BioC 3.4: CHECK report for chipenrich on zin1

Package: chipenrich

Version: 1.11.4

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings chipenrich_1.11.4.tar.gz

StartedAt: 2016-09-20 04:23:36 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 04:26:07 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 151.1 seconds

RetCode: 0

Status:  OK

CheckDir: chipenrich.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings chipenrich_1.11.4.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/chipenrich.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.11.4’
* 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
plot_spline_length 18.620  0.024  18.651
chipenrich         14.564  0.016  14.604
plot_gene_coverage  6.636  0.004   6.640
* 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	0.260	0.012	0.283
assign_peaks	0.552	0.000	0.555
calc_peak_gene_overlap	0.656	0.000	0.658
chipenrich	14.564	0.016	14.604
load_peaks	0.236	0.000	0.250
num_peaks_per_gene	0.496	0.008	0.503
plot_dist_to_tss	0.3	0.0	0.3
plot_gene_coverage	6.636	0.004	6.640
plot_spline_length	18.620	0.024	18.651
read_bed	0.048	0.000	0.050
read_bedgff	0.028	0.000	0.031
supported_genesets	0.004	0.000	0.005
supported_genomes	0.000	0.004	0.002
supported_locusdefs	0.004	0.000	0.003
supported_methods	0.000	0.000	0.001
supported_read_lengths	0.004	0.004	0.006