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This page was generated on 2025-01-23 12:05 -0500 (Thu, 23 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4746
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4493
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4517
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4469
taishanLinux (openEuler 24.03 LTS)aarch644.4.2 (2024-10-31) -- "Pile of Leaves" 4394
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1367/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
multiGSEA 1.16.2  (landing page)
Sebastian Canzler
Snapshot Date: 2025-01-20 13:00 -0500 (Mon, 20 Jan 2025)
git_url: https://git.bioconductor.org/packages/multiGSEA
git_branch: RELEASE_3_20
git_last_commit: dfe6f08
git_last_commit_date: 2024-11-25 02:40:46 -0500 (Mon, 25 Nov 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    ERROR  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    TIMEOUT  skippedskipped
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    TIMEOUT  skipped


CHECK results for multiGSEA on nebbiolo2

To the developers/maintainers of the multiGSEA package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/multiGSEA.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: multiGSEA
Version: 1.16.2
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
StartedAt: 2025-01-21 00:15:34 -0500 (Tue, 21 Jan 2025)
EndedAt: 2025-01-21 00:25:58 -0500 (Tue, 21 Jan 2025)
EllapsedTime: 624.8 seconds
RetCode: 1
Status:   ERROR  
CheckDir: multiGSEA.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### 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.


Installation output

multiGSEA.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL multiGSEA
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘multiGSEA’ ...
** 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)

Tests output

multiGSEA.Rcheck/tests/testthat.Rout.fail


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 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(multiGSEA)
loading from cache
> 
> test_check("multiGSEA")
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Timeout was reached [graphiteweb.bio.unipd.it]: SSL connection timeout
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Timeout was reached [graphiteweb.bio.unipd.it]: SSL connection timeout
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Timeout was reached [graphiteweb.bio.unipd.it]: SSL connection timeout
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Timeout was reached [graphiteweb.bio.unipd.it]: SSL connection timeout
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Timeout was reached [graphiteweb.bio.unipd.it]: SSL connection timeout
[ 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:::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:::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:::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:::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

Example timings

multiGSEA.Rcheck/multiGSEA-Ex.timings

nameusersystemelapsed
combinePvalues0.0050.0000.005