##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:multiGSEA.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings multiGSEA_1.16.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/multiGSEA.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘multiGSEA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘multiGSEA’ version ‘1.16.2’
* 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 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 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]: SSL connection timeout
Error in fetchRemote(name, path) : 
  cannot download pathway data: are you offline?
Calls: getMultiOmicsFeatures ... lapply -> FUN -> <Anonymous> -> loadData -> 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:
   6.           └─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:::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 re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘multiGSEA.rmd’ using rmarkdown

Quitting from lines 269-279 [calculate_enrichment] (multiGSEA.rmd)
Error: processing vignette 'multiGSEA.rmd' failed with diagnostics:
cannot download pathway data: are you offline?
--- failed re-building ‘multiGSEA.rmd’

SUMMARY: processing the following file failed:
  ‘multiGSEA.rmd’

Error: Vignette re-building failed.
Execution halted

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

Status: 3 ERRORs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/multiGSEA.Rcheck/00check.log’
for details.