##############################################################################
##############################################################################
###
### 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 ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 88.907  4.093  88.502
read_rnaseq_counts       27.652  2.228  29.658
plot_exprs_per_coef      22.602  0.185  22.619
plot_exprs               22.157  0.173  22.121
rm_diann_contaminants    18.858  0.696  19.388
default_formula          14.864  0.329  14.737
fit                      13.109  0.408  12.318
read_somascan            12.037  0.385  12.312
analyze                  12.094  0.161  12.136
plot_summary             11.722  0.132  11.706
read_metabolon           11.711  0.063  11.638
plot_volcano              9.376  0.032   9.336
plot_densities            8.534  0.242   8.640
ftype                     6.627  0.075   6.286
code                      6.133  0.033   6.129
fcluster                  5.519  0.349   5.767
plot_sample_nas           5.501  0.056   5.486
read_fragpipe             5.334  0.128   5.207
extract_coef_features     4.964  0.371   5.313
* 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.