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### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:Gviz.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings Gviz_1.40.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/Gviz.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Gviz/DESCRIPTION’ ... OK
* this is package ‘Gviz’ version ‘1.40.1’
* 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 ‘Gviz’ 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
AlignmentsTrack-class 12.141  1.172  13.316
AnnotationTrack-class  7.303  0.268   7.571
GeneRegionTrack-class  6.426  0.104   6.531
plotTracks             5.124  0.088   5.213
* 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:
    4.     │ ├─BiocGenerics::eval(expression, envir = callEnv)
    5.     │ └─base::eval(expression, envir = callEnv)
    6.     │   └─base::eval(expression, envir = callEnv)
    7.     └─Gviz:::.getBiomart(genome)
    8.       └─biomaRt::useEnsembl(biomart = "ensembl", dataset = map$dataset)
    9.         └─biomaRt:::.useMart(...)
   10.           └─biomaRt::useDataset(mart = mart, dataset = dataset, verbose = verbose)
   11.             └─biomaRt:::.getFilters(mart, verbose = verbose)
   12.               └─biomaRt:::.getAttrFilt(mart = mart, verbose = verbose, type = "filters")
   13.                 └─biomaRt:::bmRequest(...)
   14.                   └─httr::stop_for_status(result)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 293 ]
  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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/Gviz.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL Gviz
###
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* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘Gviz’ ...
** using staged installation
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Gviz)

R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-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(Gviz)
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min


Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: grid
> 
> test_check("Gviz")
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:grid':

    pattern

The following object is masked from 'package:base':

    strsplit

Loading required package: rtracklayer
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 293 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_AllClasses.R:175'): interaction with biomart works ─────────────
<http_504/http_500/http_error/error/condition>
Error in `bmRequest(request = request, httr_config = martHTTRConfig(mart), 
    verbose = verbose)`: Gateway Timeout (HTTP 504).
Backtrace:
     ▆
  1. └─Gviz::BiomartGeneRegionTrack(...) at test_AllClasses.R:175:4
  2.   └─Gviz:::.genome2Dataset(genome)
  3.     ├─Gviz::.doCache(...)
  4.     │ ├─BiocGenerics::eval(expression, envir = callEnv)
  5.     │ └─base::eval(expression, envir = callEnv)
  6.     │   └─base::eval(expression, envir = callEnv)
  7.     └─Gviz:::.getBiomart(genome)
  8.       └─biomaRt::useEnsembl(biomart = "ensembl", dataset = map$dataset)
  9.         └─biomaRt:::.useMart(...)
 10.           └─biomaRt::useDataset(mart = mart, dataset = dataset, verbose = verbose)
 11.             └─biomaRt:::.getFilters(mart, verbose = verbose)
 12.               └─biomaRt:::.getAttrFilt(mart = mart, verbose = verbose, type = "filters")
 13.                 └─biomaRt:::bmRequest(...)
 14.                   └─httr::stop_for_status(result)

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 293 ]
Error: Test failures
Execution halted