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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:graphite.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings graphite_1.57.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/graphite.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘graphite/DESCRIPTION’ ... OK
* this is package ‘graphite’ version ‘1.57.0’
* 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 ‘graphite’ 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
runClipper 5.352  0.145   5.639
* 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 ('test_topologygsa.R:37:3'): (code run outside of `test_that()`) ──────
  Error in `fetchRemote(name, path)`: cannot download pathway data: are you offline?
  Backtrace:
      ▆
   1. └─graphite (local) load_pathways() at test_topologygsa.R:47:1
   2.   └─graphite::pathways("hsapiens", "kegg") at test_topologygsa.R:37:3
   3.     └─graphite:::loadData(paste(species, database, sep = "-"))
   4.       └─graphite:::withArchiveDir(...)
   5.         └─graphite (local) func(path)
   6.           └─graphite:::fetchRemote(name, path)
  
  [ FAIL 5 | WARN 0 | SKIP 0 | PASS 81 ]
  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
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/graphite.Rcheck/00check.log’
for details.

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###
### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL graphite
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’
* installing *source* package ‘graphite’ ...
** this is package ‘graphite’ version ‘1.57.0’
** using staged installation
** R
** 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 (graphite)

R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
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(graphite)
> 
> test_check("graphite")
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Timeout was reached [graphiteweb.bio.unipd.it]:
Connection timed out after 10003 milliseconds
Saving _problems/test_fetch-24.R
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Timeout was reached [graphiteweb.bio.unipd.it]:
Connection timed out after 10004 milliseconds
Saving _problems/test_graph-102.R
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Timeout was reached [graphiteweb.bio.unipd.it]:
Connection timed out after 10003 milliseconds
Saving _problems/test_graph-110.R
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Timeout was reached [graphiteweb.bio.unipd.it]:
Connection timed out after 10003 milliseconds
Saving _problems/test_spia-38.R
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Timeout was reached [graphiteweb.bio.unipd.it]:
Connection timed out after 10003 milliseconds
Saving _problems/test_topologygsa-37.R
[ FAIL 5 | WARN 0 | SKIP 0 | PASS 81 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_fetch.R:24:3'): Mus musculus pathways can be downloaded ────────
Error in `fetchRemote(name, path)`: cannot download pathway data: are you offline?
Backtrace:
    ▆
 1. └─graphite::pathways("mmusculus", "kegg") at test_fetch.R:24:3
 2.   └─graphite:::loadData(paste(species, database, sep = "-"))
 3.     └─graphite:::withArchiveDir(...)
 4.       └─graphite (local) func(path)
 5.         └─graphite:::fetchRemote(name, path)
── Error ('test_graph.R:102:3'): graphNEL includes metabolites from pathway ────
Error in `fetchRemote(name, path)`: cannot download pathway data: are you offline?
Backtrace:
    ▆
 1. └─graphite::pathways("hsapiens", "kegg") at test_graph.R:102:3
 2.   └─graphite:::loadData(paste(species, database, sep = "-"))
 3.     └─graphite:::withArchiveDir(...)
 4.       └─graphite (local) func(path)
 5.         └─graphite:::fetchRemote(name, path)
── Error ('test_graph.R:110:3'): Selection of an invalid type of edge is rejected ──
Error in `fetchRemote(name, path)`: cannot download pathway data: are you offline?
Backtrace:
    ▆
 1. └─graphite::pathways("hsapiens", "kegg") at test_graph.R:110:3
 2.   └─graphite:::loadData(paste(species, database, sep = "-"))
 3.     └─graphite:::withArchiveDir(...)
 4.       └─graphite (local) func(path)
 5.         └─graphite:::fetchRemote(name, path)
── Error ('test_spia.R:38:3'): analysis result contains one row for each pathway ──
Error in `fetchRemote(name, path)`: cannot download pathway data: are you offline?
Backtrace:
    ▆
 1. └─graphite::pathways("hsapiens", "kegg") at test_spia.R:38:3
 2.   └─graphite:::loadData(paste(species, database, sep = "-"))
 3.     └─graphite:::withArchiveDir(...)
 4.       └─graphite (local) func(path)
 5.         └─graphite:::fetchRemote(name, path)
── Error ('test_topologygsa.R:37:3'): (code run outside of `test_that()`) ──────
Error in `fetchRemote(name, path)`: cannot download pathway data: are you offline?
Backtrace:
    ▆
 1. └─graphite (local) load_pathways() at test_topologygsa.R:47:1
 2.   └─graphite::pathways("hsapiens", "kegg") at test_topologygsa.R:37:3
 3.     └─graphite:::loadData(paste(species, database, sep = "-"))
 4.       └─graphite:::withArchiveDir(...)
 5.         └─graphite (local) func(path)
 6.           └─graphite:::fetchRemote(name, path)

[ FAIL 5 | WARN 0 | SKIP 0 | PASS 81 ]
Error:
! Test failures.
Execution halted