##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cogeqc.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cogeqc_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/cogeqc.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cogeqc/DESCRIPTION’ ... OK
* this is package ‘cogeqc’ version ‘1.10.0’
* 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 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: get_genome_stats
> ### Title: Get summary statistics for genomes on NCBI using the NCBI
> ###   Datasets API
> ### Aliases: get_genome_stats
> 
> ### ** Examples
> 
> # Example 1: Search for A. thaliana genomes by tax ID
> ex1 <- get_genome_stats(taxon = 3702)
Warning in open.connection(con, "rb") :
  cannot open URL 'https://api.ncbi.nlm.nih.gov/datasets/v2alpha/genome/taxon/3702/dataset_report?page_size=1000': HTTP status was '500 Internal Server Error'
Error in open.connection(con, "rb") : 
  cannot open the connection to 'https://api.ncbi.nlm.nih.gov/datasets/v2alpha/genome/taxon/3702/dataset_report?page_size=1000'
Calls: get_genome_stats ... parse_and_simplify -> parseJSON -> parse_con -> open -> open.connection
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:
  Error in `open.connection(con, "rb")`: cannot open the connection to 'https://api.ncbi.nlm.nih.gov/datasets/v2alpha/genome/taxon/Zea%20mays/dataset_report?page_size=1000'
  Backtrace:
      ▆
   1. └─cogeqc::get_genome_stats(taxon = "Zea mays") at test-genome_assembly.R:53:5
   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 2 | WARN 2 | SKIP 0 | PASS 51 ]
  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: 2 ERRORs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/cogeqc.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL cogeqc
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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 version 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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 2 | WARN 2 | SKIP 0 | PASS 51 ]

══ 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")
── Error ('test-genome_assembly.R:53:5'): compare_genome_stats() compares genome assembly stats ──
Error in `open.connection(con, "rb")`: cannot open the connection to 'https://api.ncbi.nlm.nih.gov/datasets/v2alpha/genome/taxon/Zea%20mays/dataset_report?page_size=1000'
Backtrace:
    ▆
 1. └─cogeqc::get_genome_stats(taxon = "Zea mays") at test-genome_assembly.R:53:5
 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 2 | WARN 2 | SKIP 0 | PASS 51 ]
Error: Test failures
Execution halted