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CHECK report for clusterProfiler on tokay2

This page was generated on 2020-10-17 11:56:19 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE clusterProfiler PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 319/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clusterProfiler 3.16.1
Guangchuang Yu
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/clusterProfiler
Branch: RELEASE_3_11
Last Commit: f1702b8
Last Changed Date: 2020-08-18 08:33:52 -0400 (Tue, 18 Aug 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: clusterProfiler
Version: 3.16.1
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:clusterProfiler.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings clusterProfiler_3.16.1.tar.gz
StartedAt: 2020-10-17 02:42:35 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 02:48:28 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 353.4 seconds
RetCode: 0
Status:  OK  
CheckDir: clusterProfiler.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:clusterProfiler.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings clusterProfiler_3.16.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/clusterProfiler.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'clusterProfiler/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'clusterProfiler' version '3.16.1'
* 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 'clusterProfiler' 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
groupGO 58.81   5.96   64.86
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
         user system elapsed
groupGO 49.59   1.62   51.22
* 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

clusterProfiler.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/clusterProfiler_3.16.1.tar.gz && rm -rf clusterProfiler.buildbin-libdir && mkdir clusterProfiler.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=clusterProfiler.buildbin-libdir clusterProfiler_3.16.1.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL clusterProfiler_3.16.1.zip && rm clusterProfiler_3.16.1.tar.gz clusterProfiler_3.16.1.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
100 2538k  100 2538k    0     0  24.8M      0 --:--:-- --:--:-- --:--:-- 26.6M

install for i386

* installing *source* package 'clusterProfiler' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'clusterProfiler'
    finding HTML links ... done
    DataSet                                 html  
    GSEA                                    html  
    Gff2GeneTable                           html  
    KEGG_path2extid                         html  
    bitr                                    html  
    bitr_kegg                               html  
    browseKEGG                              html  
    buildGOmap                              html  
    clusterProfiler-package                 html  
    compareCluster                          html  
    finding level-2 HTML links ... done

    download_KEGG                           html  
    dropGO                                  html  
    enrichDAVID                             html  
    enrichGO                                html  
    enrichKEGG                              html  
    enrichMKEGG                             html  
    enricher                                html  
    go2ont                                  html  
    go2term                                 html  
    gofilter                                html  
    groupGO                                 html  
    groupGOResult-class                     html  
    gseGO                                   html  
    gseKEGG                                 html  
    gseMKEGG                                html  
    idType                                  html  
    ko2name                                 html  
    merge_result                            html  
    plotGOgraph                             html  
    read.gmt                                html  
    reexports                               html  
    search_kegg_organism                    html  
    simplify-methods                        html  
    uniprot_get                             html  
    viewKEGG                                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 'clusterProfiler' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'clusterProfiler' as clusterProfiler_3.16.1.zip
* DONE (clusterProfiler)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'clusterProfiler' successfully unpacked and MD5 sums checked

Tests output

clusterProfiler.Rcheck/tests_i386/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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(clusterProfiler)

clusterProfiler v3.16.1  For help: https://guangchuangyu.github.io/software/clusterProfiler

If you use clusterProfiler in published research, please cite:
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: A Journal of Integrative Biology. 2012, 16(5):284-287.

Attaching package: 'clusterProfiler'

The following object is masked from 'package:stats':

    filter

> 
> test_check("clusterProfiler")
== testthat results  ===========================================================
[ OK: 2 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  10.06    0.79   14.68 

clusterProfiler.Rcheck/tests_x64/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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(clusterProfiler)

clusterProfiler v3.16.1  For help: https://guangchuangyu.github.io/software/clusterProfiler

If you use clusterProfiler in published research, please cite:
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: A Journal of Integrative Biology. 2012, 16(5):284-287.

Attaching package: 'clusterProfiler'

The following object is masked from 'package:stats':

    filter

> 
> test_check("clusterProfiler")
== testthat results  ===========================================================
[ OK: 2 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   9.60    0.51   13.87 

Example timings

clusterProfiler.Rcheck/examples_i386/clusterProfiler-Ex.timings

nameusersystemelapsed
compareCluster000
enrichGO000
enrichKEGG0.570.104.50
groupGO58.81 5.9664.86

clusterProfiler.Rcheck/examples_x64/clusterProfiler-Ex.timings

nameusersystemelapsed
compareCluster000
enrichGO000
enrichKEGG0.500.054.50
groupGO49.59 1.6251.22