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CHECK report for ChIPseeker on tokay1

This page was generated on 2018-04-12 13:24:15 -0400 (Thu, 12 Apr 2018).

Package 221/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPseeker 1.14.2
Guangchuang Yu
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/ChIPseeker
Branch: RELEASE_3_6
Last Commit: 00d5ed9
Last Changed Date: 2018-02-27 02:08:55 -0400 (Tue, 27 Feb 2018)
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: ChIPseeker
Version: 1.14.2
Command: rm -rf ChIPseeker.buildbin-libdir ChIPseeker.Rcheck && mkdir ChIPseeker.buildbin-libdir ChIPseeker.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ChIPseeker.buildbin-libdir ChIPseeker_1.14.2.tar.gz >ChIPseeker.Rcheck\00install.out 2>&1 && cp ChIPseeker.Rcheck\00install.out ChIPseeker-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=ChIPseeker.buildbin-libdir --install="check:ChIPseeker-install.out" --force-multiarch --no-vignettes --timings ChIPseeker_1.14.2.tar.gz
StartedAt: 2018-04-11 22:52:11 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 22:58:02 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 351.2 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: ChIPseeker.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf ChIPseeker.buildbin-libdir ChIPseeker.Rcheck && mkdir ChIPseeker.buildbin-libdir ChIPseeker.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ChIPseeker.buildbin-libdir ChIPseeker_1.14.2.tar.gz >ChIPseeker.Rcheck\00install.out 2>&1 && cp ChIPseeker.Rcheck\00install.out ChIPseeker-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=ChIPseeker.buildbin-libdir --install="check:ChIPseeker-install.out" --force-multiarch --no-vignettes --timings ChIPseeker_1.14.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/ChIPseeker.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 'ChIPseeker/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ChIPseeker' version '1.14.2'
* 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 'ChIPseeker' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWQh948/R.INSTALL18d03057e1d/ChIPseeker/man/enrichPeakOverlap.Rd:26: missing file link 'mclapply'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWQh948/R.INSTALL18d03057e1d/ChIPseeker/man/reexports.Rd:14: missing file link 'GRangesList'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/ChIPseeker.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
** running examples for arch 'x64' ... OK
* 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/ChIPseeker.Rcheck/00check.log'
for details.

Installation output

ChIPseeker.Rcheck/00install.out


install for i386

* installing *source* package 'ChIPseeker' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ChIPseeker'
    finding HTML links ... done
    ChIPseeker-package                      html  
    annotatePeak                            html  
    as.GRanges                              html  
    as.data.frame.csAnno                    html  
    covplot                                 html  
    csAnno-class                            html  
    dotFun                                  html  
    downloadGEObedFiles                     html  
    downloadGSMbedFiles                     html  
    dropAnno                                html  
    enrichAnnoOverlap                       html  
    enrichPeakOverlap                       html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWQh948/R.INSTALL18d03057e1d/ChIPseeker/man/enrichPeakOverlap.Rd:26: missing file link 'mclapply'
    getBioRegion                            html  
    getGEOInfo                              html  
    getGEOgenomeVersion                     html  
    getGEOspecies                           html  
    getGeneAnno                             html  
    getGenomicAnnotation                    html  
    getNearestFeatureIndicesAndDistances    html  
    getPromoters                            html  
    getSampleFiles                          html  
    getTagMatrix                            html  
    info                                    html  
    overlap                                 html  
    peakHeatmap                             html  
    plotAnnoBar-methods                     html  
    plotAnnoBar.data.frame                  html  
    plotAnnoPie-methods                     html  
    plotAnnoPie.csAnno                      html  
    plotAvgProf                             html  
    plotAvgProf2                            html  
    plotDistToTSS-methods                   html  
    plotDistToTSS.data.frame                html  
    readPeakFile                            html  
    reexports                               html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWQh948/R.INSTALL18d03057e1d/ChIPseeker/man/reexports.Rd:14: missing file link 'GRangesList'
    seq2gene                                html  
    show-methods                            html  
    shuffle                                 html  
    tagHeatmap                              html  
    upsetplot-methods                       html  
    vennpie-methods                         html  
    vennplot                                html  
    vennplot.peakfile                       html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'ChIPseeker' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ChIPseeker' as ChIPseeker_1.14.2.zip
* DONE (ChIPseeker)
In R CMD INSTALL
In R CMD INSTALL

Tests output

ChIPseeker.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(ChIPseeker)

ChIPseeker v1.14.2  For help: https://guangchuangyu.github.io/ChIPseeker

If you use ChIPseeker in published research, please cite:
Guangchuang Yu, Li-Gen Wang, Qing-Yu He. ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization. Bioinformatics 2015, 31(14):2382-2383
> 
> test_check("ChIPseeker")
== testthat results  ===========================================================
OK: 8 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  13.14    0.51   13.65

ChIPseeker.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(ChIPseeker)

ChIPseeker v1.14.2  For help: https://guangchuangyu.github.io/ChIPseeker

If you use ChIPseeker in published research, please cite:
Guangchuang Yu, Li-Gen Wang, Qing-Yu He. ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization. Bioinformatics 2015, 31(14):2382-2383
> 
> test_check("ChIPseeker")
== testthat results  ===========================================================
OK: 8 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  15.23    0.39   15.60

Example timings

ChIPseeker.Rcheck/examples_i386/ChIPseeker-Ex.timings

nameusersystemelapsed
annotatePeak000
dotFun000
plotAnnoPie.csAnno000
plotDistToTSS.data.frame000
readPeakFile0.280.000.28
vennplot000

ChIPseeker.Rcheck/examples_x64/ChIPseeker-Ex.timings

nameusersystemelapsed
annotatePeak000
dotFun000
plotAnnoPie.csAnno000
plotDistToTSS.data.frame000
readPeakFile0.300.010.31
vennplot000