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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:Gviz.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings Gviz_1.43.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/Gviz.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 ‘Gviz/DESCRIPTION’ ... OK
* this is package ‘Gviz’ version ‘1.43.1’
* 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 ... NOTE
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    extdata   2.5Mb
* 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        14.253  1.052  15.309
AnnotationTrack-class         9.182  0.268   9.451
GeneRegionTrack-class         9.030  0.120   9.151
plotTracks                    6.602  0.308   6.910
SequenceTrack-class           4.758  0.843   5.628
GenomeAxisTrack-class         5.317  0.100   5.418
BiomartGeneRegionTrack-class  5.117  0.052   5.172
* 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:
    7.     └─Gviz:::.getBiomart(genome)
    8.       └─biomaRt::useEnsembl(biomart = "ensembl", dataset = map$dataset)
    9.         └─biomaRt::useDataset(mart = mart, dataset = dataset, verbose = verbose)
   10.           └─biomaRt:::.getAttributes(mart, verbose = verbose)
   11.             └─biomaRt:::.getAttrFilt(mart = mart, verbose = verbose, type = "attributes")
   12.               └─biomaRt:::bmRequest(...)
   13.                 └─httr::GET(...)
   14.                   └─httr:::request_perform(req, hu$handle$handle)
   15.                     ├─httr:::request_fetch(req$output, req$url, handle)
   16.                     └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   17.                       └─curl::curl_fetch_memory(url, handle = handle)
  
  [ 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 ...
  ‘Gviz.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/Gviz.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL Gviz
###
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* installing to library ‘/home/biocbuild/bbs-3.17-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 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(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, aperm, 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 ─────────────
Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached: [www.ensembl.org:443] Operation timed out after 10000 milliseconds with 189407 bytes received
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$dataset)
  9.         └─biomaRt::useDataset(mart = mart, dataset = dataset, verbose = verbose)
 10.           └─biomaRt:::.getAttributes(mart, verbose = verbose)
 11.             └─biomaRt:::.getAttrFilt(mart = mart, verbose = verbose, type = "attributes")
 12.               └─biomaRt:::bmRequest(...)
 13.                 └─httr::GET(...)
 14.                   └─httr:::request_perform(req, hu$handle$handle)
 15.                     ├─httr:::request_fetch(req$output, req$url, handle)
 16.                     └─httr:::request_fetch.write_memory(req$output, req$url, handle)
 17.                       └─curl::curl_fetch_memory(url, handle = handle)

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