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CHECK report for multiGSEA on tokay1

This page was generated on 2021-05-05 12:12:33 -0400 (Wed, 05 May 2021).

To the developers/maintainers of the multiGSEA package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1179/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
multiGSEA 1.0.2  (landing page)
Sebastian Canzler
Snapshot Date: 2021-05-04 14:50:13 -0400 (Tue, 04 May 2021)
URL: https://git.bioconductor.org/packages/multiGSEA
Branch: RELEASE_3_12
Last Commit: 2dc0f3c
Last Changed Date: 2021-04-21 15:08:46 -0400 (Wed, 21 Apr 2021)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: multiGSEA
Version: 1.0.2
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:multiGSEA.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings multiGSEA_1.0.2.tar.gz
StartedAt: 2021-05-05 04:58:09 -0400 (Wed, 05 May 2021)
EndedAt: 2021-05-05 05:07:47 -0400 (Wed, 05 May 2021)
EllapsedTime: 578.0 seconds
RetCode: 0
Status:   OK   
CheckDir: multiGSEA.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:multiGSEA.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings multiGSEA_1.0.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/multiGSEA.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '1.0.2'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
getMetaboliteMapping 33.84   2.84   37.29
multiGSEA             4.98   0.28   24.91
extractPvalues        3.75   0.19   27.35
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
getMetaboliteMapping 26.84   0.89   28.39
multiGSEA             4.80   0.10   27.36
extractPvalues        2.68   0.06   23.11
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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: OK


Installation output

multiGSEA.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/multiGSEA_1.0.2.tar.gz && rm -rf multiGSEA.buildbin-libdir && mkdir multiGSEA.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=multiGSEA.buildbin-libdir multiGSEA_1.0.2.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL multiGSEA_1.0.2.zip && rm multiGSEA_1.0.2.tar.gz multiGSEA_1.0.2.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  2  568k    2 12897    0     0  89612      0  0:00:06 --:--:--  0:00:06 89562
100  568k  100  568k    0     0  3817k      0 --:--:-- --:--:-- --:--:-- 3816k

install for i386

* 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

install for x64

* installing *source* package 'multiGSEA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'multiGSEA' as multiGSEA_1.0.2.zip
* DONE (multiGSEA)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'multiGSEA' successfully unpacked and MD5 sums checked

Tests output

multiGSEA.Rcheck/tests_i386/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 
  39.32    3.35   99.79 

multiGSEA.Rcheck/tests_x64/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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 
  45.78    1.53   99.40 

Example timings

multiGSEA.Rcheck/examples_i386/multiGSEA-Ex.timings

nameusersystemelapsed
combinePvalues0.020.000.01
extractPvalues 3.75 0.1927.35
getFeatures0.850.161.00
getGeneMapping0.890.060.95
getMetaboliteMapping33.84 2.8437.29
getMultiOmicsFeatures0.520.050.56
getOrganisms000
initOmicsDataStructure000
metabolome0.020.000.02
multiGSEA 4.98 0.2824.91
proteome0.030.000.03
rankFeatures000
rename_duplicates000
transcriptome0.050.020.06

multiGSEA.Rcheck/examples_x64/multiGSEA-Ex.timings

nameusersystemelapsed
combinePvalues000
extractPvalues 2.68 0.0623.11
getFeatures0.550.060.61
getGeneMapping0.390.050.44
getMetaboliteMapping26.84 0.8928.39
getMultiOmicsFeatures0.360.090.45
getOrganisms000
initOmicsDataStructure000
metabolome0.020.000.02
multiGSEA 4.80 0.1027.36
proteome0.030.010.05
rankFeatures000
rename_duplicates000
transcriptome0.040.000.04