##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:immunotation.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings immunotation_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/immunotation.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'immunotation/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'immunotation' version '1.3.0'
* 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 ... NOTE
  installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R         3.8Mb
    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 R 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
plot_allele_frequency       2.54   0.25   13.39
query_haplotype_frequencies 0.48   0.01    9.54
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  'D:/biocbuild/bbs-3.15-bioc/meat/immunotation.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL immunotation
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'immunotation' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'immunotation'
    finding HTML links ... done
    assemble_protein_complex                html  
    build_allele_group                      html  
    check_geographics                       html  
    check_hla_locus                         html  
    check_hla_selection                     html  
    check_population                        html  
    check_sample_size                       html  
    check_standard                          html  
    create_encode_handle                    html  
    decode_MAC                              html  
    encode_MAC                              html  
    extract_population_id                   html  
    extract_population_info                 html  
    extract_population_name                 html  
    extract_sample_info                     html  
    fetch_encoded_MAC                       html  
    getURL                                  html  
    get_G_group                             html  
    get_P_group                             html  
    get_external_file                       html  
    get_mhcpan_input                        html  
    get_nb_pages                            html  
    get_serotypes                           html  
    get_valid_geographics                   html  
    get_valid_organisms                     html  
    human_protein_complex_table             html  
    load_mro                                html  
    mro.obo                                 html  
    parse_allele_freq_html                  html  
    parse_haplotype_freq_html               html  
    plot_allele_frequency                   html  
    query_allele_frequencies                html  
    query_haplotype_frequencies             html  
    query_population_detail                 html  
    read_complete_freq_table                html  
    read_population_detail                  html  
    retrieve_chain_lookup_table             html  
    verify_parameters                       html  
** 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)
Making 'packages.html' ... done

R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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 0 | WARN 0 | SKIP 0 | PASS 146 ]
Warning messages:
1: closing unused connection 9 (https://iamnotanurl) 
2: closing unused connection 8 (https://iamnotanurl) 
3: closing unused connection 6 (https://iamnotanurl) 
4: closing unused connection 5 (https://iamnotanurl) 
5: closing unused connection 4 (https://iamnotanurl) 
> 
> 
> proc.time()
   user  system elapsed 
  47.75    2.92   85.82