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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_1.14.8.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/autonomics.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 12.3.1 (openEuler 12.3.1-36.oe2403)
* 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 ‘1.14.8’
* 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       40.748  1.278  45.448
plot_exprs               35.144  0.254  36.199
plot_exprs_per_coef      35.026  0.255  35.641
read_diann_proteingroups 33.796  0.810  35.472
default_formula          24.096  0.299  24.401
read_metabolon           19.029  0.303  20.559
analyze                  19.090  0.223  19.358
read_somascan            19.005  0.276  19.325
fit                      18.562  0.295  18.902
plot_summary             18.041  0.080  18.346
plot_volcano             15.178  0.127  15.864
plot_densities           13.073  0.139  13.242
read_fragpipe             9.876  0.356  10.797
ftype                     9.931  0.111  10.109
code                      9.703  0.024   9.747
fcluster                  8.541  0.180   8.742
extract_coef_features     8.217  0.307   8.546
plot_sample_nas           8.170  0.016   8.266
rm_diann_contaminants     7.701  0.183  10.897
biplot_covariates         7.290  0.084   7.389
reset_fit                 7.245  0.032   7.291
subtract_baseline         6.338  0.235   6.607
fit_lmx                   6.316  0.020   6.358
plot_subgroup_points      6.151  0.028   6.192
plot_violins              5.720  0.104   6.079
dot-plot_survival         5.542  0.136   5.693
biplot                    5.185  0.219   5.417
explore_transformations   5.053  0.244   5.309
modelvar                  5.074  0.055   5.154
log2transform             4.967  0.036   5.027
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’/home/biocbuild/R/R/bin/BATCH: line 60: 1517446 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 ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/autonomics.Rcheck/00check.log’
for details.