##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:graphite.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings graphite_1.56.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/graphite.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘graphite/DESCRIPTION’ ... OK
* this is package ‘graphite’ version ‘1.56.0’
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
runClipper         9.900  0.481  10.383
convertIdentifiers 5.173  0.148   5.324
* 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 re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘metabolites.pdf.asis’ using asis
--- finished re-building ‘metabolites.pdf.asis’

--- re-building ‘graphite.Rnw’ using Sweave
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: ‘generics’

The following objects are masked from ‘package:base’:

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Timeout was reached [graphiteweb.bio.unipd.it]:
SSL connection timeout

Error: processing vignette 'graphite.Rnw' failed with diagnostics:
 chunk 3 (label = base1) 
Error in fetchRemote(name, path) : 
  cannot download pathway data: are you offline?

--- failed re-building ‘graphite.Rnw’

SUMMARY: processing the following file failed:
  ‘graphite.Rnw’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/graphite.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL graphite
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘graphite’ ...
** this is package ‘graphite’ version ‘1.56.0’
** 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 version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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(graphite)
> 
> test_check("graphite")
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Timeout was reached [graphiteweb.bio.unipd.it]:
SSL connection timeout
Saving _problems/test_fetch-24.R
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Timeout was reached [graphiteweb.bio.unipd.it]:
SSL connection timeout
Saving _problems/test_graph-102.R
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Timeout was reached [graphiteweb.bio.unipd.it]:
SSL connection timeout
Saving _problems/test_graph-110.R
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Timeout was reached [graphiteweb.bio.unipd.it]:
SSL connection timeout
Saving _problems/test_spia-38.R
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Timeout was reached [graphiteweb.bio.unipd.it]:
SSL connection timeout
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