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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_1.12.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/autonomics.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘autonomics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘autonomics’ version ‘1.12.1’
* 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 ... NOTE
checkRd: (-1) dequantify.Rd:24: Lost braces; missing escapes or markup?
    24 | Encode {channel} as suffix.
       |        ^
* 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 233.598  3.124 268.352
read_rnaseq_counts        62.174  2.901  74.660
plot_exprs                54.060  0.434  62.232
rm_diann_contaminants     49.128  0.773  57.593
plot_exprs_per_coef       48.851  0.337  55.624
default_formula           36.609  0.739  41.842
analyze                   32.590  0.274  38.128
plot_summary              31.396  0.239  36.881
read_somascan             31.225  0.273  37.205
fit                       31.074  0.400  36.593
read_metabolon            30.125  0.258  34.630
plot_volcano              24.829  0.231  28.779
plot_densities            20.641  0.305  24.006
plot_sample_nas           15.253  0.108  17.757
read_fragpipe             14.406  0.309  16.708
biplot_covariates         13.505  0.176  16.100
code                      13.130  0.189  14.549
extract_coef_features     12.883  0.278  15.573
plot_subgroup_points      11.744  0.146  13.920
fit_lmx                   11.221  0.150  13.352
subtract_baseline         11.056  0.146  12.750
reset_fit                 10.653  0.167  13.314
plot_violins               9.834  0.145  11.709
biplot                     9.472  0.139  11.184
log2transform              9.032  0.126  10.508
dot-plot_survival          8.482  0.671  10.803
explore_transformations    8.839  0.289  10.387
biplot_corrections         8.333  0.145   9.759
impute                     7.853  0.084   9.207
pca                        7.383  0.122   8.795
plot_contrastogram         5.823  0.265   7.154
add_facetvars              5.133  0.210   6.119
sumexp_to_longdt           4.674  0.195   5.587
plot_contrast_venn         4.726  0.102   5.739
plot_fit_summary           4.718  0.095   5.412
center                     4.557  0.061   5.339
plot_heatmap               4.371  0.029   5.036
modelvar                   4.223  0.133   5.097
annotate_uniprot_rest      0.143  0.021   7.822
download_contaminants      0.043  0.011   7.537
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 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

> 
> test_check("autonomics")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 159 ]
> 
> proc.time()
   user  system elapsed 
277.914  11.303 315.809