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This page was generated on 2024-05-04 11:40:49 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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 1377/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
multiGSEA 1.14.0  (landing page)
Sebastian Canzler
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/multiGSEA
git_branch: RELEASE_3_19
git_last_commit: 7fd1d9a
git_last_commit_date: 2024-04-30 11:24:57 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    TIMEOUT  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for multiGSEA on kunpeng2


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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: multiGSEA
Version: 1.14.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:multiGSEA.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings multiGSEA_1.14.0.tar.gz
StartedAt: 2024-05-04 09:56:58 -0000 (Sat, 04 May 2024)
EndedAt: 2024-05-04 10:10:14 -0000 (Sat, 04 May 2024)
EllapsedTime: 795.6 seconds
RetCode: 1
Status:   ERROR  
CheckDir: multiGSEA.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:multiGSEA.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings multiGSEA_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/multiGSEA.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘multiGSEA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘multiGSEA’ version ‘1.14.0’
* 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 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] Connection timeout after 10000 ms
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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/multiGSEA.Rcheck/00check.log’
for details.


Installation output

multiGSEA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL multiGSEA
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/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 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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$path, handle = handle) : 
  Timeout was reached: [graphiteweb.bio.unipd.it] Connection timeout after 10001 ms
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Timeout was reached: [graphiteweb.bio.unipd.it] Connection timeout after 10001 ms
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Timeout was reached: [graphiteweb.bio.unipd.it] Connection timeout after 10001 ms
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Timeout was reached: [graphiteweb.bio.unipd.it] Connection timeout after 10001 ms
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Timeout was reached: [graphiteweb.bio.unipd.it] Connection timeout after 10000 ms
[ 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
combinePvalues0.0070.0000.007