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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:lineagespot.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings lineagespot_1.9.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/lineagespot.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 ‘lineagespot/DESCRIPTION’ ... OK
* this is package ‘lineagespot’ version ‘1.9.0’
* 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'
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 ‘lineagespot’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 ... 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 ... ERROR
Running examples in ‘lineagespot-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_lineage_report
> ### Title: get_lineage_report
> ### Aliases: get_lineage_report
> 
> ### ** Examples
> 
> 
> 
> get_lineage_report(lineages = c("B.1.1.7", "B.1.617.2"))
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [api.outbreak.info] Resolving timed out after 10009 milliseconds
Calls: get_lineage_report ... request_fetch -> request_fetch.write_memory -> <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:
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_get_lineage_report.R:5:5'): get lineage report runs properly ───
  Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached: [api.outbreak.info] Resolving timed out after 10029 milliseconds
  Backtrace:
      ▆
   1. └─lineagespot::get_lineage_report(lineages = c("B.1.1.7", "B.1.617.2")) at test_get_lineage_report.R:5:5
   2.   └─httr::GET(paste0(base.url, l))
   3.     └─httr:::request_perform(req, hu$handle$handle)
   4.       ├─httr:::request_fetch(req$output, req$url, handle)
   5.       └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   6.         └─curl::curl_fetch_memory(url, handle = handle)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 16 ]
  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/lineagespot.Rcheck/00check.log’
for details.