##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:TEKRABber.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings TEKRABber_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/TEKRABber.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘TEKRABber/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TEKRABber’ version ‘1.14.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘TEKRABber’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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 loading without being on the library search path ... 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 ... OK
* checking Rd \usage sections ... OK
* 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,
+     version = 105
+ )
Error in `req_perform()`:
! HTTP 500 Internal Server Error.
Backtrace:
     ▆
  1. └─TEKRABber::orthologScale(...)
  2.   └─biomaRt::useEnsembl("ensembl", dataset = geneRef, 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_failure_cnd(req, resp, error_call = error_call)
 10.                   ├─rlang::catch_cnd(...)
 11.                   │ ├─rlang::eval_bare(...)
 12.                   │ ├─base::tryCatch(...)
 13.                   │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 14.                   │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 15.                   │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 16.                   │ └─base::force(expr)
 17.                   └─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:
    8.               └─httr2:::handle_resp(req, resp, error_call = error_call)
    9.                 └─httr2:::resp_failure_cnd(req, resp, error_call = error_call)
   10.                   ├─rlang::catch_cnd(...)
   11.                   │ ├─rlang::eval_bare(...)
   12.                   │ ├─base::tryCatch(...)
   13.                   │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   14.                   │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   15.                   │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
   16.                   │ └─base::force(expr)
   17.                   └─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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/TEKRABber.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL TEKRABber
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘TEKRABber’ ...
** this is package ‘TEKRABber’ version ‘1.14.0’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c rcpp_corr.cpp -o rcpp_corr.o
rcpp_corr.cpp:23: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
   23 |     #pragma omp parallel for
      | 
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o TEKRABber.so RcppExports.o rcpp_corr.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/R/site-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 version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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")
Saving _problems/test-orthologScale-30.R
[ FAIL 1 | WARN 0 | SKIP 1 | PASS 5 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• On CRAN (1): 'test-corrOrthologTE.R:29:1'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-orthologScale.R:21:5'): orthologScale returns orthology information and scaling factor ──
<httr2_http_500/httr2_http/httr2_error/rlang_error/rlang_error/error/condition>
Error in `req_perform(request)`: HTTP 500 Internal Server Error.
Backtrace:
     ▆
  1. └─TEKRABber::orthologScale(...) at test-orthologScale.R:21:5
  2.   └─biomaRt::useEnsembl("ensembl", dataset = geneRef, version = version)
  3.     └─biomaRt::useDataset(mart = mart, dataset = dataset, verbose = verbose)
  4.       └─biomaRt:::.getFilters(mart, verbose = verbose)
  5.         └─biomaRt:::.getAttrFilt(mart = mart, verbose = verbose, type = "filters")
  6.           └─biomaRt:::bmRequest(...)
  7.             └─httr2::req_perform(request)
  8.               └─httr2:::handle_resp(req, resp, error_call = error_call)
  9.                 └─httr2:::resp_failure_cnd(req, resp, error_call = error_call)
 10.                   ├─rlang::catch_cnd(...)
 11.                   │ ├─rlang::eval_bare(...)
 12.                   │ ├─base::tryCatch(...)
 13.                   │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 14.                   │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 15.                   │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 16.                   │ └─base::force(expr)
 17.                   └─rlang::abort(...)

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