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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PanViz.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PanViz_1.5.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/PanViz.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-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 Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PanViz/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PanViz’ version ‘1.5.0’
* 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 ‘PanViz’ 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘PanViz-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: decompose_IMON
> ### Title: decompose_IMON
> ### Aliases: decompose_IMON
> 
> ### ** Examples
> 
> data("er_snp_vector")
> G <- PanViz::get_IMON(snp_list = er_snp_vector, ego = 5, save_file = FALSE)

  |                                                                            
  |                                                                      |   0%Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [eutils.ncbi.nlm.nih.gov] Failed to connect to eutils.ncbi.nlm.nih.gov port 443 after 10090 ms: Timeout was reached
Calls: <Anonymous> ... request_fetch -> request_fetch.write_memory -> <Anonymous>
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:
    7.     │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
    8.     │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
    9.     │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
   10.     └─rentrez::entrez_summary(db = "snp", id = split_data[[i]])
   11.       ├─base::do.call(make_entrez_query, args)
   12.       └─rentrez (local) `<fn>`(...)
   13.         └─httr::GET(uri, query = args, config = config)
   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)
  
  [ FAIL 1 | WARN 31 | SKIP 0 | PASS 16 ]
  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-3.19-bioc/meat/PanViz.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL PanViz
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘PanViz’ ...
** using staged installation
** R
** data
** 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 (PanViz)

R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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(PanViz)
> Sys.setenv(R_TESTS="")
> test_check("PanViz")
This graph was created by an old(er) igraph version.
  Call upgrade_graph() on it to use with the current igraph version
  For now we convert it on the fly...

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[ FAIL 1 | WARN 31 | SKIP 0 | PASS 16 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_get_IMON.R:5:3'): tests that get_IMON produces an igraph object and throws correct errors on bad inputs ──
Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached: [eutils.ncbi.nlm.nih.gov] Failed to connect to eutils.ncbi.nlm.nih.gov port 443 after 10000 ms: Timeout was reached
Backtrace:
     ▆
  1. ├─testthat::expect_equal(...) at test_get_IMON.R:5:3
  2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
  3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
  4. └─PanViz::get_IMON(snp_list = er_snp_vector, ego = 5, save_file = FALSE)
  5.   └─PanViz:::NCBI_dbSNP_query(snp_list, progress_bar)
  6.     ├─base::tryCatch(...)
  7.     │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  8.     │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  9.     │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 10.     └─rentrez::entrez_summary(db = "snp", id = split_data[[i]])
 11.       ├─base::do.call(make_entrez_query, args)
 12.       └─rentrez (local) `<fn>`(...)
 13.         └─httr::GET(uri, query = args, config = config)
 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)

[ FAIL 1 | WARN 31 | SKIP 0 | PASS 16 ]
Error: Test failures
Execution halted