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This page was generated on 2024-06-15 12:33 -0400 (Sat, 15 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4685
lconwaymacOS 12.7.1 Montereyx86_644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4400
kjohnson3macOS 13.6.5 Venturaarm644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4349
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 1341/2242HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
multiGSEA 1.15.0  (landing page)
Sebastian Canzler
Snapshot Date: 2024-06-14 14:00 -0400 (Fri, 14 Jun 2024)
git_url: https://git.bioconductor.org/packages/multiGSEA
git_branch: devel
git_last_commit: f1d6c36
git_last_commit_date: 2024-04-30 11:24:57 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    TIMEOUT  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


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: 1.15.0
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_1.15.0.tar.gz
StartedAt: 2024-06-15 01:19:34 -0400 (Sat, 15 Jun 2024)
EndedAt: 2024-06-15 01:59:34 -0400 (Sat, 15 Jun 2024)
EllapsedTime: 2400.0 seconds
RetCode: None
Status:   TIMEOUT  
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_1.15.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/multiGSEA.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘multiGSEA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘multiGSEA’ version ‘1.15.0’
* 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 ... NOTE
Error: .onLoad failed in loadNamespace() for 'metaboliteIDmapping', details:
  call: NULL
  error: failed to load resource
  name: AH91792
  title: Mapping table of metabolite IDs and common names
  reason: 1 resources failed to download
Call sequence:
6: stop(gettextf("%s failed in %s() for '%s', details:\n  call: %s\n  error: %s", 
       hookname, "loadNamespace", pkgname, deparse(conditionCall(res))[1L], 
       conditionMessage(res)), call. = FALSE, domain = NA)
5: runHook(".onLoad", env, package.lib, package)
4: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
3: asNamespace(ns)
2: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, 
       .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
1: loadNamespace(package, lib.loc)
Execution halted
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
extractPvalues 12.534  1.066  10.692
multiGSEA       7.556  1.019   5.487
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ...

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


R version 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"
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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 50 ]
> 
> proc.time()
   user  system elapsed 
 39.981   3.282  40.224 

Example timings

multiGSEA.Rcheck/multiGSEA-Ex.timings

nameusersystemelapsed
combinePvalues0.0060.0000.006
extractPvalues12.534 1.06610.692
getFeatures0.6410.1600.801
getGeneMapping0.5410.0440.585
getMetaboliteMapping0.3490.0240.373
getMultiOmicsFeatures0.6880.2240.913
getOrganisms0.0000.0000.001
initOmicsDataStructure000
metabolome0.0020.0060.007
multiGSEA7.5561.0195.487
proteome0.0140.0000.014
rankFeatures0.0010.0000.000
rename_duplicates0.0010.0000.001
transcriptome0.0120.0040.016