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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:GenVisR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings GenVisR_1.31.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/GenVisR.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* 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 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘GenVisR/DESCRIPTION’ ... OK
* this is package ‘GenVisR’ version ‘1.31.1’
* 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 ‘GenVisR’ 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 ... NOTE
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
setTierTwo,data.table : a: no visible binding for global variable ‘tmp’
toLolliplot,GMS: no visible binding for global variable ‘missingINdex’
Undefined global functions or variables:
  missingINdex tmp
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
Lolliplot-class 25.968  1.589  40.640
geneViz          7.933  0.232   8.166
genCov           7.405  0.252   7.662
cnFreq           7.209  0.252   7.462
cnSpec           5.454  0.120   5.575
* 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:
  • MutSpectra-class/mutspectra-frequency-plot-custom-pallette.svg
  • MutSpectra-class/mutspectra-frequency-plot.svg
  • MutSpectra-class/mutspectra-proportion-plot-add-layer.svg
  • MutSpectra-class/mutspectra-proportion-plot-custom-pallette.svg
  • MutSpectra-class/mutspectra-proportion-plot.svg
  • Rainfall-class/density-main-plot.svg
  • Rainfall-class/density-plot-add-layer.svg
  • Rainfall-class/drawplot-rainfall.svg
  • Rainfall-class/final-rainfall-alter-section-hieghts.svg
  • Rainfall-class/final-rainfall-base.svg
  • Rainfall-class/rainfall-main-plot.svg
  • Rainfall-class/rainfall-plot-add-layer.svg
  • Rainfall-class/rainfall-plot-aesthetic-options.svg
  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 ...
  ‘Intro.Rmd’ using ‘UTF-8’... OK
  ‘waterfall_introduction.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/GenVisR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL GenVisR
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library’
* installing *source* package ‘GenVisR’ ...
** 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 (GenVisR)

R Under development (unstable) (2023-03-12 r83975) -- "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(GenVisR)
> 
> test_check("GenVisR")
[ FAIL 3 | WARN 17 | SKIP 44 | PASS 579 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Bioconductor (44)

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-Lolliplot-class.R:80:5'): retreiveMart works in verbose mode ───
Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached: [www.ensembl.org:443] Operation timed out after 10000 milliseconds with 401149 bytes received
Backtrace:
     ▆
  1. ├─testthat::expect_message(...) at test-Lolliplot-class.R:80:4
  2. │ └─testthat:::quasi_capture(enquo(object), label, capture_messages)
  3. │   ├─testthat (local) .capture(...)
  4. │   │ └─base::withCallingHandlers(...)
  5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  6. ├─GenVisR:::retrieveMart(...)
  7. └─GenVisR:::retrieveMart(...)
  8.   └─GenVisR (local) .local(object, ...)
  9.     └─biomaRt::useDataset(as.character(dataset[index]), mart = ensembl_mart)
 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)
── Failure ('test-Lolliplot-class.R:526:5'): setDomainHeights domains are nested correctly ──
`expected` not equivalent to `actual`.
1/1 mismatches
[1] 2 - 9 == -7
── Error ('test-Lolliplot-class.R:551:5'): (code run outside of `test_that()`) ──
Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached: [www.ensembl.org:80] Operation timed out after 10000 milliseconds with 47558 bytes received
Backtrace:
     ▆
  1. ├─base::suppressWarnings(...) at test-Lolliplot-class.R:551:4
  2. │ └─base::withCallingHandlers(...)
  3. └─GenVisR:::LolliplotData(...)
  4.   ├─GenVisR:::retrieveMart(object = species, host = host, verbose = verbose)
  5.   └─GenVisR:::retrieveMart(object = species, host = host, verbose = verbose)
  6.     └─GenVisR (local) .local(object, ...)
  7.       └─biomaRt::useDataset(as.character(dataset[index]), mart = ensembl_mart)
  8.         └─biomaRt:::.getAttributes(mart, verbose = verbose)
  9.           └─biomaRt:::.getAttrFilt(mart = mart, verbose = verbose, type = "attributes")
 10.             └─biomaRt:::bmRequest(...)
 11.               └─httr::GET(...)
 12.                 └─httr:::request_perform(req, hu$handle$handle)
 13.                   ├─httr:::request_fetch(req$output, req$url, handle)
 14.                   └─httr:::request_fetch.write_memory(req$output, req$url, handle)
 15.                     └─curl::curl_fetch_memory(url, handle = handle)

[ FAIL 3 | WARN 17 | SKIP 44 | PASS 579 ]
Deleting unused snapshots:
• Lolliplot-class/drawplot-lolliplot.svg
• Lolliplot-class/final-lolliplot-alter-section-height.svg
• Lolliplot-class/final-lolliplot-base.svg
• Lolliplot-class/lolliplot-density-plot-layer.svg
• Lolliplot-class/lolliplot-density-plot.svg
• Lolliplot-class/lolliplot-plot-base-add-domain-palette.svg
• Lolliplot-class/lolliplot-plot-base-add-labels.svg
• Lolliplot-class/lolliplot-plot-base-add-layer.svg
• Lolliplot-class/lolliplot-plot-base-add-mutation-palette.svg
• Lolliplot-class/lolliplot-plot-base.svg
• MutSpectra-class/drawplot-mutspectra.svg
• MutSpectra-class/final-mutspectra-alter-section-heights.svg
• MutSpectra-class/final-mutspectra-base.svg
• MutSpectra-class/mutspectra-clinical.svg
• MutSpectra-class/mutspectra-frequency-plot-add-layer.svg
• MutSpectra-class/mutspectra-frequency-plot-custom-pallette.svg
• MutSpectra-class/mutspectra-frequency-plot.svg
• MutSpectra-class/mutspectra-proportion-plot-add-layer.svg
• MutSpectra-class/mutspectra-proportion-plot-custom-pallette.svg
• MutSpectra-class/mutspectra-proportion-plot.svg
• Rainfall-class/density-main-plot.svg
• Rainfall-class/density-plot-add-layer.svg
• Rainfall-class/drawplot-rainfall.svg
• Rainfall-class/final-rainfall-alter-section-hieghts.svg
• Rainfall-class/final-rainfall-base.svg
• Rainfall-class/rainfall-main-plot.svg
• Rainfall-class/rainfall-plot-add-layer.svg
• Rainfall-class/rainfall-plot-aesthetic-options.svg
Error: Test failures
Execution halted