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CHECK report for chipenrich on tokay1

This page was generated on 2018-04-12 13:23:15 -0400 (Thu, 12 Apr 2018).

Package 217/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chipenrich 2.2.0
Raymond G. Cavalcante
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/chipenrich
Branch: RELEASE_3_6
Last Commit: 33e1b38
Last Changed Date: 2017-10-30 12:40:07 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: chipenrich
Version: 2.2.0
Command: rm -rf chipenrich.buildbin-libdir chipenrich.Rcheck && mkdir chipenrich.buildbin-libdir chipenrich.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=chipenrich.buildbin-libdir chipenrich_2.2.0.tar.gz >chipenrich.Rcheck\00install.out 2>&1 && cp chipenrich.Rcheck\00install.out chipenrich-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=chipenrich.buildbin-libdir --install="check:chipenrich-install.out" --force-multiarch --no-vignettes --timings chipenrich_2.2.0.tar.gz
StartedAt: 2018-04-11 22:51:03 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 23:04:36 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 812.4 seconds
RetCode: 0
Status:  OK  
CheckDir: chipenrich.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf chipenrich.buildbin-libdir chipenrich.Rcheck && mkdir chipenrich.buildbin-libdir chipenrich.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=chipenrich.buildbin-libdir chipenrich_2.2.0.tar.gz >chipenrich.Rcheck\00install.out 2>&1 && cp chipenrich.Rcheck\00install.out chipenrich-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=chipenrich.buildbin-libdir --install="check:chipenrich-install.out" --force-multiarch --no-vignettes --timings chipenrich_2.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/chipenrich.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 'chipenrich/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'chipenrich' version '2.2.0'
* 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 '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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 ... NOTE
test_polyenrich_weighted: no visible binding for global variable
  'gene_id'
Undefined global functions or variables:
  gene_id
* 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            10.27   0.10   10.61
polyenrich              7.61   0.03    7.64
plot_chipenrich_spline  3.28   0.05    5.83
chipenrich              3.15   0.04    6.09
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
broadenrich 11.50   0.03   11.53
polyenrich   7.79   0.03    7.83
* 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-3.6-bioc/meat/chipenrich.Rcheck/00check.log'
for details.



Installation output

chipenrich.Rcheck/00install.out


install for i386

* installing *source* package 'chipenrich' ...
** R
** inst
** preparing 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  
    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_2.2.0.zip
* DONE (chipenrich)
In R CMD INSTALL
In R CMD INSTALL

Tests output

chipenrich.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(chipenrich)





> 
> test_check("chipenrich")
== testthat results  ===========================================================
OK: 195 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 183.01    1.70  197.40 

chipenrich.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(chipenrich)





> 
> test_check("chipenrich")
== testthat results  ===========================================================
OK: 195 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 193.84    0.98  194.90 

Example timings

chipenrich.Rcheck/examples_i386/chipenrich-Ex.timings

nameusersystemelapsed
assign_peak_segments0.730.013.95
assign_peaks0.870.032.52
broadenrich10.27 0.1010.61
calc_peak_gene_overlap0.400.000.41
chipenrich3.150.046.09
load_peaks0.060.000.07
num_peaks_per_gene0.480.010.50
plot_chipenrich_spline3.280.055.83
plot_dist_to_tss0.350.000.34
plot_gene_coverage0.900.030.94
plot_polyenrich_spline3.240.053.34
polyenrich7.610.037.64
read_bed0.170.000.17
supported_genesets0.010.000.02
supported_genomes000
supported_locusdefs000
supported_methods0.020.000.01
supported_read_lengths000

chipenrich.Rcheck/examples_x64/chipenrich-Ex.timings

nameusersystemelapsed
assign_peak_segments0.560.000.56
assign_peaks1.950.041.99
broadenrich11.50 0.0311.53
calc_peak_gene_overlap0.420.000.42
chipenrich3.660.003.66
load_peaks0.050.000.04
num_peaks_per_gene0.540.000.55
plot_chipenrich_spline4.190.034.22
plot_dist_to_tss0.350.000.34
plot_gene_coverage1.20.01.2
plot_polyenrich_spline4.180.094.28
polyenrich7.790.037.83
read_bed0.210.000.20
supported_genesets000
supported_genomes000
supported_locusdefs0.000.020.02
supported_methods000
supported_read_lengths000