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CHECK report for chipenrich on tokay1

This page was generated on 2019-04-13 11:23:09 -0400 (Sat, 13 Apr 2019).

Package 244/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chipenrich 2.6.1
Raymond G. Cavalcante
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/chipenrich
Branch: RELEASE_3_8
Last Commit: 3b0d5f2
Last Changed Date: 2019-01-04 13:25:09 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: chipenrich
Version: 2.6.1
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:chipenrich.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings chipenrich_2.6.1.tar.gz
StartedAt: 2019-04-13 01:09:07 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 01:20:48 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 701.7 seconds
RetCode: 0
Status:  OK  
CheckDir: chipenrich.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:chipenrich.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings chipenrich_2.6.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/chipenrich.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'chipenrich/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'chipenrich' version '2.6.1'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 'chipenrich' 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
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
broadenrich 7.64   0.27    7.97
polyenrich  6.36   0.02    6.39
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
broadenrich 7.33   0.06    7.39
polyenrich  6.86   0.00    6.86
* 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: OK


Installation output

chipenrich.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/chipenrich_2.6.1.tar.gz && rm -rf chipenrich.buildbin-libdir && mkdir chipenrich.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=chipenrich.buildbin-libdir chipenrich_2.6.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL chipenrich_2.6.1.zip && rm chipenrich_2.6.1.tar.gz chipenrich_2.6.1.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
100  344k  100  344k    0     0  8939k      0 --:--:-- --:--:-- --:--:-- 9835k

install for i386

* installing *source* package 'chipenrich' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'chipenrich'
    finding HTML links ... done
    assign_peak_segments                    html  
    assign_peaks                            html  
    broadenrich                             html  
    calc_peak_gene_overlap                  html  
    chipenrich                              html  
    chipenrich_package                      html  
    filter_genesets                         html  
    genome_to_organism                      html  
    genome_to_orgdb                         html  
    get_test_method                         html  
    hybridenrich                            html  
    load_peaks                              html  
    num_peaks_per_gene                      html  
    peaks2genes                             html  
    plot_chipenrich_spline                  html  
    plot_dist_to_tss                        html  
    plot_gene_coverage                      html  
    plot_polyenrich_spline                  html  
    polyenrich                              html  
    post_process_enrichments                html  
    postprocess_peak_grs                    html  
    read_bed                                html  
    read_geneset                            html  
    read_ldef                               html  
    read_mappa                              html  
    recode_peaks                            html  
    reset_ncores_for_windows                html  
    setup_genesets                          html  
    setup_locusdef                          html  
    setup_mappa                             html  
    supported_genesets                      html  
    supported_genomes                       html  
    supported_locusdefs                     html  
    supported_methods                       html  
    supported_read_lengths                  html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'chipenrich' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'chipenrich' as chipenrich_2.6.1.zip
* DONE (chipenrich)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'chipenrich' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

chipenrich.Rcheck/tests_i386/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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(chipenrich)





> 
> test_check("chipenrich")
== testthat results  ===========================================================
OK: 194 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 150.39    2.57  158.43 

chipenrich.Rcheck/tests_x64/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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(chipenrich)





> 
> test_check("chipenrich")
== testthat results  ===========================================================
OK: 194 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 145.20    1.37  146.57 

Example timings

chipenrich.Rcheck/examples_i386/chipenrich-Ex.timings

nameusersystemelapsed
assign_peak_segments0.170.000.17
assign_peaks0.500.060.56
broadenrich7.640.277.97
calc_peak_gene_overlap0.340.000.34
chipenrich2.380.012.39
load_peaks0.040.000.05
num_peaks_per_gene0.430.000.42
peaks2genes0.450.000.45
plot_chipenrich_spline1.530.061.66
plot_dist_to_tss0.330.000.33
plot_gene_coverage1.030.001.03
plot_polyenrich_spline3.360.133.48
polyenrich6.360.026.39
read_bed0.170.000.18
supported_genesets0.020.000.01
supported_genomes000
supported_locusdefs000
supported_methods000
supported_read_lengths0.010.000.02

chipenrich.Rcheck/examples_x64/chipenrich-Ex.timings

nameusersystemelapsed
assign_peak_segments0.220.000.22
assign_peaks0.420.020.44
broadenrich7.330.067.39
calc_peak_gene_overlap0.330.000.33
chipenrich1.570.031.60
load_peaks0.050.000.05
num_peaks_per_gene0.450.020.47
peaks2genes0.490.000.48
plot_chipenrich_spline2.230.002.24
plot_dist_to_tss0.300.010.31
plot_gene_coverage0.830.000.83
plot_polyenrich_spline2.620.032.66
polyenrich6.860.006.86
read_bed0.190.000.18
supported_genesets000
supported_genomes000
supported_locusdefs000
supported_methods000
supported_read_lengths0.000.020.01