##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:autonomics.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings autonomics_1.14.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/autonomics.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘autonomics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘autonomics’ version ‘1.14.7’
* 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_diann_proteingroups 92.100  0.969  88.329
read_rnaseq_counts       28.045  1.501  29.324
plot_exprs_per_coef      23.026  0.202  23.120
plot_exprs               23.027  0.051  22.956
rm_diann_contaminants    19.461  0.782  20.098
default_formula          15.021  0.352  14.979
read_somascan            12.672  0.762  13.361
fit                      13.192  0.073  12.121
analyze                  12.670  0.144  12.722
read_metabolon           12.355  0.121  12.373
plot_summary             12.236  0.012  12.103
plot_volcano             10.252  0.043  10.188
plot_densities            9.056  0.160   9.140
read_fragpipe             6.957  0.101   6.765
ftype                     6.875  0.076   6.682
code                      6.233  0.030   6.242
subtract_baseline         5.646  0.214   5.762
plot_sample_nas           5.638  0.062   5.654
fcluster                  5.416  0.013   5.372
reset_fit                 4.870  0.163   4.922
* 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 2 | PASS 156 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* 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.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL autonomics
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 0 | SKIP 2 | PASS 156 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• empty test (2): 'test-8_fit.R:89:5', 'test-8_fit.R:99:5'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-8_fit.R:76:9'):  fit: mcclain21  ───────────────────────────────
<assertionError/assertionCondition/simpleError/error/condition>
Error in `.read_rnaseq_counts(file, sfile = sfile, by.y = "rna_id")`: is_existing_file : Some or all of the files specified by file do not exist.
/home/biocbuild/.cache/R/autonomics/datasets/mcclain21/GSE161731_counts.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.   └─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 2 | PASS 156 ]
Error: Test failures
Execution halted