Package: chipenrich

Version: 2.6.1

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:chipenrich.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings chipenrich_2.6.1.tar.gz

StartedAt: 2019-04-15 22:49:06 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-15 22:56:37 -0400 (Mon, 15 Apr 2019)

EllapsedTime: 451.5 seconds

RetCode: 0

Status:  OK

CheckDir: chipenrich.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:chipenrich.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings chipenrich_2.6.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/chipenrich.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 ... 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 for sufficient/correct file permissions ... 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
* 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 ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
broadenrich 8.748  0.052   8.836
polyenrich  6.984  0.012   7.007
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL chipenrich
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘chipenrich’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (chipenrich)

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
185.580   0.732 188.143 

name	user	system	elapsed
assign_peak_segments	0.268	0.000	0.337
assign_peaks	0.768	0.012	0.802
broadenrich	8.748	0.052	8.836
calc_peak_gene_overlap	0.496	0.000	0.500
chipenrich	2.260	0.000	2.275
load_peaks	0.052	0.000	0.052
num_peaks_per_gene	0.416	0.004	0.421
peaks2genes	0.444	0.004	0.448
plot_chipenrich_spline	1.924	0.004	1.951
plot_dist_to_tss	0.296	0.000	0.294
plot_gene_coverage	0.772	0.000	0.772
plot_polyenrich_spline	2.404	0.020	2.427
polyenrich	6.984	0.012	7.007
read_bed	0.220	0.004	0.239
supported_genesets	0.008	0.000	0.009
supported_genomes	0.004	0.000	0.003
supported_locusdefs	0.008	0.000	0.008
supported_methods	0.004	0.000	0.001
supported_read_lengths	0.004	0.000	0.005