Package: chipenrich

Version: 2.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings chipenrich_2.2.0.tar.gz

StartedAt: 2018-04-12 01:31:24 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 01:39:01 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 456.6 seconds

RetCode: 0

Status:  OK

CheckDir: chipenrich.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings chipenrich_2.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/chipenrich.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘2.2.0’
* 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 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 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 ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
broadenrich 10.240  0.236  10.719
polyenrich   6.696  0.259   7.084
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/chipenrich.Rcheck/00check.log’
for details.

* installing *source* package ‘chipenrich’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (chipenrich)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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 
168.439   8.150 180.461 

name	user	system	elapsed
assign_peak_segments	1.013	0.032	1.073
assign_peaks	1.252	0.017	1.298
broadenrich	10.240	0.236	10.719
calc_peak_gene_overlap	0.400	0.011	0.423
chipenrich	2.816	0.104	2.995
load_peaks	0.050	0.001	0.051
num_peaks_per_gene	0.527	0.019	0.553
plot_chipenrich_spline	2.686	0.151	2.881
plot_dist_to_tss	0.355	0.011	0.379
plot_gene_coverage	1.448	0.059	1.521
plot_polyenrich_spline	3.105	0.287	3.466
polyenrich	6.696	0.259	7.084
read_bed	0.211	0.003	0.220
supported_genesets	0.009	0.001	0.009
supported_genomes	0.003	0.000	0.003
supported_locusdefs	0.010	0.001	0.011
supported_methods	0.001	0.001	0.000
supported_read_lengths	0.009	0.001	0.009