BioC 3.2: CHECK report for chipenrich on oaxaca

Package: chipenrich

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings chipenrich_1.8.0.tar.gz

StartedAt: 2016-04-22 22:35:29 -0700 (Fri, 22 Apr 2016)

EndedAt: 2016-04-22 22:40:37 -0700 (Fri, 22 Apr 2016)

EllapsedTime: 308.2 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_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/chipenrich.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.8.0’
* 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 ... [13s/14s] 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:
  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 ... [114s/115s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
chipenrich          44.702  1.248  46.184
plot_expected_peaks 26.249  0.871  27.159
plot_spline_length  25.927  1.132  27.073
plot_gene_coverage   6.537  0.085   6.657
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [62s/62s]
 [62s/62s] 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-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)

name	user	system	elapsed
chipenrich	44.702	1.248	46.184
plot_dist_to_tss	1.122	0.037	1.160
plot_expected_peaks	26.249	0.871	27.159
plot_gene_coverage	6.537	0.085	6.657
plot_spline_length	25.927	1.132	27.073
supported_genesets	0.002	0.000	0.003
supported_genomes	0.002	0.000	0.002
supported_locusdefs	0.002	0.000	0.002
supported_methods	0	0	0
supported_read_lengths	0.004	0.000	0.004