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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TEKRABber.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TEKRABber_1.7.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/TEKRABber.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* 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 ‘TEKRABber/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TEKRABber’ version ‘1.7.2’
* 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 ‘TEKRABber’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 ... NOTE
Problems with news in ‘NEWS.md’:
No news entries found.
* 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 whether startup messages can be suppressed ... 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 ... NOTE
File ‘TEKRABber/R/zzz.R’:
  .onLoad calls:
    packageStartupMessage(paste(messages, collapse = "\n"))

See section ‘Good practice’ in '?.onAttach'.

appTEKRABber: no visible global function definition for ‘grid_page’
appTEKRABber: no visible global function definition for
  ‘grid_card_text’
appTEKRABber: no visible global function definition for ‘grid_card’
appTEKRABber: no visible global function definition for ‘card_header’
appTEKRABber: no visible global function definition for ‘card_body’
appTEKRABber: no visible global function definition for
  ‘selectizeInput’
appTEKRABber: no visible global function definition for ‘actionButton’
appTEKRABber: no visible global function definition for ‘plotlyOutput’
appTEKRABber: no visible global function definition for ‘plotOutput’
appTEKRABber : server: no visible global function definition for
  ‘renderPlotly’
appTEKRABber : server: no visible global function definition for
  ‘plot_ly’
appTEKRABber : server: no visible global function definition for
  ‘observeEvent’
appTEKRABber : server: no visible global function definition for
  ‘renderPlot’
appTEKRABber : server: no visible global function definition for
  ‘ggplot’
appTEKRABber : server: no visible global function definition for ‘aes’
appTEKRABber : server: no visible binding for global variable ‘gene’
appTEKRABber : server: no visible binding for global variable ‘TE’
appTEKRABber : server: no visible global function definition for
  ‘geom_point’
appTEKRABber : server: no visible global function definition for ‘labs’
appTEKRABber : server: no visible global function definition for
  ‘geom_smooth’
appTEKRABber : server: no visible global function definition for
  ‘theme_bw’
appTEKRABber : server: no visible global function definition for
  ‘ggtitle’
appTEKRABber : server: no visible global function definition for
  ‘ggviolin’
appTEKRABber : server: no visible global function definition for ‘ylab’
appTEKRABber : server: no visible global function definition for ‘xlab’
appTEKRABber : server: no visible global function definition for
  ‘theme’
appTEKRABber: no visible global function definition for ‘shinyApp’
corrOrthologTE: no visible binding for global variable ‘i’
corrOrthologTE: no visible binding for global variable ‘j’
corrOrthologTE: no visible global function definition for ‘cor.test’
orthologScale: no visible global function definition for ‘desc’
orthologScale: no visible binding for global variable
  ‘orthologyConfidence’
orthologScale: no visible binding for global variable ‘refLength’
orthologScale: no visible binding for global variable ‘compareLength’
orthologScale: no visible global function definition for ‘across’
orthologScale: no visible binding for global variable ‘refLen’
orthologScale: no visible binding for global variable ‘compareLen’
prepareRMSK: no visible binding for global variable ‘repEnd’
prepareRMSK: no visible binding for global variable ‘repStart’
prepareRMSK: no visible binding for global variable ‘repName’
prepareRMSK: no visible binding for global variable ‘repClass’
prepareRMSK: no visible binding for global variable ‘rLen’
prepareRMSK: no visible binding for global variable ‘cLen’
Undefined global functions or variables:
  TE across actionButton aes cLen card_body card_header compareLen
  compareLength cor.test desc gene geom_point geom_smooth ggplot
  ggtitle ggviolin grid_card grid_card_text grid_page i j labs
  observeEvent orthologyConfidence plotOutput plot_ly plotlyOutput rLen
  refLen refLength renderPlot renderPlotly repClass repEnd repName
  repStart selectizeInput shinyApp theme theme_bw xlab ylab
Consider adding
  importFrom("stats", "cor.test")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'corrOrthologTE.Rd':
corrOrthologTE
  Code: function(geneInput, teInput, corrMethod = "pearson", padjMethod
                 = "fdr", numCore = 1, fileDir = NULL, fileName =
                 "TEKRABber_geneTECorrResult.csv")
  Docs: function(geneInput, teInput, corrMethod = "pearson", padjMethod
                 = "fdr", fileDir = NULL, fileName =
                 "TEKRABber_geneTECorrResult.csv")
  Argument names in code not in docs:
    numCore
  Mismatches in argument names:
    Position: 5 Code: numCore Docs: fileDir
    Position: 6 Code: fileDir Docs: fileName

Codoc mismatches from Rd file 'orthologScale.Rd':
orthologScale
  Code: function(speciesRef, speciesCompare, geneCountRef,
                 geneCountCompare, teCountRef, teCountCompare, rmsk,
                 version = NULL)
  Docs: function(speciesRef, speciesCompare, geneCountRef,
                 geneCountCompare, teCountRef, teCountCompare, rmsk)
  Argument names in code not in docs:
    version

* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in Rd file 'corrOrthologTE.Rd':
  ‘numCore’

Documented arguments not in \usage in Rd file 'orthologScale.Rd':
  ‘version’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘TEKRABber-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DECorrInputs
> ### Title: Generate all the input files for TEKRABber downstream analysis
> ### Aliases: DECorrInputs
> 
> ### ** Examples
> 
> data(speciesCounts)
> data(hg38_panTro6_rmsk)
> hmGene <- speciesCounts$hmGene
> chimpGene <- speciesCounts$chimpGene
> hmTE <- speciesCounts$hmTE
> chimpTE <- speciesCounts$chimpTE
> 
> ## For demonstration, here we only select 1000 rows to save time
> set.seed(1234)
> hmGeneSample <- hmGene[sample(nrow(hmGene), 1000), ]
> chimpGeneSample <- chimpGene[sample(nrow(chimpGene), 1000), ]
> 
> fetchData <- orthologScale(
+     speciesRef = "hsapiens",
+     speciesCompare = "ptroglodytes",
+     geneCountRef = hmGeneSample,
+     geneCountCompare = chimpGeneSample,
+     teCountRef = hmTE,
+     teCountCompare = chimpTE,
+     rmsk = hg38_panTro6_rmsk
+ )
Error in `httr2::req_perform()`:
! HTTP 500 Internal Server Error.
Backtrace:
    ▆
 1. └─TEKRABber::orthologScale(...)
 2.   └─biomaRt::getLDS(...)
 3.     └─biomaRt:::.submitQueryXML(...)
 4.       └─httr2::req_perform(req)
 5.         └─httr2:::handle_resp(req, resp, error_call = error_call)
 6.           └─httr2:::resp_abort(resp, req, body, call = error_call)
 7.             └─rlang::abort(...)
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:
       ▆
    1. └─TEKRABber::orthologScale(...) at test-orthologScale.R:21:5
    2.   └─biomaRt::useEnsembl("ensembl", dataset = geneCompare, version = version)
    3.     └─biomaRt::useDataset(mart = mart, dataset = dataset, verbose = verbose)
    4.       └─biomaRt:::checkDataset(dataset = dataset, mart = mart)
    5.         └─biomaRt:::.listDatasets(mart, sort = FALSE)
    6.           └─biomaRt:::bmRequest(...)
    7.             └─httr2::req_perform(request)
    8.               └─httr2:::handle_resp(req, resp, error_call = error_call)
    9.                 └─httr2:::resp_abort(resp, req, body, call = error_call)
   10.                   └─rlang::abort(...)
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 5 ]
  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, 2 WARNINGs, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/TEKRABber.Rcheck/00check.log’
for details.