  0.310  69.282
rm_diann_contaminants     47.470  0.570  48.737
default_formula           37.700  0.645  40.433
analyze                   33.932  0.211  35.384
fit                       32.085  0.311  34.137
plot_summary              32.207  0.157  33.566
read_metabolon            30.806  0.189  31.846
read_somascan             30.708  0.234  33.004
plot_volcano              25.153  0.179  27.770
plot_densities            20.972  0.291  23.210
code                      17.294  0.149  18.554
ftype                     16.926  0.421  18.220
read_fragpipe             16.029  0.221  17.068
plot_sample_nas           14.776  0.071  15.677
fcluster                  13.977  0.106  14.701
extract_coef_features     13.271  0.114  13.886
biplot_covariates         12.844  0.118  13.385
plot_subgroup_points      11.478  0.108  12.224
reset_fit                 11.326  0.113  11.628
fit_lmx                   10.946  0.105  11.663
subtract_baseline         10.376  0.233  10.701
modelvar                   9.219  0.109   9.772
plot_violins               9.201  0.107   9.765
biplot                     8.989  0.096   9.271
log2transform              8.848  0.075   9.969
explore_transformations    8.432  0.243   9.271
dot-plot_survival          8.111  0.551   9.050
plot_contrastogram         7.874  0.168   8.474
biplot_corrections         7.948  0.088   8.277
impute                     7.375  0.058   7.754
pca                        7.202  0.099   7.967
plot_contrast_venn         5.899  0.082   6.279
add_facetvars              5.175  0.106   5.476
sumexp_to_longdt           4.700  0.211   9.123
summarize_fit              4.457  0.119   8.992
sumexplist_to_longdt       3.956  0.036   7.911
write_xl                   2.013  0.092   5.261
* 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.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL autonomics
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘autonomics’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (autonomics)

R version 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(autonomics)

Attaching package: 'autonomics'

The following objects are masked from 'package:stats':

    biplot, loadings

The following object is masked from 'package:base':

    beta

> 
> test_check("autonomics")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 158 ]
> 
> proc.time()
   user  system elapsed 
278.758  21.782 396.519