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### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:autonomics.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings autonomics_1.14.9.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/autonomics.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* 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 loading without being on the library search path ... 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       40.210  2.286  53.146
plot_exprs_per_coef      35.513  0.191  39.303
plot_exprs               34.627  0.318  38.283
read_diann_proteingroups 34.220  0.318  39.729
default_formula          22.732  0.477  26.468
read_somascan            19.266  0.378  23.770
fit                      19.187  0.227  20.937
analyze                  18.837  0.191  20.920
read_metabolon           18.416  0.059  22.713
plot_summary             18.238  0.036  20.850
plot_volcano             14.665  0.171  16.561
plot_densities           13.254  0.148  16.603
ftype                     9.983  0.092  10.964
code                      9.375  0.163  10.282
rm_diann_contaminants     8.752  0.203  10.418
plot_sample_nas           8.558  0.087  10.099
read_fragpipe             8.496  0.032   9.107
fcluster                  8.136  0.032   9.771
extract_coef_features     7.775  0.087   9.109
reset_fit                 7.085  0.204   8.688
biplot_covariates         7.101  0.155   7.711
plot_subgroup_points      6.467  0.036   7.312
fit_lmx                   6.376  0.028   6.576
subtract_baseline         5.893  0.056   7.723
plot_violins              5.392  0.088   6.168
dot-plot_survival         5.187  0.203   6.133
log2transform             5.250  0.055   5.651
modelvar                  5.155  0.008   5.598
biplot                    4.976  0.180   5.640
explore_transformations   4.874  0.147   5.485
annotate_uniprot_rest     0.232  0.020   5.886
* 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
  ‘/home/biocbuild/bbs-3.20-bioc/meat/autonomics.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL autonomics
###
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* installing to library ‘/home/biocbuild/R/R-4.4.3/site-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: aarch64-unknown-linux-gnu

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 
179.698   2.334 192.327