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### Running command:
###
###   /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) (2024-03-18 r86148)
* 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 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 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:
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test-corrOrthologTE.R:31:5'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-orthologScale.R:21:5'): orthologScale returns orthology information and scaling factor ──
  Error in `.chooseEnsemblMirror(mirror = mirror, http_config = http_config)`: Unable to query any Ensembl site
  Backtrace:
      ▆
   1. └─TEKRABber::orthologScale(...) at test-orthologScale.R:21:5
   2.   └─biomaRt::useEnsembl("ensembl", dataset = geneRef, version = version)
   3.     └─biomaRt:::.chooseEnsemblMirror(mirror = mirror, http_config = http_config)
  
  [ 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.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL TEKRABber
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘TEKRABber’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++11 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++11 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c rcpp_corr.cpp -o rcpp_corr.o
clang++ -arch x86_64 -std=gnu++11 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o TEKRABber.so RcppExports.o rcpp_corr.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-TEKRABber/00new/TEKRABber/libs
** R
** data
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (TEKRABber)

R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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("TEKRABber")
Welcome to TEKRABber version 1.8.0
+ New function: prepareRMSK() for getting repeatmasker
+ New parameter: `numCore` in corrOrthologTE() for parallel computing
> test_check("TEKRABber")
[ FAIL 1 | WARN 0 | SKIP 1 | PASS 5 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• On CRAN (1): 'test-corrOrthologTE.R:31:5'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-orthologScale.R:21:5'): orthologScale returns orthology information and scaling factor ──
Error in `.chooseEnsemblMirror(mirror = mirror, http_config = http_config)`: Unable to query any Ensembl site
Backtrace:
    ▆
 1. └─TEKRABber::orthologScale(...) at test-orthologScale.R:21:5
 2.   └─biomaRt::useEnsembl("ensembl", dataset = geneRef, version = version)
 3.     └─biomaRt:::.chooseEnsemblMirror(mirror = mirror, http_config = http_config)

[ FAIL 1 | WARN 0 | SKIP 1 | PASS 5 ]
Error: Test failures
Execution halted