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CHECK report for clusterProfiler on tokay1

This page was generated on 2018-04-12 13:20:43 -0400 (Thu, 12 Apr 2018).

Package 250/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clusterProfiler 3.6.0
Guangchuang Yu
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/clusterProfiler
Branch: RELEASE_3_6
Last Commit: ff15e3d
Last Changed Date: 2017-10-30 12:39:33 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: clusterProfiler
Version: 3.6.0
Command: rm -rf clusterProfiler.buildbin-libdir clusterProfiler.Rcheck && mkdir clusterProfiler.buildbin-libdir clusterProfiler.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=clusterProfiler.buildbin-libdir clusterProfiler_3.6.0.tar.gz >clusterProfiler.Rcheck\00install.out 2>&1 && cp clusterProfiler.Rcheck\00install.out clusterProfiler-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=clusterProfiler.buildbin-libdir --install="check:clusterProfiler-install.out" --force-multiarch --no-vignettes --timings clusterProfiler_3.6.0.tar.gz
StartedAt: 2018-04-11 22:59:52 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 23:04:20 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 267.7 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: clusterProfiler.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf clusterProfiler.buildbin-libdir clusterProfiler.Rcheck && mkdir clusterProfiler.buildbin-libdir clusterProfiler.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=clusterProfiler.buildbin-libdir clusterProfiler_3.6.0.tar.gz >clusterProfiler.Rcheck\00install.out 2>&1 && cp clusterProfiler.Rcheck\00install.out clusterProfiler-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=clusterProfiler.buildbin-libdir --install="check:clusterProfiler-install.out" --force-multiarch --no-vignettes --timings clusterProfiler_3.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/clusterProfiler.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '3.6.0'
* 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-3.6-bioc/tmpdir/RtmpyEl9ja/R.INSTALL1330e497e11/clusterProfiler/man/plotGOgraph.Rd:33: missing file link 'showSigOfNodes'
See 'C:/Users/biocbuild/bbs-3.6-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 installed files from 'inst/doc' ... 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    44.54   3.11   47.64
enrichKEGG  2.70   0.55    5.39
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
         user system elapsed
groupGO 41.95   1.89   43.85
* 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-3.6-bioc/meat/clusterProfiler.Rcheck/00check.log'
for details.

Installation output

clusterProfiler.Rcheck/00install.out


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  
    plot-methods                            html  
    plotGOgraph                             html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyEl9ja/R.INSTALL1330e497e11/clusterProfiler/man/plotGOgraph.Rd:33: missing file link 'showSigOfNodes'
    plotting.clusterProfile                 html  
    read.gmt                                html  
    search_kegg_organism                    html  
    simplify-methods                        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_3.6.0.zip
* DONE (clusterProfiler)
In R CMD INSTALL
In R CMD INSTALL

Tests output

clusterProfiler.Rcheck/tests_i386/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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)
Loading required package: DOSE

DOSE v3.4.0  For help: https://guangchuangyu.github.io/DOSE

If you use DOSE in published research, please cite:
Guangchuang Yu, Li-Gen Wang, Guang-Rong Yan, Qing-Yu He. DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis. Bioinformatics 2015, 31(4):608-609

clusterProfiler v3.6.0  For help: https://guangchuangyu.github.io/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 
  11.23    2.20   18.23

clusterProfiler.Rcheck/tests_x64/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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)
Loading required package: DOSE

DOSE v3.4.0  For help: https://guangchuangyu.github.io/DOSE

If you use DOSE in published research, please cite:
Guangchuang Yu, Li-Gen Wang, Guang-Rong Yan, Qing-Yu He. DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis. Bioinformatics 2015, 31(4):608-609

clusterProfiler v3.6.0  For help: https://guangchuangyu.github.io/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 
  10.40    2.23   14.18

Example timings

clusterProfiler.Rcheck/examples_i386/clusterProfiler-Ex.timings

nameusersystemelapsed
compareCluster000
enrichGO000
enrichKEGG2.700.555.39
groupGO44.54 3.1147.64

clusterProfiler.Rcheck/examples_x64/clusterProfiler-Ex.timings

nameusersystemelapsed
compareCluster000
enrichGO000
enrichKEGG2.050.584.23
groupGO41.95 1.8943.85