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###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:immunotation.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings immunotation_1.17.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/immunotation.Rcheck'
* using R version 4.5.0 (2025-04-11 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'immunotation/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'immunotation' version '1.17.0'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'immunotation' can be installed ... OK
* checking installed package size ... INFO
  installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R         3.2Mb
    extdata   2.2Mb
* 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 ... 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 'immunotation-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_allele_frequency
> ### Title: Plotting allele frequencies
> ### Aliases: plot_allele_frequency
> 
> ### ** Examples
> 
> 
> # select frequency of given allele
> sel_allele_freq <- query_allele_frequencies(hla_selection = "A*02:01", 
+ hla_sample_size_pattern = "bigger_than", 
+ hla_sample_size = 10000, standard="g")
Error in getURL(url, read_method = "html") : 'getURL()' failed:
  URL: http://www.allelefrequencies.net/hla6006a.asp?hla_locus_type=Classical&hla_locus=&hla_selection=A*02:01&hla_population=&hla_country=&hla_dataset=&hla_region=&hla_ethnic=&hla_study=&hla_order=order_1&hla_sample_size_pattern=bigger_than&hla_sample_size=10000&standard=g
  error: cannot open the connection
Calls: query_allele_frequencies -> rbind -> read_complete_freq_table -> getURL
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:
  Error in `getURL(url, read_method = "html")`: 'getURL()' failed:
    URL: http://www.allelefrequencies.net/pop6001c.asp?pop_id=3725
    error: cannot open the connection
  Backtrace:
      ▆
   1. └─immunotation::query_population_detail(3725) at test_4_AFND.R:190:5
   2.   ├─base::rbind(pop_df, query_single_population_detail(pop_id))
   3.   │ └─base::rbind(deparse.level, ...)
   4.   └─immunotation:::query_single_population_detail(pop_id)
   5.     └─immunotation:::read_population_detail(pop_url, population_id)
   6.       └─immunotation:::getURL(url, read_method = "html")
  
  [ FAIL 4 | WARN 4 | SKIP 0 | PASS 139 ]
  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
See
  'F:/biocbuild/bbs-3.22-bioc/meat/immunotation.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL immunotation
###
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* installing to library 'F:/biocbuild/bbs-3.22-bioc/R/library'
* installing *source* package 'immunotation' ...
** this is package 'immunotation' version '1.17.0'
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (immunotation)

R version 4.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(immunotation)
> 
> test_check("immunotation")
[ FAIL 4 | WARN 4 | SKIP 0 | PASS 139 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_4_AFND.R:48:5'): query_allele_frequencies() returns expected results ──
Error in `getURL(url, read_method = "html")`: 'getURL()' failed:
  URL: http://www.allelefrequencies.net/hla6006a.asp?hla_locus_type=Classical&hla_locus=&hla_selection=A*02:01&hla_population=&hla_country=&hla_dataset=&hla_region=&hla_ethnic=&hla_study=&hla_order=order_1&hla_sample_size_pattern=bigger_than&hla_sample_size=10000&standard=g
  error: cannot open the connection
Backtrace:
    ▆
 1. └─immunotation::query_allele_frequencies(...) at test_4_AFND.R:48:5
 2.   ├─base::rbind(...)
 3.   └─immunotation:::read_complete_freq_table(queryurl, type = "allele")
 4.     └─immunotation:::getURL(url, read_method = "html")
── Error ('test_4_AFND.R:148:5'): query_haplotype_frequencies() returns expected results ──
Error in `getURL(url, read_method = "html")`: 'getURL()' failed:
  URL: http://www.allelefrequencies.net/hla6003a.asp?hla_locus1=A*02:01&hla_locus2=B*&hla_locus3=C*&hla_locus4=DRB1_not&hla_locus5=DPA1_not&hla_locus6=DPB1_not&hla_locus7=DQA1_not&hla_locus8=DQB1_not&hla_population=&hla_country=&hla_dataset=&hla_region=Europe&hla_ethnic=&hla_study=&hla_order=order_1&hla_sample_size_pattern=&hla_sample_size=&hla_sample_year_pattern=equal&hla_sample_year=&hla_loci=
  error: cannot open the connection
Backtrace:
    ▆
 1. └─immunotation::query_haplotype_frequencies(...) at test_4_AFND.R:148:5
 2.   └─immunotation:::read_complete_freq_table(queryurl, type = "haplotype")
 3.     └─immunotation:::getURL(url, read_method = "html")
── Error ('test_4_AFND.R:170:5'): plot_allele_frequency() returns expected results ──
Error in `getURL(url, read_method = "html")`: 'getURL()' failed:
  URL: http://www.allelefrequencies.net/hla6006a.asp?hla_locus_type=Classical&hla_locus=&hla_selection=A*02:01&hla_population=&hla_country=&hla_dataset=&hla_region=&hla_ethnic=&hla_study=&hla_order=order_1&hla_sample_size_pattern=bigger_than&hla_sample_size=10000&standard=g
  error: cannot open the connection
Backtrace:
    ▆
 1. └─immunotation::query_allele_frequencies(...) at test_4_AFND.R:170:5
 2.   ├─base::rbind(...)
 3.   └─immunotation:::read_complete_freq_table(queryurl, type = "allele")
 4.     └─immunotation:::getURL(url, read_method = "html")
── Error ('test_4_AFND.R:190:5'): query_population_detail() returns expected results ──
Error in `getURL(url, read_method = "html")`: 'getURL()' failed:
  URL: http://www.allelefrequencies.net/pop6001c.asp?pop_id=3725
  error: cannot open the connection
Backtrace:
    ▆
 1. └─immunotation::query_population_detail(3725) at test_4_AFND.R:190:5
 2.   ├─base::rbind(pop_df, query_single_population_detail(pop_id))
 3.   │ └─base::rbind(deparse.level, ...)
 4.   └─immunotation:::query_single_population_detail(pop_id)
 5.     └─immunotation:::read_population_detail(pop_url, population_id)
 6.       └─immunotation:::getURL(url, read_method = "html")

[ FAIL 4 | WARN 4 | SKIP 0 | PASS 139 ]
Error: Test failures
Execution halted