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### Running command:
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###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:annotatr.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings annotatr_1.30.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/annotatr.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘annotatr/DESCRIPTION’ ... OK
* this is package ‘annotatr’ version ‘1.30.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘annotatr’ 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 ... NOTE
plot_coannotations: no visible binding for global variable ‘.’
plot_numerical_coannotations: no visible binding for global variable
  ‘.’
Undefined global functions or variables:
  .
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
build_annotations 4.827  0.688   5.515
build_ah_annots   3.883  1.062   6.111
* 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:
    2.   ├─base::suppressWarnings(build_cpg_annots(genome = genome, annotations = cpg_annotations))
    3.   │ └─base::withCallingHandlers(...)
    4.   └─annotatr:::build_cpg_annots(genome = genome, annotations = cpg_annotations)
    5.     ├─ah[[ID]]
    6.     └─ah[[ID]]
    7.       └─AnnotationHub (local) .local(x, i, j = j, ...)
    8.         └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
    9.           └─base::tryCatch(...)
   10.             └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   11.               └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   12.                 └─value[[3L]](cond)
  
  [ FAIL 1 | WARN 4 | SKIP 0 | PASS 71 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘annotatr-vignette.Rmd’ using rmarkdown

Quitting from lines 154-171 [unnamed-chunk-8] (annotatr-vignette.Rmd)
Error: processing vignette 'annotatr-vignette.Rmd' failed with diagnostics:
failed to load resource
  name: AH5086
  title: CpG Islands
  reason: error in evaluating the argument 'x' in selecting a method for function 'get': bad restore file magic number (file may be corrupted) -- no data loaded
--- failed re-building ‘annotatr-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘annotatr-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/annotatr.Rcheck/00check.log’
for details.