BioC 3.1: CHECK report for chipenrich on zin2

Package: chipenrich

Version: 1.6.1

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings chipenrich_1.6.1.tar.gz

StartedAt: 2015-10-08 23:17:18 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 23:21:30 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 252.7 seconds

RetCode: 0

Status:  OK

CheckDir: chipenrich.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings chipenrich_1.6.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/chipenrich.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.6.1’
* 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 ... [10s/12s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Authors@R field gives more than one person with maintainer role:
  Ryan P. Welch <welchr@umich.edu> [aut, cre, cph]
  Chee Lee <cheelee@umich.edu> [aut, cre]
  Raymond G. Cavalcante <rcavalca@umich.edu> [aut, cre]
* 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
chipenrich: no visible binding for global variable ‘P.value’
load_peaks: no visible binding for global variable ‘chrom’
randomize_locusdef : <anonymous>: no visible binding for global
  variable ‘chrom’
read_bed: no visible binding for global variable ‘chrom’
read_bedgff: no visible binding for global variable ‘chrom’
read_peaks: no visible binding for global variable ‘chrom’
setup_ldef: no visible binding for global variable ‘chrom’
test_approx: no visible binding for global variable ‘geneid’
test_binomial: no visible binding for global variable ‘geneid’
test_fisher_exact: no visible binding for global variable ‘geneid’
test_gam: no visible binding for global variable ‘geneid’
test_gam_ratio: no visible binding for global variable ‘geneid’
test_gam_ratio_splineless: no visible binding for global variable
  ‘geneid’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [103s/122s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
chipenrich          42.210  0.078  51.136
plot_spline_length  24.564  0.038  29.509
plot_expected_peaks 24.358  0.016  28.055
plot_gene_coverage   5.873  0.004   7.129
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.1-bioc/meat/chipenrich.Rcheck/00check.log’
for details.

* installing *source* package ‘chipenrich’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (chipenrich)

name	user	system	elapsed
chipenrich	42.210	0.078	51.136
plot_dist_to_tss	0.601	0.000	0.602
plot_expected_peaks	24.358	0.016	28.055
plot_gene_coverage	5.873	0.004	7.129
plot_spline_length	24.564	0.038	29.509
supported_genesets	0.002	0.000	0.002
supported_genomes	0.002	0.000	0.001
supported_locusdefs	0.002	0.000	0.002
supported_methods	0.001	0.000	0.000
supported_read_lengths	0.003	0.000	0.003