Package: ChIPseeker

Version: 1.16.1

Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChIPseeker.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings ChIPseeker_1.16.1.tar.gz

StartedAt: 2018-10-17 01:04:33 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 01:10:50 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 376.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: ChIPseeker.Rcheck

Warnings: 1

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### Running command:
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###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChIPseeker.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings ChIPseeker_1.16.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/ChIPseeker.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '1.16.1'
* 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-3.7-bioc/tmpdir/RtmpmErzNu/R.INSTALL107c22446bca/ChIPseeker/man/enrichPeakOverlap.Rd:26: file link 'mclapply' in package 'parallel' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpmErzNu/R.INSTALL107c22446bca/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-3.7-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-3.7-bioc/meat/ChIPseeker.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/ChIPseeker_1.16.1.tar.gz && rm -rf ChIPseeker.buildbin-libdir && mkdir ChIPseeker.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ChIPseeker.buildbin-libdir ChIPseeker_1.16.1.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL ChIPseeker_1.16.1.zip && rm ChIPseeker_1.16.1.tar.gz ChIPseeker_1.16.1.zip
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

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100 2700k  100 2700k    0     0  28.7M      0 --:--:-- --:--:-- --:--:-- 31.0M

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-3.7-bioc/tmpdir/RtmpmErzNu/R.INSTALL107c22446bca/ChIPseeker/man/enrichPeakOverlap.Rd:26: 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-3.7-bioc/tmpdir/RtmpmErzNu/R.INSTALL107c22446bca/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
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_1.16.1.zip
* DONE (ChIPseeker)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'ChIPseeker' successfully unpacked and MD5 sums checked
In R CMD INSTALL

R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
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 v1.16.1  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 
  18.14    1.07   19.36 

R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
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 v1.16.1  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 
  19.71    0.64   20.36