Multiple platform build/check report for BioC 3.13 - CHECK results for clusterProfiler on tokay2

Package: clusterProfiler

Version: 4.0.5

Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:clusterProfiler.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings clusterProfiler_4.0.5.tar.gz

StartedAt: 2021-10-14 21:13:32 -0400 (Thu, 14 Oct 2021)

EndedAt: 2021-10-14 21:19:26 -0400 (Thu, 14 Oct 2021)

EllapsedTime: 353.1 seconds

RetCode: 0

Status: OK

CheckDir: clusterProfiler.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:clusterProfiler.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings clusterProfiler_4.0.5.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/clusterProfiler.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '4.0.5'
* 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    52.82   5.30   58.12
enrichKEGG  0.77   0.06    6.08
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
groupGO    47.59   1.95   49.54
enrichKEGG  0.70   0.05    5.43
* 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

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/clusterProfiler_4.0.5.tar.gz && rm -rf clusterProfiler.buildbin-libdir && mkdir clusterProfiler.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=clusterProfiler.buildbin-libdir clusterProfiler_4.0.5.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL clusterProfiler_4.0.5.zip && rm clusterProfiler_4.0.5.tar.gz clusterProfiler_4.0.5.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
  1 2554k    1 47037    0     0   297k      0  0:00:08 --:--:--  0:00:08  298k
100 2554k  100 2554k    0     0  3248k      0 --:--:-- --:--:-- --:--:-- 3246k

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  
    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  
    enrichWP                                html  
    enricher                                html  
    get_wp_organisms                        html  
    go2ont                                  html  
    go2term                                 html  
    gofilter                                html  
    groupGO                                 html  
    groupGOResult-class                     html  
    gseGO                                   html  
    gseKEGG                                 html  
    gseMKEGG                                html  
    gseWP                                   html  
    hgmlist                                 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  
** 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_4.0.5.zip
* DONE (clusterProfiler)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'clusterProfiler' successfully unpacked and MD5 sums checked


R version 4.1.1 (2021-08-10) -- "Kick Things"
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(clusterProfiler)

clusterProfiler v4.0.5  For help: https://yulab-smu.top/biomedical-knowledge-mining-book/

If you use clusterProfiler in published research, please cite:
T Wu, E Hu, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou, W Tang, L Zhan, X Fu, S Liu, X Bo, and G Yu. clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. The Innovation. 2021, 2(3):100141. doi: 10.1016/j.xinn.2021.100141

Attaching package: 'clusterProfiler'

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

    filter

> 
> test_check("clusterProfiler")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ]
> 
> proc.time()
   user  system elapsed 
   8.65    0.85   14.28


R version 4.1.1 (2021-08-10) -- "Kick Things"
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(clusterProfiler)

clusterProfiler v4.0.5  For help: https://yulab-smu.top/biomedical-knowledge-mining-book/

If you use clusterProfiler in published research, please cite:
T Wu, E Hu, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou, W Tang, L Zhan, X Fu, S Liu, X Bo, and G Yu. clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. The Innovation. 2021, 2(3):100141. doi: 10.1016/j.xinn.2021.100141

Attaching package: 'clusterProfiler'

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

    filter

> 
> test_check("clusterProfiler")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ]
> 
> proc.time()
   user  system elapsed 
   8.51    0.53   13.81

name	user	system	elapsed
compareCluster	0	0	0
enrichGO	0	0	0
enrichKEGG	0.77	0.06	6.08
groupGO	52.82	5.30	58.12

name	user	system	elapsed
compareCluster	0	0	0
enrichGO	0	0	0
enrichKEGG	0.70	0.05	5.43
groupGO	47.59	1.95	49.54

CHECK results for clusterProfiler on tokay2

Summary

Command output

Installation output

Tests output

Example timings