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###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:immunotation.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings immunotation_1.4.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/immunotation.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'immunotation/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'immunotation' version '1.4.0'
* 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  6.2Mb
  sub-directories of 1Mb or more:
    R         3.9Mb
    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       2.98   0.27  115.83
query_haplotype_frequencies 0.76   0.03   71.68
query_allele_frequencies    0.10   0.00    7.43
query_population_detail     0.03   0.00    8.84
* 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:
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 145 ]
  Error: Test failures
  In addition: Warning messages:
  1: In .Internal(lapply(X, FUN)) :
    closing unused connection 9 (https://iamnotanurl)
  2: In .Internal(lapply(X, FUN)) :
    closing unused connection 8 (https://iamnotanurl)
  3: In .Internal(lapply(X, FUN)) :
    closing unused connection 6 (https://iamnotanurl)
  4: In .Internal(lapply(X, FUN)) :
    closing unused connection 5 (https://iamnotanurl)
  5: In .Internal(lapply(X, FUN)) :
    closing unused connection 4 (https://iamnotanurl)
  Execution halted
* 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 ERROR, 1 NOTE
See
  'F:/biocbuild/bbs-3.15-bioc/meat/immunotation.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL immunotation
###
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* installing to library 'F:/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
** 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 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid"
Copyright (C) 2022 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 1 | WARN 0 | SKIP 0 | PASS 145 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_3_name_conversions.R:72'): encode_MAC() returns error when arguments not adequate ──
encode_MAC("foo") not equal to "A service failures was logged.  Contact administrator for more information".
1/1 mismatches
x[1]: "No Locus for allele: foo"
y[1]: "A service failures was logged.  Contact administrator for more informatio
y[1]: n"

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 145 ]
Error: Test failures
In addition: Warning messages:
1: In .Internal(lapply(X, FUN)) :
  closing unused connection 9 (https://iamnotanurl)
2: In .Internal(lapply(X, FUN)) :
  closing unused connection 8 (https://iamnotanurl)
3: In .Internal(lapply(X, FUN)) :
  closing unused connection 6 (https://iamnotanurl)
4: In .Internal(lapply(X, FUN)) :
  closing unused connection 5 (https://iamnotanurl)
5: In .Internal(lapply(X, FUN)) :
  closing unused connection 4 (https://iamnotanurl)
Execution halted