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This page was generated on 2022-01-17 11:07:52 -0500 (Mon, 17 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4161
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4056
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3998
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4115
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

CHECK results for multiGSEA on riesling1


To the developers/maintainers of the multiGSEA package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1237/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
multiGSEA 1.5.0  (landing page)
Sebastian Canzler
Snapshot Date: 2022-01-16 13:55:18 -0500 (Sun, 16 Jan 2022)
git_url: https://git.bioconductor.org/packages/multiGSEA
git_branch: master
git_last_commit: 0ad0e32
git_last_commit_date: 2021-10-26 13:00:40 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'graphite' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  NO, package depends on 'fgsea' which is not available

Summary

Package: multiGSEA
Version: 1.5.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:multiGSEA.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings multiGSEA_1.5.0.tar.gz
StartedAt: 2022-01-16 19:34:55 -0500 (Sun, 16 Jan 2022)
EndedAt: 2022-01-16 19:38:53 -0500 (Sun, 16 Jan 2022)
EllapsedTime: 237.8 seconds
RetCode: 0
Status:   OK  
CheckDir: multiGSEA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:multiGSEA.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings multiGSEA_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/multiGSEA.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'multiGSEA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'multiGSEA' version '1.5.0'
* 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 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 R 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 ... NOTE
getMetaboliteMapping: no visible binding for global variable
  'metabolitesMapping'
getMetaboliteMapping: no visible binding for global variable 'Mapped'
Undefined global functions or variables:
  Mapped metabolitesMapping
* 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
getMetaboliteMapping 15.05   0.84   16.53
multiGSEA             5.02   0.05   20.86
extractPvalues        4.17   0.11   19.77
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  'D:/biocbuild/bbs-3.15-bioc/meat/multiGSEA.Rcheck/00check.log'
for details.



Installation output

multiGSEA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL multiGSEA
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'multiGSEA' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'multiGSEA'
    finding HTML links ... done
    archiveDir                              html  
    archivePath                             html  
    combinePvalues                          html  
    extractPvalues                          html  
    getFeatures                             html  
    getGeneMapping                          html  
    getIDMappingDatabase                    html  
    getMappedFeatures                       html  
    getMetaboliteMapping                    html  
    getMultiOmicsFeatures                   html  
    getOrganisms                            html  
    initOmicsDataStructure                  html  
    loadLocal                               html  
    mapIDType                               html  
    metabolome                              html  
    multiGSEA                               html  
    proteome                                html  
    rankFeatures                            html  
    rename_duplicates                       html  
    transcriptome                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (multiGSEA)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'MIGSA' is missing or broken
 done

Tests output

multiGSEA.Rcheck/tests/testthat.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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)
> 
> test_check("multiGSEA")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 50 ]
> 
> proc.time()
   user  system elapsed 
  30.75    1.31   59.23 

Example timings

multiGSEA.Rcheck/multiGSEA-Ex.timings

nameusersystemelapsed
combinePvalues000
extractPvalues 4.17 0.1119.77
getFeatures0.550.050.59
getGeneMapping0.360.020.38
getMetaboliteMapping15.05 0.8416.53
getMultiOmicsFeatures0.390.140.53
getOrganisms000
initOmicsDataStructure000
metabolome0.010.000.02
multiGSEA 5.02 0.0520.86
proteome000
rankFeatures000
rename_duplicates000
transcriptome0.020.000.02