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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:biomaRt.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings biomaRt_2.55.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/biomaRt.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘biomaRt/DESCRIPTION’ ... OK
* this is package ‘biomaRt’ version ‘2.55.3’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘biomaRt’ 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 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 ... NOTE
Unexported object imported by a ':::' call: ‘AnnotationDbi:::smartKeys’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.biomartCacheLocation’
* 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 ... NOTE
checkRd: (-1) getBM.Rd:16: Escaped LaTeX specials: \_
checkRd: (-1) getGene.Rd:9: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_
* 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
* 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:
    1. ├─testthat::expect_silent(...) at test_utilityFunctions.R:112:2
    2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ ├─withr::with_output_sink(...)
    5. │   │ │ └─base::force(code)
    6. │   │ ├─base::withCallingHandlers(...)
    7. │   │ └─base::withVisible(code)
    8. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    9. └─biomaRt:::.fetchHTMLresults(host, query, httr_config = httr_config)
   10.   └─base::gsub(...)
   11.     └─base::is.factor(x)
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 146 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘accessing_ensembl.Rmd’ using ‘UTF-8’... OK
  ‘accessing_other_marts.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/biomaRt.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL biomaRt
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library’
* installing *source* package ‘biomaRt’ ...
** 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 (biomaRt)

R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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(mockery)
> library(biomaRt)
> 
> test_check("biomaRt", encoding = "UTF-8")
[ FAIL 1 | WARN 0 | SKIP 1 | PASS 146 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Linux (1)

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_utilityFunctions.R:112:3'): TSV and HTML result tables match ───
Error in `is.factor(x)`: object 'query' not found
Backtrace:
     ▆
  1. ├─testthat::expect_silent(...) at test_utilityFunctions.R:112:2
  2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
  3. │   ├─testthat (local) .capture(...)
  4. │   │ ├─withr::with_output_sink(...)
  5. │   │ │ └─base::force(code)
  6. │   │ ├─base::withCallingHandlers(...)
  7. │   │ └─base::withVisible(code)
  8. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  9. └─biomaRt:::.fetchHTMLresults(host, query, httr_config = httr_config)
 10.   └─base::gsub(...)
 11.     └─base::is.factor(x)

[ FAIL 1 | WARN 0 | SKIP 1 | PASS 146 ]
Error: Test failures
Execution halted