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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no autonomics_1.14.7.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc-longtests/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
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* 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 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 ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘LT3.1_rnaseq_bams.R’
  Running ‘LT3.2_proteingroups_1fasta.R’
  Running ‘LT8_fit.R’
 ERROR
Running the tests in ‘longtests/LT3.1_rnaseq_bams.R’ failed.
Last 13 lines of output:
  +         expect_true('log2cpm' %in% SummarizedExperiment::assayNames(object))
  +         expect_true(any(stri_detect_fixed(         svars(object),  'pca1')))
  +         expect_true(any(stri_detect_fixed(         fvars(object),  'pca1')))
  +         expect_true(any(stri_detect_fixed(names(metadata(object)), 'pca' )))
  +     })
  + 
  +     test_that("read_rnaseq_counts(file, fit = 'limma')", {
  +         object <- read_rnaseq_bams(file, paired = TRUE, genome = 'hg38', fit = 'limma')
  +         expect_s4_class(object, 'SummarizedExperiment')
  +         expect_true(any(stri_detect_fixed(fvars(object), 'limma')))
  +     })
  + }
  Error in download_data("billing16.bam.zip") : 
    could not find function "download_data"
  Execution halted
Running the tests in ‘longtests/LT3.2_proteingroups_1fasta.R’ failed.
Complete output:
  > #============================================================================
  > #
  > #                     read_fastahdrs
  > #                    parse_fastahdrs
  > #
  > #============================================================================
  > 
  > context('`read_fastahdrs/parse_fastahdrs`')
  Error in context("`read_fastahdrs/parse_fastahdrs`") : 
    could not find function "context"
  Execution halted
Running the tests in ‘longtests/LT8_fit.R’ failed.
Last 13 lines of output:
  > 
  >     # Prepare minimal full-feature datset: subgroup, block, weights
  >         require(magrittr)
  Loading required package: magrittr
  
  Attaching package: 'magrittr'
  
  The following objects are masked from 'package:testthat':
  
      equals, is_less_than, not
  
  >         object <- .read_rnaseq_counts(file, sfile = sfile, by.y = 'rna_id')
  Error in .read_rnaseq_counts(file, sfile = sfile, by.y = "rna_id") : 
    could not find function ".read_rnaseq_counts"
  Execution halted
* DONE

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