Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-09-24 15:06:05 -0400 (Fri, 24 Sep 2021).

CHECK results for ChIPseeker on tokay2

To the developers/maintainers of the ChIPseeker package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ChIPseeker.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 296/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPseeker 1.28.3  (landing page)
Guangchuang Yu
Snapshot Date: 2021-09-23 04:50:12 -0400 (Thu, 23 Sep 2021)
git_url: https://git.bioconductor.org/packages/ChIPseeker
git_branch: RELEASE_3_13
git_last_commit: 2c3e718
git_last_commit_date: 2021-05-21 05:08:25 -0400 (Fri, 21 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ChIPseeker
Version: 1.28.3
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChIPseeker.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ChIPseeker_1.28.3.tar.gz
StartedAt: 2021-09-23 20:19:12 -0400 (Thu, 23 Sep 2021)
EndedAt: 2021-09-23 20:26:10 -0400 (Thu, 23 Sep 2021)
EllapsedTime: 417.5 seconds
RetCode: 0
Status:   OK  
CheckDir: ChIPseeker.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChIPseeker.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ChIPseeker_1.28.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/ChIPseeker.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.28.3'
* 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 ... OK
* checking installed package size ... NOTE
  installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
* 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 (user + system) or elapsed time > 5s
          user system elapsed
seq2gene 11.34   0.94   12.28
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
         user system elapsed
seq2gene 12.3   0.43   12.73
* 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/ChIPseeker.Rcheck/00check.log'
for details.



Installation output

ChIPseeker.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/ChIPseeker_1.28.3.tar.gz && rm -rf ChIPseeker.buildbin-libdir && mkdir ChIPseeker.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ChIPseeker.buildbin-libdir ChIPseeker_1.28.3.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL ChIPseeker_1.28.3.zip && rm ChIPseeker_1.28.3.tar.gz ChIPseeker_1.28.3.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 50 6397k   50 3221k    0     0  3984k      0  0:00:01 --:--:--  0:00:01 3982k
100 6397k  100 6397k    0     0  4760k      0  0:00:01  0:00:01 --:--:-- 4763k

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  
    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                             html  
    plotAnnoPie-methods                     html  
    plotAnnoPie                             html  
    plotAvgProf                             html  
    plotAvgProf2                            html  
    plotDistToTSS-methods                   html  
    plotDistToTSS.data.frame                html  
    readPeakFile                            html  
    reexports                               html  
    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_1.28.3.zip
* DONE (ChIPseeker)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'ChIPseeker' successfully unpacked and MD5 sums checked

Tests output

ChIPseeker.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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 v1.28.3  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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 8 ]
> 
> proc.time()
   user  system elapsed 
  11.75    1.23   12.95 

ChIPseeker.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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 v1.28.3  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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 8 ]
> 
> proc.time()
   user  system elapsed 
  14.76    0.73   15.48 

Example timings

ChIPseeker.Rcheck/examples_i386/ChIPseeker-Ex.timings

nameusersystemelapsed
annotatePeak000
dotFun000
plotAnnoPie000
plotDistToTSS.data.frame000
readPeakFile0.110.000.11
seq2gene11.34 0.9412.28
vennplot000

ChIPseeker.Rcheck/examples_x64/ChIPseeker-Ex.timings

nameusersystemelapsed
annotatePeak000
dotFun000
plotAnnoPie000
plotDistToTSS.data.frame000
readPeakFile0.150.000.16
seq2gene12.30 0.4312.73
vennplot000