##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GenVisR.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings GenVisR_1.31.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/GenVisR.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'GenVisR/DESCRIPTION' ... OK
* this is package 'GenVisR' version '1.31.0'
* 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 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 ... WARNING
Undocumented code objects:
  'lolliplot'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 14.73   0.59   64.86
geneViz          6.47   0.14    6.61
genCov           6.02   0.44    6.51
* 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:
    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:::checkDataset(dataset = dataset, mart = mart)
    9.           └─biomaRt:::.listDatasets(mart, sort = FALSE)
   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 21 | SKIP 44 | PASS 580 ]
  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, 1 WARNING, 2 NOTEs
See
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/GenVisR.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL GenVisR
###
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* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/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) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 21 | SKIP 44 | PASS 580 ]

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

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-Lolliplot-class.R:526'): setDomainHeights domains are nested correctly ──
`expected` not equivalent to `actual`.
Lengths differ: 1 is not 0
── Failure ('test-Lolliplot-class.R:530'): setDomainHeights domains are nested correctly ──
`expected` not equivalent to `actual`.
Lengths differ: 1 is not 0
── Error ('test-Lolliplot-class.R:559'): (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 10013 milliseconds with 0 bytes received
Backtrace:
     ▆
  1. ├─base::suppressWarnings(...) at test-Lolliplot-class.R:559:4
  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:::checkDataset(dataset = dataset, mart = mart)
  9.           └─biomaRt:::.listDatasets(mart, sort = FALSE)
 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 21 | SKIP 44 | PASS 580 ]
Error: Test failures
Execution halted