BioC 3.5: CHECK report for chipenrich on veracruz2

Package: chipenrich

Version: 2.0.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings chipenrich_2.0.1.tar.gz

StartedAt: 2017-10-18 01:32:27 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 01:39:23 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 415.7 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_2.0.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/chipenrich.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘2.0.1’
* 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 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 ... 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 7.566  0.292   8.056
polyenrich  5.667  0.160   5.997
* 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

* 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)

name	user	system	elapsed
assign_peak_segments	0.577	0.006	0.605
assign_peaks	1.660	0.015	1.750
broadenrich	7.566	0.292	8.056
calc_peak_gene_overlap	0.438	0.015	0.465
chipenrich	2.858	0.070	3.042
load_peaks	0.055	0.001	0.056
num_peaks_per_gene	0.411	0.015	0.441
plot_chipenrich_spline	2.524	0.132	2.750
plot_dist_to_tss	0.269	0.013	0.292
plot_gene_coverage	0.953	0.057	1.050
plot_polyenrich_spline	3.475	0.261	3.866
polyenrich	5.667	0.160	5.997
read_bed	0.196	0.002	0.202
supported_genesets	0.007	0.001	0.008
supported_genomes	0.002	0.000	0.003
supported_locusdefs	0.009	0.002	0.011
supported_methods	0.001	0.000	0.001
supported_read_lengths	0.008	0.001	0.009