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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:DominoEffect.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings DominoEffect_1.30.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/DominoEffect.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 ‘DominoEffect/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DominoEffect’ version ‘1.30.0’
* 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 ‘DominoEffect’ 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 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 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
import_txdb: no visible binding for global variable ‘TXTYPE’
Undefined global functions or variables:
  TXTYPE
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘DominoEffect-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DominoEffect
> ### Title: Identification of significant mutation hotspot residues.
> ### Aliases: DominoEffect
> 
> ### ** Examples
> 
> data("SnpData", package = "DominoEffect")
> data("TestData", package = "DominoEffect")
> data("DominoData", package = "DominoEffect")
> 
> hotspot_mutations <- DominoEffect(mutation_dataset = TestData, 
+ gene_data = DominoData, snp_data = SnpData)
  There are in total 5 protein residues with 5 or more mutation.
  ***Checking potential hotspots.***
  Obtaining sequences of proteins encoded by the representative Ensembl transcripts.
Error in map_to_func_elem(results, write_to_file, ens_release = ens_release) : 
  'useMart()' failed:
  error: HTTP 500 Internal Server Error.
Calls: DominoEffect -> map_to_func_elem
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’
 ERROR
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  Backtrace:
      ▆
   1. └─DominoEffect::DominoEffect(...) at test_functions.R:58:5
   2.   └─DominoEffect::map_to_func_elem(results, write_to_file, ens_release = ens_release)
  ── Error ('test_functions.R:79:5'): map_to_func_elem ───────────────────────────
  Error in `map_to_func_elem(hotspot_mutations)`: 'useMart()' failed:
    error: HTTP 500 Internal Server Error.
  Backtrace:
      ▆
   1. └─DominoEffect::map_to_func_elem(hotspot_mutations) at test_functions.R:79:5
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 10 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘Vignette.Rmd’ using rmarkdown

Quitting from Vignette.Rmd:60-63 [unnamed-chunk-6]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `map_to_func_elem()`:
! 'useMart()' failed:
  error: HTTP 500 Internal Server Error.
---
Backtrace:
    ▆
 1. └─DominoEffect::DominoEffect(...)
 2.   └─DominoEffect::map_to_func_elem(results, write_to_file, ens_release = ens_release)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Vignette.Rmd' failed with diagnostics:
'useMart()' failed:
  error: HTTP 500 Internal Server Error.
--- failed re-building ‘Vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘Vignette.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 3 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/DominoEffect.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL DominoEffect
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘DominoEffect’ ...
** this is package ‘DominoEffect’ version ‘1.30.0’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (DominoEffect)

R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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)
> test_check("DominoEffect")
Loading required package: DominoEffect
Saving _problems/test_functions-60.R
Saving _problems/test_functions-79.R
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 10 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_functions.R:58:5'): DominoEffect ───────────────────────────────
Error in `map_to_func_elem(results, write_to_file, ens_release = ens_release)`: 'useMart()' failed:
  error: HTTP 500 Internal Server Error.
Backtrace:
    ▆
 1. └─DominoEffect::DominoEffect(...) at test_functions.R:58:5
 2.   └─DominoEffect::map_to_func_elem(results, write_to_file, ens_release = ens_release)
── Error ('test_functions.R:79:5'): map_to_func_elem ───────────────────────────
Error in `map_to_func_elem(hotspot_mutations)`: 'useMart()' failed:
  error: HTTP 500 Internal Server Error.
Backtrace:
    ▆
 1. └─DominoEffect::map_to_func_elem(hotspot_mutations) at test_functions.R:79:5

[ FAIL 2 | WARN 0 | SKIP 0 | PASS 10 ]
Error:
! Test failures.
Execution halted