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CHECK report for clusterProfiler on tokay2

This page was generated on 2018-10-17 08:35:14 -0400 (Wed, 17 Oct 2018).

Package 263/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clusterProfiler 3.8.1
Guangchuang Yu
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/clusterProfiler
Branch: RELEASE_3_7
Last Commit: 81e1a7a
Last Changed Date: 2018-09-17 21:30:59 -0400 (Mon, 17 Sep 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: clusterProfiler
Version: 3.8.1
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:clusterProfiler.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings clusterProfiler_3.8.1.tar.gz
StartedAt: 2018-10-17 01:11:02 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 01:18:23 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 440.7 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: clusterProfiler.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:clusterProfiler.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings clusterProfiler_3.8.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/clusterProfiler.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '3.8.1'
* 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 ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2vUl2S/R.INSTALL1d0c66157bf9/clusterProfiler/man/plotGOgraph.Rd:30: file link 'showSigOfNodes' in package 'topGO' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/clusterProfiler.Rcheck/00install.out' for details.
* 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 or elapsed time > 5s
            user system elapsed
groupGO    96.68  17.83  114.53
enrichKEGG  4.28   0.94   13.23
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
groupGO    99.28   3.72  103.02
enrichKEGG  3.38   0.87    8.31
* 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: 1 WARNING
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/clusterProfiler.Rcheck/00check.log'
for details.

Installation output

clusterProfiler.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/clusterProfiler_3.8.1.tar.gz && rm -rf clusterProfiler.buildbin-libdir && mkdir clusterProfiler.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=clusterProfiler.buildbin-libdir clusterProfiler_3.8.1.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL clusterProfiler_3.8.1.zip && rm clusterProfiler_3.8.1.tar.gz clusterProfiler_3.8.1.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 4222k  100 4222k    0     0  38.8M      0 --:--:-- --:--:-- --:--:-- 41.6M

install for i386

* installing *source* package 'clusterProfiler' ...
** 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  
    compareClusterResult-class              html  
    finding level-2 HTML links ... done

    dotplot-methods                         html  
    download_KEGG                           html  
    dropGO                                  html  
    enrichDAVID                             html  
    enrichGO                                html  
    enrichKEGG                              html  
    enrichMKEGG                             html  
    enricher                                html  
    fortify                                 html  
    getGOLevel                              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  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2vUl2S/R.INSTALL1d0c66157bf9/clusterProfiler/man/plotGOgraph.Rd:30: file link 'showSigOfNodes' in package 'topGO' does not exist and so has been treated as a topic
    plotting.clusterProfile                 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
In R CMD INSTALL

install for x64

* installing *source* package 'clusterProfiler' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'clusterProfiler' as clusterProfiler_3.8.1.zip
* DONE (clusterProfiler)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'clusterProfiler' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

clusterProfiler.Rcheck/tests_i386/testthat.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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 v3.8.1  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.
> 
> test_check("clusterProfiler")
== testthat results  ===========================================================
OK: 2 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  14.70    2.98   21.37

clusterProfiler.Rcheck/tests_x64/testthat.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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 v3.8.1  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.
> 
> test_check("clusterProfiler")
== testthat results  ===========================================================
OK: 2 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  13.26    2.35   20.35

Example timings

clusterProfiler.Rcheck/examples_i386/clusterProfiler-Ex.timings

nameusersystemelapsed
compareCluster000
enrichGO000
enrichKEGG 4.28 0.9413.23
groupGO 96.68 17.83114.53

clusterProfiler.Rcheck/examples_x64/clusterProfiler-Ex.timings

nameusersystemelapsed
compareCluster000
enrichGO000
enrichKEGG3.380.878.31
groupGO 99.28 3.72103.02