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### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:cogeqc.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings cogeqc_1.13.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/cogeqc.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cogeqc/DESCRIPTION’ ... OK
* this is package ‘cogeqc’ version ‘1.13.0’
* 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 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 code 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 loading without being on the library search path ... 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
plot_genome_stats 9.520  0.032  11.738
get_genome_stats  1.215  0.023   9.062
* 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:
  Error in `open.connection(con, "rb")`: cannot open the connection to 'https://api.ncbi.nlm.nih.gov/datasets/v2alpha/genome/taxon/spermatophyta/dataset_report?page_size=1000&filters.assembly_level=chromosome'
  Backtrace:
      ▆
   1. └─cogeqc::get_genome_stats(taxon = "spermatophyta", filters = list(filters.assembly_level = "chromosome")) at test-genome_assembly.R:40:5
   2.   └─jsonlite::read_json(base_url, simplifyVector = TRUE)
   3.     └─jsonlite::parse_json(...)
   4.       └─jsonlite:::parse_and_simplify(...)
   5.         └─jsonlite:::parseJSON(txt, bigint_as_char)
   6.           └─jsonlite:::parse_con(txt, bigint_as_char)
   7.             ├─base::open(con, "rb")
   8.             └─base::open.connection(con, "rb")
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 55 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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-3.22-bioc/meat/cogeqc.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD INSTALL cogeqc
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* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘cogeqc’ ...
** this is package ‘cogeqc’ version ‘1.13.0’
** 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 version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 55 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-genome_assembly.R:40:5'): get_genome_stats() returns a data frame of NCBI genome stats ──
Error in `open.connection(con, "rb")`: cannot open the connection to 'https://api.ncbi.nlm.nih.gov/datasets/v2alpha/genome/taxon/spermatophyta/dataset_report?page_size=1000&filters.assembly_level=chromosome'
Backtrace:
    ▆
 1. └─cogeqc::get_genome_stats(taxon = "spermatophyta", filters = list(filters.assembly_level = "chromosome")) at test-genome_assembly.R:40:5
 2.   └─jsonlite::read_json(base_url, simplifyVector = TRUE)
 3.     └─jsonlite::parse_json(...)
 4.       └─jsonlite:::parse_and_simplify(...)
 5.         └─jsonlite:::parseJSON(txt, bigint_as_char)
 6.           └─jsonlite:::parse_con(txt, bigint_as_char)
 7.             ├─base::open(con, "rb")
 8.             └─base::open.connection(con, "rb")

[ FAIL 1 | WARN 1 | SKIP 0 | PASS 55 ]
Error: Test failures
Execution halted