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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:annotatr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings annotatr_1.31.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/annotatr.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘annotatr/DESCRIPTION’ ... OK
* this is package ‘annotatr’ version ‘1.31.0’
* 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'
Warning: unable to access index for repository https://bioconductor.org/packages/3.19/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.19/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.19/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.19/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.19/data/experiment/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 ... 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 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 ... ERROR
Running examples in ‘annotatr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: build_ah_annots
> ### Title: A helper function to build arbitrary annotatinos from
> ###   AnnotationHub
> ### Aliases: build_ah_annots
> 
> ### ** Examples
> 
> 
> # Create a named vector for the AnnotationHub accession codes with desired names
> h3k4me3_code = c('Gm12878' = 'AH23256')
> # Fetch ah_codes from AnnotationHub and create annotations annotatr understands
> build_ah_annots(genome = 'hg19', ah_codes = h3k4me3_code, annotation_class = 'H3K4me3')
Cannot connect to AnnotationHub server, using 'localHub=TRUE' instead
Warning: Could not check database for updates.
  Database source currently unreachable.
  This should only be a temporary interruption. 
  Using previously cached version.
Error in value[[3L]](cond) : failed to connect
  reason: Timeout was reached: [bioconductor.org] Resolving timed out after 10044 milliseconds
  Consider rerunning with 'localHub=TRUE'
Calls: build_ah_annots ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
* 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:
    7.         └─GenomeInfoDb:::.get_chrom_info_for_registered_UCSC_genome(...)
    8.           └─GenomeInfoDb:::.get_raw_chrom_info_for_registered_UCSC_genome(...)
    9.             └─GenomeInfoDb:::.fetch_raw_chrom_info_from_UCSC(...)
   10.               └─GenomeInfoDb (local) FETCH_ORDERED_CHROM_SIZES(goldenPath.url = goldenPath.url)
   11.                 └─GenomeInfoDb:::fetch_chrom_sizes_from_UCSC(GENOME, goldenPath.url = goldenPath.url)
   12.                   └─GenomeInfoDb:::.fetch_chrom_sizes_from_UCSC_database(...)
   13.                     └─GenomeInfoDb:::fetch_table_dump_from_UCSC(...)
   14.                       └─GenomeInfoDb:::fetch_table_from_url(...)
   15.                         ├─base::suppressWarnings(download.file(url, destfile, quiet = TRUE))
   16.                         │ └─base::withCallingHandlers(...)
   17.                         └─utils::download.file(url, destfile, quiet = TRUE)
  
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 40 ]
  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: 2 ERRORs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/annotatr.Rcheck/00check.log’
for details.