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CHECK report for ChIPseeker on tokay1

This page was generated on 2020-08-07 12:04:05 -0400 (Fri, 07 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE ChIPseeker PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 276/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPseeker 1.25.0
Guangchuang Yu
Snapshot Date: 2020-08-06 14:50:46 -0400 (Thu, 06 Aug 2020)
URL: https://git.bioconductor.org/packages/ChIPseeker
Branch: master
Last Commit: 1a47dba
Last Changed Date: 2020-04-27 23:36:28 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 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
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ChIPseeker
Version: 1.25.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChIPseeker.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings ChIPseeker_1.25.0.tar.gz
StartedAt: 2020-08-07 01:29:20 -0400 (Fri, 07 Aug 2020)
EndedAt: 2020-08-07 01:36:39 -0400 (Fri, 07 Aug 2020)
EllapsedTime: 439.1 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: ChIPseeker.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChIPseeker.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings ChIPseeker_1.25.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/ChIPseeker.Rcheck'
* using R version 4.0.2 (2020-06-22)
* 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 '1.25.0'
* package encoding: UTF-8
* 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-3.12-bioc/tmpdir/RtmpeM0Aht/R.INSTALL2b485a42e7b/ChIPseeker/man/enrichPeakOverlap.Rd:34: file link 'mclapply' in package 'parallel' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpeM0Aht/R.INSTALL2b485a42e7b/ChIPseeker/man/reexports.Rd:14: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.12-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 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-3.12-bioc/meat/ChIPseeker.Rcheck/00check.log'
for details.



Installation output

ChIPseeker.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/ChIPseeker_1.25.0.tar.gz && rm -rf ChIPseeker.buildbin-libdir && mkdir ChIPseeker.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ChIPseeker.buildbin-libdir ChIPseeker_1.25.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL ChIPseeker_1.25.0.zip && rm ChIPseeker_1.25.0.tar.gz ChIPseeker_1.25.0.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
 98 4166k   98 4112k    0     0  31.2M      0 --:--:-- --:--:-- --:--:-- 31.8M
100 4166k  100 4166k    0     0  31.5M      0 --:--:-- --:--:-- --:--:-- 32.2M

install for i386

* installing *source* package 'ChIPseeker' ...
** using staged installation
** 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-3.12-bioc/tmpdir/RtmpeM0Aht/R.INSTALL2b485a42e7b/ChIPseeker/man/enrichPeakOverlap.Rd:34: file link 'mclapply' in package 'parallel' does not exist and so has been treated as a topic
    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-3.12-bioc/tmpdir/RtmpeM0Aht/R.INSTALL2b485a42e7b/ChIPseeker/man/reexports.Rd:14: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
    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 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 'ChIPseeker' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ChIPseeker' as ChIPseeker_1.25.0.zip
* DONE (ChIPseeker)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'ChIPseeker' successfully unpacked and MD5 sums checked

Tests output

ChIPseeker.Rcheck/tests_i386/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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 v1.25.0  For help: https://guangchuangyu.github.io/software/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 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  17.06    1.54   18.61 

ChIPseeker.Rcheck/tests_x64/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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 v1.25.0  For help: https://guangchuangyu.github.io/software/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 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  20.67    0.85   21.53 

Example timings

ChIPseeker.Rcheck/examples_i386/ChIPseeker-Ex.timings

nameusersystemelapsed
annotatePeak000
dotFun000
plotAnnoPie.csAnno000
plotDistToTSS.data.frame000
readPeakFile0.200.000.21
vennplot000

ChIPseeker.Rcheck/examples_x64/ChIPseeker-Ex.timings

nameusersystemelapsed
annotatePeak000
dotFun000
plotAnnoPie.csAnno000
plotDistToTSS.data.frame000
readPeakFile0.230.000.23
vennplot000