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### Running command:
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###   /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_1.18.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/autonomics.Rcheck’
* using R version 4.5.0 (2025-04-11)
* 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 ‘1.18.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 32 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ... NOTE
Non-topic package-anchored link(s) in Rd file 'reexports.Rd':
  ‘[magrittr:compound]{%<>%}’ ‘[magrittr:pipe]{%>%}’
  ‘[magrittr:aliases]{extract}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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
write_xl                  227.224  1.658 229.913
awblinmod                  60.233  0.211  60.646
read_diann_proteingroups   59.633  0.629  62.767
read_rnaseq_counts         40.519  0.563  43.041
LINMOD                     33.436  0.610  34.165
plot_exprs                 29.756  0.115  31.147
plot_exprs_per_coef        28.395  0.115  28.892
default_formula            25.785  0.430  26.561
plot_summary               19.487  0.147  20.113
analyze                    18.405  0.076  18.524
read_somascan              18.289  0.116  18.828
read_metabolon             17.970  0.156  18.190
plot_volcano               17.879  0.075  19.050
explore-transforms         15.257  0.148  15.469
fit_survival               14.886  0.127  15.061
plot_densities             14.806  0.142  15.432
rm_diann_contaminants      13.496  0.223  14.104
fcluster                   13.163  0.024  13.407
ftype                      11.294  0.128  11.430
plot_detections            10.698  0.136  11.116
biplot_covariates           9.589  0.004   9.618
read_fragpipe               8.568  0.024   8.491
plot_xy_density             8.504  0.024  10.391
plot_subgroup_points        8.383  0.036   8.471
log2transform               6.976  0.028   7.295
subtract_baseline           6.744  0.032   6.795
reset_fit                   6.451  0.087   6.769
extract_contrast_features   6.448  0.044   6.514
code                        6.398  0.016   6.428
plot_violins                6.323  0.072   6.410
sbind                       5.530  0.012   5.557
biplot                      5.129  0.024   5.163
plot_contrastogram          4.245  0.036   5.404
annotate_uniprot_rest       0.113  0.004   5.305
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’/home/biocbuild/R/R-4.5.0/bin/BATCH: line 60: 1706408 Killed                  ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1

 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > 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")
* 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 ...