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CHECK report for clusterProfiler on machv2

This page was generated on 2020-10-17 11:58:15 -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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:clusterProfiler.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings clusterProfiler_3.16.1.tar.gz
StartedAt: 2020-10-16 23:47:46 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 23:52:48 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 302.6 seconds
RetCode: 0
Status:  OK 
CheckDir: clusterProfiler.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:clusterProfiler.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings clusterProfiler_3.16.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/clusterProfiler.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... 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
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
groupGO    73.517  4.275  78.325
enrichKEGG  1.233  0.041   5.781
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL clusterProfiler
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘clusterProfiler’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (clusterProfiler)

Tests output

clusterProfiler.Rcheck/tests/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-apple-darwin17.0 (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 
 12.116   0.657  17.935 

Example timings

clusterProfiler.Rcheck/clusterProfiler-Ex.timings

nameusersystemelapsed
compareCluster0.0000.0010.002
enrichGO000
enrichKEGG1.2330.0415.781
groupGO73.517 4.27578.325