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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:multiGSEA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings multiGSEA_1.21.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/multiGSEA.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 ‘multiGSEA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘multiGSEA’ version ‘1.21.0’
* 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 ‘multiGSEA’ 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 ‘multiGSEA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: extractPvalues
> ### Title: Create a reshaped data frame from multiGSEA output.
> ### Aliases: extractPvalues
> 
> ### ** Examples
> 
> # Download pathway definition and extract features
> pathways <- getMultiOmicsFeatures(dbs = c("kegg"), layer = c("transcriptome", "proteome"))
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Timeout was reached [graphiteweb.bio.unipd.it]:
Connection timed out after 10006 milliseconds
Error in fetchRemote(name, path) : 
  cannot download pathway data: are you offline?
Calls: getMultiOmicsFeatures ... <Anonymous> -> loadData -> withArchiveDir -> func -> fetchRemote
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:
  Backtrace:
      ▆
   1. └─multiGSEA::getMultiOmicsFeatures(dbs = dbs, organism = "hsapiens") at test_pathway_features.R:45:3
   2.   └─base::lapply(...)
   3.     └─multiGSEA (local) FUN(X[[i]], ...)
   4.       └─graphite::pathways(organism, x)
   5.         └─graphite:::loadData(paste(species, database, sep = "-"))
   6.           └─graphite:::withArchiveDir(...)
   7.             └─graphite (local) func(path)
   8.               └─graphite:::fetchRemote(name, path)
  
  [ FAIL 5 | WARN 0 | SKIP 0 | PASS 17 ]
  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-3.23-bioc/meat/multiGSEA.Rcheck/00check.log’
for details.

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL multiGSEA
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’
* installing *source* package ‘multiGSEA’ ...
** this is package ‘multiGSEA’ version ‘1.21.0’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
loading from cache
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
loading from cache
** testing if installed package can be loaded from final location
loading from cache
** testing if installed package keeps a record of temporary installation path
* DONE (multiGSEA)

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(multiGSEA)
loading from cache
> 
> test_check("multiGSEA")
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Timeout was reached [graphiteweb.bio.unipd.it]:
Connection timed out after 10009 milliseconds
Saving _problems/test_pathway_enrichment-34.R
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Timeout was reached [graphiteweb.bio.unipd.it]:
Connection timed out after 10003 milliseconds
Saving _problems/test_pathway_features-7.R
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Timeout was reached [graphiteweb.bio.unipd.it]:
Connection timed out after 10007 milliseconds
Saving _problems/test_pathway_features-20.R
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Timeout was reached [graphiteweb.bio.unipd.it]:
Connection timed out after 10003 milliseconds
Saving _problems/test_pathway_features-33.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_pathway_features-45.R
[ FAIL 5 | WARN 0 | SKIP 0 | PASS 17 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_pathway_enrichment.R:34:3'): pathway enrichment works. ─────────
Error in `fetchRemote(name, path)`: cannot download pathway data: are you offline?
Backtrace:
    ▆
 1. └─multiGSEA::getMultiOmicsFeatures(dbs = dbs) at test_pathway_enrichment.R:34:3
 2.   └─base::lapply(...)
 3.     └─multiGSEA (local) FUN(X[[i]], ...)
 4.       └─graphite::pathways(organism, x)
 5.         └─graphite:::loadData(paste(species, database, sep = "-"))
 6.           └─graphite:::withArchiveDir(...)
 7.             └─graphite (local) func(path)
 8.               └─graphite:::fetchRemote(name, path)
── Error ('test_pathway_features.R:7:3'): transcriptomic features get mapped ───
Error in `fetchRemote(name, path)`: cannot download pathway data: are you offline?
Backtrace:
    ▆
 1. └─multiGSEA::getMultiOmicsFeatures(dbs = dbs, layer = layer) at test_pathway_features.R:7:3
 2.   └─base::lapply(...)
 3.     └─multiGSEA (local) FUN(X[[i]], ...)
 4.       └─graphite::pathways(organism, x)
 5.         └─graphite:::loadData(paste(species, database, sep = "-"))
 6.           └─graphite:::withArchiveDir(...)
 7.             └─graphite (local) func(path)
 8.               └─graphite:::fetchRemote(name, path)
── Error ('test_pathway_features.R:20:3'): proteomic features get mapped ───────
Error in `fetchRemote(name, path)`: cannot download pathway data: are you offline?
Backtrace:
    ▆
 1. └─multiGSEA::getMultiOmicsFeatures(dbs = dbs, layer = layer) at test_pathway_features.R:20:3
 2.   └─base::lapply(...)
 3.     └─multiGSEA (local) FUN(X[[i]], ...)
 4.       └─graphite::pathways(organism, x)
 5.         └─graphite:::loadData(paste(species, database, sep = "-"))
 6.           └─graphite:::withArchiveDir(...)
 7.             └─graphite (local) func(path)
 8.               └─graphite:::fetchRemote(name, path)
── Error ('test_pathway_features.R:33:3'): metabolomic features get mapped ─────
Error in `fetchRemote(name, path)`: cannot download pathway data: are you offline?
Backtrace:
    ▆
 1. └─multiGSEA::getMultiOmicsFeatures(dbs = dbs, layer = layer) at test_pathway_features.R:33:3
 2.   └─base::lapply(...)
 3.     └─multiGSEA (local) FUN(X[[i]], ...)
 4.       └─graphite::pathways(organism, x)
 5.         └─graphite:::loadData(paste(species, database, sep = "-"))
 6.           └─graphite:::withArchiveDir(...)
 7.             └─graphite (local) func(path)
 8.               └─graphite:::fetchRemote(name, path)
── Error ('test_pathway_features.R:45:3'): each layer has equal length ─────────
Error in `fetchRemote(name, path)`: cannot download pathway data: are you offline?
Backtrace:
    ▆
 1. └─multiGSEA::getMultiOmicsFeatures(dbs = dbs, organism = "hsapiens") at test_pathway_features.R:45:3
 2.   └─base::lapply(...)
 3.     └─multiGSEA (local) FUN(X[[i]], ...)
 4.       └─graphite::pathways(organism, x)
 5.         └─graphite:::loadData(paste(species, database, sep = "-"))
 6.           └─graphite:::withArchiveDir(...)
 7.             └─graphite (local) func(path)
 8.               └─graphite:::fetchRemote(name, path)

[ FAIL 5 | WARN 0 | SKIP 0 | PASS 17 ]
Error:
! Test failures.
Execution halted