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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_1.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/autonomics.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* 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-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘autonomics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘autonomics’ version ‘1.16.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 30 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
read_rnaseq_counts       51.093  1.333  59.358
fit_linmod               47.704  0.143  48.306
plot_exprs_per_coef      36.951  0.067  39.297
plot_exprs               36.232  0.128  36.727
default_formula          25.493  0.453  27.382
analyze                  23.973  0.387  24.723
read_metabolon           22.463  0.163  23.061
read_somascan            22.271  0.102  23.894
plot_summary             21.837  0.128  23.437
plot_volcano             20.081  0.116  21.060
plot_densities           14.180  0.052  14.271
fcluster                 13.475  0.035  14.351
ftype                    12.073  0.092  12.788
plot_sample_nas          10.828  0.143  11.596
biplot_covariates         9.822  0.100  10.151
extract_coef_features     9.842  0.015  10.674
read_fragpipe             8.752  0.056   9.020
plot_subgroup_points      8.420  0.028   8.984
log2transform             7.750  0.067   7.984
code                      7.507  0.150   7.887
fit_survival              7.645  0.004   7.952
reset_fit                 7.155  0.027   7.463
plot_violins              6.749  0.107   7.736
biplot                    6.502  0.216   6.735
subtract_baseline         6.669  0.040   6.921
biplot_corrections        6.172  0.135   6.329
plot_joint_density        5.846  0.028   5.990
plot_survival             5.467  0.020   5.989
impute                    5.066  0.020   5.100
modelvar                  4.957  0.072   5.039
read_diann_proteingroups  4.946  0.031   5.216
annotate_uniprot_rest     0.118  0.028   7.410
* 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:
  [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. │ └─object %<>% ...
   3. └─autonomics::merge_sample_file(...)
   4.   └─autonomics:::assert_all_are_existing_files(sfile)
   5.     └─autonomics:::assert_engine(...)
   6.       └─autonomics:::give_feedback(handler_type, msg, predicate_name)
  
  [ FAIL 1 | WARN 4 | SKIP 0 | PASS 157 ]
  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
  ‘/home/biocbuild/bbs-3.21-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-devel_2025-02-19/site-library’
* installing *source* package ‘autonomics’ ...
** this is package ‘autonomics’ version ‘1.16.0’
** 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 Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
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 1 | WARN 4 | SKIP 0 | PASS 157 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-8_fit.R:76:9'):  fit: mcclain21  ───────────────────────────────
<assertionError/assertionCondition/simpleError/error/condition>
Error in `merge_sample_file(., sfile = sfile, by.x = "sample_id", by.y = by.y)`: is_existing_file : Some or all of the files specified by sfile do not exist.
/home/biocbuild/.cache/R/autonomics/datasets/mcclain21/GSE161731_counts_key.csv.gz 
                                                                             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. │ └─object %<>% ...
 3. └─autonomics::merge_sample_file(...)
 4.   └─autonomics:::assert_all_are_existing_files(sfile)
 5.     └─autonomics:::assert_engine(...)
 6.       └─autonomics:::give_feedback(handler_type, msg, predicate_name)

[ FAIL 1 | WARN 4 | SKIP 0 | PASS 157 ]
Error: Test failures
Execution halted