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### Running command:
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###   /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: aarch64-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 Ventura 13.6.6
* 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 105.708  3.096 114.068
read_rnaseq_counts        30.597  1.530  34.026
rm_diann_contaminants     21.141  0.616  21.092
plot_exprs                20.443  0.228  21.041
plot_exprs_per_coef       20.017  0.246  20.348
default_formula           18.539  0.633  17.458
fit                       16.991  0.620  13.229
analyze                   12.629  0.168  13.558
plot_summary              12.463  0.135  13.510
read_metabolon            12.338  0.147  13.605
read_somascan             12.224  0.087  12.637
plot_densities            10.969  0.263  11.578
plot_volcano              10.552  0.150  10.907
read_fragpipe              8.299  0.270   8.686
plot_sample_nas            6.584  0.066   7.120
fit_lmx                    5.603  0.212   4.756
dot-plot_survival          5.318  0.350   5.733
biplot_covariates          5.503  0.096   5.420
code                       5.111  0.095   5.042
subtract_baseline          5.089  0.112   4.827
plot_subgroup_points       4.733  0.092   5.359
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
                                                                                                    FALSE 
  attr(,"cause")
  [1] nonexistent
  attr(,"class")
  [1] "vector_with_cause" "logical"          
  Backtrace:
      ▆
   1. └─autonomics::.read_rnaseq_counts(file, sfile = sfile, by.y = "rna_id") at test-8_fit.R:76:9
   2.   └─autonomics:::assert_all_are_existing_files(file)
   3.     └─autonomics:::assert_engine(...)
   4.       └─autonomics:::give_feedback(handler_type, msg, predicate_name)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 158 ]
  Error: Test failures
  Execution halted
* 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, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/autonomics.Rcheck/00check.log’
for details.