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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:TEKRABber.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings TEKRABber_1.3.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/TEKRABber.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* 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 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘TEKRABber/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TEKRABber’ version ‘1.3.0’
* 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 11.3.0-1ubuntu1~22.04) 11.3.0’
* 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 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 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: orthologScale
> ### Title: Get orthology information from Ensembl
> ### Aliases: orthologScale
> 
> ### ** Examples
> 
> data(speciesCounts)
> hmGene <- speciesCounts$hmGene
> chimpGene <- speciesCounts$chimpGene
> 
> ## 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
+ )
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [dec2021.archive.ensembl.org:443] Operation timed out after 10000 milliseconds with 238009 bytes received
Calls: orthologScale ... request_fetch -> request_fetch.write_memory -> <Anonymous>
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:18:4
    2.   └─biomaRt::useEnsembl("ensembl", dataset = geneRef, version = "105")
    3.     └─biomaRt::useDataset(mart = mart, dataset = dataset, verbose = verbose)
    4.       └─biomaRt:::.getAttributes(mart, verbose = verbose)
    5.         └─biomaRt:::.getAttrFilt(mart = mart, verbose = verbose, type = "attributes")
    6.           └─biomaRt:::bmRequest(...)
    7.             └─httr::GET(...)
    8.               └─httr:::request_perform(req, hu$handle$handle)
    9.                 ├─httr:::request_fetch(req$output, req$url, handle)
   10.                 └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   11.                   └─curl::curl_fetch_memory(url, handle = handle)
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 13 ]
  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 ...
  ‘TEKRABber.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

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

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL TEKRABber
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘TEKRABber’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c rcpp_corr.cpp -o rcpp_corr.o
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o TEKRABber.so RcppExports.o rcpp_corr.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/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) (2023-01-14 r83615) -- "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("TEKRABber")
> test_check("TEKRABber")
[ FAIL 1 | WARN 0 | SKIP 1 | PASS 13 ]

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

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-orthologScale.R:18'): orthologScale returns orthology information and scaling factor ──
Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached: [dec2021.archive.ensembl.org:443] Operation timed out after 10001 milliseconds with 493877 bytes received
Backtrace:
     ▆
  1. └─TEKRABber::orthologScale(...) at test-orthologScale.R:18:4
  2.   └─biomaRt::useEnsembl("ensembl", dataset = geneRef, version = "105")
  3.     └─biomaRt::useDataset(mart = mart, dataset = dataset, verbose = verbose)
  4.       └─biomaRt:::.getAttributes(mart, verbose = verbose)
  5.         └─biomaRt:::.getAttrFilt(mart = mart, verbose = verbose, type = "attributes")
  6.           └─biomaRt:::bmRequest(...)
  7.             └─httr::GET(...)
  8.               └─httr:::request_perform(req, hu$handle$handle)
  9.                 ├─httr:::request_fetch(req$output, req$url, handle)
 10.                 └─httr:::request_fetch.write_memory(req$output, req$url, handle)
 11.                   └─curl::curl_fetch_memory(url, handle = handle)

[ FAIL 1 | WARN 0 | SKIP 1 | PASS 13 ]
Error: Test failures
Execution halted