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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 4.4.1 (2024-06-14)
* 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 ‘1.12.1’
* 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 244.967  3.808 297.161
read_rnaseq_counts        62.250  3.039  77.733
plot_exprs                53.951  0.420  63.684
rm_diann_contaminants     50.231  0.614  59.276
plot_exprs_per_coef       50.256  0.448  59.476
default_formula           40.946  0.932  49.882
analyze                   32.522  0.343  37.619
read_somascan             31.536  0.231  40.028
plot_summary              31.344  0.285  36.693
fit                       31.101  0.495  38.226
read_metabolon            30.240  0.272  37.345
plot_volcano              24.936  0.257  29.311
plot_densities            20.706  0.437  24.861
read_fragpipe             16.744  0.367  20.703
plot_sample_nas           15.353  0.109  18.050
biplot_covariates         13.204  0.176  16.141
code                      13.049  0.157  15.977
extract_coef_features     12.518  0.155  15.131
plot_subgroup_points      11.423  0.153  13.939
subtract_baseline         11.351  0.202  12.971
fit_lmx                   11.134  0.166  13.979
reset_fit                 10.559  0.161  12.632
plot_violins               9.719  0.155  11.526
biplot                     9.176  0.135  11.292
log2transform              8.997  0.089  10.789
dot-plot_survival          8.156  0.701  10.588
explore_transformations    8.561  0.086  10.303
biplot_corrections         8.184  0.134  10.112
pca                        7.513  0.124   8.889
impute                     7.503  0.067   8.897
plot_contrastogram         5.866  0.265   7.287
plot_contrast_venn         4.861  0.115   5.778
sumexp_to_longdt           4.700  0.215   5.475
plot_fit_summary           4.685  0.107   5.495
add_facetvars              4.345  0.207   5.194
plot_heatmap               4.447  0.029   5.059
modelvar                   4.235  0.108   5.153
* 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 4.4.1 (2024-06-14) -- "Race for Your Life"
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 
288.322  11.922 343.517