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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:graphite.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings graphite_1.45.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/graphite.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* 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 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘graphite/DESCRIPTION’ ... OK
* this is package ‘graphite’ version ‘1.45.0’
* 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 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 ... WARNING
checkRd: (5) PathwayList-class.Rd:24-27: \item in \describe must have non-empty label
checkRd: (5) PathwayList-class.Rd:28-31: \item in \describe must have non-empty label
checkRd: (5) PathwayList-class.Rd:32-35: \item in \describe must have non-empty label
checkRd: (5) PathwayList-class.Rd:36-40: \item in \describe must have non-empty label
checkRd: (5) PathwayList-class.Rd:41-44: \item in \describe must have non-empty label
checkRd: (5) PathwayList-class.Rd:45-48: \item in \describe must have non-empty label
checkRd: (5) PathwayList-class.Rd:49-52: \item in \describe must have non-empty label
checkRd: (5) PathwayList-class.Rd:53-56: \item in \describe must have non-empty label
checkRd: (5) PathwayList-class.Rd:57-60: \item in \describe must have non-empty label
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
runClipper         14.485  0.384  14.876
convertIdentifiers  5.559  0.128   5.687
* 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:
    Timeout was reached: [graphiteweb.bio.unipd.it] Resolving timed out after 10000 milliseconds
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 94 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_fetch.R:24'): 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:24:2
   2.   └─graphite:::loadData(paste(species, database, sep = "-"))
   3.     └─graphite:::fetchRemote(name, path)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 94 ]
  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 ...
  ‘metabolites.pdf.asis’... OK
  ‘graphite.Rnw’ using ‘UTF-8’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/graphite.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL graphite
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘graphite’ ...
** 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) (2023-01-14 r83615) -- "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(graphite)
> 
> test_check("graphite")
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Timeout was reached: [graphiteweb.bio.unipd.it] Resolving timed out after 10000 milliseconds
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 94 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_fetch.R:24'): 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:24:2
 2.   └─graphite:::loadData(paste(species, database, sep = "-"))
 3.     └─graphite:::fetchRemote(name, path)

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 94 ]
Error: Test failures
Execution halted