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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:cogeqc.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings cogeqc_1.3.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/cogeqc.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 ‘cogeqc/DESCRIPTION’ ... OK
* this is package ‘cogeqc’ version ‘1.3.1’
* 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 ‘cogeqc’ 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 ... ERROR
Running examples in ‘cogeqc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_genome_stats
> ### Title: Plot statistics on genome assemblies on the NCBI
> ### Aliases: plot_genome_stats
> 
> ### ** Examples
> 
> # Example 1: plot stats on maize genomes on the NCBI
> ## Obtain stats for maize genomes on the NCBI
> ncbi_stats <- get_genome_stats(taxon = "Zea mays")
> 
> plot_genome_stats(ncbi_stats)
Error in reshapeLong(data, idvar = idvar, timevar = timevar, varying = varying,  : 
  'idvar' must uniquely identify records
Calls: plot_genome_stats -> <Anonymous> -> reshapeLong
Execution halted
* 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:
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-visualization.R:72:5'): plot_genome_stats() returns a plot composition ──
  Error in `reshapeLong(data, idvar = idvar, timevar = timevar, varying = varying, 
      v.names = v.names, drop = drop, times = times, ids = ids, 
      new.row.names = new.row.names)`: 'idvar' must uniquely identify records
  Backtrace:
      ▆
   1. └─cogeqc::plot_genome_stats(ncbi_stats) at test-visualization.R:72:4
   2.   └─stats::reshape(...)
   3.     └─stats (local) reshapeLong(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 56 ]
  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 ...
  ‘vignette_01_assessing_genome_assembly.Rmd’ using ‘UTF-8’... OK
  ‘vignette_02_assessing_orthogroup_inference.Rmd’ using ‘UTF-8’... OK
  ‘vignette_03_assessing_synteny.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette_01_assessing_genome_assembly.Rmd’ using rmarkdown
Quitting from lines 171-173 (vignette_01_assessing_genome_assembly.Rmd) 
Error: processing vignette 'vignette_01_assessing_genome_assembly.Rmd' failed with diagnostics:
'idvar' must uniquely identify records
--- failed re-building ‘vignette_01_assessing_genome_assembly.Rmd’

--- re-building ‘vignette_02_assessing_orthogroup_inference.Rmd’ using rmarkdown
--- finished re-building ‘vignette_02_assessing_orthogroup_inference.Rmd’

--- re-building ‘vignette_03_assessing_synteny.Rmd’ using rmarkdown
--- finished re-building ‘vignette_03_assessing_synteny.Rmd’

SUMMARY: processing the following file failed:
  ‘vignette_01_assessing_genome_assembly.Rmd’

Error: Vignette re-building failed.
Execution halted

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

Status: 3 ERRORs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/cogeqc.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL cogeqc
###
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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 ‘cogeqc’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (cogeqc)

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(cogeqc)
> 
> test_check("cogeqc")
More than 1 BUSCO summary file found. Using only the first.
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 56 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-visualization.R:72:5'): plot_genome_stats() returns a plot composition ──
Error in `reshapeLong(data, idvar = idvar, timevar = timevar, varying = varying, 
    v.names = v.names, drop = drop, times = times, ids = ids, 
    new.row.names = new.row.names)`: 'idvar' must uniquely identify records
Backtrace:
    ▆
 1. └─cogeqc::plot_genome_stats(ncbi_stats) at test-visualization.R:72:4
 2.   └─stats::reshape(...)
 3.     └─stats (local) reshapeLong(...)

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 56 ]
Error: Test failures
Execution halted